Starting phenix.real_space_refine (version: 1.19rc7) on Wed Jan 6 05:43:18 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sp2_10279/01_2021/6sp2_10279_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sp2_10279/01_2021/6sp2_10279.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sp2_10279/01_2021/6sp2_10279_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sp2_10279/01_2021/6sp2_10279_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sp2_10279/01_2021/6sp2_10279_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sp2_10279/01_2021/6sp2_10279.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sp2_10279/01_2021/6sp2_10279.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sp2_10279/01_2021/6sp2_10279_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sp2_10279/01_2021/6sp2_10279_updated.pdb" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.136 Set model interpretation parameters Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/modules/chem_data/mon_lib" Total number of atoms: 18498 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2834 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 12, 'TRANS': 352} Chain breaks: 3 Chain: "B" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2834 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 12, 'TRANS': 352} Chain breaks: 3 Chain: "C" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2834 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 12, 'TRANS': 352} Chain breaks: 3 Chain: "D" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2834 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 12, 'TRANS': 352} Chain breaks: 3 Chain: "E" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2834 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 12, 'TRANS': 352} Chain breaks: 3 Chain: "F" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2834 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 12, 'TRANS': 352} Chain breaks: 3 Chain: "A" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 249 Unusual residues: {'CDL': 1, 'LMN': 2} Classifications: {'undetermined': 3, 'peptide': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 249 Unusual residues: {'CDL': 1, 'LMN': 2} Classifications: {'undetermined': 3, 'peptide': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 249 Unusual residues: {'CDL': 1, 'LMN': 2} Classifications: {'undetermined': 3, 'peptide': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 249 Unusual residues: {'CDL': 1, 'LMN': 2} Classifications: {'undetermined': 3, 'peptide': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 10 Chain: "E" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 249 Unusual residues: {'CDL': 1, 'LMN': 2} Classifications: {'undetermined': 3, 'peptide': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 10 Chain: "F" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 249 Unusual residues: {'CDL': 1, 'LMN': 2} Classifications: {'undetermined': 3, 'peptide': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 9.58, per 1000 atoms: 0.52 Found NCS groups: ncs_group { reference = (chain 'A' and resid 30 through 461) selection = (chain 'B' and resid 30 through 461) selection = (chain 'C' and resid 30 through 461) selection = (chain 'D' and resid 30 through 461) selection = (chain 'E' and resid 30 through 461) selection = (chain 'F' and resid 30 through 461) } Number of scatterers: 18498 At special positions: 0 Unit cell: (133.86, 144.9, 78.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 156 16.00 P 18 15.00 O 3348 8.00 N 2640 7.00 C 12336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 95 " distance=2.04 Simple disulfide: pdb=" SG CYS A 238 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 71 " - pdb=" SG CYS B 95 " distance=2.04 Simple disulfide: pdb=" SG CYS B 238 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 71 " - pdb=" SG CYS C 95 " distance=2.04 Simple disulfide: pdb=" SG CYS C 238 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS D 71 " - pdb=" SG CYS D 95 " distance=2.04 Simple disulfide: pdb=" SG CYS D 238 " - pdb=" SG CYS D 299 " distance=2.03 Simple disulfide: pdb=" SG CYS E 71 " - pdb=" SG CYS E 95 " distance=2.04 Simple disulfide: pdb=" SG CYS E 238 " - pdb=" SG CYS E 299 " distance=2.03 Simple disulfide: pdb=" SG CYS F 71 " - pdb=" SG CYS F 95 " distance=2.04 Simple disulfide: pdb=" SG CYS F 238 " - pdb=" SG CYS F 299 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.57 Conformation dependent library (CDL) restraints added in 2.7 seconds 4284 Ramachandran restraints generated. 2142 Oldfield and 0 Emsley and 2142 emsley8k. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4080 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 0 sheets defined 68.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 31 through 54 removed outlier: 3.568A pdb=" N ALA A 43 " --> pdb=" O ARG A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 91 through 97 Processing helix chain 'A' and resid 99 through 121 removed outlier: 3.938A pdb=" N GLY A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 134 Processing helix chain 'A' and resid 140 through 156 removed outlier: 4.092A pdb=" N PHE A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 200 Processing helix chain 'A' and resid 207 through 231 removed outlier: 4.176A pdb=" N THR A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 258 removed outlier: 3.583A pdb=" N SER A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER A 256 " --> pdb=" O CYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 267 removed outlier: 4.290A pdb=" N ARG A 267 " --> pdb=" O ALA A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 293 removed outlier: 4.198A pdb=" N ASN A 293 " --> pdb=" O SER A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 347 Processing helix chain 'A' and resid 397 through 415 removed outlier: 4.106A pdb=" N HIS A 401 " --> pdb=" O TRP A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 453 removed outlier: 3.896A pdb=" N VAL A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 460 Processing helix chain 'B' and resid 31 through 54 removed outlier: 3.568A pdb=" N ALA B 43 " --> pdb=" O ARG B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 91 through 97 Processing helix chain 'B' and resid 99 through 121 removed outlier: 3.939A pdb=" N GLY B 110 " --> pdb=" O ARG B 106 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 134 Processing helix chain 'B' and resid 140 through 156 removed outlier: 4.092A pdb=" N PHE B 156 " --> pdb=" O ILE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 200 Processing helix chain 'B' and resid 207 through 231 removed outlier: 4.175A pdb=" N THR B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 258 removed outlier: 3.584A pdb=" N SER B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER B 256 " --> pdb=" O CYS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 267 removed outlier: 4.290A pdb=" N ARG B 267 " --> pdb=" O ALA B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 293 removed outlier: 4.199A pdb=" N ASN B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 347 Processing helix chain 'B' and resid 397 through 415 removed outlier: 4.107A pdb=" N HIS B 401 " --> pdb=" O TRP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 453 removed outlier: 3.897A pdb=" N VAL B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 460 Processing helix chain 'C' and resid 31 through 54 removed outlier: 3.568A pdb=" N ALA C 43 " --> pdb=" O ARG C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 99 through 121 removed outlier: 3.938A pdb=" N GLY C 110 " --> pdb=" O ARG C 106 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET C 111 " --> pdb=" O VAL C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 134 Processing helix chain 'C' and resid 140 through 156 removed outlier: 4.092A pdb=" N PHE C 156 " --> pdb=" O ILE C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 200 Processing helix chain 'C' and resid 207 through 231 removed outlier: 4.176A pdb=" N THR C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 258 removed outlier: 3.584A pdb=" N SER C 246 " --> pdb=" O LYS C 242 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER C 256 " --> pdb=" O CYS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 267 removed outlier: 4.290A pdb=" N ARG C 267 " --> pdb=" O ALA C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 293 removed outlier: 4.199A pdb=" N ASN C 293 " --> pdb=" O SER C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 347 Processing helix chain 'C' and resid 397 through 415 removed outlier: 4.106A pdb=" N HIS C 401 " --> pdb=" O TRP C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 453 removed outlier: 3.897A pdb=" N VAL C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 460 Processing helix chain 'D' and resid 31 through 54 removed outlier: 3.568A pdb=" N ALA D 43 " --> pdb=" O ARG D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 67 No H-bonds generated for 'chain 'D' and resid 65 through 67' Processing helix chain 'D' and resid 91 through 97 Processing helix chain 'D' and resid 99 through 121 removed outlier: 3.938A pdb=" N GLY D 110 " --> pdb=" O ARG D 106 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET D 111 " --> pdb=" O VAL D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 134 Processing helix chain 'D' and resid 140 through 156 removed outlier: 4.092A pdb=" N PHE D 156 " --> pdb=" O ILE D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 200 Processing helix chain 'D' and resid 207 through 231 removed outlier: 4.176A pdb=" N THR D 214 " --> pdb=" O LEU D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 258 removed outlier: 3.584A pdb=" N SER D 246 " --> pdb=" O LYS D 242 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER D 256 " --> pdb=" O CYS D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 267 removed outlier: 4.290A pdb=" N ARG D 267 " --> pdb=" O ALA D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 293 removed outlier: 4.198A pdb=" N ASN D 293 " --> pdb=" O SER D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 347 Processing helix chain 'D' and resid 397 through 415 removed outlier: 4.107A pdb=" N HIS D 401 " --> pdb=" O TRP D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 453 removed outlier: 3.897A pdb=" N VAL D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 460 Processing helix chain 'E' and resid 31 through 54 removed outlier: 3.568A pdb=" N ALA E 43 " --> pdb=" O ARG E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 67 No H-bonds generated for 'chain 'E' and resid 65 through 67' Processing helix chain 'E' and resid 91 through 97 Processing helix chain 'E' and resid 99 through 121 removed outlier: 3.938A pdb=" N GLY E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET E 111 " --> pdb=" O VAL E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 134 Processing helix chain 'E' and resid 140 through 156 removed outlier: 4.093A pdb=" N PHE E 156 " --> pdb=" O ILE E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 200 Processing helix chain 'E' and resid 207 through 231 removed outlier: 4.176A pdb=" N THR E 214 " --> pdb=" O LEU E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 258 removed outlier: 3.583A pdb=" N SER E 246 " --> pdb=" O LYS E 242 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER E 256 " --> pdb=" O CYS E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 267 removed outlier: 4.291A pdb=" N ARG E 267 " --> pdb=" O ALA E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 293 removed outlier: 4.198A pdb=" N ASN E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 347 Processing helix chain 'E' and resid 397 through 415 removed outlier: 4.106A pdb=" N HIS E 401 " --> pdb=" O TRP E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 453 removed outlier: 3.896A pdb=" N VAL E 437 " --> pdb=" O ALA E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 460 Processing helix chain 'F' and resid 31 through 54 removed outlier: 3.568A pdb=" N ALA F 43 " --> pdb=" O ARG F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 67 No H-bonds generated for 'chain 'F' and resid 65 through 67' Processing helix chain 'F' and resid 91 through 97 Processing helix chain 'F' and resid 99 through 121 removed outlier: 3.938A pdb=" N GLY F 110 " --> pdb=" O ARG F 106 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET F 111 " --> pdb=" O VAL F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 134 Processing helix chain 'F' and resid 140 through 156 removed outlier: 4.091A pdb=" N PHE F 156 " --> pdb=" O ILE F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 200 Processing helix chain 'F' and resid 207 through 231 removed outlier: 4.176A pdb=" N THR F 214 " --> pdb=" O LEU F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 258 removed outlier: 3.584A pdb=" N SER F 246 " --> pdb=" O LYS F 242 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER F 256 " --> pdb=" O CYS F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 267 removed outlier: 4.289A pdb=" N ARG F 267 " --> pdb=" O ALA F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 293 removed outlier: 4.199A pdb=" N ASN F 293 " --> pdb=" O SER F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 347 Processing helix chain 'F' and resid 397 through 415 removed outlier: 4.106A pdb=" N HIS F 401 " --> pdb=" O TRP F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 453 removed outlier: 3.897A pdb=" N VAL F 437 " --> pdb=" O ALA F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 460 1086 hydrogen bonds defined for protein. 3240 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.62 Time building geometry restraints manager: 8.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2692 1.32 - 1.45: 5412 1.45 - 1.58: 10586 1.58 - 1.70: 36 1.70 - 1.83: 234 Bond restraints: 18960 Sorted by residual: bond pdb=" C1 LMN E1002 " pdb=" O5 LMN E1002 " ideal model delta sigma weight residual 1.535 1.412 0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" C1 LMN F1002 " pdb=" O5 LMN F1002 " ideal model delta sigma weight residual 1.535 1.412 0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" C1 LMN C1002 " pdb=" O5 LMN C1002 " ideal model delta sigma weight residual 1.535 1.413 0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C1 LMN B1002 " pdb=" O5 LMN B1002 " ideal model delta sigma weight residual 1.535 1.413 0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C1 LMN A 604 " pdb=" O5 LMN A 604 " ideal model delta sigma weight residual 1.535 1.413 0.122 2.00e-02 2.50e+03 3.72e+01 ... (remaining 18955 not shown) Histogram of bond angle deviations from ideal: 98.92 - 105.94: 390 105.94 - 112.96: 10579 112.96 - 119.98: 7004 119.98 - 127.00: 7422 127.00 - 134.02: 249 Bond angle restraints: 25644 Sorted by residual: angle pdb=" N PRO B 69 " pdb=" CA PRO B 69 " pdb=" C PRO B 69 " ideal model delta sigma weight residual 113.53 119.00 -5.47 1.39e+00 5.18e-01 1.55e+01 angle pdb=" N PRO E 69 " pdb=" CA PRO E 69 " pdb=" C PRO E 69 " ideal model delta sigma weight residual 113.53 118.99 -5.46 1.39e+00 5.18e-01 1.55e+01 angle pdb=" N VAL D 352 " pdb=" CA VAL D 352 " pdb=" C VAL D 352 " ideal model delta sigma weight residual 112.98 108.07 4.91 1.25e+00 6.40e-01 1.54e+01 angle pdb=" N PRO D 69 " pdb=" CA PRO D 69 " pdb=" C PRO D 69 " ideal model delta sigma weight residual 113.53 118.98 -5.45 1.39e+00 5.18e-01 1.54e+01 angle pdb=" N VAL F 352 " pdb=" CA VAL F 352 " pdb=" C VAL F 352 " ideal model delta sigma weight residual 112.98 108.08 4.90 1.25e+00 6.40e-01 1.54e+01 ... (remaining 25639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.55: 10548 30.55 - 61.09: 216 61.09 - 91.64: 12 91.64 - 122.18: 12 122.18 - 152.73: 12 Dihedral angle restraints: 10800 sinusoidal: 4452 harmonic: 6348 Sorted by residual: dihedral pdb=" CB CYS D 71 " pdb=" SG CYS D 71 " pdb=" SG CYS D 95 " pdb=" CB CYS D 95 " ideal model delta sinusoidal sigma weight residual 93.00 152.59 -59.59 1 1.00e+01 1.00e-02 4.74e+01 dihedral pdb=" CB CYS F 71 " pdb=" SG CYS F 71 " pdb=" SG CYS F 95 " pdb=" CB CYS F 95 " ideal model delta sinusoidal sigma weight residual 93.00 152.58 -59.58 1 1.00e+01 1.00e-02 4.74e+01 dihedral pdb=" CB CYS C 71 " pdb=" SG CYS C 71 " pdb=" SG CYS C 95 " pdb=" CB CYS C 95 " ideal model delta sinusoidal sigma weight residual 93.00 152.56 -59.56 1 1.00e+01 1.00e-02 4.74e+01 ... (remaining 10797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.023: 2994 1.023 - 2.045: 0 2.045 - 3.068: 0 3.068 - 4.090: 0 4.090 - 5.113: 6 Chirality restraints: 3000 Sorted by residual: chirality pdb=" CA4 CDL D1001 " pdb=" CA3 CDL D1001 " pdb=" CA6 CDL D1001 " pdb=" OA6 CDL D1001 " both_signs ideal model delta sigma weight residual False 2.70 -2.42 5.11 2.00e-01 2.50e+01 6.54e+02 chirality pdb=" CA4 CDL A 603 " pdb=" CA3 CDL A 603 " pdb=" CA6 CDL A 603 " pdb=" OA6 CDL A 603 " both_signs ideal model delta sigma weight residual False 2.70 -2.42 5.11 2.00e-01 2.50e+01 6.53e+02 chirality pdb=" CA4 CDL B1001 " pdb=" CA3 CDL B1001 " pdb=" CA6 CDL B1001 " pdb=" OA6 CDL B1001 " both_signs ideal model delta sigma weight residual False 2.70 -2.42 5.11 2.00e-01 2.50e+01 6.53e+02 ... (remaining 2997 not shown) Planarity restraints: 2904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F 268 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.63e+00 pdb=" N PRO F 269 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO F 269 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 269 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 268 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO B 269 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 269 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 269 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 268 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.62e+00 pdb=" N PRO A 269 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 269 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 269 " 0.023 5.00e-02 4.00e+02 ... (remaining 2901 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 6 2.25 - 2.91: 7586 2.91 - 3.58: 26438 3.58 - 4.24: 39017 4.24 - 4.90: 68154 Nonbonded interactions: 141201 Sorted by model distance: nonbonded pdb=" O3 LMN F1002 " pdb=" OAU LMN F1002 " model vdw 1.590 2.440 nonbonded pdb=" O3 LMN A 604 " pdb=" OAU LMN A 604 " model vdw 1.590 2.440 nonbonded pdb=" O3 LMN D1002 " pdb=" OAU LMN D1002 " model vdw 1.590 2.440 nonbonded pdb=" O3 LMN E1002 " pdb=" OAU LMN E1002 " model vdw 1.590 2.440 nonbonded pdb=" O3 LMN B1002 " pdb=" OAU LMN B1002 " model vdw 1.590 2.440 ... (remaining 141196 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints 17004 18498 True True No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 156 5.16 5 C 12336 2.51 5 N 2640 2.21 5 O 3348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 Set model interpretation parameters: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.750 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.070 Process input model: 52.210 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.520 Internal consistency checks: 0.000 Total: 63.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.011 0.123 18960 Angle : 1.069 11.015 25644 Chirality : 0.233 5.113 3000 Planarity : 0.005 0.041 2904 Dihedral : 13.999 152.727 6684 Min Nonbonded Distance : 1.590 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.17), residues: 2142 helix: 0.38 (0.12), residues: 1434 sheet: None (None), residues: 0 loop : -1.86 (0.24), residues: 708 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield and 0 Emsley and 2142 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield and 0 Emsley and 2142 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1872 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 308 time to evaluate : 1.732 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.3115 time to fit residues: 99.2024 Evaluate side-chains 215 residues out of total 1872 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.912 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.4980 chunk 163 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 55 optimal weight: 0.2980 chunk 110 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 196 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN A 422 HIS ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 HIS C 422 HIS D 136 GLN D 332 ASN D 422 HIS E 422 HIS ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.029 18960 Angle : 0.580 11.152 25644 Chirality : 0.039 0.139 3000 Planarity : 0.004 0.032 2904 Dihedral : 13.188 121.532 3078 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.18), residues: 2142 helix: 2.03 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -1.42 (0.25), residues: 708 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield and 0 Emsley and 2142 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield and 0 Emsley and 2142 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1872 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 271 time to evaluate : 2.176 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.3064 time to fit residues: 86.5842 Evaluate side-chains 206 residues out of total 1872 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 206 time to evaluate : 2.050 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 163 optimal weight: 0.0470 chunk 133 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 212 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 GLN ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.067 18960 Angle : 0.571 11.431 25644 Chirality : 0.039 0.132 3000 Planarity : 0.003 0.039 2904 Dihedral : 11.933 98.388 3078 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.19), residues: 2142 helix: 2.50 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : -1.27 (0.26), residues: 714 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield and 0 Emsley and 2142 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield and 0 Emsley and 2142 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1872 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 272 time to evaluate : 2.224 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.3104 time to fit residues: 88.0186 Evaluate side-chains 206 residues out of total 1872 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 206 time to evaluate : 2.055 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 1.9990 chunk 147 optimal weight: 0.0670 chunk 101 optimal weight: 0.0370 chunk 21 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 197 optimal weight: 0.9980 chunk 208 optimal weight: 0.1980 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.073 18960 Angle : 0.551 10.878 25644 Chirality : 0.039 0.155 3000 Planarity : 0.003 0.039 2904 Dihedral : 10.805 94.098 3078 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.19), residues: 2142 helix: 2.75 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : -1.24 (0.26), residues: 714 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield and 0 Emsley and 2142 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield and 0 Emsley and 2142 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1872 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 309 time to evaluate : 2.186 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.3041 time to fit residues: 97.1658 Evaluate side-chains 210 residues out of total 1872 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 210 time to evaluate : 2.112 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 0.4980 chunk 118 optimal weight: 5.9990 chunk 3 optimal weight: 0.0020 chunk 155 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 178 optimal weight: 0.9980 chunk 144 optimal weight: 10.0000 chunk 0 optimal weight: 10.9990 chunk 106 optimal weight: 0.9990 chunk 187 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 ASN B 270 HIS C 429 ASN D 332 ASN D 429 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.053 18960 Angle : 0.584 11.237 25644 Chirality : 0.040 0.188 3000 Planarity : 0.003 0.041 2904 Dihedral : 10.670 89.053 3078 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.19), residues: 2142 helix: 2.93 (0.13), residues: 1422 sheet: None (None), residues: 0 loop : -1.17 (0.26), residues: 720 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield and 0 Emsley and 2142 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield and 0 Emsley and 2142 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1872 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 3 poor density : 298 time to evaluate : 2.135 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 301 average time/residue: 0.3120 time to fit residues: 97.7595 Evaluate side-chains 232 residues out of total 1872 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 232 time to evaluate : 2.052 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.7980 chunk 188 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 96 optimal weight: 0.0170 chunk 17 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN B 270 HIS B 322 HIS F 322 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.077 18960 Angle : 0.581 10.973 25644 Chirality : 0.040 0.152 3000 Planarity : 0.003 0.031 2904 Dihedral : 10.421 77.187 3078 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.19), residues: 2142 helix: 3.03 (0.13), residues: 1422 sheet: None (None), residues: 0 loop : -1.12 (0.26), residues: 720 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield and 0 Emsley and 2142 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield and 0 Emsley and 2142 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1872 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 293 time to evaluate : 1.925 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.2935 time to fit residues: 89.2275 Evaluate side-chains 239 residues out of total 1872 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 239 time to evaluate : 1.977 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 126 optimal weight: 0.0010 chunk 96 optimal weight: 0.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 322 HIS E 138 ASN F 322 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.058 18960 Angle : 0.655 11.773 25644 Chirality : 0.042 0.166 3000 Planarity : 0.003 0.032 2904 Dihedral : 11.229 66.708 3078 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.19), residues: 2142 helix: 2.87 (0.13), residues: 1422 sheet: None (None), residues: 0 loop : -1.16 (0.26), residues: 720 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield and 0 Emsley and 2142 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield and 0 Emsley and 2142 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1872 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 271 time to evaluate : 2.070 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.3163 time to fit residues: 89.1108 Evaluate side-chains 217 residues out of total 1872 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 217 time to evaluate : 2.121 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 163 optimal weight: 0.9990 chunk 189 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 GLN E 136 GLN F 322 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.055 18960 Angle : 0.609 11.242 25644 Chirality : 0.041 0.203 3000 Planarity : 0.003 0.032 2904 Dihedral : 10.973 63.499 3078 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.19), residues: 2142 helix: 2.98 (0.13), residues: 1422 sheet: None (None), residues: 0 loop : -1.21 (0.26), residues: 720 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield and 0 Emsley and 2142 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield and 0 Emsley and 2142 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1872 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 260 time to evaluate : 2.216 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.3073 time to fit residues: 83.3744 Evaluate side-chains 220 residues out of total 1872 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 220 time to evaluate : 2.124 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 0.4980 chunk 181 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 116 optimal weight: 0.0270 chunk 84 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 183 optimal weight: 0.0270 chunk 193 optimal weight: 0.7980 chunk 127 optimal weight: 0.1980 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 270 HIS C 136 GLN F 138 ASN F 322 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.055 18960 Angle : 0.569 10.525 25644 Chirality : 0.039 0.161 3000 Planarity : 0.003 0.031 2904 Dihedral : 10.140 58.707 3078 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.19), residues: 2142 helix: 3.23 (0.13), residues: 1422 sheet: None (None), residues: 0 loop : -1.21 (0.26), residues: 720 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield and 0 Emsley and 2142 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield and 0 Emsley and 2142 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1872 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 296 time to evaluate : 2.209 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.3030 time to fit residues: 93.5974 Evaluate side-chains 234 residues out of total 1872 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 234 time to evaluate : 2.164 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 0.0030 chunk 125 optimal weight: 0.3980 chunk 97 optimal weight: 8.9990 chunk 142 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 198 optimal weight: 0.8980 chunk 171 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 105 optimal weight: 0.0770 chunk 136 optimal weight: 3.9990 overall best weight: 0.4148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 270 HIS C 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.053 18960 Angle : 0.574 10.704 25644 Chirality : 0.039 0.165 3000 Planarity : 0.003 0.032 2904 Dihedral : 10.031 59.659 3078 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.19), residues: 2142 helix: 3.16 (0.13), residues: 1446 sheet: None (None), residues: 0 loop : -1.06 (0.26), residues: 696 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield and 0 Emsley and 2142 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield and 0 Emsley and 2142 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1872 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 275 time to evaluate : 1.955 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.2966 time to fit residues: 84.8663 Evaluate side-chains 220 residues out of total 1872 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 220 time to evaluate : 1.956 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 3.9990 chunk 52 optimal weight: 0.0470 chunk 158 optimal weight: 0.7980 chunk 25 optimal weight: 0.0970 chunk 47 optimal weight: 0.8980 chunk 171 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 21 optimal weight: 0.0070 chunk 31 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 overall best weight: 0.3094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 270 HIS C 270 HIS D 138 ASN D 270 HIS ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.183110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.144023 restraints weight = 22008.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.148835 restraints weight = 11998.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.151883 restraints weight = 8663.786| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.002 0.054 18960 ANGLE : 0.563 10.382 25644 CHIRALITY : 0.039 0.156 3000 PLANARITY : 0.003 0.030 2904 DIHEDRAL : 9.723 59.310 3078 MIN NONBONDED DISTANCE : 2.316 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 5.90 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 4.06 % FAVORED : 95.94 % ROTAMER OUTLIERS : 0.00 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 0.00 % CIS-GENERAL : 0.00 % TWISTED PROLINE : 0.00 % TWISTED GENERAL : 0.00 % RAMA-Z (RAMACHANDRAN PLOT Z-SCORE): INTERPRETATION: BAD |RAMA-Z| > 3; SUSPICIOUS 2 < |RAMA-Z| < 3; GOOD |RAMA-Z| < 2. SCORES FOR WHOLE/HELIX/SHEET/LOOP ARE SCALED INDEPENDENTLY; THEREFORE, THE VALUES ARE NOT RELATED IN A SIMPLE MANNER. WHOLE: 2.83 (0.19), RESIDUES: 2142 HELIX: 3.25 (0.13), RESIDUES: 1440 SHEET: NONE (NONE), RESIDUES: 0 LOOP : -1.27 (0.26), RESIDUES: 702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.054 18960 Angle : 0.563 10.382 25644 Chirality : 0.039 0.156 3000 Planarity : 0.003 0.030 2904 Dihedral : 9.723 59.310 3078 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.19), residues: 2142 helix: 3.25 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : -1.27 (0.26), residues: 702 =============================================================================== Job complete usr+sys time: 3033.27 seconds wall clock time: 57 minutes 18.25 seconds (3438.25 seconds total)