On Thu, Jan 9, 2025 at 11:13 AM Oleg Sobolev <osobolev(a)lbl.gov> wrote:
> Hi Tom,
>
> I fished out the following from my Spam folder, but it is on PhenixBB. Can
> you please take a look?
>
> Best regards,
> Oleg Sobolev.
>
> ---------- Forwarded message ---------
> From: <fnsoxt(a)qq.com>
> Date: Sun, Jan 5, 2025 at 8:03 PM
> Subject: [phenixbb] phenix.predict_and_build, proccess normal and no
> error, but not generate the PredictAndBuild_0_overall_best.pdb
> To: <phenixbb(a)phenix-online.org>
>
>
> 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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>
--
Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Email: tterwilliger(a)newmexicoconsortium.org
Tel: 505-431-0010
