Starting phenix.real_space_refine on Mon Aug 25 13:54:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hk6_34847/08_2025/8hk6_34847.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hk6_34847/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8hk6_34847/08_2025/8hk6_34847.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hk6_34847/08_2025/8hk6_34847.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hk6_34847/08_2025/8hk6_34847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hk6_34847/08_2025/8hk6_34847.map" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.051 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ASP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 2, 'TRP:plan': 1} 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: {'ASP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 2, 'TRP:plan': 1} 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: {'ASP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 2, 'TRP:plan': 1} 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: {'ASP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 2, 'TRP:plan': 1} 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: 7.26, per 1000 atoms: 0.25 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: 2.51 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.31 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: 6.64 Time building geometry restraints manager: 3.29 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 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 32.580 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:9.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.760 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (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 ARG 0.009 0.001 ARG D 133 TYR 0.019 0.002 TYR D 351 PHE 0.032 0.002 PHE A 268 TRP 0.095 0.002 TRP A 169 HIS 0.013 0.001 HIS D 291 Details of bonding type rmsd covalent geometry : bond 0.00582 (29344) covalent geometry : angle 0.79909 (39812) hydrogen bonds : bond 0.21307 ( 1401) hydrogen bonds : angle 7.15424 ( 3903) metal coordination : bond 0.01290 ( 16) metal coordination : angle 4.17147 ( 12) 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 : 1.094 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: 0.7951 time to fit residues: 521.6659 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 : 1.131 ------------------------------------------------------------------------------- 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 197 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.3980 chunk 298 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 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 298 ASN C 440 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 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: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.129424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.096955 restraints weight = 50481.662| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.11 r_work: 0.3172 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 29361 Z= 0.164 Angle : 0.604 11.182 39824 Z= 0.313 Chirality : 0.044 0.288 4548 Planarity : 0.006 0.135 4992 Dihedral : 5.775 59.381 3971 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.86 % Favored : 96.91 % Rotamer: Outliers : 4.00 % Allowed : 20.08 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.14), residues: 3532 helix: 0.42 (0.12), residues: 1692 sheet: -0.84 (0.24), residues: 348 loop : -0.16 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 600 TYR 0.018 0.002 TYR A 403 PHE 0.016 0.002 PHE A 283 TRP 0.023 0.001 TRP A 228 HIS 0.007 0.001 HIS C1046 Details of bonding type rmsd covalent geometry : bond 0.00395 (29344) covalent geometry : angle 0.60227 (39812) hydrogen bonds : bond 0.04739 ( 1401) hydrogen bonds : angle 5.04240 ( 3903) metal coordination : bond 0.01372 ( 16) metal coordination : angle 2.61427 ( 12) Misc. bond : bond 0.00008 ( 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 654 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 528 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8622 (mp) REVERT: A 200 LYS cc_start: 0.4167 (OUTLIER) cc_final: 0.3779 (tppt) REVERT: A 232 ARG cc_start: 0.8102 (ttm170) cc_final: 0.7324 (ttm170) REVERT: A 275 PHE cc_start: 0.7334 (t80) cc_final: 0.7047 (t80) REVERT: A 415 GLN cc_start: 0.8498 (mt0) cc_final: 0.8111 (mp10) REVERT: A 516 MET cc_start: 0.9023 (mtm) cc_final: 0.8416 (mtm) REVERT: A 548 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8053 (tp40) REVERT: A 604 LYS cc_start: 0.8068 (ptmm) cc_final: 0.7566 (tptp) REVERT: A 883 VAL cc_start: 0.8347 (OUTLIER) cc_final: 0.8002 (m) REVERT: A 972 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.7391 (pp) REVERT: B 180 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7385 (tp40) REVERT: B 415 GLN cc_start: 0.8446 (mt0) cc_final: 0.8004 (mp10) REVERT: B 428 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7563 (mtt180) REVERT: B 516 MET cc_start: 0.9026 (mtm) cc_final: 0.8429 (mtm) REVERT: B 604 LYS cc_start: 0.8164 (mttt) cc_final: 0.7693 (tptp) REVERT: B 794 LYS cc_start: 0.7964 (tptt) cc_final: 0.7547 (mppt) REVERT: B 883 VAL cc_start: 0.8389 (OUTLIER) cc_final: 0.8078 (m) REVERT: B 947 LYS cc_start: 0.7788 (mttp) cc_final: 0.7494 (mttt) REVERT: C 200 LYS cc_start: 0.3559 (OUTLIER) cc_final: 0.3129 (tptp) REVERT: C 252 MET cc_start: 0.5795 (OUTLIER) cc_final: 0.5589 (tpt) REVERT: C 305 PHE cc_start: 0.8659 (t80) cc_final: 0.8450 (t80) REVERT: C 415 GLN cc_start: 0.8341 (mt0) cc_final: 0.7965 (mp10) REVERT: C 516 MET cc_start: 0.9046 (mtm) cc_final: 0.8481 (mtm) REVERT: C 604 LYS cc_start: 0.8096 (ptmm) cc_final: 0.7611 (tptp) REVERT: C 794 LYS cc_start: 0.8230 (ttpp) cc_final: 0.7216 (mppt) REVERT: C 883 VAL cc_start: 0.8454 (OUTLIER) cc_final: 0.8203 (m) REVERT: D 200 LYS cc_start: 0.2776 (OUTLIER) cc_final: 0.2487 (tppp) REVERT: D 228 TRP cc_start: 0.5209 (OUTLIER) cc_final: 0.3955 (m100) REVERT: D 252 MET cc_start: 0.7268 (mtp) cc_final: 0.7003 (tmt) REVERT: D 355 GLU cc_start: 0.8128 (tt0) cc_final: 0.7849 (mm-30) REVERT: D 415 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7964 (mp10) REVERT: D 516 MET cc_start: 0.9034 (mtm) cc_final: 0.8446 (mtm) REVERT: D 548 GLN cc_start: 0.8346 (tp40) cc_final: 0.8116 (tp-100) REVERT: D 794 LYS cc_start: 0.8321 (tttp) cc_final: 0.7451 (mppt) REVERT: D 828 ARG cc_start: 0.8462 (ttm170) cc_final: 0.8105 (ttm110) REVERT: D 883 VAL cc_start: 0.8298 (OUTLIER) cc_final: 0.8000 (m) REVERT: D 1151 GLU cc_start: 0.7520 (pp20) cc_final: 0.7225 (pp20) outliers start: 126 outliers final: 54 residues processed: 603 average time/residue: 0.7597 time to fit residues: 530.0955 Evaluate side-chains 573 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 504 time to evaluate : 1.219 ------------------------------------------------------------------------------- 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 331 VAL Chi-restraints excluded: chain A residue 334 MET 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 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 972 ILE Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain B residue 131 ILE 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 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 600 ARG Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 876 TYR 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 B residue 1017 LEU 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 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 883 VAL Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1143 ARG 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 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 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 1017 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 100 optimal weight: 10.0000 chunk 266 optimal weight: 0.3980 chunk 86 optimal weight: 0.0050 chunk 194 optimal weight: 5.9990 chunk 309 optimal weight: 0.4980 chunk 83 optimal weight: 0.1980 chunk 28 optimal weight: 0.9980 chunk 329 optimal weight: 2.9990 chunk 277 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1046 HIS ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 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 C 952 ASN C1046 HIS ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.130399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.098307 restraints weight = 50840.154| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.09 r_work: 0.3201 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 29361 Z= 0.114 Angle : 0.559 18.892 39824 Z= 0.283 Chirality : 0.044 0.950 4548 Planarity : 0.005 0.131 4992 Dihedral : 5.202 57.954 3928 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.72 % Favored : 97.06 % Rotamer: Outliers : 4.13 % Allowed : 20.36 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.14), residues: 3532 helix: 0.76 (0.13), residues: 1696 sheet: -0.81 (0.24), residues: 352 loop : -0.00 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.046 0.000 ARG A1137 TYR 0.016 0.001 TYR B 351 PHE 0.015 0.001 PHE C 212 TRP 0.017 0.001 TRP A 228 HIS 0.007 0.001 HIS B 291 Details of bonding type rmsd covalent geometry : bond 0.00275 (29344) covalent geometry : angle 0.55794 (39812) hydrogen bonds : bond 0.03884 ( 1401) hydrogen bonds : angle 4.68070 ( 3903) metal coordination : bond 0.00567 ( 16) metal coordination : angle 1.91874 ( 12) Misc. bond : bond 0.00132 ( 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 659 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 529 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.4178 (OUTLIER) cc_final: 0.3728 (tppt) REVERT: A 232 ARG cc_start: 0.8085 (ttm170) cc_final: 0.7628 (ttm170) REVERT: A 267 MET cc_start: 0.8274 (ttm) cc_final: 0.7729 (ttm) REVERT: A 275 PHE cc_start: 0.7367 (t80) cc_final: 0.7033 (t80) REVERT: A 413 ASP cc_start: 0.8025 (t0) cc_final: 0.7790 (t0) REVERT: A 415 GLN cc_start: 0.8355 (mt0) cc_final: 0.8018 (mp10) REVERT: A 428 ARG cc_start: 0.8526 (mtt180) cc_final: 0.8244 (mtm-85) REVERT: A 461 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7039 (mt-10) REVERT: A 548 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8028 (tp40) REVERT: A 604 LYS cc_start: 0.8057 (ptmm) cc_final: 0.7411 (tptp) REVERT: A 828 ARG cc_start: 0.8474 (ttm170) cc_final: 0.8265 (ttp-110) REVERT: A 883 VAL cc_start: 0.8298 (OUTLIER) cc_final: 0.8056 (t) REVERT: B 415 GLN cc_start: 0.8347 (mt0) cc_final: 0.7946 (mp10) REVERT: B 604 LYS cc_start: 0.8142 (mttt) cc_final: 0.7667 (tptp) REVERT: B 794 LYS cc_start: 0.7957 (tptt) cc_final: 0.7566 (mppt) REVERT: B 828 ARG cc_start: 0.8491 (ttm170) cc_final: 0.8264 (ttp-110) REVERT: B 883 VAL cc_start: 0.8362 (OUTLIER) cc_final: 0.8046 (m) REVERT: C 174 MET cc_start: 0.7086 (tpp) cc_final: 0.6802 (tpt) REVERT: C 200 LYS cc_start: 0.3615 (OUTLIER) cc_final: 0.3137 (tptp) REVERT: C 267 MET cc_start: 0.7668 (ttp) cc_final: 0.7193 (ttm) REVERT: C 275 PHE cc_start: 0.7295 (t80) cc_final: 0.7060 (t80) REVERT: C 415 GLN cc_start: 0.8248 (mt0) cc_final: 0.7912 (mp10) REVERT: C 566 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7159 (ttp) REVERT: C 883 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.8068 (m) REVERT: C 988 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8722 (mmm) REVERT: D 200 LYS cc_start: 0.2703 (OUTLIER) cc_final: 0.2451 (tppp) REVERT: D 228 TRP cc_start: 0.5387 (OUTLIER) cc_final: 0.4115 (m100) REVERT: D 267 MET cc_start: 0.8334 (ttm) cc_final: 0.8029 (tpp) REVERT: D 275 PHE cc_start: 0.7360 (t80) cc_final: 0.6965 (t80) REVERT: D 334 MET cc_start: 0.8281 (tpp) cc_final: 0.8038 (mmm) REVERT: D 351 TYR cc_start: 0.7629 (t80) cc_final: 0.7201 (t80) REVERT: D 355 GLU cc_start: 0.8059 (tt0) cc_final: 0.7772 (mm-30) REVERT: D 415 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7814 (mp10) REVERT: D 548 GLN cc_start: 0.8239 (tp40) cc_final: 0.7985 (tp-100) REVERT: D 566 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7086 (ttp) REVERT: D 794 LYS cc_start: 0.8277 (tttp) cc_final: 0.7576 (mppt) REVERT: D 828 ARG cc_start: 0.8425 (ttm170) cc_final: 0.8144 (ttm-80) REVERT: D 883 VAL cc_start: 0.8253 (OUTLIER) cc_final: 0.7959 (m) REVERT: D 1151 GLU cc_start: 0.7483 (pp20) cc_final: 0.7178 (pp20) outliers start: 130 outliers final: 55 residues processed: 605 average time/residue: 0.7333 time to fit residues: 514.5057 Evaluate side-chains 581 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 512 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 171 GLU 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 461 GLU Chi-restraints excluded: chain A residue 473 LEU 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 1017 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 320 VAL Chi-restraints excluded: chain B residue 341 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 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 969 VAL Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain C residue 162 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 566 MET Chi-restraints excluded: chain C residue 600 ARG Chi-restraints excluded: chain C residue 783 LYS 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 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 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 566 MET 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 1017 LEU Chi-restraints excluded: chain D residue 1162 LEU Chi-restraints excluded: chain D residue 1187 ASP 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 341 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 72 optimal weight: 0.0980 chunk 55 optimal weight: 0.6980 chunk 270 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 343 optimal weight: 0.8980 chunk 262 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 ASN A1046 HIS ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 GLN 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 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 440 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.129335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.097051 restraints weight = 50650.548| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.09 r_work: 0.3158 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1685 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= 0.161 Angle : 0.579 22.404 39824 Z= 0.291 Chirality : 0.044 0.541 4548 Planarity : 0.006 0.216 4992 Dihedral : 5.199 57.395 3923 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.80 % Favored : 96.97 % Rotamer: Outliers : 4.35 % Allowed : 21.32 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.14), residues: 3532 helix: 0.87 (0.13), residues: 1696 sheet: -0.93 (0.24), residues: 356 loop : 0.06 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A1137 TYR 0.014 0.001 TYR A 403 PHE 0.023 0.001 PHE C 268 TRP 0.012 0.001 TRP A 228 HIS 0.007 0.001 HIS B 291 Details of bonding type rmsd covalent geometry : bond 0.00401 (29344) covalent geometry : angle 0.57863 (39812) hydrogen bonds : bond 0.04009 ( 1401) hydrogen bonds : angle 4.62332 ( 3903) metal coordination : bond 0.00627 ( 16) metal coordination : angle 1.75211 ( 12) Misc. bond : bond 0.01277 ( 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: 137 poor density : 534 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.3925 (OUTLIER) cc_final: 0.3518 (tppt) REVERT: A 232 ARG cc_start: 0.8112 (ttm170) cc_final: 0.7672 (ttm170) REVERT: A 267 MET cc_start: 0.8271 (ttm) cc_final: 0.7736 (ttm) REVERT: A 275 PHE cc_start: 0.7457 (t80) cc_final: 0.7079 (t80) REVERT: A 413 ASP cc_start: 0.8187 (t0) cc_final: 0.7927 (t0) REVERT: A 415 GLN cc_start: 0.8395 (mt0) cc_final: 0.8068 (mp10) REVERT: A 428 ARG cc_start: 0.8530 (mtt180) cc_final: 0.8259 (mtm-85) REVERT: A 461 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6832 (mt-10) REVERT: A 604 LYS cc_start: 0.8128 (ptmm) cc_final: 0.7436 (tptp) REVERT: A 883 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.7998 (m) REVERT: B 180 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7286 (tp40) REVERT: B 231 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7266 (tp) REVERT: B 413 ASP cc_start: 0.7877 (t0) cc_final: 0.7572 (t0) REVERT: B 415 GLN cc_start: 0.8356 (mt0) cc_final: 0.7892 (mp10) REVERT: B 428 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.6997 (mtm180) REVERT: B 461 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6898 (mt-10) REVERT: B 604 LYS cc_start: 0.8221 (mttt) cc_final: 0.7637 (tptp) REVERT: B 794 LYS cc_start: 0.8052 (tptt) cc_final: 0.7434 (mppt) REVERT: B 844 HIS cc_start: 0.7931 (p-80) cc_final: 0.7587 (p-80) REVERT: B 859 MET cc_start: 0.8820 (ttm) cc_final: 0.8595 (ttm) REVERT: B 883 VAL cc_start: 0.8393 (OUTLIER) cc_final: 0.8083 (m) REVERT: C 174 MET cc_start: 0.7543 (tpp) cc_final: 0.7289 (tpp) REVERT: C 200 LYS cc_start: 0.3343 (OUTLIER) cc_final: 0.2855 (tptp) REVERT: C 252 MET cc_start: 0.5997 (OUTLIER) cc_final: 0.5278 (tpt) REVERT: C 267 MET cc_start: 0.7738 (ttp) cc_final: 0.7294 (ttm) REVERT: C 275 PHE cc_start: 0.7269 (t80) cc_final: 0.7024 (t80) REVERT: C 413 ASP cc_start: 0.8208 (t0) cc_final: 0.7951 (t0) REVERT: C 415 GLN cc_start: 0.8279 (mt0) cc_final: 0.7959 (mp10) REVERT: C 604 LYS cc_start: 0.8205 (ptmm) cc_final: 0.7452 (tptp) REVERT: C 794 LYS cc_start: 0.8192 (ttpp) cc_final: 0.7223 (mppt) REVERT: C 883 VAL cc_start: 0.8317 (OUTLIER) cc_final: 0.8074 (m) REVERT: C 1137 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.6476 (ttt-90) REVERT: D 136 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8566 (mp) REVERT: D 200 LYS cc_start: 0.2696 (OUTLIER) cc_final: 0.2442 (tppp) REVERT: D 228 TRP cc_start: 0.5424 (OUTLIER) cc_final: 0.4215 (m100) REVERT: D 267 MET cc_start: 0.8395 (ttm) cc_final: 0.8163 (tpp) REVERT: D 275 PHE cc_start: 0.7381 (t80) cc_final: 0.6989 (t80) REVERT: D 334 MET cc_start: 0.8242 (tpp) cc_final: 0.8026 (mmm) REVERT: D 415 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7966 (mp10) REVERT: D 516 MET cc_start: 0.9058 (mtm) cc_final: 0.8434 (mtm) REVERT: D 538 ARG cc_start: 0.8100 (mpt180) cc_final: 0.7772 (mmp80) REVERT: D 548 GLN cc_start: 0.8261 (tp40) cc_final: 0.7978 (tp-100) REVERT: D 604 LYS cc_start: 0.8166 (ptmm) cc_final: 0.7412 (tptp) REVERT: D 794 LYS cc_start: 0.8328 (tttp) cc_final: 0.7518 (mppt) REVERT: D 799 LYS cc_start: 0.8848 (mmmt) cc_final: 0.8425 (mmtp) REVERT: D 828 ARG cc_start: 0.8486 (ttm170) cc_final: 0.8154 (ttm-80) REVERT: D 883 VAL cc_start: 0.8284 (OUTLIER) cc_final: 0.7968 (m) outliers start: 137 outliers final: 73 residues processed: 609 average time/residue: 0.7451 time to fit residues: 526.2918 Evaluate side-chains 605 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 515 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 171 GLU 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 461 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 1017 LEU Chi-restraints excluded: chain A residue 1038 ILE 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 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 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 969 VAL Chi-restraints excluded: chain B residue 972 ILE 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 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 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 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 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 831 LEU 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 1033 SER Chi-restraints excluded: chain D residue 1038 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 215 optimal weight: 0.0470 chunk 222 optimal weight: 0.9990 chunk 168 optimal weight: 0.0270 chunk 11 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 212 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 257 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 chunk 319 optimal weight: 9.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- 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 298 ASN B 490 GLN B 603 ASN B 952 ASN 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 614 HIS 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.129882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.097689 restraints weight = 50677.473| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.09 r_work: 0.3183 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 29361 Z= 0.123 Angle : 0.557 17.896 39824 Z= 0.280 Chirality : 0.044 0.892 4548 Planarity : 0.005 0.126 4992 Dihedral : 5.067 56.560 3923 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.58 % Favored : 97.20 % Rotamer: Outliers : 4.10 % Allowed : 21.76 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.14), residues: 3532 helix: 1.03 (0.13), residues: 1692 sheet: -0.84 (0.24), residues: 352 loop : 0.14 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.000 ARG A1137 TYR 0.017 0.001 TYR D 351 PHE 0.026 0.001 PHE C 268 TRP 0.016 0.001 TRP A 169 HIS 0.007 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00304 (29344) covalent geometry : angle 0.55646 (39812) hydrogen bonds : bond 0.03615 ( 1401) hydrogen bonds : angle 4.51011 ( 3903) metal coordination : bond 0.00397 ( 16) metal coordination : angle 1.54366 ( 12) Misc. bond : bond 0.00928 ( 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 647 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 518 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 ILE cc_start: 0.7323 (tp) cc_final: 0.6835 (pt) REVERT: A 174 MET cc_start: 0.6204 (tpp) cc_final: 0.5874 (mmm) REVERT: A 200 LYS cc_start: 0.3902 (OUTLIER) cc_final: 0.3516 (tppt) REVERT: A 210 VAL cc_start: 0.5008 (OUTLIER) cc_final: 0.4626 (p) REVERT: A 228 TRP cc_start: 0.6209 (m-90) cc_final: 0.5555 (t60) REVERT: A 232 ARG cc_start: 0.8148 (ttm170) cc_final: 0.7668 (ttm110) REVERT: A 267 MET cc_start: 0.8254 (ttm) cc_final: 0.7698 (ttm) REVERT: A 275 PHE cc_start: 0.7174 (t80) cc_final: 0.6725 (t80) REVERT: A 413 ASP cc_start: 0.8189 (t0) cc_final: 0.7865 (t0) REVERT: A 415 GLN cc_start: 0.8385 (mt0) cc_final: 0.8066 (mp10) REVERT: A 428 ARG cc_start: 0.8512 (mtt180) cc_final: 0.8305 (mtm-85) REVERT: A 604 LYS cc_start: 0.8131 (ptmm) cc_final: 0.7391 (tptp) REVERT: A 883 VAL cc_start: 0.8310 (OUTLIER) cc_final: 0.7987 (m) REVERT: A 950 ARG cc_start: 0.7889 (ttm170) cc_final: 0.7671 (mtm180) REVERT: A 988 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8696 (mmm) REVERT: B 136 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8367 (mp) REVERT: B 180 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7138 (tp40) REVERT: B 415 GLN cc_start: 0.8347 (mt0) cc_final: 0.7954 (mp10) REVERT: B 428 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7023 (mtm180) REVERT: B 604 LYS cc_start: 0.8335 (mttt) cc_final: 0.7652 (tptp) REVERT: B 794 LYS cc_start: 0.8092 (tptt) cc_final: 0.7458 (mppt) REVERT: B 828 ARG cc_start: 0.8490 (ttp-110) cc_final: 0.8008 (ttm110) REVERT: B 844 HIS cc_start: 0.7890 (p-80) cc_final: 0.7534 (p-80) REVERT: B 859 MET cc_start: 0.8791 (ttm) cc_final: 0.8576 (ttm) REVERT: B 883 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.8081 (m) REVERT: C 174 MET cc_start: 0.7693 (tpp) cc_final: 0.7202 (tpt) REVERT: C 200 LYS cc_start: 0.3136 (OUTLIER) cc_final: 0.2674 (tptp) REVERT: C 231 LEU cc_start: 0.7740 (mt) cc_final: 0.7282 (tt) REVERT: C 252 MET cc_start: 0.5948 (OUTLIER) cc_final: 0.5266 (tpt) REVERT: C 267 MET cc_start: 0.7740 (ttp) cc_final: 0.7336 (ttm) REVERT: C 275 PHE cc_start: 0.7231 (t80) cc_final: 0.6973 (t80) REVERT: C 438 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7797 (mtpt) REVERT: C 604 LYS cc_start: 0.8124 (ptmm) cc_final: 0.7406 (tptp) REVERT: C 794 LYS cc_start: 0.8155 (ttpp) cc_final: 0.7896 (tmmt) REVERT: C 859 MET cc_start: 0.8705 (ttt) cc_final: 0.8476 (ttm) REVERT: C 883 VAL cc_start: 0.8306 (OUTLIER) cc_final: 0.8071 (m) REVERT: C 948 ARG cc_start: 0.7587 (mtm-85) cc_final: 0.7366 (mtm-85) REVERT: C 950 ARG cc_start: 0.7637 (ttm170) cc_final: 0.7398 (mtm180) REVERT: C 988 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8709 (mmm) REVERT: C 1137 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6361 (ttt-90) REVERT: D 200 LYS cc_start: 0.2671 (OUTLIER) cc_final: 0.2445 (tppp) REVERT: D 267 MET cc_start: 0.8343 (ttm) cc_final: 0.8010 (tpp) REVERT: D 275 PHE cc_start: 0.7348 (t80) cc_final: 0.6933 (t80) REVERT: D 334 MET cc_start: 0.8232 (tpp) cc_final: 0.8022 (mmm) REVERT: D 415 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7920 (mp10) REVERT: D 538 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7744 (mmp80) REVERT: D 544 GLU cc_start: 0.8179 (mp0) cc_final: 0.7929 (pp20) REVERT: D 548 GLN cc_start: 0.8208 (tp40) cc_final: 0.7908 (tp-100) REVERT: D 604 LYS cc_start: 0.8157 (ptmm) cc_final: 0.7380 (tptp) REVERT: D 794 LYS cc_start: 0.8304 (tttp) cc_final: 0.7480 (mppt) REVERT: D 799 LYS cc_start: 0.8864 (mmmt) cc_final: 0.8418 (mmtt) REVERT: D 828 ARG cc_start: 0.8483 (ttm170) cc_final: 0.8109 (ttm110) REVERT: D 859 MET cc_start: 0.8798 (ttm) cc_final: 0.8588 (ttm) REVERT: D 883 VAL cc_start: 0.8262 (OUTLIER) cc_final: 0.7964 (m) outliers start: 129 outliers final: 65 residues processed: 596 average time/residue: 0.7194 time to fit residues: 497.0283 Evaluate side-chains 594 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 511 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 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 B residue 1176 THR Chi-restraints excluded: chain B residue 1187 ASP Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 281 LEU 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 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 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 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 523 CYS Chi-restraints excluded: chain D residue 538 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 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 1204 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 65 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 298 optimal weight: 0.7980 chunk 190 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 319 optimal weight: 0.6980 chunk 202 optimal weight: 2.9990 chunk 262 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 298 ASN B 440 GLN B 490 GLN 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 490 GLN C 603 ASN 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 = 0.3882 r_free = 0.3882 target = 0.130451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.097972 restraints weight = 51427.671| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.15 r_work: 0.3181 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1998 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= 0.120 Angle : 0.554 12.799 39824 Z= 0.278 Chirality : 0.042 0.265 4548 Planarity : 0.006 0.173 4992 Dihedral : 5.008 56.445 3923 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.58 % Favored : 97.20 % Rotamer: Outliers : 3.65 % Allowed : 22.33 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.14), residues: 3532 helix: 1.08 (0.13), residues: 1720 sheet: -0.78 (0.25), residues: 352 loop : 0.23 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A1137 TYR 0.018 0.001 TYR B 351 PHE 0.025 0.001 PHE D 235 TRP 0.014 0.001 TRP B 169 HIS 0.006 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00298 (29344) covalent geometry : angle 0.55317 (39812) hydrogen bonds : bond 0.03511 ( 1401) hydrogen bonds : angle 4.44688 ( 3903) metal coordination : bond 0.00384 ( 16) metal coordination : angle 1.55501 ( 12) Misc. bond : bond 0.00488 ( 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 647 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 532 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 ILE cc_start: 0.7461 (tp) cc_final: 0.6970 (pt) REVERT: A 171 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7745 (mp0) REVERT: A 200 LYS cc_start: 0.4001 (OUTLIER) cc_final: 0.3593 (tppt) REVERT: A 210 VAL cc_start: 0.4701 (OUTLIER) cc_final: 0.4307 (p) REVERT: A 228 TRP cc_start: 0.6263 (m-90) cc_final: 0.5632 (t60) REVERT: A 232 ARG cc_start: 0.8083 (ttm170) cc_final: 0.7637 (ttm170) REVERT: A 267 MET cc_start: 0.8174 (ttm) cc_final: 0.7593 (ttm) REVERT: A 275 PHE cc_start: 0.7184 (t80) cc_final: 0.6741 (t80) REVERT: A 413 ASP cc_start: 0.8194 (t0) cc_final: 0.7829 (t0) REVERT: A 415 GLN cc_start: 0.8361 (mt0) cc_final: 0.8054 (mp10) REVERT: A 516 MET cc_start: 0.8959 (mtm) cc_final: 0.8419 (mtm) REVERT: A 604 LYS cc_start: 0.8088 (ptmm) cc_final: 0.7404 (tptp) REVERT: A 786 LYS cc_start: 0.7965 (mppt) cc_final: 0.7559 (mmmm) REVERT: A 859 MET cc_start: 0.8798 (ttm) cc_final: 0.8564 (ttm) REVERT: A 883 VAL cc_start: 0.8264 (OUTLIER) cc_final: 0.7979 (m) REVERT: B 136 LEU cc_start: 0.8663 (mp) cc_final: 0.8377 (mp) REVERT: B 180 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7151 (mm110) REVERT: B 220 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7471 (pt) REVERT: B 348 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6986 (mp0) REVERT: B 352 LEU cc_start: 0.8076 (mt) cc_final: 0.7851 (mm) REVERT: B 413 ASP cc_start: 0.7881 (t0) cc_final: 0.7470 (t0) REVERT: B 415 GLN cc_start: 0.8340 (mt0) cc_final: 0.7879 (mp10) REVERT: B 794 LYS cc_start: 0.8018 (tptt) cc_final: 0.7485 (mppt) REVERT: B 828 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7979 (ttm110) REVERT: B 844 HIS cc_start: 0.7845 (p-80) cc_final: 0.7506 (p-80) REVERT: B 859 MET cc_start: 0.8766 (ttm) cc_final: 0.8559 (ttm) REVERT: B 883 VAL cc_start: 0.8354 (OUTLIER) cc_final: 0.8108 (m) REVERT: B 950 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7408 (ttp-170) REVERT: B 988 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8693 (mmm) REVERT: C 200 LYS cc_start: 0.3260 (OUTLIER) cc_final: 0.2760 (tptp) REVERT: C 216 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.7086 (mpt) REVERT: C 231 LEU cc_start: 0.7670 (mt) cc_final: 0.7247 (tt) REVERT: C 252 MET cc_start: 0.6031 (OUTLIER) cc_final: 0.5350 (tpt) REVERT: C 267 MET cc_start: 0.7683 (ttp) cc_final: 0.7350 (ttm) REVERT: C 275 PHE cc_start: 0.7238 (t80) cc_final: 0.6990 (t80) REVERT: C 604 LYS cc_start: 0.8083 (ptmm) cc_final: 0.7436 (tptp) REVERT: C 794 LYS cc_start: 0.8171 (ttpp) cc_final: 0.7923 (tmmt) REVERT: C 808 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7941 (tm-30) REVERT: C 859 MET cc_start: 0.8691 (ttt) cc_final: 0.8445 (ttm) REVERT: C 883 VAL cc_start: 0.8309 (OUTLIER) cc_final: 0.8084 (m) REVERT: C 950 ARG cc_start: 0.7562 (ttm170) cc_final: 0.7322 (mtm180) REVERT: C 988 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8696 (mmm) REVERT: C 1137 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.6447 (ttt-90) REVERT: D 136 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8528 (mp) REVERT: D 176 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8055 (mm) REVERT: D 200 LYS cc_start: 0.2854 (OUTLIER) cc_final: 0.2620 (tppp) REVERT: D 267 MET cc_start: 0.8264 (ttm) cc_final: 0.8004 (tpp) REVERT: D 275 PHE cc_start: 0.7365 (t80) cc_final: 0.6930 (t80) REVERT: D 415 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7870 (mp10) REVERT: D 538 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7682 (mmp80) REVERT: D 548 GLN cc_start: 0.8180 (tp40) cc_final: 0.7893 (tp-100) REVERT: D 604 LYS cc_start: 0.8073 (ptmm) cc_final: 0.7386 (tptp) REVERT: D 794 LYS cc_start: 0.8290 (tttp) cc_final: 0.7545 (mmtm) REVERT: D 799 LYS cc_start: 0.8751 (mmmt) cc_final: 0.8373 (mmtt) REVERT: D 828 ARG cc_start: 0.8371 (ttm170) cc_final: 0.8108 (ttm110) REVERT: D 844 HIS cc_start: 0.7820 (p-80) cc_final: 0.7459 (p-80) REVERT: D 883 VAL cc_start: 0.8258 (OUTLIER) cc_final: 0.7993 (m) REVERT: D 988 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8716 (mmm) outliers start: 115 outliers final: 62 residues processed: 595 average time/residue: 0.6912 time to fit residues: 477.7129 Evaluate side-chains 603 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 517 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLU 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 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 134 VAL 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 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 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 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 134 VAL Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 281 LEU 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 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 1038 ILE Chi-restraints excluded: chain C residue 1137 ARG Chi-restraints excluded: chain C residue 1143 ARG 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 473 LEU 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 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 1176 THR Chi-restraints excluded: chain D residue 1187 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 330 optimal weight: 0.9990 chunk 331 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 243 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 218 optimal weight: 0.6980 chunk 268 optimal weight: 6.9990 chunk 223 optimal weight: 9.9990 chunk 315 optimal weight: 0.0020 chunk 177 optimal weight: 3.9990 chunk 262 optimal weight: 7.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- 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 298 ASN B 440 GLN B 490 GLN B 952 ASN B1046 HIS ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 GLN C 614 HIS 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 788 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 = 0.3886 r_free = 0.3886 target = 0.130726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.098431 restraints weight = 51056.826| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.14 r_work: 0.3186 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2144 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= 0.115 Angle : 0.542 15.715 39824 Z= 0.273 Chirality : 0.042 0.265 4548 Planarity : 0.005 0.121 4992 Dihedral : 4.867 55.955 3921 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.41 % Favored : 97.37 % Rotamer: Outliers : 3.91 % Allowed : 22.71 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.14), residues: 3532 helix: 1.17 (0.13), residues: 1720 sheet: -0.72 (0.25), residues: 352 loop : 0.25 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1143 TYR 0.020 0.001 TYR B 351 PHE 0.030 0.001 PHE D 268 TRP 0.012 0.001 TRP B 169 HIS 0.005 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00286 (29344) covalent geometry : angle 0.54175 (39812) hydrogen bonds : bond 0.03383 ( 1401) hydrogen bonds : angle 4.37874 ( 3903) metal coordination : bond 0.00305 ( 16) metal coordination : angle 1.51586 ( 12) Misc. bond : bond 0.00022 ( 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 642 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 519 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 ILE cc_start: 0.7462 (tp) cc_final: 0.7010 (pt) REVERT: A 200 LYS cc_start: 0.4004 (OUTLIER) cc_final: 0.3579 (tppt) REVERT: A 210 VAL cc_start: 0.4951 (OUTLIER) cc_final: 0.4559 (p) REVERT: A 220 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7618 (pt) REVERT: A 228 TRP cc_start: 0.6157 (m-90) cc_final: 0.5559 (t60) REVERT: A 232 ARG cc_start: 0.8107 (ttm170) cc_final: 0.7565 (ttm170) REVERT: A 267 MET cc_start: 0.8222 (ttm) cc_final: 0.7656 (ttm) REVERT: A 275 PHE cc_start: 0.7176 (t80) cc_final: 0.6693 (t80) REVERT: A 413 ASP cc_start: 0.8172 (t0) cc_final: 0.7789 (t0) REVERT: A 415 GLN cc_start: 0.8434 (mt0) cc_final: 0.8091 (mp10) REVERT: A 604 LYS cc_start: 0.8119 (ptmm) cc_final: 0.7379 (tptp) REVERT: A 883 VAL cc_start: 0.8285 (OUTLIER) cc_final: 0.7993 (m) REVERT: A 988 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8684 (mmm) REVERT: B 131 ILE cc_start: 0.8113 (mm) cc_final: 0.7841 (OUTLIER) REVERT: B 180 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.6966 (mm110) REVERT: B 220 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7488 (pt) REVERT: B 291 HIS cc_start: 0.8616 (t70) cc_final: 0.8407 (t70) REVERT: B 349 LEU cc_start: 0.8624 (mt) cc_final: 0.8379 (mt) REVERT: B 352 LEU cc_start: 0.8061 (mt) cc_final: 0.7824 (mm) REVERT: B 413 ASP cc_start: 0.7880 (t0) cc_final: 0.7432 (t0) REVERT: B 415 GLN cc_start: 0.8405 (mt0) cc_final: 0.7888 (mp10) REVERT: B 461 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6815 (mt-10) REVERT: B 794 LYS cc_start: 0.8067 (tptt) cc_final: 0.7484 (mppt) REVERT: B 828 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7967 (ttm110) REVERT: B 844 HIS cc_start: 0.7889 (p-80) cc_final: 0.7537 (p-80) REVERT: B 859 MET cc_start: 0.8721 (ttm) cc_final: 0.8497 (ttm) REVERT: B 883 VAL cc_start: 0.8372 (OUTLIER) cc_final: 0.8118 (m) REVERT: B 950 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7457 (ttp-170) REVERT: B 988 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8694 (mmm) REVERT: C 174 MET cc_start: 0.7455 (tpt) cc_final: 0.6898 (tpt) REVERT: C 200 LYS cc_start: 0.3036 (OUTLIER) cc_final: 0.2616 (tptp) REVERT: C 216 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.7232 (mpt) REVERT: C 231 LEU cc_start: 0.7634 (mt) cc_final: 0.7192 (tt) REVERT: C 252 MET cc_start: 0.5976 (OUTLIER) cc_final: 0.5288 (tpt) REVERT: C 267 MET cc_start: 0.7672 (ttp) cc_final: 0.7358 (ttm) REVERT: C 275 PHE cc_start: 0.7328 (t80) cc_final: 0.7052 (t80) REVERT: C 604 LYS cc_start: 0.8100 (ptmm) cc_final: 0.7386 (tptp) REVERT: C 794 LYS cc_start: 0.8156 (ttpp) cc_final: 0.7860 (tmmt) REVERT: C 808 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7971 (tm-30) REVERT: C 859 MET cc_start: 0.8627 (ttt) cc_final: 0.8382 (ttm) REVERT: C 876 TYR cc_start: 0.8049 (OUTLIER) cc_final: 0.7422 (p90) REVERT: C 883 VAL cc_start: 0.8304 (OUTLIER) cc_final: 0.8101 (m) REVERT: C 950 ARG cc_start: 0.7657 (ttm170) cc_final: 0.7434 (mtm180) REVERT: C 988 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8701 (mmm) REVERT: C 1137 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.6464 (ttt-90) REVERT: D 200 LYS cc_start: 0.2795 (OUTLIER) cc_final: 0.2572 (tppp) REVERT: D 232 ARG cc_start: 0.7819 (mmm-85) cc_final: 0.7425 (ttm170) REVERT: D 415 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7832 (mp10) REVERT: D 428 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.7037 (mtm180) REVERT: D 538 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7741 (mmp80) REVERT: D 548 GLN cc_start: 0.8213 (tp40) cc_final: 0.7928 (tp-100) REVERT: D 604 LYS cc_start: 0.8094 (ptmm) cc_final: 0.7307 (tptp) REVERT: D 786 LYS cc_start: 0.7878 (mppt) cc_final: 0.7469 (mmmm) REVERT: D 799 LYS cc_start: 0.8807 (mmmt) cc_final: 0.8385 (mmtt) REVERT: D 828 ARG cc_start: 0.8453 (ttm170) cc_final: 0.8115 (ttm110) REVERT: D 844 HIS cc_start: 0.7896 (p-80) cc_final: 0.7521 (p-80) REVERT: D 876 TYR cc_start: 0.8034 (OUTLIER) cc_final: 0.7504 (p90) REVERT: D 883 VAL cc_start: 0.8279 (OUTLIER) cc_final: 0.8016 (m) REVERT: D 988 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8717 (mmm) outliers start: 123 outliers final: 66 residues processed: 594 average time/residue: 0.6748 time to fit residues: 466.1643 Evaluate side-chains 600 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 509 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL 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 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 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 422 ILE 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 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 988 MET 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 162 ILE Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 281 LEU 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 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 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 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 523 CYS Chi-restraints excluded: chain D residue 538 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 988 MET Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain D residue 1038 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 342 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 306 optimal weight: 0.9990 chunk 320 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 201 optimal weight: 7.9990 chunk 286 optimal weight: 0.9990 chunk 339 optimal weight: 0.0470 chunk 315 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 195 optimal weight: 8.9990 overall best weight: 0.7082 ------------------------------------------------------------------------------- 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 298 ASN B 490 GLN B 952 ASN 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 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.130826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.098597 restraints weight = 51197.342| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.12 r_work: 0.3192 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2219 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= 0.116 Angle : 0.554 16.329 39824 Z= 0.276 Chirality : 0.042 0.261 4548 Planarity : 0.005 0.120 4992 Dihedral : 4.744 55.412 3919 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.55 % Favored : 97.23 % Rotamer: Outliers : 3.56 % Allowed : 23.41 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.14), residues: 3532 helix: 1.21 (0.13), residues: 1720 sheet: -0.70 (0.25), residues: 352 loop : 0.27 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1143 TYR 0.020 0.001 TYR A 351 PHE 0.029 0.001 PHE D 268 TRP 0.012 0.001 TRP B 169 HIS 0.005 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00289 (29344) covalent geometry : angle 0.55356 (39812) hydrogen bonds : bond 0.03360 ( 1401) hydrogen bonds : angle 4.36002 ( 3903) metal coordination : bond 0.00289 ( 16) metal coordination : angle 1.49393 ( 12) Misc. bond : bond 0.00034 ( 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 625 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 513 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 ILE cc_start: 0.7620 (tp) cc_final: 0.6977 (pt) REVERT: A 171 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: A 200 LYS cc_start: 0.4007 (OUTLIER) cc_final: 0.3577 (tppt) REVERT: A 210 VAL cc_start: 0.4601 (OUTLIER) cc_final: 0.4209 (p) REVERT: A 220 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7545 (pt) REVERT: A 228 TRP cc_start: 0.6278 (m-90) cc_final: 0.5565 (t60) REVERT: A 232 ARG cc_start: 0.8107 (ttm170) cc_final: 0.7552 (ttm170) REVERT: A 267 MET cc_start: 0.8299 (ttm) cc_final: 0.7468 (tpp) REVERT: A 275 PHE cc_start: 0.7208 (t80) cc_final: 0.6699 (t80) REVERT: A 413 ASP cc_start: 0.8130 (t0) cc_final: 0.7746 (t0) REVERT: A 415 GLN cc_start: 0.8403 (mt0) cc_final: 0.8080 (mp10) REVERT: A 461 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6816 (mt-10) REVERT: A 604 LYS cc_start: 0.8104 (ptmm) cc_final: 0.7385 (tptp) REVERT: A 786 LYS cc_start: 0.7917 (mppt) cc_final: 0.7524 (mmmm) REVERT: A 883 VAL cc_start: 0.8289 (OUTLIER) cc_final: 0.7990 (m) REVERT: A 988 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8684 (mmm) REVERT: B 129 LEU cc_start: 0.8758 (tp) cc_final: 0.8426 (tt) REVERT: B 131 ILE cc_start: 0.8134 (mm) cc_final: 0.7911 (OUTLIER) REVERT: B 180 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.7280 (tp40) REVERT: B 220 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7499 (pt) REVERT: B 228 TRP cc_start: 0.6994 (t-100) cc_final: 0.6654 (t60) REVERT: B 291 HIS cc_start: 0.8631 (t70) cc_final: 0.8367 (t70) REVERT: B 349 LEU cc_start: 0.8577 (mt) cc_final: 0.8319 (mt) REVERT: B 352 LEU cc_start: 0.8124 (mt) cc_final: 0.7893 (mm) REVERT: B 413 ASP cc_start: 0.7873 (t0) cc_final: 0.7430 (t0) REVERT: B 415 GLN cc_start: 0.8343 (mt0) cc_final: 0.7860 (mp10) REVERT: B 461 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6841 (mt-10) REVERT: B 548 GLN cc_start: 0.8107 (tp-100) cc_final: 0.7849 (tp-100) REVERT: B 794 LYS cc_start: 0.8053 (tptt) cc_final: 0.7491 (mppt) REVERT: B 828 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7972 (ttt90) REVERT: B 844 HIS cc_start: 0.7802 (p-80) cc_final: 0.7471 (p-80) REVERT: B 883 VAL cc_start: 0.8371 (OUTLIER) cc_final: 0.8116 (m) REVERT: B 950 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7447 (ttp-170) REVERT: B 988 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8701 (mmm) REVERT: B 1140 LEU cc_start: 0.8202 (mt) cc_final: 0.7967 (tp) REVERT: C 200 LYS cc_start: 0.3126 (OUTLIER) cc_final: 0.2641 (tptp) REVERT: C 216 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7367 (mpt) REVERT: C 231 LEU cc_start: 0.7632 (mt) cc_final: 0.7187 (tt) REVERT: C 252 MET cc_start: 0.6014 (OUTLIER) cc_final: 0.5345 (tpt) REVERT: C 267 MET cc_start: 0.7616 (ttp) cc_final: 0.7381 (ttm) REVERT: C 275 PHE cc_start: 0.7325 (t80) cc_final: 0.7019 (t80) REVERT: C 604 LYS cc_start: 0.8079 (ptmm) cc_final: 0.7377 (tptp) REVERT: C 748 GLU cc_start: 0.6467 (mm-30) cc_final: 0.6250 (mm-30) REVERT: C 794 LYS cc_start: 0.8171 (ttpp) cc_final: 0.7875 (tmmt) REVERT: C 808 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7968 (tm-30) REVERT: C 876 TYR cc_start: 0.8073 (OUTLIER) cc_final: 0.7459 (p90) REVERT: C 883 VAL cc_start: 0.8321 (OUTLIER) cc_final: 0.8121 (m) REVERT: C 950 ARG cc_start: 0.7627 (ttm170) cc_final: 0.7408 (mtm180) REVERT: C 988 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8701 (mmm) REVERT: C 1137 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.6546 (ttt-90) REVERT: C 1151 GLU cc_start: 0.7591 (pp20) cc_final: 0.7385 (pp20) REVERT: D 200 LYS cc_start: 0.2828 (OUTLIER) cc_final: 0.2628 (tppp) REVERT: D 232 ARG cc_start: 0.7818 (mmm-85) cc_final: 0.7403 (ttm170) REVERT: D 415 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7768 (mp10) REVERT: D 428 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.7030 (mtm180) REVERT: D 538 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7727 (mmp80) REVERT: D 548 GLN cc_start: 0.8177 (tp40) cc_final: 0.7873 (tp-100) REVERT: D 566 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7142 (ttp) REVERT: D 604 LYS cc_start: 0.8062 (ptmm) cc_final: 0.7295 (tptp) REVERT: D 783 LYS cc_start: 0.7723 (ptmm) cc_final: 0.7522 (pptt) REVERT: D 799 LYS cc_start: 0.8779 (mmmt) cc_final: 0.8385 (mmtp) REVERT: D 828 ARG cc_start: 0.8422 (ttm170) cc_final: 0.8138 (ttt90) REVERT: D 844 HIS cc_start: 0.7832 (p-80) cc_final: 0.7502 (p-80) REVERT: D 876 TYR cc_start: 0.8052 (OUTLIER) cc_final: 0.7467 (p90) REVERT: D 883 VAL cc_start: 0.8284 (OUTLIER) cc_final: 0.8025 (m) REVERT: D 968 ARG cc_start: 0.8547 (mmp80) cc_final: 0.8322 (mmp-170) REVERT: D 988 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8720 (mmm) outliers start: 112 outliers final: 60 residues processed: 583 average time/residue: 0.6799 time to fit residues: 461.0488 Evaluate side-chains 588 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 500 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 171 GLU 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 331 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 461 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 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 422 ILE 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 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 988 MET Chi-restraints excluded: chain B residue 1038 ILE Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 216 MET 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 1137 ARG Chi-restraints excluded: chain C residue 1143 ARG 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 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 523 CYS Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 566 MET 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 988 MET 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 101 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 317 optimal weight: 3.9990 chunk 304 optimal weight: 2.9990 chunk 126 optimal weight: 0.2980 chunk 289 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 chunk 338 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 357 GLN B 490 GLN B 952 ASN 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 470 GLN D 490 GLN 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 = 0.3871 r_free = 0.3871 target = 0.130146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.097920 restraints weight = 50968.178| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.11 r_work: 0.3168 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 29361 Z= 0.160 Angle : 0.583 15.998 39824 Z= 0.292 Chirality : 0.043 0.263 4548 Planarity : 0.005 0.118 4992 Dihedral : 4.712 55.331 3914 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.75 % Favored : 97.03 % Rotamer: Outliers : 3.53 % Allowed : 23.70 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.14), residues: 3532 helix: 1.13 (0.13), residues: 1724 sheet: -0.84 (0.25), residues: 356 loop : 0.22 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B1143 TYR 0.018 0.001 TYR D 351 PHE 0.032 0.002 PHE A 268 TRP 0.013 0.001 TRP B 169 HIS 0.005 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00403 (29344) covalent geometry : angle 0.58265 (39812) hydrogen bonds : bond 0.03686 ( 1401) hydrogen bonds : angle 4.42611 ( 3903) metal coordination : bond 0.00344 ( 16) metal coordination : angle 1.71578 ( 12) Misc. bond : bond 0.00047 ( 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 621 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 510 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ILE cc_start: 0.7648 (tp) cc_final: 0.7049 (pt) REVERT: A 171 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7549 (mp0) REVERT: A 200 LYS cc_start: 0.4034 (OUTLIER) cc_final: 0.3561 (tppt) REVERT: A 210 VAL cc_start: 0.4623 (OUTLIER) cc_final: 0.4238 (p) REVERT: A 228 TRP cc_start: 0.6258 (m-90) cc_final: 0.5541 (t60) REVERT: A 232 ARG cc_start: 0.8132 (ttm170) cc_final: 0.7608 (ttm170) REVERT: A 275 PHE cc_start: 0.7228 (t80) cc_final: 0.6693 (t80) REVERT: A 413 ASP cc_start: 0.8170 (t0) cc_final: 0.7746 (t0) REVERT: A 415 GLN cc_start: 0.8441 (mt0) cc_final: 0.8094 (mp10) REVERT: A 461 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6918 (mt-10) REVERT: A 604 LYS cc_start: 0.8162 (ptmm) cc_final: 0.7398 (tptp) REVERT: A 883 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.8054 (m) REVERT: A 927 MET cc_start: 0.8441 (mtt) cc_final: 0.8181 (mtt) REVERT: B 129 LEU cc_start: 0.8777 (tp) cc_final: 0.8426 (tt) REVERT: B 180 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7256 (tp40) REVERT: B 220 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7424 (pt) REVERT: B 228 TRP cc_start: 0.6958 (t-100) cc_final: 0.6634 (t60) REVERT: B 291 HIS cc_start: 0.8607 (t70) cc_final: 0.8308 (t70) REVERT: B 349 LEU cc_start: 0.8564 (mt) cc_final: 0.8317 (mt) REVERT: B 413 ASP cc_start: 0.7936 (t0) cc_final: 0.7508 (t0) REVERT: B 415 GLN cc_start: 0.8380 (mt0) cc_final: 0.7859 (mp10) REVERT: B 461 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6926 (mt-10) REVERT: B 786 LYS cc_start: 0.7810 (mppt) cc_final: 0.7326 (mmmm) REVERT: B 794 LYS cc_start: 0.8120 (tptt) cc_final: 0.7466 (mppt) REVERT: B 828 ARG cc_start: 0.8425 (ttp-110) cc_final: 0.7953 (mtm-85) REVERT: B 844 HIS cc_start: 0.7881 (p-80) cc_final: 0.7569 (p-80) REVERT: B 883 VAL cc_start: 0.8403 (OUTLIER) cc_final: 0.8147 (m) REVERT: B 930 MET cc_start: 0.6491 (tmm) cc_final: 0.6077 (mmm) REVERT: B 950 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7447 (ttp-170) REVERT: C 200 LYS cc_start: 0.3213 (OUTLIER) cc_final: 0.2718 (tptp) REVERT: C 216 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7378 (mpt) REVERT: C 231 LEU cc_start: 0.7648 (mt) cc_final: 0.7203 (tt) REVERT: C 252 MET cc_start: 0.5982 (OUTLIER) cc_final: 0.5368 (tpt) REVERT: C 267 MET cc_start: 0.7632 (ttp) cc_final: 0.7361 (ttm) REVERT: C 275 PHE cc_start: 0.7286 (t80) cc_final: 0.6983 (t80) REVERT: C 604 LYS cc_start: 0.8112 (ptmm) cc_final: 0.7392 (tptp) REVERT: C 794 LYS cc_start: 0.8197 (ttpp) cc_final: 0.7888 (tmmt) REVERT: C 808 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7992 (tm-30) REVERT: C 876 TYR cc_start: 0.8194 (OUTLIER) cc_final: 0.7565 (p90) REVERT: C 883 VAL cc_start: 0.8320 (OUTLIER) cc_final: 0.8116 (m) REVERT: C 930 MET cc_start: 0.6491 (tmm) cc_final: 0.6059 (mmm) REVERT: C 950 ARG cc_start: 0.7654 (ttm170) cc_final: 0.7435 (mtm180) REVERT: C 1137 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.6535 (ttt-90) REVERT: D 136 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8470 (mp) REVERT: D 200 LYS cc_start: 0.2606 (OUTLIER) cc_final: 0.2258 (tppt) REVERT: D 232 ARG cc_start: 0.7836 (mmm-85) cc_final: 0.7448 (ttm170) REVERT: D 418 ARG cc_start: 0.8259 (ttm110) cc_final: 0.7976 (mtm-85) REVERT: D 428 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.6974 (mtm180) REVERT: D 538 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7754 (mmp80) REVERT: D 548 GLN cc_start: 0.8209 (tp40) cc_final: 0.7897 (tp-100) REVERT: D 604 LYS cc_start: 0.8087 (ptmm) cc_final: 0.7330 (tptp) REVERT: D 786 LYS cc_start: 0.7897 (mppt) cc_final: 0.7472 (mmmm) REVERT: D 794 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.8056 (ttmt) REVERT: D 799 LYS cc_start: 0.8806 (mmmt) cc_final: 0.8391 (mmtp) REVERT: D 828 ARG cc_start: 0.8478 (ttm170) cc_final: 0.8164 (ttt90) REVERT: D 876 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.7582 (p90) REVERT: D 883 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.8038 (m) outliers start: 111 outliers final: 72 residues processed: 578 average time/residue: 0.7379 time to fit residues: 494.7582 Evaluate side-chains 594 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 499 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 171 GLU 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 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 422 ILE Chi-restraints excluded: chain A residue 461 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 1017 LEU 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 131 ILE 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 422 ILE 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 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 1038 ILE Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 216 MET 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 1038 ILE Chi-restraints excluded: chain C residue 1137 ARG Chi-restraints excluded: chain C residue 1143 ARG 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 414 VAL 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 789 SER Chi-restraints excluded: chain D residue 794 LYS 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 1033 SER 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 238 optimal weight: 0.7980 chunk 211 optimal weight: 0.0570 chunk 349 optimal weight: 6.9990 chunk 263 optimal weight: 0.7980 chunk 248 optimal weight: 0.8980 chunk 48 optimal weight: 0.0000 chunk 90 optimal weight: 6.9990 chunk 257 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 0.0050 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 GLN A 632 ASN A 952 ASN A1046 HIS ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN B 357 GLN B 490 GLN B 952 ASN 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 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 = 0.3900 r_free = 0.3900 target = 0.131601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.098877 restraints weight = 50966.806| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.37 r_work: 0.3183 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2410 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= 0.106 Angle : 0.564 17.757 39824 Z= 0.280 Chirality : 0.041 0.256 4548 Planarity : 0.005 0.116 4992 Dihedral : 4.522 54.718 3914 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.21 % Favored : 97.57 % Rotamer: Outliers : 2.86 % Allowed : 24.81 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.14), residues: 3532 helix: 1.31 (0.13), residues: 1696 sheet: -0.62 (0.25), residues: 352 loop : 0.26 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 133 TYR 0.020 0.001 TYR C 351 PHE 0.032 0.001 PHE A 268 TRP 0.023 0.001 TRP A 169 HIS 0.004 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00262 (29344) covalent geometry : angle 0.56346 (39812) hydrogen bonds : bond 0.03158 ( 1401) hydrogen bonds : angle 4.30758 ( 3903) metal coordination : bond 0.00313 ( 16) metal coordination : angle 1.54207 ( 12) Misc. bond : bond 0.00043 ( 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 602 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 512 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ILE cc_start: 0.7274 (tp) cc_final: 0.6709 (pt) REVERT: A 200 LYS cc_start: 0.3945 (OUTLIER) cc_final: 0.3489 (tppt) REVERT: A 210 VAL cc_start: 0.4882 (OUTLIER) cc_final: 0.4491 (p) REVERT: A 228 TRP cc_start: 0.6195 (m-90) cc_final: 0.5419 (t60) REVERT: A 232 ARG cc_start: 0.8111 (ttm170) cc_final: 0.7720 (ttm110) REVERT: A 267 MET cc_start: 0.8227 (ttm) cc_final: 0.7748 (tpp) REVERT: A 275 PHE cc_start: 0.7149 (t80) cc_final: 0.6593 (t80) REVERT: A 413 ASP cc_start: 0.8140 (t0) cc_final: 0.7721 (t0) REVERT: A 415 GLN cc_start: 0.8446 (mt0) cc_final: 0.8071 (mp10) REVERT: A 604 LYS cc_start: 0.8102 (ptmm) cc_final: 0.7364 (tptp) REVERT: A 786 LYS cc_start: 0.7992 (mppt) cc_final: 0.7504 (mmmm) REVERT: A 808 GLU cc_start: 0.8348 (tt0) cc_final: 0.8126 (tm-30) REVERT: A 829 LYS cc_start: 0.8765 (mtmt) cc_final: 0.8231 (mttm) REVERT: A 883 VAL cc_start: 0.8293 (OUTLIER) cc_final: 0.8028 (m) REVERT: A 988 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8692 (mmm) REVERT: B 129 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8251 (tt) REVERT: B 131 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7670 (OUTLIER) REVERT: B 174 MET cc_start: 0.7335 (tpp) cc_final: 0.7048 (tpt) REVERT: B 179 ILE cc_start: 0.7810 (tt) cc_final: 0.7602 (tp) REVERT: B 180 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7280 (tp40) REVERT: B 220 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7409 (pt) REVERT: B 349 LEU cc_start: 0.8436 (mt) cc_final: 0.8189 (mt) REVERT: B 548 GLN cc_start: 0.8116 (tp-100) cc_final: 0.7850 (tp-100) REVERT: B 794 LYS cc_start: 0.8066 (tptt) cc_final: 0.7472 (mppt) REVERT: B 828 ARG cc_start: 0.8419 (ttp-110) cc_final: 0.7964 (ttm110) REVERT: B 830 GLU cc_start: 0.7638 (pt0) cc_final: 0.7392 (tp30) REVERT: B 844 HIS cc_start: 0.7804 (p-80) cc_final: 0.7464 (p-80) REVERT: B 883 VAL cc_start: 0.8379 (OUTLIER) cc_final: 0.8123 (m) REVERT: B 930 MET cc_start: 0.6191 (tmm) cc_final: 0.5760 (mmm) REVERT: B 950 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7374 (ttp-170) REVERT: B 988 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8702 (mmm) REVERT: C 200 LYS cc_start: 0.3125 (OUTLIER) cc_final: 0.2632 (tptp) REVERT: C 216 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7217 (mpt) REVERT: C 231 LEU cc_start: 0.7560 (mt) cc_final: 0.7112 (tt) REVERT: C 252 MET cc_start: 0.5970 (OUTLIER) cc_final: 0.5456 (tpt) REVERT: C 275 PHE cc_start: 0.7244 (t80) cc_final: 0.6921 (t80) REVERT: C 349 LEU cc_start: 0.8523 (tp) cc_final: 0.8270 (mt) REVERT: C 604 LYS cc_start: 0.8085 (ptmm) cc_final: 0.7343 (tptp) REVERT: C 794 LYS cc_start: 0.8126 (ttpp) cc_final: 0.7909 (tmmt) REVERT: C 808 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7942 (tm-30) REVERT: C 876 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.7428 (p90) REVERT: C 930 MET cc_start: 0.6155 (tmm) cc_final: 0.5726 (mmm) REVERT: C 950 ARG cc_start: 0.7576 (ttm170) cc_final: 0.7294 (mtm180) REVERT: C 988 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8703 (mmm) REVERT: C 1137 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.6511 (ttt-90) REVERT: D 200 LYS cc_start: 0.2785 (OUTLIER) cc_final: 0.2435 (tppt) REVERT: D 418 ARG cc_start: 0.8237 (ttm110) cc_final: 0.7925 (mtm-85) REVERT: D 428 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7036 (mtm180) REVERT: D 538 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7697 (mmp80) REVERT: D 548 GLN cc_start: 0.8086 (tp40) cc_final: 0.7811 (tp-100) REVERT: D 604 LYS cc_start: 0.8032 (ptmm) cc_final: 0.7255 (tptp) REVERT: D 799 LYS cc_start: 0.8785 (mmmt) cc_final: 0.8374 (mmtp) REVERT: D 828 ARG cc_start: 0.8455 (ttm170) cc_final: 0.8155 (ttt90) REVERT: D 829 LYS cc_start: 0.8736 (mtmt) cc_final: 0.8182 (mttm) REVERT: D 883 VAL cc_start: 0.8292 (OUTLIER) cc_final: 0.8030 (m) REVERT: D 930 MET cc_start: 0.5975 (tmm) cc_final: 0.5674 (mmm) REVERT: D 968 ARG cc_start: 0.8538 (mmp80) cc_final: 0.8327 (mmp-170) REVERT: D 988 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8727 (mmm) outliers start: 90 outliers final: 54 residues processed: 569 average time/residue: 0.7455 time to fit residues: 491.4040 Evaluate side-chains 571 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 496 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL 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 301 LEU Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 422 ILE 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 988 MET Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 132 VAL 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 422 ILE 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 1176 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 335 ILE 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 969 VAL Chi-restraints excluded: chain C residue 988 MET 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 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 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 428 ARG 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 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 988 MET Chi-restraints excluded: chain D residue 1143 ARG Chi-restraints excluded: chain D residue 1162 LEU Chi-restraints excluded: chain D residue 1176 THR 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 125 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 263 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 137 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 227 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 307 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 GLN A 490 GLN A 632 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 952 ASN B1046 HIS ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 GLN C 844 HIS 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 844 HIS D 952 ASN D1046 HIS ** D1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.130780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.098573 restraints weight = 51163.542| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.12 r_work: 0.3185 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2366 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= 0.136 Angle : 0.583 16.035 39824 Z= 0.290 Chirality : 0.042 0.256 4548 Planarity : 0.005 0.116 4992 Dihedral : 4.567 53.911 3914 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.72 % Favored : 97.06 % Rotamer: Outliers : 2.80 % Allowed : 25.03 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.14), residues: 3532 helix: 1.28 (0.13), residues: 1700 sheet: -0.68 (0.25), residues: 356 loop : 0.27 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1143 TYR 0.017 0.001 TYR D 351 PHE 0.032 0.002 PHE A 268 TRP 0.025 0.001 TRP A 169 HIS 0.006 0.001 HIS D 291 Details of bonding type rmsd covalent geometry : bond 0.00341 (29344) covalent geometry : angle 0.58201 (39812) hydrogen bonds : bond 0.03450 ( 1401) hydrogen bonds : angle 4.34005 ( 3903) metal coordination : bond 0.00297 ( 16) metal coordination : angle 1.64679 ( 12) Misc. bond : bond 0.00047 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14466.90 seconds wall clock time: 246 minutes 27.67 seconds (14787.67 seconds total)