phenix.predict_and_build, proccess normal and no error, but not generate the PredictAndBuild_0_overall_best.pdb

6 Jan 2025

      How can i deal with it? This is the log file

Starting phenix.predict_and_build
on Wed Jan  1 20:55:50 2025 by xukui
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  No files found

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    full_map=/data2/xukui/data/jobs_pab/6b3o/6b3o.mrc
    seq_file=/data2/xukui/data/jobs_pab/6b3o/6b3o.fasta
    resolution=4.1
    nproc=20
    predicted_model=/data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb
    process_predicted_model.chunk_size=10000
    predict_and_build.chunk_size=10000
    process_predicted_model.break_into_chunks_if_length_is=10000
    predict_and_build.break_into_chunks_if_length_is=10000

Warning: Ambiguous parameter definition: resolution = 4.1
Best matches:
  crystal_info.resolution
  prediction.resolution
Assuming crystal_info.resolution was intended.
Warning: Ambiguous parameter definition: nproc = 20
Best matches:
  prediction.nproc
  control.nproc
Assuming control.nproc was intended.
Processing files from PHIL:
-------------------------------------------------------------------------------

  Found model, /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb
  Found sequence, /data2/xukui/data/jobs_pab/6b3o/6b3o.fasta
  Found real_map, /data2/xukui/data/jobs_pab/6b3o/6b3o.mrc

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    sequence_files = "/data2/xukui/data/jobs_pab/6b3o/6b3o.fasta"
    default_sequence = "/data2/xukui/data/jobs_pab/6b3o/6b3o.fasta"
    real_map_files = "/data2/xukui/data/jobs_pab/6b3o/6b3o.mrc"
    default_real_map = "/data2/xukui/data/jobs_pab/6b3o/6b3o.mrc"
    model {
      file = "/data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb"
    }
    default_model = "/data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb"
  }
  predict_and_build {
    break_into_chunks_if_length_is = 10000
    chunk_size = 10000
  }
  input_files {
    seq_file = /data2/xukui/data/jobs_pab/6b3o/6b3o.fasta
    map_model {
      full_map = /data2/xukui/data/jobs_pab/6b3o/6b3o.mrc
    }
    predicted_model = /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb
  }
  crystal_info {
    resolution = 4.1
  }
  process_predicted_model {
    break_into_chunks_if_length_is = 10000
    chunk_size = 10000
  }
  control {
    nproc = 20
  }

Starting job
===============================================================================

************************************************************
          PHENIX predict_and_build  Wed Jan  1 20:55:59 2025
************************************************************

Working directory:  /data2/xukui/data/jobs_pab/6b3o 

PHENIX VERSION:  1.21.1-5286 

Base directory is /data2/xukui/data/jobs_pab/6b3o
Creating jobname of 'PredictAndBuild_0'
Working directory /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0_CarryOn will be created in base directory
Output prefix for files will be: /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0_CarryOn/PredictAndBuild_0_rebuilt
Running in Standard mode...
Turning off all building steps except refinement

Running with a cryo-EM map
Mean B-iso in af2_group_0.pdb: 80.9577007535 A**2
Added predicted model /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb_A with plddt=80.96 
Mean value in B-factor field for /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb (converted from plddt to plddt): 80.96 
Set random_seed_iterations to 5
No templates read from templates_as_string...
Total of 0 templates to be used
Setting density_modify_with_model = False (default for cryo-EM)

Set rmsd_for_similar_placement to 4.10 A
Working directory will be based on jobname: PredictAndBuild_0
Created new temp dir: PredictAndBuild_0 ...
temp-dir will be deleted at end

================================================================================
Running predict_and_build
================================================================================

Starting data:
Map file: Map manager (from /data2/xukui/data/jobs_pab/6b3o/6b3o.mrc)
Unit cell: (435.2, 435.2, 435.2, 90, 90, 90) Space group: P 1 (No. 1), 
Unit-cell grid: (320, 320, 320), (present: (320, 320, 320)), origin shift (0, 0, 0) 
Working coordinate shift (-0.0, -0.0, -0.0)
NCS object with 0 groups: 

List of sequences:
MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK
MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK
MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK

List of models:
af2_group_0.pdb Chain A extracted

List of chain IDs and sequences to use
A (6b3o_A): MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK
B (6b3o_A): MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK
C (6b3o_A): MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK

================================================================================
Running cycle 1 of predict_and_build
================================================================================
Not using any supplied msas
No supplied templates will be used in prediction this cycle

================================================================================
Predicting models for 0 chains with alphafold

Updating chain names in model list...
Chain A: MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK
Total of 1 working models
Total MSAs obtained: 0

Updating chain IDs
Previous ID: 'A'  New ID: 'A' 
MODEL: af2_group_0.pdb

Getting processed (trimmed, B-values updated) models 
B-value field interpreted as pLDDT (0 - 100)
Maximum rmsd of 1.50 A used
Maximum B-value to be included: 59.22 A**2
Removing short segments: (chain A and resseq 537:539)
Total of 492 of 605 residues kept after B-factor filtering

Selection string for B-factor filtering:  (chain A and resseq 15:20)  or  (chain A and resseq 25:136)  or  (chain A and resseq 145:157)  or  (chain A and resseq 174:200)  or  (chain A and resseq 207:494)  or  (chain A and resseq 541:586) 

Selecting domains as compact chains
Clusters: 15   Threshold: 3.90 
Clusters: 5   Threshold: 4.40 
Clusters: 6   Threshold: 4.82 
Clusters: 5   Threshold: 4.34 
Clusters: 3   Threshold: 3.27 
Clusters: 2   Threshold: 2.14 
Clusters: 3   Threshold: 3.98 
Clusters: 2   Threshold: 1.81 
Clusters: 3   Threshold: 3.74 
Clusters: 2   Threshold: 1.80 
Best resolution for domains is 35.0 A giving 3 regions

Selection list based on domains:
(resseq 15:20) or (resseq 25:136) or (resseq 145:157) or (resseq 174:200) or (resseq 207:494) or (resseq 541:586) (492 residues)  
Total of 1 regions identified
Obtained processed model from af2_group_0.pdb with 492 residues (of 605)
=============================================================================== 
Finished with prediction (Job PredictAndBuild_0 cycle 1 at 2025-01-01 20:56:19) 
=============================================================================== 

=============================================================================== 
Getting scaffold model... (Job PredictAndBuild_0 cycle 1 at 2025-01-01 20:56:19) 
=============================================================================== 

Checking whether scaffold model is complete...

================================================================================
Getting new scaffold model in /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0_CarryOn/PredictAndBuild_0_scaffold_cycle_1.pdb
================================================================================

================================================================================
Docking 1 models (to represent 3 sequences) in map to create a scaffold

================================================================================
Model to dock: af2_group_0.pdb: MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK
Calculating how many copies of each sequence
Model: A MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK
Model copies: 1 Sequence copies:  3
Remainder copies:  {'MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK': 0} remainder: 0
Copies to use:  3
Setting up model for dock_and_rebuild
Added model af2_group_0.pdb (A) for dock_and_rebuild

Running dock_and_rebuild to dock models

Total of 1 predicted models
MODEL: MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK

================================================================================
Running dock_and_rebuild on total of 3 chains
Chain 1 (chain A from af2_group_0.pdb) 
Chain 2 (chain A from af2_group_0.pdb) 
Chain 3 (chain A from af2_group_0.pdb) 
================================================================================

================================================================================
Running on chain 1 (chain A from af2_group_0.pdb)
================================================================================
Working directory for this chain: PredictAndBuild_0/local_dock_and_rebuild_1_0
No docked model for chain A ...
Running search...

Running standard docking...

 =============================================================================== 
    Processing input model 
 =============================================================================== 

B-value field interpreted as pLDDT (0 - 100)
Maximum rmsd of 1.50 A used
Maximum B-value to be included: 59.22 A**2
Removing short segments: (chain A and resseq 537:539)
Total of 492 of 605 residues kept after B-factor filtering

Selection string for B-factor filtering:  (chain A and resseq 15:20)  or  (chain A and resseq 25:136)  or  (chain A and resseq 145:157)  or  (chain A and resseq 174:200)  or  (chain A and resseq 207:494)  or  (chain A and resseq 541:586) 

Selecting domains as compact chains
Clusters: 15   Threshold: 3.90 
Clusters: 5   Threshold: 4.40 
Clusters: 6   Threshold: 4.82 
Clusters: 5   Threshold: 4.34 
Clusters: 3   Threshold: 3.27 
Clusters: 2   Threshold: 2.14 
Clusters: 3   Threshold: 3.98 
Clusters: 2   Threshold: 1.81 
Clusters: 3   Threshold: 3.74 
Clusters: 2   Threshold: 1.80 
Best resolution for domains is 35.0 A giving 3 regions

Selection list based on domains:
(resseq 15:20) or (resseq 25:136) or (resseq 145:157) or (resseq 174:200) or (resseq 207:494) or (resseq 541:586) (492 residues)  
Total of 1 regions identified
Obtained processed model with 492 residues (of 605)
Wrote processed model to /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0/local_dock_and_rebuild_1_0/working_model_processed.pdb

 =============================================================================== 
 Extracting unique part of map 
 =============================================================================== 

Setting map-model-manager and model shift to zero during run
Split model into chains: A1
Chain number: 1 id: A1  Residues: 492

 ============================================================================== 
  Searching with each chain as a seed  
 ============================================================================== 

 ============================================================================== 
  Running dock-in map on domain A1 with 492 residues 
 ============================================================================== 

Running dock-in-map at overall resolution of 4.1 A
Density radius set to: 24.6 A
Placing model in map

Map has been not been offset 
New cell after running map_box: (435.20, 424.32, 435.20, 90.00, 90.00, 90.00)
Target boxes set to 20

Choosing local part of search model to use in search...

Shifting search model coordinates (0.3, 1.9, -1.9)  to origin 
and creating search map coefficients

Docking with MR...
Using masked map data
MODEL: full_shifted_sm_1.pdb  mass: 54120 (copies: 1)
Estimated solvent fraction: 0.95
Total atoms in all copies: 3781 (volume = 66567.6 A**3)
Solvent fraction (as used) is about 0.94
Total good sites: 11268
Max clusters: 1
Wrote mtz data to PredictAndBuild_0/local_dock_and_rebuild_1_0/run_mr/mtz_data.mtz
Wrote model A1_full_shifted_sm_1.pdb to PredictAndBuild_0/local_dock_and_rebuild_1_0/run_mr/A1_full_shifted_sm_1.pdb
Wrote model A_from_cluster_0.pdb to PredictAndBuild_0/local_dock_and_rebuild_1_0/run_mr/A_from_cluster_0.pdb

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