{================================Notices:============================}
This script is used to deposit the structure factors and all of the
statistics from structure solution to final refinement.
1, Structure factors and statistics (if any) from initial data process.
2, Structure factors used for final structure refinement.
3, Statistics from molecular replacement (if any).
4, Statistics from heavy atom phasing (if any).
5, Statistics from density modification (if any).
6, Statistics and coordinates from final refinement.
7, If the software is not in the list, you can still give the software
   name that you used, but log files have to be either in CIF or PDB format.
8, Please add more entries for the log_file names below, if needed.

{* Guidelines for using this file:*}
 1 Only the strings in brackets will be parsed for evaluation. 
   Therefore, never use left or right bracket sign in the comments!!
 2 All values (strings or numbers) in brackets must be double_quoted!!



{================Structure Factor from Initial Data Process=============}
The structure factors were initially processed by softwares at the beam line
site and they are normally used for heavy atom phasing solution. If you only
have one data set and it is also used for final structure refinement, you may
skip this part.

Note:
1, If the data file is converted to CNS format, give the program name as CNS.
2, If the software is not in the above list, please give program name OTHER,
   and provide ASCII file with six values[H, K, L, I(or F), sigmaI(or sigmaF)]
   in each row and separate each value by a space.
3, You may have several crystals and each crystal may be diffracted with
   several wavelengths. It is required to deposit all the data, if all are
   used for heavy atom phasing.
4, If anomalous signals exist, please fill fprime and fdouble_prime.
5, Please add more entries, if needed.

Instruction for items in brackets below:
data_type:         I for intensity, F for amplitude.
program_name:      software name for data processing(HKL|SCALEPACK|DTREK).
crystal_number_?:  number of crystals (integers: 1, 2, 3...)
diffract_number_?: number of diffractions (integers: 1, 2, 3...)
data_file_name_?:  file name containing reflection data.
log_file_name_?:   log file generated from software (containing statistics).
wavelength_?:      wavelength used for diffractions.
fprime_?:          anomalous signal f'.
fdouble_prime_?:   anomalous signal f".

<data_type = "F" >
<program_name = "CNS" >

{Crystal 1 diffracted with wavelength 1 }
<crystal_number_1  = "1" >
<diffract_number_1 = "1" >
<data_file_name_1  = "input_data/hrm.hkl " >
<log_file_name_1   = " " >
<wavelength_1      = " " >
<fprime_1          = " " >
<fdouble_prime_1   = " " >

{Crystal 1 diffracted with wavelength 2 }
<crystal_number_1  = "1" >
<diffract_number_2 = "2" >
<data_file_name_2  = "input_data/infl.hkl " >
<log_file_name_2   = " " >
<wavelength_2      = " " >
<fprime_2          = " " >
<fdouble_prime_2   = " " >

{Crystal 1 diffracted with wavelength 3 }
<crystal_number_1  = "1" >
<diffract_number_3 = "3" >
<data_file_name_3  = "input_data/lrm.hkl " >
<log_file_name_3   = " " >
<wavelength_3      = " " >
<fprime_3          = " " >
<fdouble_prime_3   = " " >



{==================Structure Factor for Final Refinement=================}
{The structure factors were used for final structure refinement.}

 Note:
 If you use REFMAC5 for refinement, please convert the mtz file to CNS format.
 If the program is not in the above list, please give program name OTHER, and
 provide ASCII file with six values [H, K, L, I(or F), sigmaI(or sigmaF)]
 in each row and separate each value by a space.

 Instruction for items in brackets below:
 refine_data_type:      I for intensity, F for amplitude.
 refine_program_name:   software used for final refinement(CNS|SHELX|TNT).
 refine_data_file_name: file name containing reflection data.

<refine_data_type = "F" >
<refine_program_name = "CNS" >
<refine_data_file_name = " " >



{==================Molecular Replacement=================}
Information will be collected from LOG files generated from softwares
for molecular replacement (only for the last trials).

Instruction for items in brackets below:
mr_software:       (CNS|AMORE|MOLREP|EPMR).
mr_log_file_LOG_?: output file corresponding to each program.

<mr_method = " MR " >
<mr_software = " " >

<mr_log_file_LOG_1 = " " >
<mr_log_file_LOG_2 = " " >


{==================Heavy Atom Phasing And Statistics=================}
Statistics will be collected from some LOG files generated from softwares
during heavy atom phasing (only for the last trials).

Instruction for items in brackets below:
phasing_method:         (SAD|MAD|SIR|SIRAS|MIR|MIRAS).
phasing_software:       (CNS|MLPHARE|SOLVE|SHELXS|SHELXD|SNB|SHARP).
phasing_log_file_CIF_?: output file in CIF format.
phasing_log_file_PDB_?: output file in PDB format.
phasing_log_file_LOG_?: output file corresponding to each program.

<phasing_method = "MAD" >
<phasing_software = " MLPHARE" >

<phasing_log_file_CIF_1 = "input_data/mlphare.mmcif " >
<phasing_log_file_CIF_2 = " " >

<phasing_log_file_PDB_1 = " " >
<phasing_log_file_PDB_2 = " " >

<phasing_log_file_LOG_1 = "input_data/prephadata.dat " >
<phasing_log_file_LOG_2 = " " >


{================Density Modification And Statistics=================}
Statistics will be collected from some LOG files generated from softwares
during density modification (only for the last trials).

Instruction for items in brackets below:
dm_software:        (CNS|DM|RESOLVE|SOLOMON|SHELXE|SHARP).
dm_log_file_CIF_? : the output file in CIF format.
dm_log_file_PDB_? : the output file in PDB format.
dm_log_file_LOG_? : the output file corresponding to each program.

<dm_software = " DM" >

<dm_log_file_CIF_1 = " " >
<dm_log_file_PDB_1 = " " >
<dm_log_file_LOG_1 = " input_data/9_dm.log" >


{================Structure Refinement And Statistics==================}
This is the last step of structure solution. Atom coordinates as well as
statistics from refinement will be collected from files generated by the
softwares (CNS|REFMAC5|SHELXL|TNT|PROLSQ|RESTRAIN).

Instruction for items in brackets below:
refine_software:        (CNS|REFMAC5|SHELXL|TNT|PROLSQ|RESTRAIN).
refine_log_file_CIF_? : the output file in CIF format.
refine_log_file_PDB_? : the output file in PDB format.
refine_log_file_LOG_? : the output file corresponding to each program.

<refine_software = "REFMAC5" >

<refine_log_file_CIF_1 = "input_data/refmac.mmcif " >
<refine_log_file_CIF_2 = " " >

<refine_log_file_PDB_1 = "input_data/refine_gere.pdb " >
<refine_log_file_PDB_2 = " " >

<refine_log_file_LOG_1 = " " >
<refine_log_file_LOG_2 = " " >


{========================Crystallographic Data========================}
{Space group: use International Table conventions.}

<space_group = "C 1 2 1   " >

{unit cell parameters in Angstroms and degrees}

<a     = " 109.019 " >
<b     = "  61.749 " >
<c     = "  71.743 " >
<alpha = " 90.00 " >
<beta  = " 97.08 " >
<gamma = " 90.00 " >


{=========================== Output File Names===========================}
There are two output files in cif format. One is for structure factor and the
other is for the statistics. If you do not specify the output file names, the
default names (pdb_extract.mmcif and pdb_extract_sf.mmcif) will be given.

<sf_output= "script_example_2_sf.cif" >
<statistics_output= "script_example_2.cif" >


{========================Molecular Entities =========================}
A Molecular entity is defined as a unique monomer in asymmetric unit. For
 example, if there are several copies in asymmetric unit, the molecular entity
 is only one. Below is the chemical sequence extracted from the PDB coordinate
 file. The entities are automatically calculated. You need to carefully check
 the entity and modify it if necessary. If a chain is broken, four question
 marks ???? are given at the broken point. You need to replace the ? for the
 missing sequences including N and C terminals. If the residue is modified,
 you should give the full residue name and give parentheses for the residue.

 NOTE: if one molecule is assigned to several chain IDs, the calculated entity
 poly group will NOT be correct, you should manually put all the chain IDs to 
 the same entity poly group. For detailed definition of entity poly group,
 please see http://pdb.rutgers.edu/mmcif/

<ENTITY_ID="1" >
< ENTITY_TYPE="polypeptide(L)" >
< ONE_LETTER_SEQUNCE=" 
SKPLLTKREREVFELLVQDKTTKEIASELFISEKTVRNHISNAMQKLGVKGRSQAVVELLRMGELEL" >
< CHAIN_ID="A,B,C,D,E,F" >

<ENTITY_ID=" " >
< ENTITY_TYPE=" " >
< ONE_LETTER_SEQUNCE="  " >
< CHAIN_ID=" " >