Starting phenix.real_space_refine on Tue Jun 24 14:01:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hk6_34847/06_2025/8hk6_34847.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hk6_34847/06_2025/8hk6_34847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hk6_34847/06_2025/8hk6_34847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hk6_34847/06_2025/8hk6_34847.map" model { file = "/net/cci-nas-00/data/ceres_data/8hk6_34847/06_2025/8hk6_34847.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hk6_34847/06_2025/8hk6_34847.cif" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.051 sd= 0.187 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: 6 Type Number sf(0) Gaussians K 20 8.98 5 Zn 4 6.06 5 S 212 5.16 5 C 18588 2.51 5 N 4772 2.21 5 O 5108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28704 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7170 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 7170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7170 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "C" Number of atoms: 7170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7170 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "D" Number of atoms: 7170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7170 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' K': 8, ' ZN': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 4, ' ZN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 4, ' ZN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 4, ' ZN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4448 SG CYS A 777 85.572 96.078 128.620 1.00 74.69 S ATOM 4454 SG CYS A 778 86.057 99.913 128.438 1.00 82.67 S ATOM 4508 SG CYS A 785 82.677 98.393 129.556 1.00105.48 S ATOM 11618 SG CYS B 777 53.556 85.575 128.703 1.00 75.07 S ATOM 11624 SG CYS B 778 49.929 85.993 128.505 1.00 82.61 S ATOM 11678 SG CYS B 785 51.410 82.824 129.668 1.00105.30 S ATOM 18788 SG CYS C 777 64.165 53.688 128.607 1.00 73.24 S ATOM 18794 SG CYS C 778 63.708 49.848 128.422 1.00 82.57 S ATOM 18848 SG CYS C 785 67.054 51.395 129.583 1.00106.68 S ATOM 25958 SG CYS D 777 96.044 64.149 128.595 1.00 77.59 S ATOM 25964 SG CYS D 778 99.891 63.713 128.419 1.00 82.97 S ATOM 26018 SG CYS D 785 98.311 67.055 129.542 1.00106.54 S Time building chain proxies: 15.70, per 1000 atoms: 0.55 Number of scatterers: 28704 At special positions: 0 Unit cell: (150.8, 150.8, 144.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 K 20 19.00 S 212 16.00 O 5108 8.00 N 4772 7.00 C 18588 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.31 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1303 " pdb="ZN ZN A1303 " - pdb=" ND1 HIS A 787 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 777 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 778 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 785 " pdb=" ZN B1303 " pdb="ZN ZN B1303 " - pdb=" ND1 HIS B 787 " pdb="ZN ZN B1303 " - pdb=" SG CYS B 777 " pdb="ZN ZN B1303 " - pdb=" SG CYS B 778 " pdb="ZN ZN B1303 " - pdb=" SG CYS B 785 " pdb=" ZN C1303 " pdb="ZN ZN C1303 " - pdb=" ND1 HIS C 787 " pdb="ZN ZN C1303 " - pdb=" SG CYS C 777 " pdb="ZN ZN C1303 " - pdb=" SG CYS C 785 " pdb="ZN ZN C1303 " - pdb=" SG CYS C 778 " pdb=" ZN D1303 " pdb="ZN ZN D1303 " - pdb=" ND1 HIS D 787 " pdb="ZN ZN D1303 " - pdb=" SG CYS D 777 " pdb="ZN ZN D1303 " - pdb=" SG CYS D 785 " pdb="ZN ZN D1303 " - pdb=" SG CYS D 778 " Number of angles added : 12 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6888 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 21 sheets defined 53.8% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.46 Creating SS restraints... Processing helix chain 'A' and resid 110 through 136 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 173 through 198 removed outlier: 3.608A pdb=" N ALA A 178 " --> pdb=" O MET A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 228 Proline residue: A 221 - end of helix removed outlier: 3.858A pdb=" N ILE A 226 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TRP A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 removed outlier: 3.934A pdb=" N ASN A 233 " --> pdb=" O PRO A 230 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 234 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 254 removed outlier: 4.044A pdb=" N LEU A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 293 Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 324 through 357 Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 382 through 394 Processing helix chain 'A' and resid 395 through 400 removed outlier: 6.701A pdb=" N ARG A 398 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 400 " --> pdb=" O PRO A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 422 removed outlier: 3.564A pdb=" N VAL A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 427 removed outlier: 4.457A pdb=" N GLN A 427 " --> pdb=" O PRO A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 463 through 482 Processing helix chain 'A' and resid 493 through 500 removed outlier: 4.717A pdb=" N PHE A 498 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS A 499 " --> pdb=" O ASN A 496 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 500 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 523 removed outlier: 3.551A pdb=" N CYS A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 534 Processing helix chain 'A' and resid 547 through 557 Processing helix chain 'A' and resid 572 through 576 Processing helix chain 'A' and resid 579 through 592 Processing helix chain 'A' and resid 633 through 644 removed outlier: 3.612A pdb=" N PHE A 637 " --> pdb=" O SER A 633 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 638 " --> pdb=" O ALA A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 780 Processing helix chain 'A' and resid 792 through 797 removed outlier: 3.523A pdb=" N TYR A 796 " --> pdb=" O ASP A 792 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY A 797 " --> pdb=" O ALA A 793 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 792 through 797' Processing helix chain 'A' and resid 811 through 823 Proline residue: A 820 - end of helix Processing helix chain 'A' and resid 843 through 851 Processing helix chain 'A' and resid 865 through 873 Processing helix chain 'A' and resid 893 through 897 Processing helix chain 'A' and resid 898 through 912 Processing helix chain 'A' and resid 923 through 930 removed outlier: 4.053A pdb=" N ARG A 928 " --> pdb=" O SER A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 952 removed outlier: 3.681A pdb=" N SER A 943 " --> pdb=" O SER A 939 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS A 944 " --> pdb=" O LEU A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 960 removed outlier: 3.966A pdb=" N PHE A 960 " --> pdb=" O ALA A 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 957 through 960' Processing helix chain 'A' and resid 961 through 966 Processing helix chain 'A' and resid 972 through 982 removed outlier: 3.586A pdb=" N ASP A 976 " --> pdb=" O ILE A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 996 Processing helix chain 'A' and resid 1013 through 1017 removed outlier: 3.630A pdb=" N LEU A1017 " --> pdb=" O GLU A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1033 Processing helix chain 'A' and resid 1129 through 1143 Processing helix chain 'A' and resid 1144 through 1161 Processing helix chain 'B' and resid 111 through 136 Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 173 through 198 Processing helix chain 'B' and resid 211 through 218 Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 226 through 227 No H-bonds generated for 'chain 'B' and resid 226 through 227' Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 240 through 254 removed outlier: 4.033A pdb=" N LEU B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 293 Processing helix chain 'B' and resid 300 through 313 Processing helix chain 'B' and resid 324 through 357 Proline residue: B 343 - end of helix Processing helix chain 'B' and resid 382 through 394 Processing helix chain 'B' and resid 395 through 400 removed outlier: 6.664A pdb=" N ARG B 398 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN B 400 " --> pdb=" O PRO B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 422 removed outlier: 3.582A pdb=" N VAL B 419 " --> pdb=" O GLN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 427 removed outlier: 4.418A pdb=" N GLN B 427 " --> pdb=" O PRO B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 446 through 450 Processing helix chain 'B' and resid 463 through 482 Processing helix chain 'B' and resid 493 through 500 removed outlier: 4.719A pdb=" N PHE B 498 " --> pdb=" O GLU B 495 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS B 499 " --> pdb=" O ASN B 496 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 500 " --> pdb=" O LYS B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 523 removed outlier: 3.552A pdb=" N CYS B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 534 Processing helix chain 'B' and resid 547 through 557 Processing helix chain 'B' and resid 572 through 576 Processing helix chain 'B' and resid 579 through 592 Processing helix chain 'B' and resid 633 through 644 removed outlier: 3.606A pdb=" N PHE B 637 " --> pdb=" O SER B 633 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B 638 " --> pdb=" O ALA B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 780 Processing helix chain 'B' and resid 792 through 797 removed outlier: 3.612A pdb=" N TYR B 796 " --> pdb=" O ASP B 792 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 792 through 797' Processing helix chain 'B' and resid 811 through 823 Proline residue: B 820 - end of helix Processing helix chain 'B' and resid 843 through 851 Processing helix chain 'B' and resid 865 through 873 Processing helix chain 'B' and resid 893 through 897 Processing helix chain 'B' and resid 898 through 912 Processing helix chain 'B' and resid 923 through 930 removed outlier: 4.055A pdb=" N ARG B 928 " --> pdb=" O SER B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 952 removed outlier: 3.658A pdb=" N SER B 943 " --> pdb=" O SER B 939 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS B 944 " --> pdb=" O LEU B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 960 removed outlier: 3.926A pdb=" N PHE B 960 " --> pdb=" O ALA B 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 957 through 960' Processing helix chain 'B' and resid 961 through 966 Processing helix chain 'B' and resid 972 through 982 removed outlier: 3.621A pdb=" N ASP B 976 " --> pdb=" O ILE B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 996 Processing helix chain 'B' and resid 1013 through 1017 removed outlier: 3.631A pdb=" N LEU B1017 " --> pdb=" O GLU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1021 through 1033 Processing helix chain 'B' and resid 1129 through 1143 Processing helix chain 'B' and resid 1144 through 1161 Processing helix chain 'C' and resid 111 through 136 Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 173 through 198 removed outlier: 3.517A pdb=" N ALA C 178 " --> pdb=" O MET C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 225 Proline residue: C 221 - end of helix Processing helix chain 'C' and resid 226 through 227 No H-bonds generated for 'chain 'C' and resid 226 through 227' Processing helix chain 'C' and resid 228 through 232 Processing helix chain 'C' and resid 240 through 254 removed outlier: 4.038A pdb=" N LEU C 244 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 293 Processing helix chain 'C' and resid 300 through 313 Processing helix chain 'C' and resid 324 through 357 Proline residue: C 343 - end of helix Processing helix chain 'C' and resid 382 through 394 Processing helix chain 'C' and resid 395 through 400 removed outlier: 6.724A pdb=" N ARG C 398 " --> pdb=" O ALA C 395 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN C 400 " --> pdb=" O PRO C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 422 removed outlier: 3.623A pdb=" N VAL C 419 " --> pdb=" O GLN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 427 removed outlier: 4.406A pdb=" N GLN C 427 " --> pdb=" O PRO C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 446 through 450 Processing helix chain 'C' and resid 463 through 482 Processing helix chain 'C' and resid 493 through 500 removed outlier: 4.723A pdb=" N PHE C 498 " --> pdb=" O GLU C 495 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS C 499 " --> pdb=" O ASN C 496 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C 500 " --> pdb=" O LYS C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 523 removed outlier: 3.554A pdb=" N CYS C 521 " --> pdb=" O LEU C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 534 Processing helix chain 'C' and resid 547 through 557 Processing helix chain 'C' and resid 572 through 576 Processing helix chain 'C' and resid 579 through 592 Processing helix chain 'C' and resid 633 through 644 removed outlier: 3.607A pdb=" N PHE C 637 " --> pdb=" O SER C 633 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS C 638 " --> pdb=" O ALA C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 775 through 780 Processing helix chain 'C' and resid 792 through 797 removed outlier: 3.535A pdb=" N TYR C 796 " --> pdb=" O ASP C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 823 Proline residue: C 820 - end of helix Processing helix chain 'C' and resid 843 through 851 Processing helix chain 'C' and resid 865 through 873 Processing helix chain 'C' and resid 893 through 897 Processing helix chain 'C' and resid 898 through 912 Processing helix chain 'C' and resid 923 through 930 removed outlier: 4.042A pdb=" N ARG C 928 " --> pdb=" O SER C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 936 through 952 removed outlier: 3.663A pdb=" N SER C 943 " --> pdb=" O SER C 939 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS C 944 " --> pdb=" O LEU C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 960 removed outlier: 4.077A pdb=" N PHE C 960 " --> pdb=" O ALA C 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 957 through 960' Processing helix chain 'C' and resid 961 through 966 Processing helix chain 'C' and resid 972 through 982 removed outlier: 3.637A pdb=" N ASP C 976 " --> pdb=" O ILE C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 996 Processing helix chain 'C' and resid 1013 through 1017 removed outlier: 3.622A pdb=" N LEU C1017 " --> pdb=" O GLU C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1021 through 1033 Processing helix chain 'C' and resid 1129 through 1143 Processing helix chain 'C' and resid 1144 through 1161 Processing helix chain 'D' and resid 111 through 137 Processing helix chain 'D' and resid 164 through 169 Processing helix chain 'D' and resid 173 through 198 removed outlier: 3.626A pdb=" N ALA D 178 " --> pdb=" O MET D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 218 Processing helix chain 'D' and resid 219 through 226 removed outlier: 3.544A pdb=" N ILE D 223 " --> pdb=" O THR D 219 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE D 226 " --> pdb=" O PHE D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 254 removed outlier: 4.060A pdb=" N LEU D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET D 252 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN D 254 " --> pdb=" O GLU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 293 Processing helix chain 'D' and resid 300 through 313 Processing helix chain 'D' and resid 324 through 357 Proline residue: D 343 - end of helix Processing helix chain 'D' and resid 382 through 394 Processing helix chain 'D' and resid 395 through 400 removed outlier: 6.762A pdb=" N ARG D 398 " --> pdb=" O ALA D 395 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN D 400 " --> pdb=" O PRO D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 421 Processing helix chain 'D' and resid 422 through 427 removed outlier: 4.421A pdb=" N GLN D 427 " --> pdb=" O PRO D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 446 through 450 Processing helix chain 'D' and resid 463 through 482 Processing helix chain 'D' and resid 493 through 500 removed outlier: 4.713A pdb=" N PHE D 498 " --> pdb=" O GLU D 495 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS D 499 " --> pdb=" O ASN D 496 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL D 500 " --> pdb=" O LYS D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 523 removed outlier: 3.545A pdb=" N CYS D 521 " --> pdb=" O LEU D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 534 Processing helix chain 'D' and resid 547 through 557 Processing helix chain 'D' and resid 572 through 576 Processing helix chain 'D' and resid 579 through 592 Processing helix chain 'D' and resid 633 through 644 removed outlier: 3.616A pdb=" N PHE D 637 " --> pdb=" O SER D 633 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS D 638 " --> pdb=" O ALA D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 775 through 780 Processing helix chain 'D' and resid 792 through 797 removed outlier: 3.520A pdb=" N TYR D 796 " --> pdb=" O ASP D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 823 Proline residue: D 820 - end of helix Processing helix chain 'D' and resid 843 through 851 Processing helix chain 'D' and resid 865 through 873 Processing helix chain 'D' and resid 893 through 897 Processing helix chain 'D' and resid 898 through 912 Processing helix chain 'D' and resid 923 through 930 removed outlier: 4.046A pdb=" N ARG D 928 " --> pdb=" O SER D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 936 through 952 removed outlier: 3.713A pdb=" N SER D 943 " --> pdb=" O SER D 939 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS D 944 " --> pdb=" O LEU D 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 957 through 960 removed outlier: 4.113A pdb=" N PHE D 960 " --> pdb=" O ALA D 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 957 through 960' Processing helix chain 'D' and resid 961 through 966 Processing helix chain 'D' and resid 972 through 982 removed outlier: 3.621A pdb=" N ASP D 976 " --> pdb=" O ILE D 972 " (cutoff:3.500A) Processing helix chain 'D' and resid 987 through 996 Processing helix chain 'D' and resid 1013 through 1017 removed outlier: 3.622A pdb=" N LEU D1017 " --> pdb=" O GLU D1014 " (cutoff:3.500A) Processing helix chain 'D' and resid 1021 through 1033 Processing helix chain 'D' and resid 1129 through 1143 Processing helix chain 'D' and resid 1144 through 1161 Processing sheet with id=AA1, first strand: chain 'A' and resid 143 through 144 Processing sheet with id=AA2, first strand: chain 'A' and resid 429 through 432 removed outlier: 6.164A pdb=" N VAL A 404 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU A 432 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE A 406 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N PHE A 454 " --> pdb=" O HIS A 373 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL A 375 " --> pdb=" O PHE A 454 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N LEU A 456 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N CYS A 377 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N CYS A 453 " --> pdb=" O TYR A 488 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLN A 490 " --> pdb=" O CYS A 453 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE A 455 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 560 through 565 removed outlier: 6.579A pdb=" N ILE A 625 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LEU A 595 " --> pdb=" O ILE A 625 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 750 through 752 Processing sheet with id=AA5, first strand: chain 'A' and resid 856 through 860 removed outlier: 6.129A pdb=" N ILE A 834 " --> pdb=" O TYR A 857 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N MET A 859 " --> pdb=" O ILE A 834 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU A 836 " --> pdb=" O MET A 859 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE A 803 " --> pdb=" O VAL A 835 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU A 837 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL A 805 " --> pdb=" O LEU A 837 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LEU A 802 " --> pdb=" O ALA A 877 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER A 916 " --> pdb=" O ASP A 878 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A 920 " --> pdb=" O VAL A 882 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1006 through 1012 removed outlier: 3.913A pdb=" N ASP A1194 " --> pdb=" O ILE A1012 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY A1039 " --> pdb=" O TYR A1197 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE A1199 " --> pdb=" O PRO A1037 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 429 through 432 removed outlier: 6.171A pdb=" N VAL B 404 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU B 432 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE B 406 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N PHE B 454 " --> pdb=" O HIS B 373 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL B 375 " --> pdb=" O PHE B 454 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N LEU B 456 " --> pdb=" O VAL B 375 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N CYS B 377 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N CYS B 453 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N GLN B 490 " --> pdb=" O CYS B 453 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE B 455 " --> pdb=" O GLN B 490 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 560 through 565 removed outlier: 6.586A pdb=" N ILE B 625 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU B 595 " --> pdb=" O ILE B 625 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 750 through 752 Processing sheet with id=AB1, first strand: chain 'B' and resid 856 through 860 removed outlier: 6.125A pdb=" N ILE B 834 " --> pdb=" O TYR B 857 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N MET B 859 " --> pdb=" O ILE B 834 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU B 836 " --> pdb=" O MET B 859 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE B 803 " --> pdb=" O VAL B 835 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LEU B 837 " --> pdb=" O ILE B 803 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL B 805 " --> pdb=" O LEU B 837 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LEU B 802 " --> pdb=" O ALA B 877 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER B 916 " --> pdb=" O ASP B 878 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B 920 " --> pdb=" O VAL B 882 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1006 through 1012 removed outlier: 3.918A pdb=" N ASP B1194 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY B1039 " --> pdb=" O TYR B1197 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B1199 " --> pdb=" O PRO B1037 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 429 through 432 removed outlier: 6.152A pdb=" N VAL C 404 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU C 432 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE C 406 " --> pdb=" O LEU C 432 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N PHE C 454 " --> pdb=" O HIS C 373 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL C 375 " --> pdb=" O PHE C 454 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU C 456 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N CYS C 377 " --> pdb=" O LEU C 456 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N CYS C 453 " --> pdb=" O TYR C 488 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLN C 490 " --> pdb=" O CYS C 453 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE C 455 " --> pdb=" O GLN C 490 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 560 through 565 removed outlier: 6.583A pdb=" N ILE C 625 " --> pdb=" O LEU C 595 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU C 595 " --> pdb=" O ILE C 625 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 750 through 752 Processing sheet with id=AB6, first strand: chain 'C' and resid 856 through 860 removed outlier: 6.132A pdb=" N ILE C 834 " --> pdb=" O TYR C 857 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N MET C 859 " --> pdb=" O ILE C 834 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU C 836 " --> pdb=" O MET C 859 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE C 803 " --> pdb=" O VAL C 835 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU C 837 " --> pdb=" O ILE C 803 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL C 805 " --> pdb=" O LEU C 837 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU C 802 " --> pdb=" O ALA C 877 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER C 916 " --> pdb=" O ASP C 878 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU C 920 " --> pdb=" O VAL C 882 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 1006 through 1012 removed outlier: 3.917A pdb=" N ASP C1194 " --> pdb=" O ILE C1012 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY C1039 " --> pdb=" O TYR C1197 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE C1199 " --> pdb=" O PRO C1037 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 429 through 432 removed outlier: 6.165A pdb=" N VAL D 404 " --> pdb=" O ILE D 430 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU D 432 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE D 406 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N CYS D 453 " --> pdb=" O TYR D 488 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N GLN D 490 " --> pdb=" O CYS D 453 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE D 455 " --> pdb=" O GLN D 490 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 560 through 565 removed outlier: 6.584A pdb=" N ILE D 625 " --> pdb=" O LEU D 595 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU D 595 " --> pdb=" O ILE D 625 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 750 through 752 Processing sheet with id=AC2, first strand: chain 'D' and resid 856 through 860 removed outlier: 6.119A pdb=" N ILE D 834 " --> pdb=" O TYR D 857 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N MET D 859 " --> pdb=" O ILE D 834 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU D 836 " --> pdb=" O MET D 859 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE D 803 " --> pdb=" O VAL D 835 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU D 837 " --> pdb=" O ILE D 803 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL D 805 " --> pdb=" O LEU D 837 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LEU D 802 " --> pdb=" O ALA D 877 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER D 916 " --> pdb=" O ASP D 878 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU D 920 " --> pdb=" O VAL D 882 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 1006 through 1012 removed outlier: 3.907A pdb=" N ASP D1194 " --> pdb=" O ILE D1012 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY D1039 " --> pdb=" O TYR D1197 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE D1199 " --> pdb=" O PRO D1037 " (cutoff:3.500A) 1401 hydrogen bonds defined for protein. 3903 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: 10.92 Time building geometry restraints manager: 7.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.22: 2 1.22 - 1.37: 9990 1.37 - 1.53: 16059 1.53 - 1.68: 2981 1.68 - 1.83: 312 Bond restraints: 29344 Sorted by residual: bond pdb=" CB PRO C 139 " pdb=" CG PRO C 139 " ideal model delta sigma weight residual 1.492 1.065 0.427 5.00e-02 4.00e+02 7.28e+01 bond pdb=" CG PRO C 139 " pdb=" CD PRO C 139 " ideal model delta sigma weight residual 1.503 1.237 0.266 3.40e-02 8.65e+02 6.11e+01 bond pdb=" C ASP C 138 " pdb=" N PRO C 139 " ideal model delta sigma weight residual 1.335 1.264 0.071 1.30e-02 5.92e+03 2.98e+01 bond pdb=" N PRO C 139 " pdb=" CA PRO C 139 " ideal model delta sigma weight residual 1.473 1.525 -0.051 1.32e-02 5.74e+03 1.51e+01 bond pdb=" CG PRO C 423 " pdb=" CD PRO C 423 " ideal model delta sigma weight residual 1.503 1.393 0.110 3.40e-02 8.65e+02 1.05e+01 ... (remaining 29339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.77: 39809 14.77 - 29.55: 2 29.55 - 44.32: 0 44.32 - 59.10: 0 59.10 - 73.87: 1 Bond angle restraints: 39812 Sorted by residual: angle pdb=" CB PRO C 139 " pdb=" CG PRO C 139 " pdb=" CD PRO C 139 " ideal model delta sigma weight residual 106.10 179.97 -73.87 3.20e+00 9.77e-02 5.33e+02 angle pdb=" N PRO C 139 " pdb=" CD PRO C 139 " pdb=" CG PRO C 139 " ideal model delta sigma weight residual 103.20 73.90 29.30 1.50e+00 4.44e-01 3.81e+02 angle pdb=" CA PRO C 139 " pdb=" CB PRO C 139 " pdb=" CG PRO C 139 " ideal model delta sigma weight residual 104.50 74.99 29.51 1.90e+00 2.77e-01 2.41e+02 angle pdb=" N PRO C 423 " pdb=" CD PRO C 423 " pdb=" CG PRO C 423 " ideal model delta sigma weight residual 103.20 94.23 8.97 1.50e+00 4.44e-01 3.58e+01 angle pdb=" N PRO A 229 " pdb=" CA PRO A 229 " pdb=" C PRO A 229 " ideal model delta sigma weight residual 110.70 117.43 -6.73 1.22e+00 6.72e-01 3.04e+01 ... (remaining 39807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 15426 17.83 - 35.66: 1633 35.66 - 53.49: 403 53.49 - 71.32: 113 71.32 - 89.15: 29 Dihedral angle restraints: 17604 sinusoidal: 6992 harmonic: 10612 Sorted by residual: dihedral pdb=" CA PRO D 149 " pdb=" C PRO D 149 " pdb=" N LYS D 150 " pdb=" CA LYS D 150 " ideal model delta harmonic sigma weight residual 180.00 152.78 27.22 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA PRO B 149 " pdb=" C PRO B 149 " pdb=" N LYS B 150 " pdb=" CA LYS B 150 " ideal model delta harmonic sigma weight residual 180.00 154.66 25.34 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA PRO A 149 " pdb=" C PRO A 149 " pdb=" N LYS A 150 " pdb=" CA LYS A 150 " ideal model delta harmonic sigma weight residual 180.00 155.03 24.97 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 17601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 4043 0.066 - 0.132: 463 0.132 - 0.198: 30 0.198 - 0.264: 3 0.264 - 0.330: 9 Chirality restraints: 4548 Sorted by residual: chirality pdb=" CA TRP C 146 " pdb=" N TRP C 146 " pdb=" C TRP C 146 " pdb=" CB TRP C 146 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA TRP D 146 " pdb=" N TRP D 146 " pdb=" C TRP D 146 " pdb=" CB TRP D 146 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA PRO D 149 " pdb=" N PRO D 149 " pdb=" C PRO D 149 " pdb=" CB PRO D 149 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 4545 not shown) Planarity restraints: 4992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 169 " 0.032 2.00e-02 2.50e+03 3.87e-02 3.74e+01 pdb=" CG TRP A 169 " -0.095 2.00e-02 2.50e+03 pdb=" CD1 TRP A 169 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 TRP A 169 " 0.016 2.00e-02 2.50e+03 pdb=" NE1 TRP A 169 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TRP A 169 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 169 " 0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 169 " 0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 169 " -0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP A 169 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 148 " -0.092 5.00e-02 4.00e+02 1.39e-01 3.07e+01 pdb=" N PRO A 149 " 0.240 5.00e-02 4.00e+02 pdb=" CA PRO A 149 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO A 149 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 148 " 0.092 5.00e-02 4.00e+02 1.38e-01 3.06e+01 pdb=" N PRO C 149 " -0.239 5.00e-02 4.00e+02 pdb=" CA PRO C 149 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO C 149 " 0.073 5.00e-02 4.00e+02 ... (remaining 4989 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.21: 22 2.21 - 2.94: 12397 2.94 - 3.67: 49918 3.67 - 4.41: 86827 4.41 - 5.14: 142549 Nonbonded interactions: 291713 Sorted by model distance: nonbonded pdb=" OE1 GLN B 415 " pdb=" NZ LYS C 438 " model vdw 1.477 3.120 nonbonded pdb=" CE1 HIS B1159 " pdb=" OE2 GLU C 848 " model vdw 2.024 3.260 nonbonded pdb=" CE1 HIS A1159 " pdb=" OE2 GLU B 848 " model vdw 2.033 3.260 nonbonded pdb=" O ASN B 163 " pdb=" OD1 ASN B 163 " model vdw 2.094 3.040 nonbonded pdb=" NE2 HIS B1159 " pdb=" OE2 GLU C 848 " model vdw 2.105 3.120 ... (remaining 291708 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 110 through 1205 or resid 1301 through 1305)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.020 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: 0.030 Extract box with map and model: 1.010 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 65.060 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.110 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:10.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 : 0.006 0.427 29361 Z= 0.321 Angle : 0.802 73.874 39824 Z= 0.398 Chirality : 0.046 0.330 4548 Planarity : 0.007 0.139 4992 Dihedral : 16.467 89.152 10716 Min Nonbonded Distance : 1.477 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.80 % Favored : 96.97 % Rotamer: Outliers : 1.62 % Allowed : 21.54 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.13), residues: 3532 helix: -0.40 (0.12), residues: 1684 sheet: -0.81 (0.24), residues: 356 loop : -0.38 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.095 0.002 TRP A 169 HIS 0.013 0.001 HIS D 291 PHE 0.032 0.002 PHE A 268 TYR 0.019 0.002 TYR D 351 ARG 0.009 0.001 ARG D 133 Details of bonding type rmsd hydrogen bonds : bond 0.21307 ( 1401) hydrogen bonds : angle 7.15424 ( 3903) metal coordination : bond 0.01290 ( 16) metal coordination : angle 4.17147 ( 12) covalent geometry : bond 0.00582 (29344) covalent geometry : angle 0.79909 (39812) Misc. bond : bond 0.40622 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 532 time to evaluate : 3.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 ARG cc_start: 0.7958 (ttm170) cc_final: 0.7417 (ttm110) REVERT: A 275 PHE cc_start: 0.7159 (t80) cc_final: 0.6876 (t80) REVERT: B 604 LYS cc_start: 0.8043 (mttt) cc_final: 0.7799 (tptp) REVERT: B 794 LYS cc_start: 0.7698 (tptt) cc_final: 0.7399 (mmtm) REVERT: C 179 ILE cc_start: 0.7849 (mt) cc_final: 0.7618 (mp) REVERT: D 232 ARG cc_start: 0.7581 (mmm-85) cc_final: 0.7361 (mmm-85) REVERT: D 252 MET cc_start: 0.6810 (mtp) cc_final: 0.6539 (tmt) REVERT: D 603 ASN cc_start: 0.7574 (m-40) cc_final: 0.7056 (m110) REVERT: D 794 LYS cc_start: 0.8097 (tttp) cc_final: 0.7298 (mppt) outliers start: 51 outliers final: 36 residues processed: 571 average time/residue: 1.6264 time to fit residues: 1071.3490 Evaluate side-chains 534 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 498 time to evaluate : 3.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 1159 HIS Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain B residue 627 ILE Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 783 LYS Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 831 LEU Chi-restraints excluded: chain C residue 975 LEU Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1176 THR Chi-restraints excluded: chain C residue 1187 ASP Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 438 LYS Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 627 ILE Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 1176 THR Chi-restraints excluded: chain D residue 1204 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 0.0370 chunk 269 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 182 optimal weight: 20.0000 chunk 144 optimal weight: 9.9990 chunk 279 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 323 optimal weight: 8.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 218 ASN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 GLN A 490 GLN A 505 HIS A 535 HIS A 603 ASN A 632 ASN A 981 GLN A1046 HIS ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN B 218 ASN B 298 ASN B 440 GLN B 490 GLN B 505 HIS B 535 HIS B 548 GLN B 952 ASN B 981 GLN B1046 HIS ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN C 218 ASN ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 HIS C 298 ASN ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 GLN C 490 GLN C 505 HIS C 535 HIS C 632 ASN C 952 ASN C 981 GLN ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN D 218 ASN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 GLN D 470 GLN D 490 GLN D 505 HIS D 535 HIS D 548 GLN D 632 ASN D 981 GLN D1046 HIS ** D1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.128342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.095645 restraints weight = 50352.154| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.13 r_work: 0.3139 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.108 29361 Z= 0.274 Angle : 0.672 11.036 39824 Z= 0.345 Chirality : 0.048 0.290 4548 Planarity : 0.006 0.135 4992 Dihedral : 6.112 59.415 3971 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.00 % Favored : 96.77 % Rotamer: Outliers : 4.67 % Allowed : 19.63 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.14), residues: 3532 helix: 0.20 (0.12), residues: 1712 sheet: -1.06 (0.23), residues: 380 loop : -0.33 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 228 HIS 0.008 0.002 HIS B 291 PHE 0.018 0.002 PHE B 798 TYR 0.018 0.002 TYR A 403 ARG 0.010 0.001 ARG A1137 Details of bonding type rmsd hydrogen bonds : bond 0.05386 ( 1401) hydrogen bonds : angle 5.15658 ( 3903) metal coordination : bond 0.01657 ( 16) metal coordination : angle 2.89732 ( 12) covalent geometry : bond 0.00679 (29344) covalent geometry : angle 0.66974 (39812) Misc. bond : bond 0.00302 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 523 time to evaluate : 3.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8625 (mp) REVERT: A 200 LYS cc_start: 0.4252 (OUTLIER) cc_final: 0.3853 (tppt) REVERT: A 232 ARG cc_start: 0.8164 (ttm170) cc_final: 0.7451 (ttm110) REVERT: A 275 PHE cc_start: 0.7339 (t80) cc_final: 0.7079 (t80) REVERT: A 415 GLN cc_start: 0.8541 (mt0) cc_final: 0.8143 (mp10) REVERT: A 604 LYS cc_start: 0.8073 (ptmm) cc_final: 0.7559 (tptp) REVERT: A 883 VAL cc_start: 0.8397 (OUTLIER) cc_final: 0.8071 (m) REVERT: A 1146 ARG cc_start: 0.7996 (tpm-80) cc_final: 0.7789 (tpm170) REVERT: A 1151 GLU cc_start: 0.7416 (pp20) cc_final: 0.7199 (pp20) REVERT: B 180 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7405 (tp40) REVERT: B 231 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7359 (tp) REVERT: B 415 GLN cc_start: 0.8431 (mt0) cc_final: 0.8032 (mp10) REVERT: B 428 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7582 (mtt180) REVERT: B 516 MET cc_start: 0.9072 (mtm) cc_final: 0.8492 (mtm) REVERT: B 604 LYS cc_start: 0.8180 (mttt) cc_final: 0.7687 (tptp) REVERT: B 794 LYS cc_start: 0.8038 (tptt) cc_final: 0.7612 (mppt) REVERT: B 859 MET cc_start: 0.8843 (ttm) cc_final: 0.8599 (ttm) REVERT: B 883 VAL cc_start: 0.8385 (OUTLIER) cc_final: 0.8074 (m) REVERT: B 950 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7630 (ttp-170) REVERT: B 1146 ARG cc_start: 0.7961 (tpm-80) cc_final: 0.7739 (tpm170) REVERT: C 200 LYS cc_start: 0.3541 (OUTLIER) cc_final: 0.3106 (tptp) REVERT: C 215 GLU cc_start: 0.7209 (tp30) cc_final: 0.6987 (tm-30) REVERT: C 252 MET cc_start: 0.5802 (OUTLIER) cc_final: 0.5559 (mtt) REVERT: C 305 PHE cc_start: 0.8684 (t80) cc_final: 0.8468 (t80) REVERT: C 516 MET cc_start: 0.9081 (mtm) cc_final: 0.8523 (mtm) REVERT: C 604 LYS cc_start: 0.8102 (ptmm) cc_final: 0.7562 (tptp) REVERT: C 883 VAL cc_start: 0.8406 (OUTLIER) cc_final: 0.8177 (m) REVERT: D 200 LYS cc_start: 0.2931 (OUTLIER) cc_final: 0.2624 (tppp) REVERT: D 228 TRP cc_start: 0.5233 (OUTLIER) cc_final: 0.3988 (m100) REVERT: D 252 MET cc_start: 0.7286 (mtp) cc_final: 0.7009 (tmt) REVERT: D 351 TYR cc_start: 0.7617 (t80) cc_final: 0.7230 (t80) REVERT: D 355 GLU cc_start: 0.8126 (tt0) cc_final: 0.7803 (mm-30) REVERT: D 415 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.8023 (mp10) REVERT: D 516 MET cc_start: 0.9074 (mtm) cc_final: 0.8489 (mtm) REVERT: D 544 GLU cc_start: 0.8132 (mp0) cc_final: 0.7887 (mt-10) REVERT: D 548 GLN cc_start: 0.8366 (tp40) cc_final: 0.8158 (tp-100) REVERT: D 783 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7249 (ptmm) REVERT: D 794 LYS cc_start: 0.8348 (tttp) cc_final: 0.7505 (mppt) REVERT: D 883 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.8021 (m) REVERT: D 1151 GLU cc_start: 0.7533 (pp20) cc_final: 0.7244 (pp20) outliers start: 147 outliers final: 77 residues processed: 608 average time/residue: 1.4432 time to fit residues: 1021.4589 Evaluate side-chains 602 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 509 time to evaluate : 2.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1187 ASP Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 428 ARG Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 600 ARG Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 950 ARG Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1038 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 600 ARG Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 831 LEU Chi-restraints excluded: chain C residue 840 ASN Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1016 ASP Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1033 SER Chi-restraints excluded: chain C residue 1038 ILE Chi-restraints excluded: chain C residue 1143 ARG Chi-restraints excluded: chain C residue 1152 LEU Chi-restraints excluded: chain C residue 1187 ASP Chi-restraints excluded: chain C residue 1204 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 497 LYS Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 600 ARG Chi-restraints excluded: chain D residue 783 LYS Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 840 ASN Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain D residue 1152 LEU Chi-restraints excluded: chain D residue 1162 LEU Chi-restraints excluded: chain D residue 1204 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 63 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 197 optimal weight: 0.7980 chunk 175 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 171 optimal weight: 0.1980 chunk 301 optimal weight: 0.7980 chunk 290 optimal weight: 1.9990 chunk 341 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 GLN A1046 HIS ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 ASN B 981 GLN B1046 HIS ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN C 415 GLN C 440 GLN C 952 ASN C 981 GLN ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 GLN D 440 GLN D 603 ASN D 632 ASN D 952 ASN D 981 GLN D1046 HIS ** D1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.129631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.097552 restraints weight = 50491.823| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.07 r_work: 0.3183 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 29361 Z= 0.127 Angle : 0.571 18.338 39824 Z= 0.290 Chirality : 0.046 1.187 4548 Planarity : 0.006 0.132 4992 Dihedral : 5.338 57.491 3928 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.75 % Favored : 97.03 % Rotamer: Outliers : 4.35 % Allowed : 20.36 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.14), residues: 3532 helix: 0.63 (0.12), residues: 1696 sheet: -0.97 (0.24), residues: 344 loop : -0.12 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 228 HIS 0.008 0.001 HIS B 291 PHE 0.017 0.001 PHE A 212 TYR 0.017 0.001 TYR A 403 ARG 0.027 0.000 ARG A1137 Details of bonding type rmsd hydrogen bonds : bond 0.04031 ( 1401) hydrogen bonds : angle 4.73050 ( 3903) metal coordination : bond 0.00591 ( 16) metal coordination : angle 1.93872 ( 12) covalent geometry : bond 0.00305 (29344) covalent geometry : angle 0.57057 (39812) Misc. bond : bond 0.00866 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 534 time to evaluate : 3.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.4174 (OUTLIER) cc_final: 0.3745 (tppt) REVERT: A 228 TRP cc_start: 0.6286 (m-90) cc_final: 0.5511 (t60) REVERT: A 232 ARG cc_start: 0.8121 (ttm170) cc_final: 0.7681 (ttm110) REVERT: A 267 MET cc_start: 0.8266 (ttm) cc_final: 0.7694 (ttm) REVERT: A 275 PHE cc_start: 0.7384 (t80) cc_final: 0.7041 (t80) REVERT: A 298 ASN cc_start: 0.8302 (m-40) cc_final: 0.8099 (t0) REVERT: A 413 ASP cc_start: 0.8068 (t0) cc_final: 0.7851 (t0) REVERT: A 415 GLN cc_start: 0.8436 (mt0) cc_final: 0.8086 (mp10) REVERT: A 604 LYS cc_start: 0.8099 (ptmm) cc_final: 0.7407 (tptp) REVERT: A 883 VAL cc_start: 0.8321 (OUTLIER) cc_final: 0.7994 (m) REVERT: A 972 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.7455 (pp) REVERT: A 988 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8706 (mmm) REVERT: A 1151 GLU cc_start: 0.7422 (pp20) cc_final: 0.7202 (pp20) REVERT: A 1162 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8074 (mt) REVERT: B 180 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.7254 (tp40) REVERT: B 356 ARG cc_start: 0.7829 (tmm-80) cc_final: 0.7627 (tmm-80) REVERT: B 415 GLN cc_start: 0.8352 (mt0) cc_final: 0.7938 (mp10) REVERT: B 604 LYS cc_start: 0.8182 (mttt) cc_final: 0.7673 (tptp) REVERT: B 794 LYS cc_start: 0.8034 (tptt) cc_final: 0.7413 (mppt) REVERT: B 859 MET cc_start: 0.8780 (ttm) cc_final: 0.8547 (ttm) REVERT: B 883 VAL cc_start: 0.8380 (OUTLIER) cc_final: 0.8065 (m) REVERT: B 1151 GLU cc_start: 0.7540 (pp20) cc_final: 0.7328 (pp20) REVERT: C 200 LYS cc_start: 0.3593 (OUTLIER) cc_final: 0.3088 (tptp) REVERT: C 267 MET cc_start: 0.7613 (ttp) cc_final: 0.7108 (ttm) REVERT: C 275 PHE cc_start: 0.7267 (t80) cc_final: 0.7023 (t80) REVERT: C 305 PHE cc_start: 0.8616 (t80) cc_final: 0.8339 (t80) REVERT: C 604 LYS cc_start: 0.8118 (ptmm) cc_final: 0.7433 (tptp) REVERT: C 883 VAL cc_start: 0.8409 (OUTLIER) cc_final: 0.8176 (m) REVERT: C 988 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8710 (mmm) REVERT: D 200 LYS cc_start: 0.2720 (OUTLIER) cc_final: 0.2458 (tppp) REVERT: D 228 TRP cc_start: 0.5416 (OUTLIER) cc_final: 0.4160 (m100) REVERT: D 334 MET cc_start: 0.8287 (tpp) cc_final: 0.8039 (mmm) REVERT: D 355 GLU cc_start: 0.8108 (tt0) cc_final: 0.7736 (mm-30) REVERT: D 415 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7882 (mp10) REVERT: D 548 GLN cc_start: 0.8281 (tp40) cc_final: 0.8033 (tp-100) REVERT: D 794 LYS cc_start: 0.8311 (tttp) cc_final: 0.7503 (mppt) REVERT: D 828 ARG cc_start: 0.8469 (ttm170) cc_final: 0.7682 (tmt170) REVERT: D 883 VAL cc_start: 0.8305 (OUTLIER) cc_final: 0.8009 (m) REVERT: D 1151 GLU cc_start: 0.7515 (pp20) cc_final: 0.7191 (pp20) outliers start: 137 outliers final: 50 residues processed: 612 average time/residue: 1.5537 time to fit residues: 1105.4343 Evaluate side-chains 570 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 506 time to evaluate : 3.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 600 ARG Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 831 LEU Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1143 ARG Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1204 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 600 ARG Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain D residue 1162 LEU Chi-restraints excluded: chain D residue 1204 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 321 optimal weight: 0.0980 chunk 179 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 309 optimal weight: 3.9990 chunk 254 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 230 optimal weight: 0.0070 chunk 301 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 192 optimal weight: 20.0000 chunk 127 optimal weight: 2.9990 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 GLN A 981 GLN A1046 HIS ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN B 548 GLN B 952 ASN B 981 GLN B1046 HIS ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 GLN C 603 ASN C 632 ASN C 952 ASN C 981 GLN C1046 HIS ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 GLN D 490 GLN D 632 ASN D 952 ASN D 981 GLN D1046 HIS ** D1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.129225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.096994 restraints weight = 50906.919| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.09 r_work: 0.3156 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 29361 Z= 0.150 Angle : 0.574 18.885 39824 Z= 0.290 Chirality : 0.045 1.014 4548 Planarity : 0.006 0.189 4992 Dihedral : 5.248 57.078 3924 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.75 % Favored : 97.03 % Rotamer: Outliers : 4.64 % Allowed : 20.97 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.14), residues: 3532 helix: 0.79 (0.12), residues: 1696 sheet: -1.04 (0.24), residues: 348 loop : 0.00 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.007 0.001 HIS B 291 PHE 0.026 0.001 PHE C 268 TYR 0.015 0.001 TYR A 403 ARG 0.041 0.001 ARG A1137 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 1401) hydrogen bonds : angle 4.61763 ( 3903) metal coordination : bond 0.00579 ( 16) metal coordination : angle 1.78200 ( 12) covalent geometry : bond 0.00375 (29344) covalent geometry : angle 0.57339 (39812) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 525 time to evaluate : 3.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8709 (mp) REVERT: A 169 TRP cc_start: 0.8107 (m100) cc_final: 0.7852 (m100) REVERT: A 200 LYS cc_start: 0.3908 (OUTLIER) cc_final: 0.3513 (tppt) REVERT: A 232 ARG cc_start: 0.8098 (ttm170) cc_final: 0.7612 (ttm170) REVERT: A 267 MET cc_start: 0.8222 (ttm) cc_final: 0.7640 (ttm) REVERT: A 275 PHE cc_start: 0.7245 (t80) cc_final: 0.6872 (t80) REVERT: A 413 ASP cc_start: 0.8168 (t0) cc_final: 0.7854 (t0) REVERT: A 415 GLN cc_start: 0.8406 (mt0) cc_final: 0.8080 (mp10) REVERT: A 604 LYS cc_start: 0.8136 (ptmm) cc_final: 0.7432 (tptp) REVERT: A 883 VAL cc_start: 0.8333 (OUTLIER) cc_final: 0.8010 (m) REVERT: A 1151 GLU cc_start: 0.7473 (pp20) cc_final: 0.7238 (pp20) REVERT: A 1162 LEU cc_start: 0.8307 (mt) cc_final: 0.8063 (mt) REVERT: B 136 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8351 (mp) REVERT: B 180 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7271 (tp40) REVERT: B 413 ASP cc_start: 0.7873 (t0) cc_final: 0.7563 (t0) REVERT: B 415 GLN cc_start: 0.8345 (mt0) cc_final: 0.7870 (mp10) REVERT: B 426 SER cc_start: 0.8842 (p) cc_final: 0.8581 (p) REVERT: B 428 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.6996 (mtm180) REVERT: B 461 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6825 (mt-10) REVERT: B 516 MET cc_start: 0.9053 (mtm) cc_final: 0.8424 (mtm) REVERT: B 604 LYS cc_start: 0.8260 (mttt) cc_final: 0.7639 (tptp) REVERT: B 794 LYS cc_start: 0.8124 (tptt) cc_final: 0.7483 (mppt) REVERT: B 828 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7967 (ttm110) REVERT: B 859 MET cc_start: 0.8799 (ttm) cc_final: 0.8557 (ttm) REVERT: B 883 VAL cc_start: 0.8402 (OUTLIER) cc_final: 0.8116 (m) REVERT: B 950 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7551 (ttp-170) REVERT: C 200 LYS cc_start: 0.3391 (OUTLIER) cc_final: 0.2841 (tptp) REVERT: C 252 MET cc_start: 0.5968 (OUTLIER) cc_final: 0.5271 (tpt) REVERT: C 267 MET cc_start: 0.7753 (ttp) cc_final: 0.7322 (ttm) REVERT: C 275 PHE cc_start: 0.7243 (t80) cc_final: 0.7010 (t80) REVERT: C 604 LYS cc_start: 0.8147 (ptmm) cc_final: 0.7428 (tptp) REVERT: C 876 TYR cc_start: 0.8056 (OUTLIER) cc_final: 0.7456 (p90) REVERT: C 883 VAL cc_start: 0.8317 (OUTLIER) cc_final: 0.8080 (m) REVERT: C 1137 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.6484 (ttt-90) REVERT: D 136 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8555 (mp) REVERT: D 200 LYS cc_start: 0.2697 (OUTLIER) cc_final: 0.2439 (tppp) REVERT: D 228 TRP cc_start: 0.5426 (OUTLIER) cc_final: 0.4223 (m100) REVERT: D 275 PHE cc_start: 0.7364 (t80) cc_final: 0.6987 (t80) REVERT: D 334 MET cc_start: 0.8243 (tpp) cc_final: 0.8025 (mmm) REVERT: D 355 GLU cc_start: 0.8086 (tt0) cc_final: 0.7685 (mm-30) REVERT: D 415 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7848 (mp10) REVERT: D 428 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.6959 (mtm180) REVERT: D 516 MET cc_start: 0.9052 (mtm) cc_final: 0.8428 (mtm) REVERT: D 548 GLN cc_start: 0.8245 (tp40) cc_final: 0.7959 (tp-100) REVERT: D 604 LYS cc_start: 0.8172 (ptmm) cc_final: 0.7401 (tptp) REVERT: D 748 GLU cc_start: 0.6895 (mm-30) cc_final: 0.6681 (mm-30) REVERT: D 783 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.6811 (ptmm) REVERT: D 799 LYS cc_start: 0.8861 (mmmt) cc_final: 0.8421 (mmtt) REVERT: D 876 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.7494 (p90) REVERT: D 883 VAL cc_start: 0.8293 (OUTLIER) cc_final: 0.7993 (m) outliers start: 146 outliers final: 77 residues processed: 607 average time/residue: 1.4240 time to fit residues: 1009.1971 Evaluate side-chains 607 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 507 time to evaluate : 2.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 981 GLN Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 428 ARG Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 828 ARG Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 950 ARG Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 981 GLN Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1038 ILE Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 600 ARG Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 831 LEU Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1038 ILE Chi-restraints excluded: chain C residue 1137 ARG Chi-restraints excluded: chain C residue 1143 ARG Chi-restraints excluded: chain C residue 1152 LEU Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1176 THR Chi-restraints excluded: chain C residue 1187 ASP Chi-restraints excluded: chain C residue 1204 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 428 ARG Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 497 LYS Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 600 ARG Chi-restraints excluded: chain D residue 783 LYS Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain D residue 1038 ILE Chi-restraints excluded: chain D residue 1152 LEU Chi-restraints excluded: chain D residue 1204 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 305 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 275 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 341 optimal weight: 0.6980 chunk 297 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 GLN A1046 HIS ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 GLN B 952 ASN B1046 HIS ** B1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 ASN C 952 ASN C 981 GLN C1046 HIS ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 GLN D 490 GLN D 632 ASN D 788 ASN D 952 ASN D 981 GLN D1046 HIS ** D1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.128960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.096390 restraints weight = 50521.389| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.11 r_work: 0.3147 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 29361 Z= 0.180 Angle : 0.597 21.610 39824 Z= 0.300 Chirality : 0.045 0.689 4548 Planarity : 0.006 0.184 4992 Dihedral : 5.286 57.001 3924 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.89 % Favored : 96.89 % Rotamer: Outliers : 4.54 % Allowed : 21.63 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.14), residues: 3532 helix: 0.81 (0.12), residues: 1720 sheet: -1.06 (0.24), residues: 348 loop : 0.02 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 228 HIS 0.008 0.001 HIS A 291 PHE 0.026 0.002 PHE C 268 TYR 0.018 0.002 TYR B 351 ARG 0.018 0.000 ARG A1137 Details of bonding type rmsd hydrogen bonds : bond 0.04024 ( 1401) hydrogen bonds : angle 4.62045 ( 3903) metal coordination : bond 0.00485 ( 16) metal coordination : angle 1.79795 ( 12) covalent geometry : bond 0.00451 (29344) covalent geometry : angle 0.59676 (39812) Misc. bond : bond 0.01269 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 527 time to evaluate : 3.202 Fit side-chains revert: symmetry clash REVERT: A 135 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8516 (mp) REVERT: A 169 TRP cc_start: 0.8120 (m100) cc_final: 0.7866 (m100) REVERT: A 200 LYS cc_start: 0.3910 (OUTLIER) cc_final: 0.3498 (tppt) REVERT: A 210 VAL cc_start: 0.4691 (OUTLIER) cc_final: 0.4304 (p) REVERT: A 232 ARG cc_start: 0.8167 (ttm170) cc_final: 0.7666 (ttm110) REVERT: A 267 MET cc_start: 0.8256 (ttm) cc_final: 0.7670 (ttm) REVERT: A 275 PHE cc_start: 0.7300 (t80) cc_final: 0.6860 (t80) REVERT: A 413 ASP cc_start: 0.8204 (t0) cc_final: 0.7855 (t0) REVERT: A 415 GLN cc_start: 0.8364 (mt0) cc_final: 0.8065 (mp10) REVERT: A 417 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7955 (mtt90) REVERT: A 428 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.6851 (mtm180) REVERT: A 461 GLU cc_start: 0.7282 (tt0) cc_final: 0.7077 (tm-30) REVERT: A 604 LYS cc_start: 0.8161 (ptmm) cc_final: 0.7418 (tptp) REVERT: A 859 MET cc_start: 0.8822 (ttm) cc_final: 0.8596 (ttm) REVERT: A 883 VAL cc_start: 0.8345 (OUTLIER) cc_final: 0.8011 (m) REVERT: A 1151 GLU cc_start: 0.7489 (pp20) cc_final: 0.7256 (pp20) REVERT: A 1162 LEU cc_start: 0.8292 (mt) cc_final: 0.8024 (mt) REVERT: B 136 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8380 (mp) REVERT: B 180 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7223 (tp40) REVERT: B 220 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7605 (pp) REVERT: B 352 LEU cc_start: 0.8133 (mt) cc_final: 0.7898 (mm) REVERT: B 413 ASP cc_start: 0.7860 (t0) cc_final: 0.7471 (t0) REVERT: B 415 GLN cc_start: 0.8347 (mt0) cc_final: 0.7873 (mp10) REVERT: B 426 SER cc_start: 0.8879 (OUTLIER) cc_final: 0.8595 (p) REVERT: B 428 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.6953 (mtm180) REVERT: B 461 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6766 (mt-10) REVERT: B 604 LYS cc_start: 0.8316 (mttt) cc_final: 0.7690 (tptp) REVERT: B 794 LYS cc_start: 0.8151 (tptt) cc_final: 0.7489 (mppt) REVERT: B 844 HIS cc_start: 0.7924 (p-80) cc_final: 0.7583 (p-80) REVERT: B 883 VAL cc_start: 0.8430 (OUTLIER) cc_final: 0.8147 (m) REVERT: B 950 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7480 (ttp-170) REVERT: B 1151 GLU cc_start: 0.7576 (pp20) cc_final: 0.7368 (pp20) REVERT: C 200 LYS cc_start: 0.3227 (OUTLIER) cc_final: 0.2694 (tptp) REVERT: C 252 MET cc_start: 0.5948 (OUTLIER) cc_final: 0.5288 (tpt) REVERT: C 267 MET cc_start: 0.7774 (ttp) cc_final: 0.7348 (ttm) REVERT: C 275 PHE cc_start: 0.7277 (t80) cc_final: 0.7046 (t80) REVERT: C 604 LYS cc_start: 0.8147 (ptmm) cc_final: 0.7449 (tptp) REVERT: C 794 LYS cc_start: 0.8283 (ttpp) cc_final: 0.7992 (tmmt) REVERT: C 859 MET cc_start: 0.8740 (ttt) cc_final: 0.8492 (ttm) REVERT: C 876 TYR cc_start: 0.8142 (OUTLIER) cc_final: 0.7563 (p90) REVERT: C 883 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.8128 (m) REVERT: C 950 ARG cc_start: 0.7684 (ttm170) cc_final: 0.7456 (mtm180) REVERT: C 1137 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.6420 (ttt-90) REVERT: D 136 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8568 (mp) REVERT: D 200 LYS cc_start: 0.2691 (OUTLIER) cc_final: 0.2432 (tppp) REVERT: D 228 TRP cc_start: 0.5433 (OUTLIER) cc_final: 0.4431 (m100) REVERT: D 275 PHE cc_start: 0.7404 (t80) cc_final: 0.7007 (t80) REVERT: D 334 MET cc_start: 0.8263 (tpp) cc_final: 0.8040 (mmm) REVERT: D 415 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7793 (mp10) REVERT: D 428 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.6932 (mtm180) REVERT: D 548 GLN cc_start: 0.8207 (tp40) cc_final: 0.7905 (tp-100) REVERT: D 604 LYS cc_start: 0.8167 (ptmm) cc_final: 0.7404 (tptp) REVERT: D 799 LYS cc_start: 0.8865 (mmmt) cc_final: 0.8425 (mmtt) REVERT: D 876 TYR cc_start: 0.8133 (OUTLIER) cc_final: 0.7578 (p90) REVERT: D 883 VAL cc_start: 0.8326 (OUTLIER) cc_final: 0.8019 (m) outliers start: 143 outliers final: 82 residues processed: 612 average time/residue: 1.4174 time to fit residues: 1015.1016 Evaluate side-chains 619 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 511 time to evaluate : 3.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 417 ARG Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1143 ARG Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 428 ARG Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 950 ARG Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1038 ILE Chi-restraints excluded: chain B residue 1152 LEU Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain B residue 1187 ASP Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 600 ARG Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 831 LEU Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 981 GLN Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1038 ILE Chi-restraints excluded: chain C residue 1137 ARG Chi-restraints excluded: chain C residue 1143 ARG Chi-restraints excluded: chain C residue 1152 LEU Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1187 ASP Chi-restraints excluded: chain C residue 1204 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 428 ARG Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 497 LYS Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 600 ARG Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 981 GLN Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain D residue 1033 SER Chi-restraints excluded: chain D residue 1038 ILE Chi-restraints excluded: chain D residue 1162 LEU Chi-restraints excluded: chain D residue 1176 THR Chi-restraints excluded: chain D residue 1187 ASP Chi-restraints excluded: chain D residue 1204 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 329 optimal weight: 0.3980 chunk 49 optimal weight: 5.9990 chunk 174 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 239 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 chunk 269 optimal weight: 5.9990 chunk 324 optimal weight: 0.9990 chunk 312 optimal weight: 6.9990 chunk 253 optimal weight: 0.8980 chunk 313 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 GLN A1046 HIS ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 GLN B 952 ASN B 981 GLN B1046 HIS ** B1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 ASN C 981 GLN C1046 HIS ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 GLN D 490 GLN D 632 ASN D 952 ASN D 981 GLN D1046 HIS ** D1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.129869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.097619 restraints weight = 51242.747| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.11 r_work: 0.3154 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 29361 Z= 0.123 Angle : 0.560 22.395 39824 Z= 0.281 Chirality : 0.042 0.343 4548 Planarity : 0.006 0.198 4992 Dihedral : 5.134 56.414 3924 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.66 % Favored : 97.11 % Rotamer: Outliers : 4.19 % Allowed : 22.30 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.14), residues: 3532 helix: 0.98 (0.13), residues: 1720 sheet: -0.96 (0.25), residues: 352 loop : 0.07 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.006 0.001 HIS A 291 PHE 0.023 0.001 PHE C 268 TYR 0.019 0.001 TYR B 351 ARG 0.014 0.000 ARG A1137 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 1401) hydrogen bonds : angle 4.49338 ( 3903) metal coordination : bond 0.00324 ( 16) metal coordination : angle 1.65962 ( 12) covalent geometry : bond 0.00302 (29344) covalent geometry : angle 0.55909 (39812) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 525 time to evaluate : 3.040 Fit side-chains revert: symmetry clash REVERT: A 135 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8658 (mp) REVERT: A 200 LYS cc_start: 0.3938 (OUTLIER) cc_final: 0.3546 (tppt) REVERT: A 210 VAL cc_start: 0.4767 (OUTLIER) cc_final: 0.4369 (p) REVERT: A 232 ARG cc_start: 0.8150 (ttm170) cc_final: 0.7630 (ttm170) REVERT: A 267 MET cc_start: 0.8233 (ttm) cc_final: 0.7643 (ttm) REVERT: A 275 PHE cc_start: 0.7192 (t80) cc_final: 0.6726 (t80) REVERT: A 413 ASP cc_start: 0.8194 (t0) cc_final: 0.7839 (t0) REVERT: A 415 GLN cc_start: 0.8424 (mt0) cc_final: 0.8118 (mp10) REVERT: A 428 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.6841 (mtm180) REVERT: A 548 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8058 (tp40) REVERT: A 604 LYS cc_start: 0.8167 (ptmm) cc_final: 0.7429 (tptp) REVERT: A 859 MET cc_start: 0.8791 (ttm) cc_final: 0.8554 (ttm) REVERT: A 883 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.8050 (m) REVERT: A 1151 GLU cc_start: 0.7523 (pp20) cc_final: 0.7305 (pp20) REVERT: A 1162 LEU cc_start: 0.8379 (mt) cc_final: 0.8137 (mt) REVERT: B 136 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8426 (mp) REVERT: B 180 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7285 (tp40) REVERT: B 220 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7485 (pt) REVERT: B 352 LEU cc_start: 0.8095 (mt) cc_final: 0.7858 (mm) REVERT: B 413 ASP cc_start: 0.7933 (t0) cc_final: 0.7514 (t0) REVERT: B 415 GLN cc_start: 0.8413 (mt0) cc_final: 0.7919 (mp10) REVERT: B 426 SER cc_start: 0.8848 (OUTLIER) cc_final: 0.8562 (p) REVERT: B 428 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.6969 (mtm180) REVERT: B 461 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6842 (mt-10) REVERT: B 604 LYS cc_start: 0.8279 (mttt) cc_final: 0.7640 (tptp) REVERT: B 794 LYS cc_start: 0.8103 (tptt) cc_final: 0.7495 (mppt) REVERT: B 844 HIS cc_start: 0.7854 (p-80) cc_final: 0.7527 (p-80) REVERT: B 859 MET cc_start: 0.8787 (ttm) cc_final: 0.8559 (ttm) REVERT: B 883 VAL cc_start: 0.8394 (OUTLIER) cc_final: 0.8134 (m) REVERT: B 950 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7497 (ttp-170) REVERT: C 200 LYS cc_start: 0.3232 (OUTLIER) cc_final: 0.2683 (tptp) REVERT: C 216 MET cc_start: 0.7413 (mmp) cc_final: 0.7038 (mpt) REVERT: C 231 LEU cc_start: 0.7731 (mt) cc_final: 0.7252 (tt) REVERT: C 252 MET cc_start: 0.5991 (OUTLIER) cc_final: 0.5348 (tpt) REVERT: C 267 MET cc_start: 0.7697 (ttp) cc_final: 0.7337 (ttm) REVERT: C 275 PHE cc_start: 0.7280 (t80) cc_final: 0.7014 (t80) REVERT: C 604 LYS cc_start: 0.8129 (ptmm) cc_final: 0.7420 (tptp) REVERT: C 794 LYS cc_start: 0.8199 (ttpp) cc_final: 0.7959 (tmmt) REVERT: C 859 MET cc_start: 0.8680 (ttt) cc_final: 0.8427 (ttm) REVERT: C 876 TYR cc_start: 0.8137 (OUTLIER) cc_final: 0.7440 (p90) REVERT: C 883 VAL cc_start: 0.8317 (OUTLIER) cc_final: 0.8107 (m) REVERT: C 950 ARG cc_start: 0.7657 (ttm170) cc_final: 0.7440 (mtm180) REVERT: C 988 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8695 (mmm) REVERT: C 1137 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.6484 (ttt-90) REVERT: D 200 LYS cc_start: 0.2831 (OUTLIER) cc_final: 0.2612 (tppp) REVERT: D 232 ARG cc_start: 0.7776 (mmm-85) cc_final: 0.7368 (ttm170) REVERT: D 275 PHE cc_start: 0.7374 (t80) cc_final: 0.6933 (t80) REVERT: D 415 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7836 (mp10) REVERT: D 548 GLN cc_start: 0.8222 (tp40) cc_final: 0.7928 (tp-100) REVERT: D 604 LYS cc_start: 0.8143 (ptmm) cc_final: 0.7390 (tptp) REVERT: D 799 LYS cc_start: 0.8830 (mmmt) cc_final: 0.8402 (mmtt) REVERT: D 859 MET cc_start: 0.8788 (ttm) cc_final: 0.8560 (ttm) REVERT: D 876 TYR cc_start: 0.8105 (OUTLIER) cc_final: 0.7456 (p90) REVERT: D 883 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.8046 (m) REVERT: D 1151 GLU cc_start: 0.7589 (pp20) cc_final: 0.7358 (pp20) outliers start: 132 outliers final: 70 residues processed: 603 average time/residue: 1.3875 time to fit residues: 976.8965 Evaluate side-chains 609 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 515 time to evaluate : 3.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1143 ARG Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1187 ASP Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 428 ARG Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 600 ARG Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 950 ARG Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1038 ILE Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1038 ILE Chi-restraints excluded: chain C residue 1137 ARG Chi-restraints excluded: chain C residue 1143 ARG Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1176 THR Chi-restraints excluded: chain C residue 1204 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 497 LYS Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain D residue 1038 ILE Chi-restraints excluded: chain D residue 1162 LEU Chi-restraints excluded: chain D residue 1176 THR Chi-restraints excluded: chain D residue 1187 ASP Chi-restraints excluded: chain D residue 1204 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 88 optimal weight: 0.9980 chunk 69 optimal weight: 0.4980 chunk 230 optimal weight: 0.0570 chunk 305 optimal weight: 3.9990 chunk 141 optimal weight: 0.0010 chunk 99 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 267 optimal weight: 30.0000 chunk 211 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 overall best weight: 0.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 GLN A1046 HIS ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 GLN B 952 ASN B 981 GLN B1046 HIS ** B1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1175 ASN ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 ASN C 981 GLN C1046 HIS ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 GLN D 490 GLN D 632 ASN D 952 ASN D 981 GLN D1046 HIS ** D1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.130812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.098735 restraints weight = 51136.284| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.11 r_work: 0.3186 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 29361 Z= 0.108 Angle : 0.554 21.565 39824 Z= 0.277 Chirality : 0.042 0.667 4548 Planarity : 0.005 0.123 4992 Dihedral : 4.889 56.940 3922 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.60 % Favored : 97.17 % Rotamer: Outliers : 4.13 % Allowed : 22.52 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.14), residues: 3532 helix: 1.16 (0.13), residues: 1696 sheet: -0.85 (0.25), residues: 352 loop : 0.14 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 169 HIS 0.005 0.001 HIS A 291 PHE 0.030 0.001 PHE B 268 TYR 0.019 0.001 TYR B 351 ARG 0.017 0.000 ARG A1137 Details of bonding type rmsd hydrogen bonds : bond 0.03345 ( 1401) hydrogen bonds : angle 4.39393 ( 3903) metal coordination : bond 0.00338 ( 16) metal coordination : angle 1.58555 ( 12) covalent geometry : bond 0.00262 (29344) covalent geometry : angle 0.55338 (39812) Misc. bond : bond 0.02214 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 527 time to evaluate : 3.785 Fit side-chains revert: symmetry clash REVERT: A 135 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8665 (mp) REVERT: A 143 ILE cc_start: 0.7317 (tp) cc_final: 0.6862 (pt) REVERT: A 200 LYS cc_start: 0.3939 (OUTLIER) cc_final: 0.3527 (tppt) REVERT: A 210 VAL cc_start: 0.4609 (OUTLIER) cc_final: 0.4211 (p) REVERT: A 220 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7540 (pt) REVERT: A 232 ARG cc_start: 0.8137 (ttm170) cc_final: 0.7525 (ttm170) REVERT: A 267 MET cc_start: 0.8277 (ttm) cc_final: 0.7705 (ttm) REVERT: A 275 PHE cc_start: 0.7182 (t80) cc_final: 0.6704 (t80) REVERT: A 604 LYS cc_start: 0.8140 (ptmm) cc_final: 0.7421 (tptp) REVERT: A 786 LYS cc_start: 0.7940 (mppt) cc_final: 0.7529 (mmmm) REVERT: A 808 GLU cc_start: 0.8392 (tt0) cc_final: 0.8154 (tm-30) REVERT: A 844 HIS cc_start: 0.7839 (p-80) cc_final: 0.7420 (p-80) REVERT: A 859 MET cc_start: 0.8766 (ttm) cc_final: 0.8506 (ttm) REVERT: A 883 VAL cc_start: 0.8283 (OUTLIER) cc_final: 0.8019 (m) REVERT: A 988 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8704 (mmm) REVERT: A 1162 LEU cc_start: 0.8322 (mt) cc_final: 0.8031 (mt) REVERT: B 129 LEU cc_start: 0.8725 (tp) cc_final: 0.8366 (tp) REVERT: B 180 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7163 (tp40) REVERT: B 352 LEU cc_start: 0.7985 (mt) cc_final: 0.7749 (mm) REVERT: B 413 ASP cc_start: 0.7894 (t0) cc_final: 0.7450 (t0) REVERT: B 415 GLN cc_start: 0.8358 (mt0) cc_final: 0.7860 (mp10) REVERT: B 426 SER cc_start: 0.8804 (OUTLIER) cc_final: 0.8524 (p) REVERT: B 794 LYS cc_start: 0.8114 (tptt) cc_final: 0.7441 (mppt) REVERT: B 844 HIS cc_start: 0.7779 (p-80) cc_final: 0.7435 (p-80) REVERT: B 883 VAL cc_start: 0.8375 (OUTLIER) cc_final: 0.8122 (m) REVERT: B 950 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7407 (ttp-170) REVERT: B 988 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8695 (mmm) REVERT: C 200 LYS cc_start: 0.3043 (OUTLIER) cc_final: 0.2544 (tptp) REVERT: C 216 MET cc_start: 0.7553 (mmp) cc_final: 0.7031 (mpt) REVERT: C 231 LEU cc_start: 0.7599 (mt) cc_final: 0.7161 (tt) REVERT: C 252 MET cc_start: 0.5907 (OUTLIER) cc_final: 0.5267 (tpt) REVERT: C 267 MET cc_start: 0.7672 (ttp) cc_final: 0.7386 (ttm) REVERT: C 275 PHE cc_start: 0.7286 (t80) cc_final: 0.6999 (t80) REVERT: C 566 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7072 (ttp) REVERT: C 604 LYS cc_start: 0.8128 (ptmm) cc_final: 0.7359 (tptp) REVERT: C 748 GLU cc_start: 0.6626 (mm-30) cc_final: 0.6399 (mm-30) REVERT: C 794 LYS cc_start: 0.8156 (ttpp) cc_final: 0.7920 (tmmt) REVERT: C 808 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7885 (tm-30) REVERT: C 859 MET cc_start: 0.8624 (ttt) cc_final: 0.8369 (ttm) REVERT: C 876 TYR cc_start: 0.8130 (OUTLIER) cc_final: 0.7408 (p90) REVERT: C 950 ARG cc_start: 0.7605 (ttm170) cc_final: 0.7376 (mtm180) REVERT: C 988 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8709 (mmm) REVERT: C 1137 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.6445 (ttt-90) REVERT: D 200 LYS cc_start: 0.2772 (OUTLIER) cc_final: 0.2560 (tppp) REVERT: D 232 ARG cc_start: 0.7811 (mmm-85) cc_final: 0.7455 (ttm170) REVERT: D 415 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7747 (mp10) REVERT: D 544 GLU cc_start: 0.8143 (mp0) cc_final: 0.7898 (pp20) REVERT: D 548 GLN cc_start: 0.8179 (tp40) cc_final: 0.7889 (tp-100) REVERT: D 566 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7052 (ttp) REVERT: D 604 LYS cc_start: 0.8098 (ptmm) cc_final: 0.7317 (tptp) REVERT: D 786 LYS cc_start: 0.7904 (mppt) cc_final: 0.7502 (mmmm) REVERT: D 799 LYS cc_start: 0.8857 (mmmt) cc_final: 0.8414 (mmtt) REVERT: D 844 HIS cc_start: 0.7776 (p-80) cc_final: 0.7430 (p-80) REVERT: D 876 TYR cc_start: 0.8108 (OUTLIER) cc_final: 0.7431 (p90) REVERT: D 883 VAL cc_start: 0.8299 (OUTLIER) cc_final: 0.8046 (m) REVERT: D 988 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8717 (mmm) outliers start: 130 outliers final: 70 residues processed: 605 average time/residue: 1.4651 time to fit residues: 1045.5528 Evaluate side-chains 608 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 515 time to evaluate : 3.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 981 GLN Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1143 ARG Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 950 ARG Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 981 GLN Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1038 ILE Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain B residue 1187 ASP Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 566 MET Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1038 ILE Chi-restraints excluded: chain C residue 1137 ARG Chi-restraints excluded: chain C residue 1143 ARG Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1176 THR Chi-restraints excluded: chain C residue 1187 ASP Chi-restraints excluded: chain C residue 1204 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 566 MET Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain D residue 1033 SER Chi-restraints excluded: chain D residue 1038 ILE Chi-restraints excluded: chain D residue 1162 LEU Chi-restraints excluded: chain D residue 1176 THR Chi-restraints excluded: chain D residue 1187 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 69 optimal weight: 2.9990 chunk 242 optimal weight: 7.9990 chunk 175 optimal weight: 0.3980 chunk 244 optimal weight: 2.9990 chunk 288 optimal weight: 3.9990 chunk 263 optimal weight: 1.9990 chunk 347 optimal weight: 8.9990 chunk 206 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 262 optimal weight: 3.9990 chunk 52 optimal weight: 0.0270 overall best weight: 1.6844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 GLN A 981 GLN A1046 HIS ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 GLN B 952 ASN B 981 GLN B1046 HIS ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 ASN C1046 HIS ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 GLN D 490 GLN D 632 ASN D 952 ASN D1046 HIS ** D1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.129775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.097452 restraints weight = 51331.328| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.11 r_work: 0.3152 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 29361 Z= 0.168 Angle : 0.591 20.156 39824 Z= 0.295 Chirality : 0.044 0.632 4548 Planarity : 0.005 0.121 4992 Dihedral : 4.968 57.964 3920 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.89 % Favored : 96.89 % Rotamer: Outliers : 3.91 % Allowed : 23.25 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.14), residues: 3532 helix: 1.11 (0.13), residues: 1696 sheet: -0.94 (0.25), residues: 356 loop : 0.08 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 169 HIS 0.006 0.001 HIS A 291 PHE 0.032 0.002 PHE D 235 TYR 0.018 0.002 TYR D 351 ARG 0.022 0.000 ARG A1137 Details of bonding type rmsd hydrogen bonds : bond 0.03746 ( 1401) hydrogen bonds : angle 4.46105 ( 3903) metal coordination : bond 0.00326 ( 16) metal coordination : angle 1.70045 ( 12) covalent geometry : bond 0.00420 (29344) covalent geometry : angle 0.59038 (39812) Misc. bond : bond 0.01264 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 517 time to evaluate : 3.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8622 (mp) REVERT: A 143 ILE cc_start: 0.7257 (tp) cc_final: 0.6762 (pt) REVERT: A 200 LYS cc_start: 0.3970 (OUTLIER) cc_final: 0.3532 (tppt) REVERT: A 232 ARG cc_start: 0.8165 (ttm170) cc_final: 0.7728 (ttm110) REVERT: A 267 MET cc_start: 0.8304 (ttm) cc_final: 0.7475 (tpp) REVERT: A 275 PHE cc_start: 0.7213 (t80) cc_final: 0.6726 (t80) REVERT: A 415 GLN cc_start: 0.8434 (mt0) cc_final: 0.8043 (mp10) REVERT: A 604 LYS cc_start: 0.8174 (ptmm) cc_final: 0.7404 (tptp) REVERT: A 883 VAL cc_start: 0.8330 (OUTLIER) cc_final: 0.8061 (m) REVERT: A 1162 LEU cc_start: 0.8366 (mt) cc_final: 0.8100 (mt) REVERT: B 129 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8328 (tt) REVERT: B 131 ILE cc_start: 0.8116 (mm) cc_final: 0.7809 (OUTLIER) REVERT: B 136 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8327 (mp) REVERT: B 180 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7340 (tp40) REVERT: B 291 HIS cc_start: 0.8619 (t70) cc_final: 0.8382 (t70) REVERT: B 349 LEU cc_start: 0.8625 (mt) cc_final: 0.8376 (mt) REVERT: B 413 ASP cc_start: 0.7911 (t0) cc_final: 0.7467 (t0) REVERT: B 415 GLN cc_start: 0.8380 (mt0) cc_final: 0.7867 (mp10) REVERT: B 426 SER cc_start: 0.8857 (OUTLIER) cc_final: 0.8556 (p) REVERT: B 428 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.6954 (mtm180) REVERT: B 794 LYS cc_start: 0.8139 (tptt) cc_final: 0.7474 (mppt) REVERT: B 844 HIS cc_start: 0.7870 (p-80) cc_final: 0.7559 (p-80) REVERT: B 883 VAL cc_start: 0.8411 (OUTLIER) cc_final: 0.8159 (m) REVERT: B 950 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7476 (ttp-170) REVERT: C 200 LYS cc_start: 0.3208 (OUTLIER) cc_final: 0.2650 (tptp) REVERT: C 216 MET cc_start: 0.7574 (mmp) cc_final: 0.7033 (mpt) REVERT: C 231 LEU cc_start: 0.7640 (mt) cc_final: 0.7197 (tt) REVERT: C 252 MET cc_start: 0.5954 (OUTLIER) cc_final: 0.5312 (tpt) REVERT: C 267 MET cc_start: 0.7631 (ttp) cc_final: 0.7322 (ttm) REVERT: C 275 PHE cc_start: 0.7330 (t80) cc_final: 0.7047 (t80) REVERT: C 538 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.6896 (mmp80) REVERT: C 604 LYS cc_start: 0.8162 (ptmm) cc_final: 0.7409 (tptp) REVERT: C 794 LYS cc_start: 0.8198 (ttpp) cc_final: 0.7902 (tmmt) REVERT: C 808 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7893 (tm-30) REVERT: C 859 MET cc_start: 0.8681 (ttt) cc_final: 0.8434 (ttm) REVERT: C 876 TYR cc_start: 0.8203 (OUTLIER) cc_final: 0.7513 (p90) REVERT: C 950 ARG cc_start: 0.7616 (ttm170) cc_final: 0.7410 (mtm180) REVERT: C 1137 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.6511 (ttt-90) REVERT: D 136 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8490 (mp) REVERT: D 200 LYS cc_start: 0.2551 (OUTLIER) cc_final: 0.2306 (tppp) REVERT: D 232 ARG cc_start: 0.7812 (mmm-85) cc_final: 0.7455 (ttm170) REVERT: D 415 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7965 (mp10) REVERT: D 428 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.6961 (mtm180) REVERT: D 461 GLU cc_start: 0.7396 (tt0) cc_final: 0.6947 (tm-30) REVERT: D 538 ARG cc_start: 0.8078 (mpt180) cc_final: 0.7750 (mmp80) REVERT: D 544 GLU cc_start: 0.8113 (mp0) cc_final: 0.7906 (pp20) REVERT: D 548 GLN cc_start: 0.8224 (tp40) cc_final: 0.7931 (tp-100) REVERT: D 604 LYS cc_start: 0.8134 (ptmm) cc_final: 0.7424 (tptp) REVERT: D 799 LYS cc_start: 0.8822 (mmmt) cc_final: 0.8401 (mmtp) REVERT: D 876 TYR cc_start: 0.8176 (OUTLIER) cc_final: 0.7515 (p90) REVERT: D 883 VAL cc_start: 0.8326 (OUTLIER) cc_final: 0.8050 (m) outliers start: 123 outliers final: 82 residues processed: 592 average time/residue: 1.4668 time to fit residues: 1012.4537 Evaluate side-chains 605 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 503 time to evaluate : 2.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1143 ARG Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1187 ASP Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 428 ARG Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 600 ARG Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 950 ARG Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1038 ILE Chi-restraints excluded: chain B residue 1152 LEU Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain B residue 1187 ASP Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 538 ARG Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1038 ILE Chi-restraints excluded: chain C residue 1137 ARG Chi-restraints excluded: chain C residue 1143 ARG Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1176 THR Chi-restraints excluded: chain C residue 1187 ASP Chi-restraints excluded: chain C residue 1204 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 428 ARG Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 497 LYS Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 830 GLU Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain D residue 1033 SER Chi-restraints excluded: chain D residue 1038 ILE Chi-restraints excluded: chain D residue 1143 ARG Chi-restraints excluded: chain D residue 1152 LEU Chi-restraints excluded: chain D residue 1162 LEU Chi-restraints excluded: chain D residue 1176 THR Chi-restraints excluded: chain D residue 1187 ASP Chi-restraints excluded: chain D residue 1204 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 166 optimal weight: 0.6980 chunk 149 optimal weight: 0.7980 chunk 86 optimal weight: 8.9990 chunk 334 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 321 optimal weight: 0.2980 chunk 276 optimal weight: 20.0000 chunk 254 optimal weight: 1.9990 chunk 306 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 272 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 GLN A 788 ASN A 981 GLN A1046 HIS ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 GLN B 952 ASN B 981 GLN B1046 HIS ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 GLN C 952 ASN C1046 HIS ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 490 GLN D 632 ASN D 952 ASN D1046 HIS ** D1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.130636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.098551 restraints weight = 51102.037| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.11 r_work: 0.3179 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 29361 Z= 0.111 Angle : 0.561 16.599 39824 Z= 0.281 Chirality : 0.042 0.260 4548 Planarity : 0.005 0.120 4992 Dihedral : 4.828 58.510 3920 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.66 % Favored : 97.11 % Rotamer: Outliers : 3.46 % Allowed : 23.82 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.14), residues: 3532 helix: 1.22 (0.13), residues: 1696 sheet: -0.78 (0.25), residues: 352 loop : 0.16 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 169 HIS 0.006 0.001 HIS D 291 PHE 0.032 0.001 PHE D 235 TYR 0.021 0.001 TYR B 351 ARG 0.004 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.03321 ( 1401) hydrogen bonds : angle 4.37669 ( 3903) metal coordination : bond 0.00322 ( 16) metal coordination : angle 1.72651 ( 12) covalent geometry : bond 0.00274 (29344) covalent geometry : angle 0.56058 (39812) Misc. bond : bond 0.00129 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 510 time to evaluate : 3.132 Fit side-chains revert: symmetry clash REVERT: A 135 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8647 (mp) REVERT: A 143 ILE cc_start: 0.7177 (tp) cc_final: 0.6670 (pt) REVERT: A 200 LYS cc_start: 0.3946 (OUTLIER) cc_final: 0.3513 (tppt) REVERT: A 210 VAL cc_start: 0.4670 (OUTLIER) cc_final: 0.4293 (p) REVERT: A 232 ARG cc_start: 0.8129 (ttm170) cc_final: 0.7719 (ttm110) REVERT: A 267 MET cc_start: 0.8288 (ttm) cc_final: 0.7494 (tpp) REVERT: A 275 PHE cc_start: 0.7231 (t80) cc_final: 0.6722 (t80) REVERT: A 509 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7951 (tt0) REVERT: A 604 LYS cc_start: 0.8144 (ptmm) cc_final: 0.7458 (tptp) REVERT: A 808 GLU cc_start: 0.8380 (tt0) cc_final: 0.8154 (tm-30) REVERT: A 844 HIS cc_start: 0.7849 (p-80) cc_final: 0.7468 (p-80) REVERT: A 883 VAL cc_start: 0.8303 (OUTLIER) cc_final: 0.8036 (m) REVERT: A 988 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8683 (mmm) REVERT: A 1162 LEU cc_start: 0.8379 (mt) cc_final: 0.8161 (mt) REVERT: B 129 LEU cc_start: 0.8744 (tp) cc_final: 0.8300 (tt) REVERT: B 131 ILE cc_start: 0.8065 (mm) cc_final: 0.7771 (OUTLIER) REVERT: B 349 LEU cc_start: 0.8538 (mt) cc_final: 0.8284 (mt) REVERT: B 413 ASP cc_start: 0.7889 (t0) cc_final: 0.7452 (t0) REVERT: B 415 GLN cc_start: 0.8325 (mt0) cc_final: 0.7823 (mp10) REVERT: B 426 SER cc_start: 0.8813 (OUTLIER) cc_final: 0.8510 (p) REVERT: B 786 LYS cc_start: 0.7783 (mppt) cc_final: 0.7320 (mmmm) REVERT: B 794 LYS cc_start: 0.8121 (tptt) cc_final: 0.7481 (mppt) REVERT: B 828 ARG cc_start: 0.8448 (ttp-110) cc_final: 0.8029 (ttm-80) REVERT: B 844 HIS cc_start: 0.7784 (p-80) cc_final: 0.7450 (p-80) REVERT: B 883 VAL cc_start: 0.8381 (OUTLIER) cc_final: 0.8135 (m) REVERT: B 950 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7412 (ttp-170) REVERT: C 200 LYS cc_start: 0.3093 (OUTLIER) cc_final: 0.2540 (tptp) REVERT: C 216 MET cc_start: 0.7499 (mmp) cc_final: 0.6853 (mpt) REVERT: C 231 LEU cc_start: 0.7616 (mt) cc_final: 0.7172 (tt) REVERT: C 252 MET cc_start: 0.6008 (OUTLIER) cc_final: 0.5449 (tpt) REVERT: C 275 PHE cc_start: 0.7337 (t80) cc_final: 0.7044 (t80) REVERT: C 538 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7494 (mmp80) REVERT: C 604 LYS cc_start: 0.8112 (ptmm) cc_final: 0.7368 (tptp) REVERT: C 794 LYS cc_start: 0.8193 (ttpp) cc_final: 0.7885 (tmmt) REVERT: C 808 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7835 (tm-30) REVERT: C 876 TYR cc_start: 0.8139 (OUTLIER) cc_final: 0.7424 (p90) REVERT: C 950 ARG cc_start: 0.7584 (ttm170) cc_final: 0.7364 (mtm180) REVERT: C 988 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8690 (mmm) REVERT: C 1137 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.6502 (ttt-90) REVERT: D 136 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8458 (mp) REVERT: D 200 LYS cc_start: 0.2811 (OUTLIER) cc_final: 0.2436 (tppt) REVERT: D 215 GLU cc_start: 0.8150 (tp30) cc_final: 0.7721 (tp30) REVERT: D 355 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7280 (mm-30) REVERT: D 428 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7004 (mtm180) REVERT: D 538 ARG cc_start: 0.8026 (mpt180) cc_final: 0.7679 (mmp80) REVERT: D 544 GLU cc_start: 0.8114 (mp0) cc_final: 0.7907 (pp20) REVERT: D 548 GLN cc_start: 0.8169 (tp40) cc_final: 0.7864 (tp-100) REVERT: D 604 LYS cc_start: 0.8093 (ptmm) cc_final: 0.7336 (tptp) REVERT: D 786 LYS cc_start: 0.7933 (mppt) cc_final: 0.7479 (mmmm) REVERT: D 799 LYS cc_start: 0.8817 (mmmt) cc_final: 0.8395 (mmtp) REVERT: D 829 LYS cc_start: 0.8740 (mtmt) cc_final: 0.8145 (mttm) REVERT: D 876 TYR cc_start: 0.8116 (OUTLIER) cc_final: 0.7442 (p90) REVERT: D 883 VAL cc_start: 0.8304 (OUTLIER) cc_final: 0.8042 (m) REVERT: D 988 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8712 (mmm) outliers start: 109 outliers final: 63 residues processed: 575 average time/residue: 1.4990 time to fit residues: 1012.5103 Evaluate side-chains 584 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 500 time to evaluate : 3.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 950 ARG Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1038 ILE Chi-restraints excluded: chain B residue 1143 ARG Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain B residue 1187 ASP Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 538 ARG Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1137 ARG Chi-restraints excluded: chain C residue 1143 ARG Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1176 THR Chi-restraints excluded: chain C residue 1187 ASP Chi-restraints excluded: chain C residue 1204 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 428 ARG Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 600 ARG Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain D residue 1038 ILE Chi-restraints excluded: chain D residue 1162 LEU Chi-restraints excluded: chain D residue 1176 THR Chi-restraints excluded: chain D residue 1187 ASP Chi-restraints excluded: chain D residue 1204 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 290 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 162 optimal weight: 0.0000 chunk 47 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 258 optimal weight: 8.9990 chunk 118 optimal weight: 0.5980 chunk 126 optimal weight: 0.5980 chunk 101 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 GLN A 788 ASN A 981 GLN A1046 HIS ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN B 548 GLN B 952 ASN B 981 GLN B1046 HIS ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 ASN C1046 HIS ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 GLN D 490 GLN D 632 ASN D 952 ASN D1046 HIS ** D1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.129570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.097333 restraints weight = 50972.232| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.10 r_work: 0.3146 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 29361 Z= 0.181 Angle : 0.619 16.143 39824 Z= 0.309 Chirality : 0.044 0.259 4548 Planarity : 0.005 0.119 4992 Dihedral : 4.909 54.938 3918 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.06 % Favored : 96.72 % Rotamer: Outliers : 3.43 % Allowed : 24.27 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.14), residues: 3532 helix: 1.10 (0.13), residues: 1700 sheet: -0.93 (0.25), residues: 348 loop : 0.10 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 169 HIS 0.006 0.001 HIS D 291 PHE 0.032 0.002 PHE A 268 TYR 0.022 0.002 TYR A 351 ARG 0.013 0.001 ARG B1143 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 1401) hydrogen bonds : angle 4.49101 ( 3903) metal coordination : bond 0.00356 ( 16) metal coordination : angle 1.89093 ( 12) covalent geometry : bond 0.00457 (29344) covalent geometry : angle 0.61782 (39812) Misc. bond : bond 0.00346 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 502 time to evaluate : 3.338 Fit side-chains revert: symmetry clash REVERT: A 135 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8619 (mp) REVERT: A 143 ILE cc_start: 0.7151 (tp) cc_final: 0.6633 (pt) REVERT: A 200 LYS cc_start: 0.3966 (OUTLIER) cc_final: 0.3512 (tppt) REVERT: A 232 ARG cc_start: 0.8125 (ttm170) cc_final: 0.7699 (ttm110) REVERT: A 275 PHE cc_start: 0.7231 (t80) cc_final: 0.6697 (t80) REVERT: A 509 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.8022 (tt0) REVERT: A 604 LYS cc_start: 0.8136 (ptmm) cc_final: 0.7445 (tptp) REVERT: A 883 VAL cc_start: 0.8342 (OUTLIER) cc_final: 0.8073 (m) REVERT: A 1162 LEU cc_start: 0.8360 (mt) cc_final: 0.8136 (mt) REVERT: B 129 LEU cc_start: 0.8692 (tp) cc_final: 0.8267 (tt) REVERT: B 131 ILE cc_start: 0.8127 (mm) cc_final: 0.7902 (OUTLIER) REVERT: B 179 ILE cc_start: 0.7823 (tt) cc_final: 0.7614 (tp) REVERT: B 349 LEU cc_start: 0.8524 (mt) cc_final: 0.8274 (mt) REVERT: B 413 ASP cc_start: 0.7921 (t0) cc_final: 0.7497 (t0) REVERT: B 415 GLN cc_start: 0.8347 (mt0) cc_final: 0.7822 (mp10) REVERT: B 426 SER cc_start: 0.8818 (OUTLIER) cc_final: 0.8502 (p) REVERT: B 428 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7013 (mtm180) REVERT: B 461 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6823 (mt-10) REVERT: B 786 LYS cc_start: 0.7785 (mppt) cc_final: 0.7306 (mmmm) REVERT: B 794 LYS cc_start: 0.8145 (tptt) cc_final: 0.7452 (mppt) REVERT: B 828 ARG cc_start: 0.8472 (ttp-110) cc_final: 0.8030 (ttm-80) REVERT: B 844 HIS cc_start: 0.7837 (p-80) cc_final: 0.7527 (p-80) REVERT: B 883 VAL cc_start: 0.8437 (OUTLIER) cc_final: 0.8187 (m) REVERT: B 950 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7354 (ttp-170) REVERT: C 200 LYS cc_start: 0.3216 (OUTLIER) cc_final: 0.2644 (tptp) REVERT: C 216 MET cc_start: 0.7465 (mmp) cc_final: 0.6912 (mpt) REVERT: C 231 LEU cc_start: 0.7622 (mt) cc_final: 0.7166 (tt) REVERT: C 252 MET cc_start: 0.6003 (OUTLIER) cc_final: 0.5467 (tpt) REVERT: C 267 MET cc_start: 0.8235 (ttm) cc_final: 0.8013 (tpp) REVERT: C 275 PHE cc_start: 0.7306 (t80) cc_final: 0.7005 (t80) REVERT: C 538 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.6892 (mmp80) REVERT: C 604 LYS cc_start: 0.8129 (ptmm) cc_final: 0.7377 (tptp) REVERT: C 794 LYS cc_start: 0.8201 (ttpp) cc_final: 0.7852 (tmmt) REVERT: C 808 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7914 (tm-30) REVERT: C 876 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.7551 (p90) REVERT: C 950 ARG cc_start: 0.7596 (ttm170) cc_final: 0.7364 (mtm180) REVERT: C 1137 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.6420 (ttt-90) REVERT: D 173 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7657 (mmmt) REVERT: D 200 LYS cc_start: 0.2586 (OUTLIER) cc_final: 0.2234 (tppt) REVERT: D 355 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7294 (mm-30) REVERT: D 428 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.6955 (mtm180) REVERT: D 538 ARG cc_start: 0.8012 (mpt180) cc_final: 0.7683 (mmp80) REVERT: D 548 GLN cc_start: 0.8166 (tp40) cc_final: 0.7840 (tp-100) REVERT: D 604 LYS cc_start: 0.8119 (ptmm) cc_final: 0.7408 (tptp) REVERT: D 799 LYS cc_start: 0.8829 (mmmt) cc_final: 0.8395 (mmtp) REVERT: D 828 ARG cc_start: 0.8522 (ttp-110) cc_final: 0.8122 (ttm-80) REVERT: D 876 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7554 (p90) REVERT: D 883 VAL cc_start: 0.8344 (OUTLIER) cc_final: 0.8062 (m) outliers start: 108 outliers final: 71 residues processed: 567 average time/residue: 1.4329 time to fit residues: 950.0241 Evaluate side-chains 583 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 493 time to evaluate : 3.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 981 GLN Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1187 ASP Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 428 ARG Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 950 ARG Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1038 ILE Chi-restraints excluded: chain B residue 1139 SER Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain B residue 1187 ASP Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 538 ARG Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1137 ARG Chi-restraints excluded: chain C residue 1143 ARG Chi-restraints excluded: chain C residue 1152 LEU Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1176 THR Chi-restraints excluded: chain C residue 1187 ASP Chi-restraints excluded: chain C residue 1204 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 428 ARG Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain D residue 1038 ILE Chi-restraints excluded: chain D residue 1152 LEU Chi-restraints excluded: chain D residue 1162 LEU Chi-restraints excluded: chain D residue 1176 THR Chi-restraints excluded: chain D residue 1187 ASP Chi-restraints excluded: chain D residue 1204 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 116 optimal weight: 0.6980 chunk 291 optimal weight: 0.8980 chunk 213 optimal weight: 0.0970 chunk 302 optimal weight: 0.1980 chunk 129 optimal weight: 0.8980 chunk 290 optimal weight: 5.9990 chunk 296 optimal weight: 2.9990 chunk 292 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 258 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 GLN A 788 ASN A 952 ASN A 981 GLN A1046 HIS ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 GLN B 952 ASN B1046 HIS ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 ASN C1046 HIS ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 490 GLN D 632 ASN D 952 ASN D1046 HIS ** D1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.130801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.098686 restraints weight = 51092.362| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.12 r_work: 0.3177 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 29361 Z= 0.113 Angle : 0.571 16.197 39824 Z= 0.286 Chirality : 0.042 0.256 4548 Planarity : 0.005 0.117 4992 Dihedral : 4.749 54.743 3918 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.69 % Favored : 97.08 % Rotamer: Outliers : 2.99 % Allowed : 24.65 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.14), residues: 3532 helix: 1.24 (0.13), residues: 1696 sheet: -0.76 (0.25), residues: 352 loop : 0.17 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 169 HIS 0.005 0.001 HIS D 291 PHE 0.033 0.001 PHE D 235 TYR 0.022 0.001 TYR A 980 ARG 0.006 0.000 ARG B 356 Details of bonding type rmsd hydrogen bonds : bond 0.03311 ( 1401) hydrogen bonds : angle 4.37132 ( 3903) metal coordination : bond 0.00301 ( 16) metal coordination : angle 1.64295 ( 12) covalent geometry : bond 0.00279 (29344) covalent geometry : angle 0.57017 (39812) Misc. bond : bond 0.00040 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30577.72 seconds wall clock time: 527 minutes 37.69 seconds (31657.69 seconds total)