Starting phenix.real_space_refine on Mon Aug 25 12:23:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dkf_46956/08_2025/9dkf_46956.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dkf_46956/08_2025/9dkf_46956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dkf_46956/08_2025/9dkf_46956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dkf_46956/08_2025/9dkf_46956.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dkf_46956/08_2025/9dkf_46956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dkf_46956/08_2025/9dkf_46956.map" } resolution = 2.6 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 8 9.91 5 K 5 8.98 5 Mg 4 5.21 5 S 168 5.16 5 C 18112 2.51 5 N 4540 2.21 5 O 5024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 152 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27861 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 6961 Classifications: {'peptide': 890} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 34, 'TRANS': 855} Chain breaks: 6 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6, 'ASN:plan1': 6, 'GLN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "B" Number of atoms: 6961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 6961 Classifications: {'peptide': 890} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 34, 'TRANS': 855} Chain breaks: 6 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6, 'ASN:plan1': 6, 'GLN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "C" Number of atoms: 6961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 6961 Classifications: {'peptide': 890} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 34, 'TRANS': 855} Chain breaks: 6 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6, 'ASN:plan1': 6, 'GLN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "D" Number of atoms: 6961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 6961 Classifications: {'peptide': 890} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 34, 'TRANS': 855} Chain breaks: 6 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6, 'ASN:plan1': 6, 'GLN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 2, ' CA': 2, ' MG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' K': 3, ' CA': 2, ' MG': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.25, per 1000 atoms: 0.26 Number of scatterers: 27861 At special positions: 0 Unit cell: (143.505, 143.505, 122.245, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 8 19.99 K 5 19.00 S 168 16.00 Mg 4 11.99 O 5024 8.00 N 4540 7.00 C 18112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.39 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6712 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 20 sheets defined 59.7% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 15 through 44 removed outlier: 4.212A pdb=" N PHE A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY A 30 " --> pdb=" O THR A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 93 Processing helix chain 'A' and resid 96 through 123 removed outlier: 3.628A pdb=" N GLY A 104 " --> pdb=" O ARG A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 160 Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 169 through 177 removed outlier: 3.535A pdb=" N PHE A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 188 removed outlier: 3.802A pdb=" N ILE A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 204 Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 218 through 249 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 262 through 275 Processing helix chain 'A' and resid 286 through 317 removed outlier: 4.817A pdb=" N GLY A 302 " --> pdb=" O MET A 298 " (cutoff:3.500A) Proline residue: A 309 - end of helix Processing helix chain 'A' and resid 341 through 353 removed outlier: 3.607A pdb=" N ASP A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 383 Processing helix chain 'A' and resid 396 through 403 Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 421 through 440 Processing helix chain 'A' and resid 451 through 460 removed outlier: 3.794A pdb=" N LYS A 455 " --> pdb=" O GLN A 451 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA A 456 " --> pdb=" O TYR A 452 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TYR A 457 " --> pdb=" O HIS A 453 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A 458 " --> pdb=" O ASN A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 475 through 489 Processing helix chain 'A' and resid 491 through 499 Processing helix chain 'A' and resid 512 through 523 Processing helix chain 'A' and resid 532 through 536 Processing helix chain 'A' and resid 539 through 550 Processing helix chain 'A' and resid 592 through 597 Processing helix chain 'A' and resid 597 through 602 Processing helix chain 'A' and resid 604 through 608 Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 721 through 725 Processing helix chain 'A' and resid 728 through 735 Processing helix chain 'A' and resid 756 through 761 Processing helix chain 'A' and resid 762 through 765 Processing helix chain 'A' and resid 769 through 773 Processing helix chain 'A' and resid 781 through 793 removed outlier: 3.730A pdb=" N ARG A 787 " --> pdb=" O ASP A 783 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS A 790 " --> pdb=" O HIS A 786 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N THR A 791 " --> pdb=" O ARG A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 814 Processing helix chain 'A' and resid 815 through 819 Processing helix chain 'A' and resid 836 through 838 No H-bonds generated for 'chain 'A' and resid 836 through 838' Processing helix chain 'A' and resid 839 through 852 Processing helix chain 'A' and resid 882 through 886 Processing helix chain 'A' and resid 894 through 901 removed outlier: 3.768A pdb=" N GLN A 899 " --> pdb=" O SER A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 915 Processing helix chain 'A' and resid 916 through 921 Processing helix chain 'A' and resid 928 through 931 removed outlier: 4.000A pdb=" N ASP A 931 " --> pdb=" O SER A 928 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 928 through 931' Processing helix chain 'A' and resid 932 through 940 Processing helix chain 'A' and resid 940 through 952 Processing helix chain 'A' and resid 956 through 965 Processing helix chain 'A' and resid 975 through 980 Processing helix chain 'A' and resid 981 through 983 No H-bonds generated for 'chain 'A' and resid 981 through 983' Processing helix chain 'A' and resid 997 through 1002 removed outlier: 3.710A pdb=" N GLY A1001 " --> pdb=" O LEU A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1018 Processing helix chain 'B' and resid 15 through 44 removed outlier: 4.213A pdb=" N PHE B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY B 30 " --> pdb=" O THR B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 93 Processing helix chain 'B' and resid 96 through 123 Processing helix chain 'B' and resid 136 through 160 Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 169 through 177 removed outlier: 3.535A pdb=" N PHE B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 188 removed outlier: 3.802A pdb=" N ILE B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 204 Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 218 through 249 Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 262 through 275 Processing helix chain 'B' and resid 286 through 317 removed outlier: 4.816A pdb=" N GLY B 302 " --> pdb=" O MET B 298 " (cutoff:3.500A) Proline residue: B 309 - end of helix Processing helix chain 'B' and resid 341 through 353 removed outlier: 3.608A pdb=" N ASP B 351 " --> pdb=" O ASN B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 383 Processing helix chain 'B' and resid 396 through 403 Processing helix chain 'B' and resid 404 through 408 Processing helix chain 'B' and resid 421 through 440 Processing helix chain 'B' and resid 451 through 460 removed outlier: 3.794A pdb=" N LYS B 455 " --> pdb=" O GLN B 451 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA B 456 " --> pdb=" O TYR B 452 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TYR B 457 " --> pdb=" O HIS B 453 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU B 458 " --> pdb=" O ASN B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 475 through 489 Processing helix chain 'B' and resid 491 through 499 Processing helix chain 'B' and resid 512 through 523 Processing helix chain 'B' and resid 532 through 536 Processing helix chain 'B' and resid 539 through 550 Processing helix chain 'B' and resid 592 through 597 Processing helix chain 'B' and resid 597 through 602 Processing helix chain 'B' and resid 604 through 608 Processing helix chain 'B' and resid 612 through 616 Processing helix chain 'B' and resid 721 through 725 Processing helix chain 'B' and resid 728 through 735 Processing helix chain 'B' and resid 756 through 761 Processing helix chain 'B' and resid 762 through 765 Processing helix chain 'B' and resid 769 through 773 Processing helix chain 'B' and resid 781 through 793 removed outlier: 3.731A pdb=" N ARG B 787 " --> pdb=" O ASP B 783 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS B 790 " --> pdb=" O HIS B 786 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N THR B 791 " --> pdb=" O ARG B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 814 Processing helix chain 'B' and resid 815 through 819 Processing helix chain 'B' and resid 836 through 838 No H-bonds generated for 'chain 'B' and resid 836 through 838' Processing helix chain 'B' and resid 839 through 852 Processing helix chain 'B' and resid 882 through 886 Processing helix chain 'B' and resid 894 through 901 removed outlier: 3.767A pdb=" N GLN B 899 " --> pdb=" O SER B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 915 Processing helix chain 'B' and resid 916 through 921 Processing helix chain 'B' and resid 928 through 931 removed outlier: 4.001A pdb=" N ASP B 931 " --> pdb=" O SER B 928 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 928 through 931' Processing helix chain 'B' and resid 932 through 940 Processing helix chain 'B' and resid 940 through 952 Processing helix chain 'B' and resid 956 through 965 Processing helix chain 'B' and resid 975 through 980 Processing helix chain 'B' and resid 981 through 983 No H-bonds generated for 'chain 'B' and resid 981 through 983' Processing helix chain 'B' and resid 997 through 1002 removed outlier: 3.710A pdb=" N GLY B1001 " --> pdb=" O LEU B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1018 Processing helix chain 'C' and resid 15 through 44 removed outlier: 4.212A pdb=" N PHE C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY C 30 " --> pdb=" O THR C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 93 Processing helix chain 'C' and resid 96 through 123 removed outlier: 3.649A pdb=" N GLY C 104 " --> pdb=" O ARG C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 160 Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 169 through 177 removed outlier: 3.534A pdb=" N PHE C 173 " --> pdb=" O GLU C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 188 removed outlier: 3.802A pdb=" N ILE C 186 " --> pdb=" O SER C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 204 Processing helix chain 'C' and resid 205 through 213 Processing helix chain 'C' and resid 218 through 249 Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 262 through 275 Processing helix chain 'C' and resid 286 through 317 removed outlier: 4.817A pdb=" N GLY C 302 " --> pdb=" O MET C 298 " (cutoff:3.500A) Proline residue: C 309 - end of helix Processing helix chain 'C' and resid 341 through 353 removed outlier: 3.606A pdb=" N ASP C 351 " --> pdb=" O ASN C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 383 Processing helix chain 'C' and resid 396 through 403 Processing helix chain 'C' and resid 404 through 408 Processing helix chain 'C' and resid 421 through 440 Processing helix chain 'C' and resid 451 through 460 removed outlier: 3.794A pdb=" N LYS C 455 " --> pdb=" O GLN C 451 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA C 456 " --> pdb=" O TYR C 452 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TYR C 457 " --> pdb=" O HIS C 453 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU C 458 " --> pdb=" O ASN C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 475 through 489 Processing helix chain 'C' and resid 491 through 499 Processing helix chain 'C' and resid 512 through 523 Processing helix chain 'C' and resid 532 through 536 Processing helix chain 'C' and resid 539 through 550 Processing helix chain 'C' and resid 592 through 597 Processing helix chain 'C' and resid 597 through 602 Processing helix chain 'C' and resid 604 through 608 Processing helix chain 'C' and resid 612 through 616 Processing helix chain 'C' and resid 721 through 725 Processing helix chain 'C' and resid 728 through 735 Processing helix chain 'C' and resid 756 through 761 Processing helix chain 'C' and resid 762 through 765 Processing helix chain 'C' and resid 769 through 773 Processing helix chain 'C' and resid 781 through 793 removed outlier: 3.731A pdb=" N ARG C 787 " --> pdb=" O ASP C 783 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS C 790 " --> pdb=" O HIS C 786 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N THR C 791 " --> pdb=" O ARG C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 814 Processing helix chain 'C' and resid 815 through 819 Processing helix chain 'C' and resid 836 through 838 No H-bonds generated for 'chain 'C' and resid 836 through 838' Processing helix chain 'C' and resid 839 through 852 Processing helix chain 'C' and resid 882 through 886 Processing helix chain 'C' and resid 894 through 901 removed outlier: 3.767A pdb=" N GLN C 899 " --> pdb=" O SER C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 915 Processing helix chain 'C' and resid 916 through 921 Processing helix chain 'C' and resid 928 through 931 removed outlier: 4.001A pdb=" N ASP C 931 " --> pdb=" O SER C 928 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 928 through 931' Processing helix chain 'C' and resid 932 through 940 Processing helix chain 'C' and resid 940 through 952 Processing helix chain 'C' and resid 956 through 965 Processing helix chain 'C' and resid 975 through 980 Processing helix chain 'C' and resid 981 through 983 No H-bonds generated for 'chain 'C' and resid 981 through 983' Processing helix chain 'C' and resid 997 through 1002 removed outlier: 3.709A pdb=" N GLY C1001 " --> pdb=" O LEU C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1018 Processing helix chain 'D' and resid 15 through 44 removed outlier: 4.212A pdb=" N PHE D 19 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY D 30 " --> pdb=" O THR D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 93 Processing helix chain 'D' and resid 96 through 123 Processing helix chain 'D' and resid 136 through 160 Processing helix chain 'D' and resid 162 through 167 Processing helix chain 'D' and resid 169 through 177 removed outlier: 3.535A pdb=" N PHE D 173 " --> pdb=" O GLU D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 188 removed outlier: 3.802A pdb=" N ILE D 186 " --> pdb=" O SER D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 204 Processing helix chain 'D' and resid 205 through 213 Processing helix chain 'D' and resid 218 through 249 Processing helix chain 'D' and resid 250 through 254 Processing helix chain 'D' and resid 262 through 275 Processing helix chain 'D' and resid 286 through 317 removed outlier: 4.817A pdb=" N GLY D 302 " --> pdb=" O MET D 298 " (cutoff:3.500A) Proline residue: D 309 - end of helix Processing helix chain 'D' and resid 341 through 353 removed outlier: 3.607A pdb=" N ASP D 351 " --> pdb=" O ASN D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 383 Processing helix chain 'D' and resid 396 through 403 Processing helix chain 'D' and resid 404 through 408 Processing helix chain 'D' and resid 421 through 440 Processing helix chain 'D' and resid 451 through 460 removed outlier: 3.793A pdb=" N LYS D 455 " --> pdb=" O GLN D 451 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA D 456 " --> pdb=" O TYR D 452 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TYR D 457 " --> pdb=" O HIS D 453 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU D 458 " --> pdb=" O ASN D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 475 through 489 Processing helix chain 'D' and resid 491 through 499 Processing helix chain 'D' and resid 512 through 523 Processing helix chain 'D' and resid 532 through 536 Processing helix chain 'D' and resid 539 through 550 Processing helix chain 'D' and resid 592 through 597 Processing helix chain 'D' and resid 597 through 602 Processing helix chain 'D' and resid 604 through 608 Processing helix chain 'D' and resid 612 through 616 Processing helix chain 'D' and resid 721 through 725 Processing helix chain 'D' and resid 728 through 735 Processing helix chain 'D' and resid 756 through 761 Processing helix chain 'D' and resid 762 through 765 Processing helix chain 'D' and resid 769 through 773 Processing helix chain 'D' and resid 781 through 793 removed outlier: 3.730A pdb=" N ARG D 787 " --> pdb=" O ASP D 783 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS D 790 " --> pdb=" O HIS D 786 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N THR D 791 " --> pdb=" O ARG D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 807 through 814 Processing helix chain 'D' and resid 815 through 819 Processing helix chain 'D' and resid 836 through 838 No H-bonds generated for 'chain 'D' and resid 836 through 838' Processing helix chain 'D' and resid 839 through 852 Processing helix chain 'D' and resid 882 through 886 Processing helix chain 'D' and resid 894 through 901 removed outlier: 3.768A pdb=" N GLN D 899 " --> pdb=" O SER D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 912 through 915 Processing helix chain 'D' and resid 916 through 921 Processing helix chain 'D' and resid 928 through 931 removed outlier: 4.000A pdb=" N ASP D 931 " --> pdb=" O SER D 928 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 928 through 931' Processing helix chain 'D' and resid 932 through 940 Processing helix chain 'D' and resid 940 through 952 Processing helix chain 'D' and resid 956 through 965 Processing helix chain 'D' and resid 975 through 980 Processing helix chain 'D' and resid 981 through 983 No H-bonds generated for 'chain 'D' and resid 981 through 983' Processing helix chain 'D' and resid 997 through 1002 removed outlier: 3.711A pdb=" N GLY D1001 " --> pdb=" O LEU D 997 " (cutoff:3.500A) Processing helix chain 'D' and resid 1005 through 1018 Processing sheet with id=AA1, first strand: chain 'A' and resid 387 through 391 removed outlier: 6.792A pdb=" N ARG A 332 " --> pdb=" O GLU A 363 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL A 365 " --> pdb=" O ARG A 332 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL A 334 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU A 367 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL A 336 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N HIS A 333 " --> pdb=" O ALA A 410 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N LEU A 412 " --> pdb=" O HIS A 333 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL A 335 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU A 414 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS A 337 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N CYS A 411 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N GLN A 448 " --> pdb=" O CYS A 411 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL A 413 " --> pdb=" O GLN A 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 525 through 530 removed outlier: 7.101A pdb=" N GLN A 585 " --> pdb=" O ILE A 558 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE A 558 " --> pdb=" O GLN A 585 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE A 587 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 708 through 709 Processing sheet with id=AA4, first strand: chain 'A' and resid 798 through 802 removed outlier: 6.443A pdb=" N THR A 776 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU A 801 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE A 778 " --> pdb=" O LEU A 801 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL A 742 " --> pdb=" O VAL A 823 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N VAL A 825 " --> pdb=" O VAL A 742 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N CYS A 744 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N SER A 826 " --> pdb=" O GLU A 891 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 986 through 991 removed outlier: 3.694A pdb=" N GLY A1023 " --> pdb=" O TYR A1060 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU A1062 " --> pdb=" O CYS A1021 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N CYS A1021 " --> pdb=" O LEU A1062 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 387 through 391 removed outlier: 6.792A pdb=" N ARG B 332 " --> pdb=" O GLU B 363 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL B 365 " --> pdb=" O ARG B 332 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL B 334 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU B 367 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL B 336 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N HIS B 333 " --> pdb=" O ALA B 410 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N LEU B 412 " --> pdb=" O HIS B 333 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 335 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LEU B 414 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N CYS B 337 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N CYS B 411 " --> pdb=" O ILE B 446 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLN B 448 " --> pdb=" O CYS B 411 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL B 413 " --> pdb=" O GLN B 448 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 525 through 530 removed outlier: 7.102A pdb=" N GLN B 585 " --> pdb=" O ILE B 558 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE B 558 " --> pdb=" O GLN B 585 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE B 587 " --> pdb=" O LEU B 556 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 708 through 709 Processing sheet with id=AA9, first strand: chain 'B' and resid 798 through 802 removed outlier: 6.443A pdb=" N THR B 776 " --> pdb=" O SER B 799 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU B 801 " --> pdb=" O THR B 776 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE B 778 " --> pdb=" O LEU B 801 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL B 742 " --> pdb=" O VAL B 823 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL B 825 " --> pdb=" O VAL B 742 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N CYS B 744 " --> pdb=" O VAL B 825 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N SER B 826 " --> pdb=" O GLU B 891 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 986 through 991 removed outlier: 3.694A pdb=" N GLY B1023 " --> pdb=" O TYR B1060 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU B1062 " --> pdb=" O CYS B1021 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N CYS B1021 " --> pdb=" O LEU B1062 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 387 through 391 removed outlier: 6.793A pdb=" N ARG C 332 " --> pdb=" O GLU C 363 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL C 365 " --> pdb=" O ARG C 332 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL C 334 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU C 367 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL C 336 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N HIS C 333 " --> pdb=" O ALA C 410 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N LEU C 412 " --> pdb=" O HIS C 333 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL C 335 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU C 414 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS C 337 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N CYS C 411 " --> pdb=" O ILE C 446 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLN C 448 " --> pdb=" O CYS C 411 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL C 413 " --> pdb=" O GLN C 448 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 525 through 530 removed outlier: 7.102A pdb=" N GLN C 585 " --> pdb=" O ILE C 558 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE C 558 " --> pdb=" O GLN C 585 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N PHE C 587 " --> pdb=" O LEU C 556 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AB5, first strand: chain 'C' and resid 798 through 802 removed outlier: 6.443A pdb=" N THR C 776 " --> pdb=" O SER C 799 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU C 801 " --> pdb=" O THR C 776 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE C 778 " --> pdb=" O LEU C 801 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL C 742 " --> pdb=" O VAL C 823 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N VAL C 825 " --> pdb=" O VAL C 742 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N CYS C 744 " --> pdb=" O VAL C 825 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N SER C 826 " --> pdb=" O GLU C 891 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 986 through 991 removed outlier: 3.694A pdb=" N GLY C1023 " --> pdb=" O TYR C1060 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU C1062 " --> pdb=" O CYS C1021 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N CYS C1021 " --> pdb=" O LEU C1062 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 387 through 391 removed outlier: 6.792A pdb=" N ARG D 332 " --> pdb=" O GLU D 363 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N VAL D 365 " --> pdb=" O ARG D 332 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL D 334 " --> pdb=" O VAL D 365 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU D 367 " --> pdb=" O VAL D 334 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL D 336 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N HIS D 333 " --> pdb=" O ALA D 410 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N LEU D 412 " --> pdb=" O HIS D 333 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL D 335 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU D 414 " --> pdb=" O VAL D 335 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS D 337 " --> pdb=" O LEU D 414 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N CYS D 411 " --> pdb=" O ILE D 446 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N GLN D 448 " --> pdb=" O CYS D 411 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL D 413 " --> pdb=" O GLN D 448 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 525 through 530 removed outlier: 7.102A pdb=" N GLN D 585 " --> pdb=" O ILE D 558 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE D 558 " --> pdb=" O GLN D 585 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N PHE D 587 " --> pdb=" O LEU D 556 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 708 through 709 Processing sheet with id=AC1, first strand: chain 'D' and resid 798 through 802 removed outlier: 6.443A pdb=" N THR D 776 " --> pdb=" O SER D 799 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU D 801 " --> pdb=" O THR D 776 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE D 778 " --> pdb=" O LEU D 801 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL D 742 " --> pdb=" O VAL D 823 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N VAL D 825 " --> pdb=" O VAL D 742 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N CYS D 744 " --> pdb=" O VAL D 825 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N SER D 826 " --> pdb=" O GLU D 891 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 986 through 991 removed outlier: 3.693A pdb=" N GLY D1023 " --> pdb=" O TYR D1060 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU D1062 " --> pdb=" O CYS D1021 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N CYS D1021 " --> pdb=" O LEU D1062 " (cutoff:3.500A) 1478 hydrogen bonds defined for protein. 3954 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: 6.68 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5006 1.32 - 1.44: 7411 1.44 - 1.57: 15835 1.57 - 1.70: 0 1.70 - 1.83: 256 Bond restraints: 28508 Sorted by residual: bond pdb=" C ILE A 947 " pdb=" O ILE A 947 " ideal model delta sigma weight residual 1.237 1.189 0.048 1.13e-02 7.83e+03 1.81e+01 bond pdb=" C ILE C 947 " pdb=" O ILE C 947 " ideal model delta sigma weight residual 1.237 1.189 0.048 1.13e-02 7.83e+03 1.80e+01 bond pdb=" C ILE B 947 " pdb=" O ILE B 947 " ideal model delta sigma weight residual 1.237 1.189 0.048 1.13e-02 7.83e+03 1.79e+01 bond pdb=" C ILE D 947 " pdb=" O ILE D 947 " ideal model delta sigma weight residual 1.237 1.190 0.047 1.13e-02 7.83e+03 1.73e+01 bond pdb=" C HIS B 333 " pdb=" O HIS B 333 " ideal model delta sigma weight residual 1.234 1.185 0.048 1.22e-02 6.72e+03 1.57e+01 ... (remaining 28503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 28543 1.84 - 3.67: 8995 3.67 - 5.51: 1144 5.51 - 7.35: 69 7.35 - 9.19: 5 Bond angle restraints: 38756 Sorted by residual: angle pdb=" N ILE B 179 " pdb=" CA ILE B 179 " pdb=" CB ILE B 179 " ideal model delta sigma weight residual 110.45 116.22 -5.77 7.80e-01 1.64e+00 5.48e+01 angle pdb=" N ILE A 179 " pdb=" CA ILE A 179 " pdb=" CB ILE A 179 " ideal model delta sigma weight residual 110.45 116.22 -5.77 7.80e-01 1.64e+00 5.48e+01 angle pdb=" N ILE D 179 " pdb=" CA ILE D 179 " pdb=" CB ILE D 179 " ideal model delta sigma weight residual 110.45 116.20 -5.75 7.80e-01 1.64e+00 5.43e+01 angle pdb=" N ILE C 179 " pdb=" CA ILE C 179 " pdb=" CB ILE C 179 " ideal model delta sigma weight residual 110.45 116.19 -5.74 7.80e-01 1.64e+00 5.41e+01 angle pdb=" N GLY C 99 " pdb=" CA GLY C 99 " pdb=" C GLY C 99 " ideal model delta sigma weight residual 112.49 104.96 7.53 1.21e+00 6.83e-01 3.88e+01 ... (remaining 38751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 15538 17.69 - 35.37: 930 35.37 - 53.06: 172 53.06 - 70.74: 60 70.74 - 88.43: 12 Dihedral angle restraints: 16712 sinusoidal: 6332 harmonic: 10380 Sorted by residual: dihedral pdb=" CA ASP C 612 " pdb=" C ASP C 612 " pdb=" N VAL C 613 " pdb=" CA VAL C 613 " ideal model delta harmonic sigma weight residual 180.00 -151.45 -28.55 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA ASP B 612 " pdb=" C ASP B 612 " pdb=" N VAL B 613 " pdb=" CA VAL B 613 " ideal model delta harmonic sigma weight residual -180.00 -151.46 -28.54 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA ASP A 612 " pdb=" C ASP A 612 " pdb=" N VAL A 613 " pdb=" CA VAL A 613 " ideal model delta harmonic sigma weight residual -180.00 -151.47 -28.53 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 16709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 3030 0.093 - 0.186: 1211 0.186 - 0.280: 173 0.280 - 0.373: 18 0.373 - 0.466: 8 Chirality restraints: 4440 Sorted by residual: chirality pdb=" CA LEU A 458 " pdb=" N LEU A 458 " pdb=" C LEU A 458 " pdb=" CB LEU A 458 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.43e+00 chirality pdb=" CA LEU D 458 " pdb=" N LEU D 458 " pdb=" C LEU D 458 " pdb=" CB LEU D 458 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" CA LEU C 458 " pdb=" N LEU C 458 " pdb=" C LEU C 458 " pdb=" CB LEU C 458 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.33e+00 ... (remaining 4437 not shown) Planarity restraints: 4888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 167 " -0.121 2.00e-02 2.50e+03 5.94e-02 8.83e+01 pdb=" CG TRP A 167 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP A 167 " 0.051 2.00e-02 2.50e+03 pdb=" CD2 TRP A 167 " 0.036 2.00e-02 2.50e+03 pdb=" NE1 TRP A 167 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TRP A 167 " -0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP A 167 " 0.081 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 167 " -0.065 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 167 " 0.029 2.00e-02 2.50e+03 pdb=" CH2 TRP A 167 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 167 " 0.121 2.00e-02 2.50e+03 5.94e-02 8.82e+01 pdb=" CG TRP D 167 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP D 167 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 TRP D 167 " -0.036 2.00e-02 2.50e+03 pdb=" NE1 TRP D 167 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TRP D 167 " 0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP D 167 " -0.081 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 167 " 0.064 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 167 " -0.029 2.00e-02 2.50e+03 pdb=" CH2 TRP D 167 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 167 " -0.121 2.00e-02 2.50e+03 5.94e-02 8.82e+01 pdb=" CG TRP B 167 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP B 167 " 0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP B 167 " 0.036 2.00e-02 2.50e+03 pdb=" NE1 TRP B 167 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TRP B 167 " -0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP B 167 " 0.081 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 167 " -0.064 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 167 " 0.029 2.00e-02 2.50e+03 pdb=" CH2 TRP B 167 " -0.059 2.00e-02 2.50e+03 ... (remaining 4885 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.54: 74 2.54 - 3.19: 25027 3.19 - 3.84: 53389 3.84 - 4.49: 76781 4.49 - 5.14: 124260 Nonbonded interactions: 279531 Sorted by model distance: nonbonded pdb=" OE2 GLU D 363 " pdb="MG MG D1101 " model vdw 1.886 2.170 nonbonded pdb=" OE2 GLU C 363 " pdb="MG MG C1104 " model vdw 1.886 2.170 nonbonded pdb=" OE2 GLU A 363 " pdb="MG MG A1103 " model vdw 1.886 2.170 nonbonded pdb=" OE2 GLU B 363 " pdb="MG MG B1101 " model vdw 1.887 2.170 nonbonded pdb=" OE2 GLU A 388 " pdb="MG MG A1103 " model vdw 1.911 2.170 ... (remaining 279526 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 14 through 1065) selection = (chain 'B' and resid 14 through 1065) selection = (chain 'C' and resid 14 through 1065) selection = (chain 'D' and resid 14 through 1065) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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 Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file 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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 28.520 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6436 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.078 28508 Z= 0.714 Angle : 1.678 9.186 38756 Z= 1.125 Chirality : 0.093 0.466 4440 Planarity : 0.013 0.117 4888 Dihedral : 12.968 88.428 10000 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.41 % Allowed : 6.01 % Favored : 93.58 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.13), residues: 3504 helix: -0.75 (0.11), residues: 1740 sheet: 0.07 (0.27), residues: 356 loop : 0.30 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 757 TYR 0.083 0.017 TYR D 938 PHE 0.076 0.012 PHE C 500 TRP 0.121 0.024 TRP A 167 HIS 0.015 0.003 HIS B 333 Details of bonding type rmsd covalent geometry : bond 0.01184 (28508) covalent geometry : angle 1.67812 (38756) hydrogen bonds : bond 0.18285 ( 1478) hydrogen bonds : angle 6.99441 ( 3954) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.998 Fit side-chains REVERT: A 274 MET cc_start: 0.8808 (ptm) cc_final: 0.8595 (ptp) REVERT: B 274 MET cc_start: 0.8867 (ptm) cc_final: 0.8624 (ptp) REVERT: B 821 MET cc_start: 0.6540 (tpt) cc_final: 0.6316 (tpp) REVERT: B 852 MET cc_start: 0.7210 (mtm) cc_final: 0.7007 (mtp) REVERT: C 274 MET cc_start: 0.8804 (ptm) cc_final: 0.8486 (ptp) REVERT: C 821 MET cc_start: 0.6566 (tpt) cc_final: 0.6292 (tpp) REVERT: C 832 MET cc_start: 0.7766 (ptp) cc_final: 0.7323 (ppp) REVERT: C 852 MET cc_start: 0.7302 (mtm) cc_final: 0.7087 (mtp) REVERT: D 271 MET cc_start: 0.9096 (tpp) cc_final: 0.8778 (tpp) REVERT: D 274 MET cc_start: 0.8800 (ptm) cc_final: 0.8536 (ptp) REVERT: D 852 MET cc_start: 0.7185 (mtm) cc_final: 0.6972 (mtp) outliers start: 12 outliers final: 0 residues processed: 144 average time/residue: 0.6069 time to fit residues: 105.1011 Evaluate side-chains 106 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN A 582 ASN A 786 HIS ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 ASN B 582 ASN B 786 HIS C 536 ASN C 582 ASN C 786 HIS ** D 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 ASN D 582 ASN D 786 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.066813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.048319 restraints weight = 85254.749| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 3.21 r_work: 0.2717 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28508 Z= 0.132 Angle : 0.601 10.696 38756 Z= 0.310 Chirality : 0.043 0.160 4440 Planarity : 0.004 0.035 4888 Dihedral : 4.901 24.535 3808 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.18 % Allowed : 8.38 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.14), residues: 3504 helix: 0.70 (0.12), residues: 1788 sheet: 0.22 (0.26), residues: 400 loop : 0.92 (0.18), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 614 TYR 0.014 0.001 TYR C 37 PHE 0.025 0.001 PHE C 148 TRP 0.016 0.002 TRP D 514 HIS 0.004 0.001 HIS A 786 Details of bonding type rmsd covalent geometry : bond 0.00273 (28508) covalent geometry : angle 0.60135 (38756) hydrogen bonds : bond 0.04872 ( 1478) hydrogen bonds : angle 4.75360 ( 3954) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 104 time to evaluate : 1.115 Fit side-chains REVERT: B 274 MET cc_start: 0.9331 (ptm) cc_final: 0.9076 (ptp) REVERT: B 328 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7876 (mp0) REVERT: C 274 MET cc_start: 0.9341 (ptm) cc_final: 0.9100 (ptp) REVERT: C 832 MET cc_start: 0.8194 (ptp) cc_final: 0.7947 (ppp) REVERT: D 274 MET cc_start: 0.9341 (ptm) cc_final: 0.9063 (ptp) REVERT: D 328 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7891 (mp0) outliers start: 35 outliers final: 0 residues processed: 127 average time/residue: 0.7754 time to fit residues: 114.1995 Evaluate side-chains 94 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain D residue 328 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 242 optimal weight: 6.9990 chunk 210 optimal weight: 0.0670 chunk 162 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 251 optimal weight: 0.0770 chunk 350 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 191 optimal weight: 0.0970 chunk 308 optimal weight: 8.9990 chunk 345 optimal weight: 0.0870 overall best weight: 0.4654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 917 GLN B 95 GLN B 917 GLN C 917 GLN D 917 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.068143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.049628 restraints weight = 84908.691| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 3.23 r_work: 0.2760 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28508 Z= 0.102 Angle : 0.520 10.781 38756 Z= 0.261 Chirality : 0.040 0.175 4440 Planarity : 0.003 0.037 4888 Dihedral : 4.163 19.509 3808 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.96 % Allowed : 7.97 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.15), residues: 3504 helix: 1.10 (0.12), residues: 1816 sheet: 0.24 (0.27), residues: 400 loop : 1.09 (0.18), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1015 TYR 0.011 0.001 TYR B 505 PHE 0.013 0.001 PHE A 148 TRP 0.013 0.001 TRP B 514 HIS 0.004 0.000 HIS D 786 Details of bonding type rmsd covalent geometry : bond 0.00202 (28508) covalent geometry : angle 0.51979 (38756) hydrogen bonds : bond 0.03861 ( 1478) hydrogen bonds : angle 4.32233 ( 3954) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 97 time to evaluate : 0.925 Fit side-chains REVERT: A 81 MET cc_start: 0.8339 (mtm) cc_final: 0.8002 (mmt) REVERT: A 832 MET cc_start: 0.7866 (ppp) cc_final: 0.7312 (ppp) REVERT: B 81 MET cc_start: 0.8248 (mtm) cc_final: 0.7857 (mmt) REVERT: B 274 MET cc_start: 0.9225 (ptm) cc_final: 0.8965 (ptp) REVERT: B 486 SER cc_start: 0.9269 (OUTLIER) cc_final: 0.9038 (m) REVERT: B 832 MET cc_start: 0.7998 (ppp) cc_final: 0.7501 (ppp) REVERT: C 81 MET cc_start: 0.8342 (mtm) cc_final: 0.7999 (mmt) REVERT: C 274 MET cc_start: 0.9224 (ptm) cc_final: 0.8985 (ptp) REVERT: C 486 SER cc_start: 0.9251 (OUTLIER) cc_final: 0.9014 (m) REVERT: D 81 MET cc_start: 0.8393 (mtm) cc_final: 0.7966 (mmt) REVERT: D 486 SER cc_start: 0.9209 (OUTLIER) cc_final: 0.8987 (m) REVERT: D 832 MET cc_start: 0.7995 (ppp) cc_final: 0.7427 (ppp) outliers start: 58 outliers final: 1 residues processed: 142 average time/residue: 0.6395 time to fit residues: 107.4465 Evaluate side-chains 97 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 951 ILE Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain D residue 486 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 339 optimal weight: 7.9990 chunk 241 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 38 optimal weight: 0.0970 chunk 52 optimal weight: 5.9990 chunk 290 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 236 optimal weight: 4.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 786 HIS B 786 HIS C 786 HIS D 95 GLN D 786 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.066015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.047272 restraints weight = 85618.378| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 3.24 r_work: 0.2693 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 28508 Z= 0.154 Angle : 0.519 9.506 38756 Z= 0.264 Chirality : 0.041 0.135 4440 Planarity : 0.003 0.037 4888 Dihedral : 4.057 17.664 3808 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.23 % Allowed : 7.91 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.15), residues: 3504 helix: 1.25 (0.12), residues: 1820 sheet: 0.13 (0.27), residues: 392 loop : 1.20 (0.18), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1015 TYR 0.010 0.001 TYR D 37 PHE 0.014 0.001 PHE B 148 TRP 0.009 0.001 TRP D 514 HIS 0.005 0.001 HIS B 333 Details of bonding type rmsd covalent geometry : bond 0.00354 (28508) covalent geometry : angle 0.51891 (38756) hydrogen bonds : bond 0.04150 ( 1478) hydrogen bonds : angle 4.26912 ( 3954) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 97 time to evaluate : 1.187 Fit side-chains REVERT: A 832 MET cc_start: 0.7829 (ppp) cc_final: 0.7126 (ppp) REVERT: B 39 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8156 (pp) REVERT: B 832 MET cc_start: 0.7829 (ppp) cc_final: 0.7383 (ppp) REVERT: C 39 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8144 (pp) REVERT: D 39 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8053 (pp) REVERT: D 832 MET cc_start: 0.7885 (ppp) cc_final: 0.7435 (ppp) outliers start: 66 outliers final: 8 residues processed: 145 average time/residue: 0.5922 time to fit residues: 104.0733 Evaluate side-chains 104 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 940 ASN Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 209 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 316 optimal weight: 5.9990 chunk 174 optimal weight: 8.9990 chunk 290 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 282 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 171 optimal weight: 7.9990 chunk 346 optimal weight: 8.9990 chunk 182 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.065844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.047025 restraints weight = 85413.866| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.25 r_work: 0.2686 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 28508 Z= 0.153 Angle : 0.503 8.493 38756 Z= 0.255 Chirality : 0.041 0.137 4440 Planarity : 0.003 0.039 4888 Dihedral : 3.991 16.307 3808 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.23 % Allowed : 9.12 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.15), residues: 3504 helix: 1.33 (0.12), residues: 1816 sheet: 0.10 (0.27), residues: 392 loop : 1.22 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1015 TYR 0.009 0.001 TYR A 37 PHE 0.012 0.001 PHE D 500 TRP 0.009 0.001 TRP A 514 HIS 0.004 0.001 HIS C 333 Details of bonding type rmsd covalent geometry : bond 0.00356 (28508) covalent geometry : angle 0.50305 (38756) hydrogen bonds : bond 0.04010 ( 1478) hydrogen bonds : angle 4.24011 ( 3954) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 97 time to evaluate : 0.697 Fit side-chains REVERT: A 81 MET cc_start: 0.8449 (mmm) cc_final: 0.8146 (mmt) REVERT: A 832 MET cc_start: 0.7819 (ppp) cc_final: 0.7097 (ppp) REVERT: B 81 MET cc_start: 0.8397 (mmm) cc_final: 0.8080 (mmt) REVERT: B 832 MET cc_start: 0.7798 (ppp) cc_final: 0.7171 (ppp) REVERT: C 81 MET cc_start: 0.8335 (mmm) cc_final: 0.8072 (mmt) REVERT: C 832 MET cc_start: 0.7625 (ppp) cc_final: 0.7279 (ppp) REVERT: D 81 MET cc_start: 0.8377 (mmm) cc_final: 0.8061 (mmt) REVERT: D 832 MET cc_start: 0.7809 (ppp) cc_final: 0.7403 (ppp) outliers start: 66 outliers final: 12 residues processed: 149 average time/residue: 0.5378 time to fit residues: 96.9830 Evaluate side-chains 107 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 940 ASN Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 940 ASN Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain D residue 209 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 247 optimal weight: 7.9990 chunk 135 optimal weight: 0.9990 chunk 132 optimal weight: 0.3980 chunk 354 optimal weight: 0.0570 chunk 93 optimal weight: 1.9990 chunk 337 optimal weight: 1.9990 chunk 289 optimal weight: 4.9990 chunk 350 optimal weight: 0.9980 chunk 299 optimal weight: 5.9990 chunk 268 optimal weight: 20.0000 chunk 111 optimal weight: 0.7980 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 786 HIS B 786 HIS C 786 HIS D 786 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.067548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.048778 restraints weight = 85116.197| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.26 r_work: 0.2738 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 28508 Z= 0.091 Angle : 0.465 8.527 38756 Z= 0.234 Chirality : 0.039 0.141 4440 Planarity : 0.003 0.038 4888 Dihedral : 3.805 15.159 3808 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.35 % Allowed : 9.90 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.15), residues: 3504 helix: 1.39 (0.13), residues: 1828 sheet: -0.04 (0.26), residues: 444 loop : 1.46 (0.20), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1015 TYR 0.009 0.001 TYR A 37 PHE 0.011 0.001 PHE B 500 TRP 0.010 0.001 TRP A 514 HIS 0.002 0.000 HIS D 786 Details of bonding type rmsd covalent geometry : bond 0.00189 (28508) covalent geometry : angle 0.46511 (38756) hydrogen bonds : bond 0.03429 ( 1478) hydrogen bonds : angle 4.10036 ( 3954) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 99 time to evaluate : 0.793 Fit side-chains REVERT: A 81 MET cc_start: 0.8348 (mmm) cc_final: 0.8067 (mmt) REVERT: A 832 MET cc_start: 0.7865 (ppp) cc_final: 0.7113 (ppp) REVERT: A 951 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8860 (pt) REVERT: B 39 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8128 (pp) REVERT: B 81 MET cc_start: 0.8397 (mmm) cc_final: 0.8123 (mmt) REVERT: B 832 MET cc_start: 0.7839 (ppp) cc_final: 0.7161 (ppp) REVERT: C 39 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8110 (pp) REVERT: C 81 MET cc_start: 0.8293 (mmm) cc_final: 0.7991 (mmt) REVERT: C 832 MET cc_start: 0.7686 (ppp) cc_final: 0.7262 (ppp) REVERT: D 39 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8113 (pp) REVERT: D 81 MET cc_start: 0.8388 (mmm) cc_final: 0.8108 (mmt) REVERT: D 832 MET cc_start: 0.7892 (ppp) cc_final: 0.7463 (ppp) REVERT: D 951 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8892 (pt) outliers start: 40 outliers final: 6 residues processed: 129 average time/residue: 0.5593 time to fit residues: 85.7989 Evaluate side-chains 106 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 951 ILE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 951 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 100 optimal weight: 9.9990 chunk 225 optimal weight: 5.9990 chunk 289 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 346 optimal weight: 9.9990 chunk 119 optimal weight: 8.9990 chunk 175 optimal weight: 9.9990 chunk 7 optimal weight: 0.0270 chunk 232 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 228 optimal weight: 10.0000 overall best weight: 2.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1046 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.065846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.047069 restraints weight = 85026.096| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 3.22 r_work: 0.2689 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28508 Z= 0.154 Angle : 0.493 8.474 38756 Z= 0.250 Chirality : 0.040 0.135 4440 Planarity : 0.003 0.038 4888 Dihedral : 3.840 16.066 3808 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.55 % Allowed : 10.71 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.15), residues: 3504 helix: 1.44 (0.13), residues: 1820 sheet: -0.04 (0.26), residues: 448 loop : 1.46 (0.19), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 948 TYR 0.009 0.001 TYR C 938 PHE 0.012 0.001 PHE A 304 TRP 0.008 0.001 TRP D 16 HIS 0.004 0.001 HIS C 333 Details of bonding type rmsd covalent geometry : bond 0.00359 (28508) covalent geometry : angle 0.49297 (38756) hydrogen bonds : bond 0.03874 ( 1478) hydrogen bonds : angle 4.15527 ( 3954) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 96 time to evaluate : 1.167 Fit side-chains REVERT: A 81 MET cc_start: 0.8427 (mmm) cc_final: 0.8112 (mmt) REVERT: A 496 MET cc_start: 0.9016 (mtp) cc_final: 0.8795 (ttm) REVERT: A 832 MET cc_start: 0.7951 (ppp) cc_final: 0.7434 (ppp) REVERT: A 837 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9322 (mm) REVERT: B 39 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8063 (pp) REVERT: B 81 MET cc_start: 0.8451 (mmm) cc_final: 0.8141 (mmt) REVERT: B 832 MET cc_start: 0.7945 (ppp) cc_final: 0.7218 (ppp) REVERT: C 39 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8133 (pp) REVERT: C 81 MET cc_start: 0.8358 (mmm) cc_final: 0.8056 (mmt) REVERT: C 832 MET cc_start: 0.7827 (ppp) cc_final: 0.7616 (ppp) REVERT: D 39 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8108 (pp) REVERT: D 81 MET cc_start: 0.8438 (mmm) cc_final: 0.8134 (mmt) REVERT: D 832 MET cc_start: 0.7981 (ppp) cc_final: 0.7220 (ppp) outliers start: 46 outliers final: 12 residues processed: 130 average time/residue: 0.6801 time to fit residues: 104.4547 Evaluate side-chains 112 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 951 ILE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 947 ILE Chi-restraints excluded: chain D residue 951 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 313 optimal weight: 9.9990 chunk 185 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 230 optimal weight: 0.0270 chunk 155 optimal weight: 0.9990 chunk 153 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 196 optimal weight: 10.0000 chunk 177 optimal weight: 1.9990 overall best weight: 1.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 786 HIS B 786 HIS C 786 HIS D 786 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.066970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.048254 restraints weight = 85186.042| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.25 r_work: 0.2725 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 28508 Z= 0.099 Angle : 0.467 9.086 38756 Z= 0.235 Chirality : 0.039 0.140 4440 Planarity : 0.003 0.038 4888 Dihedral : 3.766 19.638 3808 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.28 % Allowed : 10.84 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.15), residues: 3504 helix: 1.42 (0.13), residues: 1832 sheet: -0.04 (0.26), residues: 444 loop : 1.53 (0.20), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1015 TYR 0.008 0.001 TYR A 37 PHE 0.012 0.001 PHE A 304 TRP 0.010 0.001 TRP B 514 HIS 0.003 0.001 HIS A 786 Details of bonding type rmsd covalent geometry : bond 0.00220 (28508) covalent geometry : angle 0.46705 (38756) hydrogen bonds : bond 0.03477 ( 1478) hydrogen bonds : angle 4.07800 ( 3954) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 98 time to evaluate : 1.132 Fit side-chains REVERT: A 81 MET cc_start: 0.8433 (mmm) cc_final: 0.8142 (mmt) REVERT: A 105 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8543 (tm) REVERT: A 496 MET cc_start: 0.9093 (mtp) cc_final: 0.8883 (ttm) REVERT: A 832 MET cc_start: 0.7972 (ppp) cc_final: 0.7565 (ppp) REVERT: A 837 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9337 (mm) REVERT: B 39 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8171 (pp) REVERT: B 81 MET cc_start: 0.8463 (mmm) cc_final: 0.8170 (mmt) REVERT: B 496 MET cc_start: 0.8947 (ttm) cc_final: 0.8740 (ttm) REVERT: B 525 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7752 (pm20) REVERT: B 832 MET cc_start: 0.7974 (ppp) cc_final: 0.7248 (ppp) REVERT: C 39 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8119 (pp) REVERT: C 81 MET cc_start: 0.8331 (mmm) cc_final: 0.8068 (mmt) REVERT: C 105 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8573 (tm) REVERT: C 525 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7779 (pm20) REVERT: D 39 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8093 (pp) REVERT: D 81 MET cc_start: 0.8442 (mmm) cc_final: 0.8162 (mmt) REVERT: D 525 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7840 (pm20) REVERT: D 832 MET cc_start: 0.7991 (ppp) cc_final: 0.7628 (ppp) REVERT: D 951 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8852 (pt) outliers start: 38 outliers final: 8 residues processed: 130 average time/residue: 0.7061 time to fit residues: 107.7878 Evaluate side-chains 114 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 951 ILE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain D residue 947 ILE Chi-restraints excluded: chain D residue 951 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 62 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 287 optimal weight: 0.8980 chunk 11 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 158 optimal weight: 0.2980 chunk 297 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 322 optimal weight: 9.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.066455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.047765 restraints weight = 85146.637| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.24 r_work: 0.2712 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28508 Z= 0.119 Angle : 0.478 8.541 38756 Z= 0.241 Chirality : 0.039 0.137 4440 Planarity : 0.003 0.038 4888 Dihedral : 3.756 20.630 3808 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.05 % Allowed : 11.22 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.15), residues: 3504 helix: 1.43 (0.13), residues: 1832 sheet: 0.10 (0.28), residues: 396 loop : 1.48 (0.19), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1015 TYR 0.008 0.001 TYR A 37 PHE 0.012 0.001 PHE A 304 TRP 0.008 0.001 TRP B 514 HIS 0.003 0.001 HIS B 333 Details of bonding type rmsd covalent geometry : bond 0.00274 (28508) covalent geometry : angle 0.47784 (38756) hydrogen bonds : bond 0.03579 ( 1478) hydrogen bonds : angle 4.08058 ( 3954) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 1.069 Fit side-chains REVERT: A 81 MET cc_start: 0.8445 (mmm) cc_final: 0.8117 (mmt) REVERT: A 105 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8558 (tm) REVERT: A 496 MET cc_start: 0.9155 (mtp) cc_final: 0.8917 (ttm) REVERT: A 832 MET cc_start: 0.7962 (ppp) cc_final: 0.7349 (ppp) REVERT: A 837 LEU cc_start: 0.9541 (OUTLIER) cc_final: 0.9320 (mm) REVERT: B 39 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8109 (pp) REVERT: B 81 MET cc_start: 0.8473 (mmm) cc_final: 0.8171 (mmt) REVERT: B 496 MET cc_start: 0.9036 (ttm) cc_final: 0.8817 (ttm) REVERT: B 519 MET cc_start: 0.8959 (mmt) cc_final: 0.8706 (mmt) REVERT: B 525 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7790 (pm20) REVERT: B 832 MET cc_start: 0.8061 (ppp) cc_final: 0.7693 (ppp) REVERT: C 39 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8117 (pp) REVERT: C 81 MET cc_start: 0.8358 (mmm) cc_final: 0.8052 (mmt) REVERT: C 519 MET cc_start: 0.8970 (mmt) cc_final: 0.8714 (mmt) REVERT: C 525 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7802 (pm20) REVERT: C 832 MET cc_start: 0.7686 (ppp) cc_final: 0.7097 (ppp) REVERT: D 39 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8095 (pp) REVERT: D 81 MET cc_start: 0.8460 (mmm) cc_final: 0.8164 (mmt) REVERT: D 525 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7809 (pm20) REVERT: D 615 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8266 (pt0) REVERT: D 832 MET cc_start: 0.7922 (ppp) cc_final: 0.7667 (ppp) outliers start: 31 outliers final: 9 residues processed: 123 average time/residue: 0.7374 time to fit residues: 106.3471 Evaluate side-chains 114 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 951 ILE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain D residue 615 GLN Chi-restraints excluded: chain D residue 947 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 330 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 219 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 315 optimal weight: 0.6980 chunk 145 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 346 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.066646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.048015 restraints weight = 85124.803| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 3.24 r_work: 0.2720 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 28508 Z= 0.108 Angle : 0.471 8.480 38756 Z= 0.237 Chirality : 0.039 0.160 4440 Planarity : 0.003 0.039 4888 Dihedral : 3.728 22.364 3808 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.78 % Allowed : 11.55 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.15), residues: 3504 helix: 1.45 (0.13), residues: 1832 sheet: 0.11 (0.28), residues: 396 loop : 1.51 (0.19), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 757 TYR 0.008 0.001 TYR A 37 PHE 0.012 0.001 PHE A 304 TRP 0.009 0.001 TRP C 514 HIS 0.003 0.001 HIS C 333 Details of bonding type rmsd covalent geometry : bond 0.00245 (28508) covalent geometry : angle 0.47115 (38756) hydrogen bonds : bond 0.03497 ( 1478) hydrogen bonds : angle 4.04562 ( 3954) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7008 Ramachandran restraints generated. 3504 Oldfield, 0 Emsley, 3504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 1.161 Fit side-chains REVERT: A 81 MET cc_start: 0.8464 (mmm) cc_final: 0.8114 (mmt) REVERT: A 105 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8562 (tm) REVERT: A 832 MET cc_start: 0.7982 (ppp) cc_final: 0.7690 (ppp) REVERT: A 837 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9308 (mm) REVERT: B 39 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8097 (pp) REVERT: B 81 MET cc_start: 0.8453 (mmm) cc_final: 0.8171 (mmt) REVERT: B 496 MET cc_start: 0.9023 (ttm) cc_final: 0.8807 (ttm) REVERT: B 525 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7794 (pm20) REVERT: B 832 MET cc_start: 0.8032 (ppp) cc_final: 0.7747 (ppp) REVERT: C 39 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8109 (pp) REVERT: C 81 MET cc_start: 0.8379 (mmm) cc_final: 0.8050 (mmt) REVERT: C 525 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7755 (pm20) REVERT: C 832 MET cc_start: 0.7723 (ppp) cc_final: 0.7193 (ppp) REVERT: D 39 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8106 (pp) REVERT: D 81 MET cc_start: 0.8479 (mmm) cc_final: 0.8186 (mmt) REVERT: D 832 MET cc_start: 0.7942 (ppp) cc_final: 0.7688 (ppp) outliers start: 23 outliers final: 7 residues processed: 115 average time/residue: 0.7535 time to fit residues: 101.5076 Evaluate side-chains 110 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 951 ILE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 525 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 345 optimal weight: 0.9980 chunk 158 optimal weight: 0.0570 chunk 60 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 337 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 289 optimal weight: 0.1980 chunk 294 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1046 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.067507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.048878 restraints weight = 84444.114| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 3.24 r_work: 0.2747 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 28508 Z= 0.090 Angle : 0.460 8.433 38756 Z= 0.231 Chirality : 0.039 0.166 4440 Planarity : 0.003 0.040 4888 Dihedral : 3.639 19.239 3808 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.64 % Allowed : 11.79 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.15), residues: 3504 helix: 1.49 (0.13), residues: 1832 sheet: 0.09 (0.28), residues: 396 loop : 1.55 (0.19), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 757 TYR 0.008 0.001 TYR A 37 PHE 0.012 0.001 PHE A 304 TRP 0.009 0.001 TRP B 514 HIS 0.002 0.000 HIS B 333 Details of bonding type rmsd covalent geometry : bond 0.00193 (28508) covalent geometry : angle 0.45962 (38756) hydrogen bonds : bond 0.03293 ( 1478) hydrogen bonds : angle 3.99678 ( 3954) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7460.57 seconds wall clock time: 128 minutes 31.43 seconds (7711.43 seconds total)