Starting phenix.real_space_refine on Wed Jun 25 01:20:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hkm_34855/06_2025/8hkm_34855.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hkm_34855/06_2025/8hkm_34855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hkm_34855/06_2025/8hkm_34855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hkm_34855/06_2025/8hkm_34855.map" model { file = "/net/cci-nas-00/data/ceres_data/8hkm_34855/06_2025/8hkm_34855.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hkm_34855/06_2025/8hkm_34855.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.033 sd= 0.123 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 11 8.98 5 Zn 4 6.06 5 P 4 5.49 5 S 212 5.16 5 C 18692 2.51 5 N 4784 2.21 5 O 5148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.53s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28855 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7188 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 7188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7188 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 7188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7188 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 7188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7188 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 27 Unusual residues: {' K': 4, ' ZN': 1, '6OU': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'6OU:plan-1': 1, '6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Unusual residues: {' K': 2, ' ZN': 1, '6OU': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'6OU:plan-1': 1, '6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 25 Unusual residues: {' K': 2, ' ZN': 1, '6OU': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'6OU:plan-1': 1, '6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 26 Unusual residues: {' K': 3, ' ZN': 1, '6OU': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'6OU:plan-1': 1, '6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 5 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4457 SG CYS A 777 97.513 66.786 13.845 1.00106.01 S ATOM 4463 SG CYS A 778 100.217 64.035 14.123 1.00106.62 S ATOM 4517 SG CYS A 785 96.837 63.244 12.492 1.00141.13 S ATOM 11645 SG CYS B 777 66.390 53.345 13.810 1.00100.38 S ATOM 11651 SG CYS B 778 63.502 50.638 14.045 1.00102.12 S ATOM 11705 SG CYS B 785 63.070 53.915 12.538 1.00120.59 S ATOM 18833 SG CYS C 777 52.812 84.392 13.755 1.00106.54 S ATOM 18839 SG CYS C 778 50.045 87.288 14.010 1.00109.23 S ATOM 18893 SG CYS C 785 53.220 87.802 12.382 1.00132.25 S ATOM 26021 SG CYS D 777 83.928 97.967 13.755 1.00 99.44 S ATOM 26027 SG CYS D 778 86.804 100.723 14.020 1.00104.05 S ATOM 26081 SG CYS D 785 87.249 97.422 12.372 1.00131.41 S Time building chain proxies: 16.97, per 1000 atoms: 0.59 Number of scatterers: 28855 At special positions: 0 Unit cell: (151.84, 151.84, 143.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 K 11 19.00 S 212 16.00 P 4 15.00 O 5148 8.00 N 4784 7.00 C 18692 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS A 280 " distance=2.04 Simple disulfide: pdb=" SG CYS B 242 " - pdb=" SG CYS B 280 " distance=1.08 Simple disulfide: pdb=" SG CYS C 242 " - pdb=" SG CYS C 280 " distance=2.03 Simple disulfide: pdb=" SG CYS D 242 " - pdb=" SG CYS D 280 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.29 Conformation dependent library (CDL) restraints added in 3.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1303 " pdb="ZN ZN A1303 " - pdb=" ND1 HIS A 787 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 785 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 778 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 777 " pdb=" ZN B1304 " pdb="ZN ZN B1304 " - pdb=" ND1 HIS B 787 " pdb="ZN ZN B1304 " - pdb=" SG CYS B 785 " pdb="ZN ZN B1304 " - pdb=" SG CYS B 777 " pdb="ZN ZN B1304 " - pdb=" SG CYS B 778 " pdb=" ZN C1304 " pdb="ZN ZN C1304 " - pdb=" SG CYS C 777 " pdb="ZN ZN C1304 " - pdb=" SG CYS C 785 " pdb="ZN ZN C1304 " - pdb=" ND1 HIS C 787 " pdb="ZN ZN C1304 " - pdb=" SG CYS C 778 " pdb=" ZN D1305 " pdb="ZN ZN D1305 " - pdb=" SG CYS D 785 " pdb="ZN ZN D1305 " - pdb=" ND1 HIS D 787 " pdb="ZN ZN D1305 " - pdb=" SG CYS D 777 " pdb="ZN ZN D1305 " - 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: 162 helices and 20 sheets defined 53.3% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.35 Creating SS restraints... Processing helix chain 'A' and resid 110 through 137 Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 173 through 198 Processing helix chain 'A' and resid 211 through 228 removed outlier: 3.587A pdb=" N GLU A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Proline residue: A 221 - end of helix removed outlier: 3.650A pdb=" N ILE A 226 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 240 through 254 removed outlier: 4.235A pdb=" N LEU A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 293 removed outlier: 4.071A pdb=" N GLN A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) 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 removed outlier: 3.711A pdb=" N GLU A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 400 removed outlier: 6.591A pdb=" N ARG A 398 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A 400 " --> pdb=" O PRO A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 421 Processing helix chain 'A' and resid 422 through 427 removed outlier: 4.585A 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 463 through 482 removed outlier: 3.516A pdb=" N VAL A 478 " --> pdb=" O ARG A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 500 removed outlier: 4.555A pdb=" N PHE A 498 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N HIS A 499 " --> pdb=" O ASN A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 521 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 removed outlier: 3.615A pdb=" N GLU A 576 " --> pdb=" O ARG A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 591 Processing helix chain 'A' and resid 633 through 644 removed outlier: 3.737A pdb=" N PHE A 637 " --> pdb=" O SER A 633 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG A 643 " --> pdb=" O GLN A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 797 removed outlier: 3.567A pdb=" N TYR A 796 " --> pdb=" O ASP A 792 " (cutoff:3.500A) removed outlier: 3.512A 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 822 removed outlier: 3.570A pdb=" N PHE A 817 " --> pdb=" O GLY A 813 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 818 " --> pdb=" O LEU A 814 " (cutoff:3.500A) Proline residue: A 820 - end of helix Processing helix chain 'A' and resid 827 through 831 removed outlier: 3.628A pdb=" N LEU A 831 " --> pdb=" O ARG A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 851 Processing helix chain 'A' and resid 865 through 873 removed outlier: 3.566A pdb=" N LEU A 869 " --> pdb=" O ASN A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 897 Processing helix chain 'A' and resid 898 through 912 removed outlier: 3.683A pdb=" N MET A 908 " --> pdb=" O ASN A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 930 removed outlier: 4.277A pdb=" N ARG A 928 " --> pdb=" O SER A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 952 removed outlier: 3.593A pdb=" N LEU A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER A 943 " --> pdb=" O SER A 939 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS A 944 " --> pdb=" O LEU A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 960 removed outlier: 3.580A pdb=" N MET A 959 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE A 960 " --> pdb=" O ALA A 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 956 through 960' Processing helix chain 'A' and resid 961 through 966 Processing helix chain 'A' and resid 973 through 982 Processing helix chain 'A' and resid 987 through 997 Processing helix chain 'A' and resid 1013 through 1017 Processing helix chain 'A' and resid 1021 through 1033 Processing helix chain 'A' and resid 1129 through 1143 removed outlier: 3.721A pdb=" N ARG A1142 " --> pdb=" O LEU A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1161 Processing helix chain 'B' and resid 111 through 137 Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 173 through 198 Processing helix chain 'B' and resid 212 through 228 Proline residue: B 221 - end of helix removed outlier: 3.639A pdb=" N ILE B 226 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 234 removed outlier: 4.182A pdb=" N ASN B 233 " --> pdb=" O PRO B 230 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 234 " --> pdb=" O LEU B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 239 No H-bonds generated for 'chain 'B' and resid 237 through 239' Processing helix chain 'B' and resid 240 through 254 removed outlier: 4.049A pdb=" N LEU B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 293 removed outlier: 4.021A pdb=" N GLN B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) 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 removed outlier: 3.709A pdb=" N GLU B 392 " --> pdb=" O ASP B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 removed outlier: 6.635A pdb=" N ARG B 398 " --> pdb=" O ALA B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 421 Processing helix chain 'B' and resid 422 through 427 removed outlier: 4.600A 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: 4.554A pdb=" N PHE B 498 " --> pdb=" O GLU B 495 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS B 499 " --> pdb=" O ASN B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 521 Processing helix chain 'B' and resid 525 through 534 Processing helix chain 'B' and resid 547 through 556 Processing helix chain 'B' and resid 557 through 559 No H-bonds generated for 'chain 'B' and resid 557 through 559' Processing helix chain 'B' and resid 572 through 576 removed outlier: 3.620A pdb=" N GLU B 576 " --> pdb=" O ARG B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 591 Processing helix chain 'B' and resid 633 through 644 removed outlier: 3.754A pdb=" N PHE B 637 " --> pdb=" O SER B 633 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG B 643 " --> pdb=" O GLN B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 797 removed outlier: 3.504A pdb=" N TYR B 796 " --> pdb=" O ASP B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 822 removed outlier: 3.570A pdb=" N PHE B 817 " --> pdb=" O GLY B 813 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 818 " --> pdb=" O LEU B 814 " (cutoff:3.500A) 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 removed outlier: 3.615A pdb=" N LEU B 869 " --> pdb=" O ASN B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 897 Processing helix chain 'B' and resid 898 through 912 removed outlier: 3.628A pdb=" N MET B 908 " --> pdb=" O ASN B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 930 removed outlier: 4.156A pdb=" N ARG B 928 " --> pdb=" O SER B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 952 removed outlier: 3.605A pdb=" N LEU B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER B 943 " --> pdb=" O SER B 939 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS B 944 " --> pdb=" O LEU B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 960 removed outlier: 3.998A 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 973 through 982 removed outlier: 3.504A pdb=" N THR B 977 " --> pdb=" O SER B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 997 Processing helix chain 'B' and resid 1013 through 1017 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 137 Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 173 through 198 Processing helix chain 'C' and resid 211 through 228 removed outlier: 3.604A pdb=" N GLU C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) Proline residue: C 221 - end of helix removed outlier: 3.554A pdb=" N ILE C 226 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE C 227 " --> pdb=" O ILE C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 232 Processing helix chain 'C' and resid 237 through 239 No H-bonds generated for 'chain 'C' and resid 237 through 239' Processing helix chain 'C' and resid 240 through 254 removed outlier: 4.309A pdb=" N LEU C 244 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 293 removed outlier: 4.030A pdb=" N GLN C 270 " --> pdb=" O ALA C 266 " (cutoff:3.500A) 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 removed outlier: 3.734A pdb=" N GLU C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 400 removed outlier: 6.646A pdb=" N ARG C 398 " --> pdb=" O ALA C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 421 Processing helix chain 'C' and resid 422 through 427 removed outlier: 4.541A 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: 4.545A pdb=" N PHE C 498 " --> pdb=" O GLU C 495 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS C 499 " --> pdb=" O ASN C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 521 Processing helix chain 'C' and resid 525 through 534 Processing helix chain 'C' and resid 547 through 556 Processing helix chain 'C' and resid 557 through 559 No H-bonds generated for 'chain 'C' and resid 557 through 559' Processing helix chain 'C' and resid 572 through 576 removed outlier: 3.596A pdb=" N GLU C 576 " --> pdb=" O ARG C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 591 Processing helix chain 'C' and resid 633 through 644 removed outlier: 3.733A pdb=" N PHE C 637 " --> pdb=" O SER C 633 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG C 643 " --> pdb=" O GLN C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 797 removed outlier: 3.629A pdb=" N TYR C 796 " --> pdb=" O ASP C 792 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY C 797 " --> pdb=" O ALA C 793 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 792 through 797' Processing helix chain 'C' and resid 811 through 822 removed outlier: 3.598A pdb=" N PHE C 817 " --> pdb=" O GLY C 813 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 818 " --> pdb=" O LEU C 814 " (cutoff:3.500A) 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 removed outlier: 3.576A pdb=" N LEU C 869 " --> pdb=" O ASN C 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 897 Processing helix chain 'C' and resid 898 through 912 removed outlier: 3.509A pdb=" N MET C 908 " --> pdb=" O ASN C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 930 removed outlier: 4.182A pdb=" N ARG C 928 " --> pdb=" O SER C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 936 through 952 removed outlier: 3.807A pdb=" N SER C 943 " --> pdb=" O SER C 939 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS C 944 " --> pdb=" O LEU C 940 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 945 " --> pdb=" O ALA C 941 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 960 removed outlier: 3.526A pdb=" N MET C 959 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE C 960 " --> pdb=" O ALA C 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 956 through 960' Processing helix chain 'C' and resid 961 through 966 Processing helix chain 'C' and resid 973 through 982 removed outlier: 3.586A pdb=" N THR C 977 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 997 Processing helix chain 'C' and resid 1013 through 1017 Processing helix chain 'C' and resid 1021 through 1033 Processing helix chain 'C' and resid 1129 through 1143 removed outlier: 3.663A pdb=" N ARG C1142 " --> pdb=" O LEU C1138 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 211 through 228 removed outlier: 3.546A pdb=" N GLU D 215 " --> pdb=" O SER D 211 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE D 217 " --> pdb=" O VAL D 213 " (cutoff:3.500A) Proline residue: D 221 - end of helix removed outlier: 3.565A pdb=" N ILE D 226 " --> pdb=" O PHE D 222 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP D 228 " --> pdb=" O ILE D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 233 removed outlier: 3.569A pdb=" N ARG D 232 " --> pdb=" O PRO D 229 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN D 233 " --> pdb=" O PRO D 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 229 through 233' Processing helix chain 'D' and resid 240 through 254 removed outlier: 3.946A pdb=" N LEU D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN D 254 " --> pdb=" O GLU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 293 removed outlier: 4.266A pdb=" N GLN D 270 " --> pdb=" O ALA D 266 " (cutoff:3.500A) 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 removed outlier: 3.670A pdb=" N GLU D 392 " --> pdb=" O ASP D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 400 removed outlier: 6.597A pdb=" N ARG D 398 " --> pdb=" O ALA D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 421 Processing helix chain 'D' and resid 422 through 427 removed outlier: 4.600A 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: 4.539A pdb=" N PHE D 498 " --> pdb=" O GLU D 495 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS D 499 " --> pdb=" O ASN D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 521 Processing helix chain 'D' and resid 525 through 534 Processing helix chain 'D' and resid 547 through 556 removed outlier: 3.518A pdb=" N ARG D 551 " --> pdb=" O GLU D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 559 No H-bonds generated for 'chain 'D' and resid 557 through 559' Processing helix chain 'D' and resid 572 through 576 removed outlier: 3.629A pdb=" N GLU D 576 " --> pdb=" O ARG D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 591 Processing helix chain 'D' and resid 633 through 644 removed outlier: 3.777A pdb=" N PHE D 637 " --> pdb=" O SER D 633 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG D 643 " --> pdb=" O GLN D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 797 removed outlier: 3.563A pdb=" N TYR D 796 " --> pdb=" O ASP D 792 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY D 797 " --> pdb=" O ALA D 793 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 792 through 797' Processing helix chain 'D' and resid 811 through 822 removed outlier: 3.522A pdb=" N PHE D 817 " --> pdb=" O GLY D 813 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE D 818 " --> pdb=" O LEU D 814 " (cutoff:3.500A) 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 removed outlier: 3.557A pdb=" N LEU D 869 " --> pdb=" O ASN D 865 " (cutoff:3.500A) Processing helix chain 'D' and resid 893 through 897 Processing helix chain 'D' and resid 898 through 912 removed outlier: 3.630A pdb=" N MET D 908 " --> pdb=" O ASN D 904 " (cutoff:3.500A) Processing helix chain 'D' and resid 923 through 930 removed outlier: 4.179A pdb=" N ARG D 928 " --> pdb=" O SER D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 936 through 952 removed outlier: 3.698A pdb=" N SER D 943 " --> pdb=" O SER D 939 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS D 944 " --> pdb=" O LEU D 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 960 removed outlier: 3.525A pdb=" N MET D 959 " --> pdb=" O LEU D 956 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE D 960 " --> pdb=" O ALA D 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 956 through 960' Processing helix chain 'D' and resid 961 through 966 Processing helix chain 'D' and resid 973 through 982 Processing helix chain 'D' and resid 987 through 997 Processing helix chain 'D' and resid 1013 through 1017 Processing helix chain 'D' and resid 1021 through 1033 Processing helix chain 'D' and resid 1129 through 1143 removed outlier: 3.522A pdb=" N ARG D1142 " --> pdb=" O LEU D1138 " (cutoff:3.500A) Processing helix chain 'D' and resid 1144 through 1161 Processing sheet with id=AA1, first strand: chain 'A' and resid 429 through 432 removed outlier: 6.266A pdb=" N VAL A 404 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU A 432 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ILE A 406 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N PHE A 454 " --> pdb=" O HIS A 373 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL A 375 " --> pdb=" O PHE A 454 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 560 through 565 removed outlier: 6.861A pdb=" N ILE A 625 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LEU A 595 " --> pdb=" O ILE A 625 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 750 through 752 Processing sheet with id=AA4, first strand: chain 'A' and resid 856 through 860 removed outlier: 6.345A pdb=" N ILE A 803 " --> pdb=" O VAL A 835 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU A 837 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL A 805 " --> pdb=" O LEU A 837 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LEU A 802 " --> pdb=" O ALA A 877 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A 879 " --> pdb=" O LEU A 802 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER A 916 " --> pdb=" O ASP A 878 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A 920 " --> pdb=" O VAL A 882 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1006 through 1012 removed outlier: 3.846A pdb=" N ASP A1194 " --> pdb=" O ILE A1012 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY A1039 " --> pdb=" O TYR A1197 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE A1199 " --> pdb=" O PRO A1037 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 429 through 433 removed outlier: 6.260A pdb=" N VAL B 404 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LEU B 432 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ILE B 406 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N PHE B 454 " --> pdb=" O HIS B 373 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL B 375 " --> pdb=" O PHE B 454 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N CYS B 453 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N GLN B 490 " --> pdb=" O CYS B 453 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE B 455 " --> pdb=" O GLN B 490 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 560 through 565 removed outlier: 6.867A pdb=" N ILE B 625 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU B 595 " --> pdb=" O ILE B 625 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 750 through 752 Processing sheet with id=AA9, first strand: chain 'B' and resid 856 through 860 removed outlier: 6.094A pdb=" N ILE B 834 " --> pdb=" O TYR B 857 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N MET B 859 " --> pdb=" O ILE B 834 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU B 836 " --> pdb=" O MET B 859 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE B 803 " --> pdb=" O VAL B 835 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU B 837 " --> pdb=" O ILE B 803 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL B 805 " --> pdb=" O LEU B 837 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU B 802 " --> pdb=" O ALA B 877 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN B 879 " --> pdb=" O LEU B 802 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER B 916 " --> pdb=" O ASP B 878 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B 920 " --> pdb=" O VAL B 882 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N PHE B 970 " --> pdb=" O ILE B 917 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR B 919 " --> pdb=" O PHE B 970 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1006 through 1012 removed outlier: 3.892A pdb=" N ASP B1194 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY B1039 " --> pdb=" O TYR B1197 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE B1199 " --> pdb=" O PRO B1037 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 429 through 433 removed outlier: 6.239A pdb=" N VAL C 404 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU C 432 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ILE C 406 " --> pdb=" O LEU C 432 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N PHE C 454 " --> pdb=" O HIS C 373 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL C 375 " --> pdb=" O PHE C 454 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N CYS C 453 " --> pdb=" O TYR C 488 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N GLN C 490 " --> pdb=" O CYS C 453 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ILE C 455 " --> pdb=" O GLN C 490 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 560 through 565 removed outlier: 6.894A pdb=" N ILE C 625 " --> pdb=" O LEU C 595 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LEU C 595 " --> pdb=" O ILE C 625 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 750 through 752 Processing sheet with id=AB5, first strand: chain 'C' and resid 856 through 860 removed outlier: 6.291A pdb=" N ILE C 803 " --> pdb=" O VAL C 835 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU C 837 " --> pdb=" O ILE C 803 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL C 805 " --> pdb=" O LEU C 837 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LEU C 802 " --> pdb=" O ALA C 877 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN C 879 " --> pdb=" O LEU C 802 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER C 916 " --> pdb=" O ASP C 878 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU C 920 " --> pdb=" O VAL C 882 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 1006 through 1012 removed outlier: 3.711A pdb=" N ASP C1194 " --> pdb=" O ILE C1012 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY C1039 " --> pdb=" O TYR C1197 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE C1199 " --> pdb=" O PRO C1037 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 429 through 432 removed outlier: 6.267A pdb=" N VAL D 404 " --> pdb=" O ILE D 430 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU D 432 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ILE D 406 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N PHE D 454 " --> pdb=" O HIS D 373 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL D 375 " --> pdb=" O PHE D 454 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 560 through 565 removed outlier: 6.870A pdb=" N ILE D 625 " --> pdb=" O LEU D 595 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU D 595 " --> pdb=" O ILE D 625 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 750 through 752 Processing sheet with id=AC1, first strand: chain 'D' and resid 856 through 860 removed outlier: 6.060A pdb=" N ILE D 834 " --> pdb=" O TYR D 857 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N MET D 859 " --> pdb=" O ILE D 834 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU D 836 " --> pdb=" O MET D 859 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE D 803 " --> pdb=" O VAL D 835 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU D 837 " --> pdb=" O ILE D 803 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL D 805 " --> pdb=" O LEU D 837 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N LEU D 802 " --> pdb=" O ALA D 877 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN D 879 " --> pdb=" O LEU D 802 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER D 916 " --> pdb=" O ASP D 878 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU D 920 " --> pdb=" O VAL D 882 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 1006 through 1012 removed outlier: 3.803A pdb=" N ASP D1194 " --> pdb=" O ILE D1012 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY D1039 " --> pdb=" O TYR D1197 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE D1199 " --> pdb=" O PRO D1037 " (cutoff:3.500A) 1362 hydrogen bonds defined for protein. 3813 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: 12.21 Time building geometry restraints manager: 7.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9063 1.34 - 1.46: 6890 1.46 - 1.58: 13233 1.58 - 1.71: 10 1.71 - 1.83: 312 Bond restraints: 29508 Sorted by residual: bond pdb=" C PRO A 149 " pdb=" N LYS A 150 " ideal model delta sigma weight residual 1.330 1.382 -0.052 1.38e-02 5.25e+03 1.41e+01 bond pdb=" CB CYS A 242 " pdb=" SG CYS A 242 " ideal model delta sigma weight residual 1.808 1.711 0.097 3.30e-02 9.18e+02 8.72e+00 bond pdb=" CB CYS C 242 " pdb=" SG CYS C 242 " ideal model delta sigma weight residual 1.808 1.728 0.080 3.30e-02 9.18e+02 5.87e+00 bond pdb=" C TRP D 228 " pdb=" N PRO D 229 " ideal model delta sigma weight residual 1.329 1.357 -0.028 1.18e-02 7.18e+03 5.43e+00 bond pdb=" CG PRO D 229 " pdb=" CD PRO D 229 " ideal model delta sigma weight residual 1.503 1.426 0.077 3.40e-02 8.65e+02 5.19e+00 ... (remaining 29503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.85: 39966 6.85 - 13.69: 46 13.69 - 20.54: 6 20.54 - 27.39: 0 27.39 - 34.23: 2 Bond angle restraints: 40020 Sorted by residual: angle pdb=" C PRO D 149 " pdb=" CA PRO D 149 " pdb=" CB PRO D 149 " ideal model delta sigma weight residual 111.56 141.12 -29.56 1.65e+00 3.67e-01 3.21e+02 angle pdb=" N LYS D 150 " pdb=" CA LYS D 150 " pdb=" C LYS D 150 " ideal model delta sigma weight residual 110.80 76.57 34.23 2.13e+00 2.20e-01 2.58e+02 angle pdb=" N LYS D 150 " pdb=" CA LYS D 150 " pdb=" CB LYS D 150 " ideal model delta sigma weight residual 110.49 128.90 -18.41 1.69e+00 3.50e-01 1.19e+02 angle pdb=" N PRO C 149 " pdb=" CA PRO C 149 " pdb=" C PRO C 149 " ideal model delta sigma weight residual 112.47 127.57 -15.10 2.06e+00 2.36e-01 5.37e+01 angle pdb=" N PRO B 149 " pdb=" CA PRO B 149 " pdb=" C PRO B 149 " ideal model delta sigma weight residual 112.47 127.55 -15.08 2.06e+00 2.36e-01 5.36e+01 ... (remaining 40015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.95: 16988 30.95 - 61.90: 667 61.90 - 92.85: 56 92.85 - 123.80: 8 123.80 - 154.75: 1 Dihedral angle restraints: 17720 sinusoidal: 7108 harmonic: 10612 Sorted by residual: dihedral pdb=" C PRO D 149 " pdb=" N PRO D 149 " pdb=" CA PRO D 149 " pdb=" CB PRO D 149 " ideal model delta harmonic sigma weight residual -120.70 -147.64 26.94 0 2.50e+00 1.60e-01 1.16e+02 dihedral pdb=" CB CYS D 242 " pdb=" SG CYS D 242 " pdb=" SG CYS D 280 " pdb=" CB CYS D 280 " ideal model delta sinusoidal sigma weight residual 93.00 -176.69 -90.31 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS B 242 " pdb=" SG CYS B 242 " pdb=" SG CYS B 280 " pdb=" CB CYS B 280 " ideal model delta sinusoidal sigma weight residual 93.00 175.34 -82.34 1 1.00e+01 1.00e-02 8.32e+01 ... (remaining 17717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.185: 4546 0.185 - 0.371: 3 0.371 - 0.556: 0 0.556 - 0.742: 2 0.742 - 0.927: 1 Chirality restraints: 4552 Sorted by residual: 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 1.79 0.93 2.00e-01 2.50e+01 2.15e+01 chirality pdb=" CA PRO C 149 " pdb=" N PRO C 149 " pdb=" C PRO C 149 " pdb=" CB PRO C 149 " both_signs ideal model delta sigma weight residual False 2.72 1.98 0.74 2.00e-01 2.50e+01 1.37e+01 chirality pdb=" CA PRO B 149 " pdb=" N PRO B 149 " pdb=" C PRO B 149 " pdb=" CB PRO B 149 " both_signs ideal model delta sigma weight residual False 2.72 2.07 0.65 2.00e-01 2.50e+01 1.05e+01 ... (remaining 4549 not shown) Planarity restraints: 5008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 149 " -0.054 2.00e-02 2.50e+03 1.03e-01 1.05e+02 pdb=" C PRO D 149 " 0.178 2.00e-02 2.50e+03 pdb=" O PRO D 149 " -0.065 2.00e-02 2.50e+03 pdb=" N LYS D 150 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 148 " -0.113 5.00e-02 4.00e+02 1.72e-01 4.75e+01 pdb=" N PRO A 149 " 0.298 5.00e-02 4.00e+02 pdb=" CA PRO A 149 " -0.102 5.00e-02 4.00e+02 pdb=" CD PRO A 149 " -0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS D 148 " -0.111 5.00e-02 4.00e+02 1.70e-01 4.62e+01 pdb=" N PRO D 149 " 0.294 5.00e-02 4.00e+02 pdb=" CA PRO D 149 " -0.100 5.00e-02 4.00e+02 pdb=" CD PRO D 149 " -0.082 5.00e-02 4.00e+02 ... (remaining 5005 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.22: 22 2.22 - 2.95: 12546 2.95 - 3.68: 50308 3.68 - 4.41: 84444 4.41 - 5.14: 141014 Nonbonded interactions: 288334 Sorted by model distance: nonbonded pdb=" O CYS D 148 " pdb=" O PRO D 149 " model vdw 1.484 3.040 nonbonded pdb=" CZ ARG D 828 " pdb=" NZ LYS D 829 " model vdw 1.790 3.350 nonbonded pdb=" NH1 ARG D 828 " pdb=" NZ LYS D 829 " model vdw 1.817 3.200 nonbonded pdb=" NH1 ARG C 538 " pdb=" NE2 GLN C 540 " model vdw 1.839 3.200 nonbonded pdb=" NH2 ARG C 538 " pdb=" OE1 GLN C 540 " model vdw 1.944 3.120 ... (remaining 288329 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 110 through 1205 or resid 1302)) selection = (chain 'B' and (resid 110 through 1205 or resid 1302)) selection = (chain 'C' and (resid 110 through 1205 or resid 1302)) selection = (chain 'D' and (resid 110 through 1205 or resid 1302)) } 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.070 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 70.550 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 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 : 0.007 0.946 29528 Z= 0.327 Angle : 0.804 61.392 40040 Z= 0.397 Chirality : 0.045 0.927 4552 Planarity : 0.006 0.172 5008 Dihedral : 16.007 154.747 10820 Min Nonbonded Distance : 1.484 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.63 % Favored : 97.25 % Rotamer: Outliers : 1.30 % Allowed : 19.11 % Favored : 79.59 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.14), residues: 3532 helix: -0.35 (0.12), residues: 1664 sheet: -1.18 (0.29), residues: 324 loop : 0.05 (0.16), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 204 HIS 0.011 0.001 HIS C 844 PHE 0.033 0.001 PHE B 275 TYR 0.021 0.001 TYR A 553 ARG 0.013 0.000 ARG C 555 Details of bonding type rmsd hydrogen bonds : bond 0.24059 ( 1362) hydrogen bonds : angle 7.60448 ( 3813) metal coordination : bond 0.17446 ( 16) metal coordination : angle 7.96409 ( 12) SS BOND : bond 0.47325 ( 4) SS BOND : angle 24.28629 ( 8) covalent geometry : bond 0.00286 (29508) covalent geometry : angle 0.71422 (40020) *********************** 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 381 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 340 time to evaluate : 3.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 PRO cc_start: 0.8685 (Cg_endo) cc_final: 0.8402 (Cg_exo) REVERT: A 876 TYR cc_start: 0.8777 (OUTLIER) cc_final: 0.8088 (p90) REVERT: B 174 MET cc_start: 0.7843 (ptp) cc_final: 0.7525 (pmm) REVERT: B 632 ASN cc_start: 0.8710 (m-40) cc_final: 0.8383 (m110) REVERT: B 844 HIS cc_start: 0.8120 (m170) cc_final: 0.7913 (m-70) REVERT: C 845 HIS cc_start: 0.8084 (t-90) cc_final: 0.7746 (t-90) REVERT: C 876 TYR cc_start: 0.8674 (OUTLIER) cc_final: 0.7964 (p90) REVERT: C 1047 VAL cc_start: 0.8163 (OUTLIER) cc_final: 0.7846 (t) REVERT: C 1138 LEU cc_start: 0.8858 (tp) cc_final: 0.8591 (tm) REVERT: D 192 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.6940 (mtm) REVERT: D 212 PHE cc_start: 0.8236 (t80) cc_final: 0.7938 (t80) REVERT: D 351 TYR cc_start: 0.7823 (t80) cc_final: 0.7615 (t80) outliers start: 41 outliers final: 33 residues processed: 374 average time/residue: 1.4081 time to fit residues: 618.4153 Evaluate side-chains 325 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 288 time to evaluate : 3.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 1188 THR Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 527 SER Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 1014 GLU Chi-restraints excluded: chain D residue 1047 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 3.9990 chunk 269 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 92 optimal weight: 20.0000 chunk 182 optimal weight: 0.3980 chunk 144 optimal weight: 0.8980 chunk 279 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 chunk 207 optimal weight: 0.0050 chunk 323 optimal weight: 7.9990 overall best weight: 1.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN A 218 ASN A 291 HIS A 427 GLN A 469 HIS A 470 GLN A 496 ASN A 505 HIS A 535 HIS A 614 HIS A 816 ASN A 871 GLN A 931 GLN B 163 ASN B 470 GLN B 496 ASN B 505 HIS B 535 HIS B 614 HIS B 816 ASN B 871 GLN B 879 ASN B 923 HIS B 931 GLN B1136 GLN C 291 HIS C 470 GLN C 496 ASN C 505 HIS C 535 HIS C 543 GLN C 632 ASN C 816 ASN C 931 GLN ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 HIS D 396 HIS D 427 GLN D 470 GLN D 496 ASN D 505 HIS D 535 HIS D 543 GLN D 871 GLN D 931 GLN D1136 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.103539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.081158 restraints weight = 64328.941| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.61 r_work: 0.3100 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 29528 Z= 0.154 Angle : 0.607 16.159 40040 Z= 0.303 Chirality : 0.043 0.288 4552 Planarity : 0.006 0.162 5008 Dihedral : 7.868 144.140 4028 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.43 % Favored : 97.48 % Rotamer: Outliers : 3.10 % Allowed : 18.99 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.14), residues: 3532 helix: 0.46 (0.12), residues: 1688 sheet: -0.95 (0.26), residues: 360 loop : -0.04 (0.17), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 243 HIS 0.008 0.001 HIS B 845 PHE 0.032 0.002 PHE B 275 TYR 0.018 0.001 TYR A 403 ARG 0.008 0.001 ARG D 538 Details of bonding type rmsd hydrogen bonds : bond 0.04938 ( 1362) hydrogen bonds : angle 4.80026 ( 3813) metal coordination : bond 0.00691 ( 16) metal coordination : angle 2.30443 ( 12) SS BOND : bond 0.01429 ( 4) SS BOND : angle 4.74865 ( 8) covalent geometry : bond 0.00361 (29508) covalent geometry : angle 0.60184 (40020) *********************** 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 423 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 325 time to evaluate : 3.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 VAL cc_start: 0.8798 (OUTLIER) cc_final: 0.8483 (p) REVERT: A 139 PRO cc_start: 0.8542 (Cg_endo) cc_final: 0.8307 (Cg_exo) REVERT: A 289 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8419 (tp) REVERT: A 566 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.6629 (tpt) REVERT: A 876 TYR cc_start: 0.8830 (OUTLIER) cc_final: 0.8314 (p90) REVERT: B 174 MET cc_start: 0.8047 (ptp) cc_final: 0.7781 (pmm) REVERT: B 212 PHE cc_start: 0.8382 (t80) cc_final: 0.7150 (t80) REVERT: B 566 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.6838 (tpt) REVERT: B 632 ASN cc_start: 0.8711 (m-40) cc_final: 0.8399 (m110) REVERT: B 876 TYR cc_start: 0.8601 (OUTLIER) cc_final: 0.8088 (p90) REVERT: C 289 ILE cc_start: 0.8835 (tp) cc_final: 0.8558 (tp) REVERT: C 356 ARG cc_start: 0.8210 (ttt180) cc_final: 0.7901 (tmm-80) REVERT: C 845 HIS cc_start: 0.7875 (t-90) cc_final: 0.7574 (t-90) REVERT: C 859 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8351 (ptm) REVERT: C 876 TYR cc_start: 0.8736 (OUTLIER) cc_final: 0.8143 (p90) REVERT: C 927 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.7597 (mpp) REVERT: C 1047 VAL cc_start: 0.8162 (OUTLIER) cc_final: 0.7856 (t) REVERT: D 212 PHE cc_start: 0.7856 (t80) cc_final: 0.7629 (t80) REVERT: D 252 MET cc_start: 0.6893 (tmt) cc_final: 0.6623 (tmm) REVERT: D 630 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.7014 (tp30) REVERT: D 1138 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8098 (mm) outliers start: 98 outliers final: 33 residues processed: 391 average time/residue: 1.3667 time to fit residues: 629.0203 Evaluate side-chains 343 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 298 time to evaluate : 3.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 927 MET Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 566 MET Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 927 MET Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 568 ASP Chi-restraints excluded: chain D residue 630 GLU Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 828 ARG Chi-restraints excluded: chain D residue 1010 MET Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1138 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 104 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 316 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 139 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 143 optimal weight: 0.1980 chunk 109 optimal weight: 2.9990 chunk 330 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 283 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 GLN B1136 GLN C 632 ASN C 844 HIS C 845 HIS ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1136 GLN D1173 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.105843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.083216 restraints weight = 64723.267| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.52 r_work: 0.3123 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 29528 Z= 0.116 Angle : 0.564 16.147 40040 Z= 0.275 Chirality : 0.041 0.260 4552 Planarity : 0.005 0.154 5008 Dihedral : 7.105 137.691 3991 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.29 % Favored : 97.62 % Rotamer: Outliers : 2.94 % Allowed : 19.75 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.14), residues: 3532 helix: 0.92 (0.12), residues: 1668 sheet: -1.08 (0.26), residues: 360 loop : 0.16 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 243 HIS 0.012 0.001 HIS C 844 PHE 0.016 0.001 PHE C 585 TYR 0.021 0.001 TYR A 553 ARG 0.008 0.000 ARG D1142 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 1362) hydrogen bonds : angle 4.36860 ( 3813) metal coordination : bond 0.00270 ( 16) metal coordination : angle 1.44848 ( 12) SS BOND : bond 0.00337 ( 4) SS BOND : angle 3.99632 ( 8) covalent geometry : bond 0.00269 (29508) covalent geometry : angle 0.56104 (40020) *********************** 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 432 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 339 time to evaluate : 3.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.8312 (mtt90) cc_final: 0.7767 (mtt90) REVERT: A 132 VAL cc_start: 0.8924 (OUTLIER) cc_final: 0.8623 (p) REVERT: A 139 PRO cc_start: 0.8539 (Cg_endo) cc_final: 0.8262 (Cg_exo) REVERT: A 168 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7381 (mp) REVERT: A 279 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8113 (mp) REVERT: A 289 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8407 (tp) REVERT: A 413 ASP cc_start: 0.7979 (t0) cc_final: 0.7749 (t0) REVERT: A 566 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.6662 (tpt) REVERT: A 876 TYR cc_start: 0.8819 (OUTLIER) cc_final: 0.8389 (p90) REVERT: B 153 TYR cc_start: 0.8010 (m-80) cc_final: 0.7711 (m-80) REVERT: B 566 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.6871 (tpt) REVERT: B 632 ASN cc_start: 0.8666 (m-40) cc_final: 0.8381 (m110) REVERT: B 876 TYR cc_start: 0.8490 (OUTLIER) cc_final: 0.8190 (p90) REVERT: B 935 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8346 (mtpp) REVERT: B 1175 ASN cc_start: 0.8282 (m-40) cc_final: 0.8062 (t0) REVERT: C 289 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8562 (tp) REVERT: C 845 HIS cc_start: 0.7756 (t70) cc_final: 0.7431 (t70) REVERT: C 859 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8341 (ptm) REVERT: C 876 TYR cc_start: 0.8721 (OUTLIER) cc_final: 0.8216 (p90) REVERT: C 927 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.7425 (mpp) REVERT: C 974 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.7239 (ptp) REVERT: C 1047 VAL cc_start: 0.8148 (OUTLIER) cc_final: 0.7850 (t) REVERT: D 212 PHE cc_start: 0.7764 (t80) cc_final: 0.7444 (t80) REVERT: D 630 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6880 (tp30) REVERT: D 1138 LEU cc_start: 0.8311 (tm) cc_final: 0.8056 (mm) outliers start: 93 outliers final: 25 residues processed: 396 average time/residue: 1.4505 time to fit residues: 673.9714 Evaluate side-chains 346 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 305 time to evaluate : 3.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 566 MET Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 935 LYS Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 927 MET Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 630 GLU Chi-restraints excluded: chain D residue 1014 GLU Chi-restraints excluded: chain D residue 1047 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 322 optimal weight: 4.9990 chunk 283 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 chunk 347 optimal weight: 5.9990 chunk 299 optimal weight: 0.7980 chunk 318 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 227 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 GLN B1175 ASN C 632 ASN D1136 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.104725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.082360 restraints weight = 65225.962| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.63 r_work: 0.3094 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 29528 Z= 0.155 Angle : 0.568 11.628 40040 Z= 0.278 Chirality : 0.042 0.252 4552 Planarity : 0.005 0.138 5008 Dihedral : 6.912 135.618 3989 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.63 % Favored : 97.28 % Rotamer: Outliers : 3.01 % Allowed : 20.22 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.14), residues: 3532 helix: 1.05 (0.13), residues: 1668 sheet: -1.12 (0.26), residues: 360 loop : 0.17 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 243 HIS 0.006 0.001 HIS B 845 PHE 0.033 0.001 PHE B 275 TYR 0.019 0.001 TYR A 553 ARG 0.010 0.000 ARG D 555 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 1362) hydrogen bonds : angle 4.27779 ( 3813) metal coordination : bond 0.00337 ( 16) metal coordination : angle 1.58469 ( 12) SS BOND : bond 0.00209 ( 4) SS BOND : angle 3.49282 ( 8) covalent geometry : bond 0.00378 (29508) covalent geometry : angle 0.56488 (40020) *********************** 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 413 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 318 time to evaluate : 3.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.8238 (mtt90) cc_final: 0.7725 (mtt90) REVERT: A 132 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8487 (p) REVERT: A 139 PRO cc_start: 0.8516 (Cg_endo) cc_final: 0.8225 (Cg_exo) REVERT: A 151 GLN cc_start: 0.8130 (mt0) cc_final: 0.7807 (mp10) REVERT: A 279 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8263 (mp) REVERT: A 289 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8463 (tp) REVERT: A 413 ASP cc_start: 0.8096 (t0) cc_final: 0.7837 (t0) REVERT: A 555 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7566 (ttm-80) REVERT: A 566 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.6669 (tpt) REVERT: A 876 TYR cc_start: 0.8821 (OUTLIER) cc_final: 0.8323 (p90) REVERT: A 927 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.7950 (mmt) REVERT: B 128 LEU cc_start: 0.8130 (mm) cc_final: 0.7927 (tp) REVERT: B 153 TYR cc_start: 0.8056 (m-80) cc_final: 0.7725 (m-80) REVERT: B 192 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.7045 (mpp) REVERT: B 351 TYR cc_start: 0.7662 (t80) cc_final: 0.7438 (t80) REVERT: B 566 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.6903 (tpt) REVERT: B 876 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.8190 (p90) REVERT: B 935 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8416 (mtpp) REVERT: C 289 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8586 (tp) REVERT: C 555 ARG cc_start: 0.7888 (ttp-110) cc_final: 0.7664 (ttp-110) REVERT: C 845 HIS cc_start: 0.7833 (t70) cc_final: 0.7511 (t70) REVERT: C 859 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8395 (ptm) REVERT: C 876 TYR cc_start: 0.8749 (OUTLIER) cc_final: 0.8241 (p90) REVERT: C 935 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8180 (mtpp) REVERT: C 1047 VAL cc_start: 0.8172 (OUTLIER) cc_final: 0.7859 (t) REVERT: C 1173 HIS cc_start: 0.5881 (OUTLIER) cc_final: 0.5632 (t70) REVERT: D 212 PHE cc_start: 0.7682 (t80) cc_final: 0.7414 (t80) REVERT: D 630 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6913 (tp30) outliers start: 95 outliers final: 34 residues processed: 373 average time/residue: 1.3923 time to fit residues: 609.2945 Evaluate side-chains 357 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 305 time to evaluate : 3.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 927 MET Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 555 ARG Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 566 MET Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 935 LYS Chi-restraints excluded: chain B residue 1010 MET Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 935 LYS Chi-restraints excluded: chain C residue 1010 MET Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1173 HIS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 630 GLU Chi-restraints excluded: chain D residue 1010 MET Chi-restraints excluded: chain D residue 1014 GLU Chi-restraints excluded: chain D residue 1047 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 242 optimal weight: 0.0870 chunk 59 optimal weight: 0.7980 chunk 149 optimal weight: 0.5980 chunk 172 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 355 optimal weight: 5.9990 chunk 335 optimal weight: 0.8980 chunk 327 optimal weight: 9.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1136 GLN B1175 ASN C 632 ASN ** C1174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 816 ASN D1136 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.105095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.082756 restraints weight = 64451.138| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.63 r_work: 0.3124 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.096 29528 Z= 0.108 Angle : 0.551 11.367 40040 Z= 0.267 Chirality : 0.041 0.265 4552 Planarity : 0.005 0.133 5008 Dihedral : 6.631 132.295 3989 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.18 % Favored : 97.73 % Rotamer: Outliers : 2.97 % Allowed : 20.54 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.14), residues: 3532 helix: 1.19 (0.13), residues: 1672 sheet: -1.24 (0.25), residues: 384 loop : 0.24 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 243 HIS 0.011 0.001 HIS B 787 PHE 0.014 0.001 PHE C 585 TYR 0.021 0.001 TYR A 553 ARG 0.007 0.000 ARG D1189 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 1362) hydrogen bonds : angle 4.12154 ( 3813) metal coordination : bond 0.00423 ( 16) metal coordination : angle 1.46563 ( 12) SS BOND : bond 0.00076 ( 4) SS BOND : angle 3.37337 ( 8) covalent geometry : bond 0.00247 (29508) covalent geometry : angle 0.54811 (40020) *********************** 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 407 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 313 time to evaluate : 3.086 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 132 VAL cc_start: 0.8777 (OUTLIER) cc_final: 0.8483 (p) REVERT: A 139 PRO cc_start: 0.8547 (Cg_endo) cc_final: 0.8216 (Cg_exo) REVERT: A 279 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8269 (mp) REVERT: A 289 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8402 (tp) REVERT: A 413 ASP cc_start: 0.8094 (t0) cc_final: 0.7839 (t0) REVERT: A 566 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.6641 (tpt) REVERT: A 876 TYR cc_start: 0.8819 (OUTLIER) cc_final: 0.8410 (p90) REVERT: B 128 LEU cc_start: 0.8148 (mm) cc_final: 0.7943 (tp) REVERT: B 351 TYR cc_start: 0.7720 (t80) cc_final: 0.7495 (t80) REVERT: B 566 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.6881 (tpt) REVERT: B 876 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.8171 (p90) REVERT: B 935 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8402 (mtpp) REVERT: C 174 MET cc_start: 0.6415 (OUTLIER) cc_final: 0.5828 (tpp) REVERT: C 289 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8543 (tp) REVERT: C 845 HIS cc_start: 0.7797 (t70) cc_final: 0.7471 (t70) REVERT: C 859 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8411 (ptm) REVERT: C 876 TYR cc_start: 0.8718 (OUTLIER) cc_final: 0.8233 (p90) REVERT: C 935 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8165 (mtpp) REVERT: C 1047 VAL cc_start: 0.8215 (OUTLIER) cc_final: 0.7917 (t) REVERT: C 1173 HIS cc_start: 0.5907 (OUTLIER) cc_final: 0.5611 (t70) REVERT: D 630 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6884 (tp30) outliers start: 94 outliers final: 37 residues processed: 366 average time/residue: 1.5039 time to fit residues: 651.7625 Evaluate side-chains 352 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 299 time to evaluate : 3.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 555 ARG Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 566 MET Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 935 LYS Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 1010 MET Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 935 LYS Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1173 HIS Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 630 GLU Chi-restraints excluded: chain D residue 838 LEU Chi-restraints excluded: chain D residue 1014 GLU Chi-restraints excluded: chain D residue 1047 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 327 optimal weight: 0.6980 chunk 271 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 215 optimal weight: 0.3980 chunk 148 optimal weight: 0.9990 chunk 118 optimal weight: 0.6980 chunk 167 optimal weight: 4.9990 chunk 354 optimal weight: 7.9990 chunk 322 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 330 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 GLN B1136 GLN C 632 ASN C1174 GLN D 614 HIS D1136 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.105020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.082761 restraints weight = 64733.892| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.63 r_work: 0.3120 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.090 29528 Z= 0.105 Angle : 0.553 13.106 40040 Z= 0.265 Chirality : 0.041 0.261 4552 Planarity : 0.005 0.131 5008 Dihedral : 6.484 130.605 3987 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.29 % Favored : 97.62 % Rotamer: Outliers : 2.72 % Allowed : 20.85 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.14), residues: 3532 helix: 1.31 (0.13), residues: 1672 sheet: -1.16 (0.25), residues: 384 loop : 0.31 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 243 HIS 0.005 0.001 HIS B 845 PHE 0.036 0.001 PHE B 275 TYR 0.023 0.001 TYR D 582 ARG 0.013 0.000 ARG C 555 Details of bonding type rmsd hydrogen bonds : bond 0.03246 ( 1362) hydrogen bonds : angle 4.03451 ( 3813) metal coordination : bond 0.00246 ( 16) metal coordination : angle 1.19921 ( 12) SS BOND : bond 0.00027 ( 4) SS BOND : angle 3.20543 ( 8) covalent geometry : bond 0.00248 (29508) covalent geometry : angle 0.55048 (40020) *********************** 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 409 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 323 time to evaluate : 3.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 VAL cc_start: 0.8832 (OUTLIER) cc_final: 0.8526 (p) REVERT: A 139 PRO cc_start: 0.8530 (Cg_endo) cc_final: 0.8154 (Cg_exo) REVERT: A 289 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8396 (tp) REVERT: A 355 GLU cc_start: 0.8580 (tt0) cc_final: 0.8371 (tt0) REVERT: A 876 TYR cc_start: 0.8830 (OUTLIER) cc_final: 0.8430 (p90) REVERT: A 1191 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7971 (mp0) REVERT: B 139 PRO cc_start: 0.9061 (Cg_endo) cc_final: 0.8639 (Cg_exo) REVERT: B 216 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7509 (ppp) REVERT: B 351 TYR cc_start: 0.7822 (t80) cc_final: 0.7573 (t80) REVERT: B 566 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.6950 (tpt) REVERT: B 876 TYR cc_start: 0.8481 (OUTLIER) cc_final: 0.8250 (p90) REVERT: B 935 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8326 (mtpp) REVERT: B 1174 GLN cc_start: 0.6231 (mm110) cc_final: 0.5266 (mt0) REVERT: C 174 MET cc_start: 0.6528 (OUTLIER) cc_final: 0.5912 (tpp) REVERT: C 289 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8559 (tp) REVERT: C 845 HIS cc_start: 0.7761 (t70) cc_final: 0.7422 (t70) REVERT: C 859 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8419 (ptm) REVERT: C 876 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.8266 (p90) REVERT: C 935 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8144 (mtpp) REVERT: C 969 VAL cc_start: 0.8981 (OUTLIER) cc_final: 0.8746 (p) REVERT: C 1047 VAL cc_start: 0.8206 (OUTLIER) cc_final: 0.7912 (t) REVERT: C 1173 HIS cc_start: 0.5890 (OUTLIER) cc_final: 0.5529 (t70) outliers start: 86 outliers final: 35 residues processed: 371 average time/residue: 1.5234 time to fit residues: 663.6870 Evaluate side-chains 355 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 304 time to evaluate : 3.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 555 ARG Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 566 MET Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 935 LYS Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 935 LYS Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1173 HIS Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 838 LEU Chi-restraints excluded: chain D residue 1014 GLU Chi-restraints excluded: chain D residue 1047 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 164 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 43 optimal weight: 0.1980 chunk 88 optimal weight: 0.8980 chunk 317 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 293 optimal weight: 0.9980 chunk 343 optimal weight: 0.9990 chunk 12 optimal weight: 20.0000 chunk 101 optimal weight: 0.0270 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 GLN A1159 HIS C 632 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.105714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.083331 restraints weight = 64765.859| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.54 r_work: 0.3134 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.090 29528 Z= 0.103 Angle : 0.553 12.803 40040 Z= 0.266 Chirality : 0.041 0.259 4552 Planarity : 0.004 0.132 5008 Dihedral : 6.346 129.316 3987 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.21 % Favored : 97.71 % Rotamer: Outliers : 2.59 % Allowed : 21.27 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.14), residues: 3532 helix: 1.40 (0.13), residues: 1668 sheet: -1.08 (0.25), residues: 384 loop : 0.40 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 243 HIS 0.008 0.001 HIS A1159 PHE 0.017 0.001 PHE B 188 TYR 0.023 0.001 TYR D 582 ARG 0.010 0.000 ARG C 600 Details of bonding type rmsd hydrogen bonds : bond 0.03186 ( 1362) hydrogen bonds : angle 3.96934 ( 3813) metal coordination : bond 0.00199 ( 16) metal coordination : angle 1.15779 ( 12) SS BOND : bond 0.00794 ( 4) SS BOND : angle 2.53915 ( 8) covalent geometry : bond 0.00243 (29508) covalent geometry : angle 0.55156 (40020) *********************** 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 394 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 312 time to evaluate : 3.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 VAL cc_start: 0.8743 (OUTLIER) cc_final: 0.8445 (p) REVERT: A 139 PRO cc_start: 0.8522 (Cg_endo) cc_final: 0.8136 (Cg_exo) REVERT: A 216 MET cc_start: 0.8310 (mmm) cc_final: 0.8077 (mmm) REVERT: A 289 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8376 (tp) REVERT: A 355 GLU cc_start: 0.8500 (tt0) cc_final: 0.7951 (tt0) REVERT: A 876 TYR cc_start: 0.8811 (OUTLIER) cc_final: 0.8480 (p90) REVERT: A 988 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8077 (mmm) REVERT: A 1191 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7997 (mp0) REVERT: B 128 LEU cc_start: 0.8244 (tp) cc_final: 0.7773 (mp) REVERT: B 139 PRO cc_start: 0.9081 (Cg_endo) cc_final: 0.8646 (Cg_exo) REVERT: B 216 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7511 (ppp) REVERT: B 351 TYR cc_start: 0.7747 (t80) cc_final: 0.7482 (t80) REVERT: B 566 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.6851 (tpt) REVERT: B 876 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.8202 (p90) REVERT: C 174 MET cc_start: 0.6616 (OUTLIER) cc_final: 0.5981 (tpp) REVERT: C 216 MET cc_start: 0.8239 (mmm) cc_final: 0.7923 (mmm) REVERT: C 289 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8533 (tp) REVERT: C 351 TYR cc_start: 0.7860 (t80) cc_final: 0.7197 (t80) REVERT: C 355 GLU cc_start: 0.8371 (tt0) cc_final: 0.8141 (mp0) REVERT: C 788 ASN cc_start: 0.7642 (p0) cc_final: 0.7432 (p0) REVERT: C 845 HIS cc_start: 0.7747 (t70) cc_final: 0.7399 (t70) REVERT: C 859 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8405 (ptm) REVERT: C 876 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.8162 (p90) REVERT: C 927 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.7528 (mpp) REVERT: C 935 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8154 (mtpp) REVERT: C 1047 VAL cc_start: 0.8187 (OUTLIER) cc_final: 0.7900 (t) REVERT: C 1139 SER cc_start: 0.8809 (t) cc_final: 0.8590 (p) REVERT: C 1173 HIS cc_start: 0.5883 (OUTLIER) cc_final: 0.5584 (t70) REVERT: D 174 MET cc_start: 0.7876 (tpt) cc_final: 0.7655 (tpt) REVERT: D 235 PHE cc_start: 0.8662 (t80) cc_final: 0.8399 (t80) REVERT: D 630 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6807 (tp30) REVERT: D 908 MET cc_start: 0.7915 (mmt) cc_final: 0.7699 (mmp) outliers start: 82 outliers final: 41 residues processed: 361 average time/residue: 1.4315 time to fit residues: 609.6572 Evaluate side-chains 359 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 301 time to evaluate : 3.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 555 ARG Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 566 MET Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 927 MET Chi-restraints excluded: chain C residue 935 LYS Chi-restraints excluded: chain C residue 1010 MET Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1173 HIS Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 630 GLU Chi-restraints excluded: chain D residue 838 LEU Chi-restraints excluded: chain D residue 1010 MET Chi-restraints excluded: chain D residue 1014 GLU Chi-restraints excluded: chain D residue 1047 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 169 optimal weight: 8.9990 chunk 188 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 182 optimal weight: 20.0000 chunk 191 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 310 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 339 optimal weight: 8.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 ASN A1136 GLN B1136 GLN C 632 ASN D1136 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.104939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.082692 restraints weight = 65324.831| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.61 r_work: 0.3102 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 29528 Z= 0.140 Angle : 0.578 13.225 40040 Z= 0.278 Chirality : 0.042 0.262 4552 Planarity : 0.005 0.133 5008 Dihedral : 6.294 129.779 3987 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.77 % Favored : 97.14 % Rotamer: Outliers : 2.66 % Allowed : 21.52 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.14), residues: 3532 helix: 1.37 (0.13), residues: 1668 sheet: -1.07 (0.25), residues: 384 loop : 0.39 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 243 HIS 0.005 0.001 HIS B 291 PHE 0.036 0.002 PHE B 275 TYR 0.022 0.001 TYR D 582 ARG 0.012 0.000 ARG C 555 Details of bonding type rmsd hydrogen bonds : bond 0.03402 ( 1362) hydrogen bonds : angle 3.99826 ( 3813) metal coordination : bond 0.00312 ( 16) metal coordination : angle 1.35883 ( 12) SS BOND : bond 0.00070 ( 4) SS BOND : angle 4.45283 ( 8) covalent geometry : bond 0.00342 (29508) covalent geometry : angle 0.57374 (40020) *********************** 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 389 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 305 time to evaluate : 3.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 VAL cc_start: 0.8773 (OUTLIER) cc_final: 0.8469 (p) REVERT: A 139 PRO cc_start: 0.8522 (Cg_endo) cc_final: 0.8130 (Cg_exo) REVERT: A 289 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8392 (tp) REVERT: A 355 GLU cc_start: 0.8551 (tt0) cc_final: 0.8012 (tt0) REVERT: A 555 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7620 (ttm-80) REVERT: A 566 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.6733 (tpt) REVERT: A 876 TYR cc_start: 0.8821 (OUTLIER) cc_final: 0.8424 (p90) REVERT: A 927 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.7490 (mmt) REVERT: A 1011 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8230 (tptm) REVERT: A 1191 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.8036 (mp0) REVERT: B 139 PRO cc_start: 0.9089 (Cg_endo) cc_final: 0.8656 (Cg_exo) REVERT: B 188 PHE cc_start: 0.7960 (t80) cc_final: 0.7599 (t80) REVERT: B 351 TYR cc_start: 0.7806 (t80) cc_final: 0.7540 (t80) REVERT: B 566 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.6940 (tpt) REVERT: B 876 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.8243 (p90) REVERT: B 1174 GLN cc_start: 0.6272 (mm110) cc_final: 0.5286 (mt0) REVERT: C 174 MET cc_start: 0.6646 (OUTLIER) cc_final: 0.6014 (tpp) REVERT: C 216 MET cc_start: 0.8199 (mmm) cc_final: 0.7879 (mmm) REVERT: C 267 MET cc_start: 0.8501 (tpp) cc_final: 0.8206 (tpt) REVERT: C 289 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8527 (tp) REVERT: C 351 TYR cc_start: 0.7820 (t80) cc_final: 0.7141 (t80) REVERT: C 355 GLU cc_start: 0.8431 (tt0) cc_final: 0.8171 (mp0) REVERT: C 788 ASN cc_start: 0.7679 (p0) cc_final: 0.7470 (p0) REVERT: C 845 HIS cc_start: 0.7843 (t70) cc_final: 0.7481 (t70) REVERT: C 876 TYR cc_start: 0.8746 (OUTLIER) cc_final: 0.8266 (p90) REVERT: C 927 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.7545 (mpp) REVERT: C 935 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8161 (mtpp) REVERT: C 1047 VAL cc_start: 0.8228 (OUTLIER) cc_final: 0.7938 (t) REVERT: C 1139 SER cc_start: 0.8835 (t) cc_final: 0.8617 (m) REVERT: C 1173 HIS cc_start: 0.5861 (OUTLIER) cc_final: 0.5381 (t70) REVERT: D 235 PHE cc_start: 0.8686 (t80) cc_final: 0.8456 (t80) REVERT: D 630 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6894 (tp30) outliers start: 84 outliers final: 43 residues processed: 355 average time/residue: 1.4704 time to fit residues: 616.4259 Evaluate side-chains 361 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 300 time to evaluate : 3.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 927 MET Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1011 LYS Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 555 ARG Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 566 MET Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 927 MET Chi-restraints excluded: chain C residue 935 LYS Chi-restraints excluded: chain C residue 1010 MET Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1173 HIS Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 630 GLU Chi-restraints excluded: chain D residue 838 LEU Chi-restraints excluded: chain D residue 1010 MET Chi-restraints excluded: chain D residue 1047 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 223 optimal weight: 9.9990 chunk 207 optimal weight: 0.4980 chunk 169 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 291 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 251 optimal weight: 4.9990 chunk 109 optimal weight: 0.2980 chunk 90 optimal weight: 0.7980 chunk 301 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 GLN B1136 GLN ** C1174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1136 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.105263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.082779 restraints weight = 64748.138| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.54 r_work: 0.3133 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 29528 Z= 0.106 Angle : 0.568 13.111 40040 Z= 0.272 Chirality : 0.041 0.262 4552 Planarity : 0.004 0.134 5008 Dihedral : 6.134 127.564 3987 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.10 % Favored : 97.82 % Rotamer: Outliers : 2.28 % Allowed : 22.18 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.14), residues: 3532 helix: 1.46 (0.13), residues: 1668 sheet: -1.03 (0.26), residues: 384 loop : 0.43 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 243 HIS 0.005 0.001 HIS B 291 PHE 0.029 0.001 PHE A 235 TYR 0.024 0.001 TYR D 582 ARG 0.011 0.000 ARG C 555 Details of bonding type rmsd hydrogen bonds : bond 0.03121 ( 1362) hydrogen bonds : angle 3.93925 ( 3813) metal coordination : bond 0.00178 ( 16) metal coordination : angle 1.09749 ( 12) SS BOND : bond 0.00840 ( 4) SS BOND : angle 2.32316 ( 8) covalent geometry : bond 0.00252 (29508) covalent geometry : angle 0.56674 (40020) *********************** 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 379 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 307 time to evaluate : 3.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8447 (p) REVERT: A 139 PRO cc_start: 0.8497 (Cg_endo) cc_final: 0.8090 (Cg_exo) REVERT: A 289 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8401 (tp) REVERT: A 355 GLU cc_start: 0.8476 (tt0) cc_final: 0.7920 (tt0) REVERT: A 566 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.6688 (tpt) REVERT: A 876 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.8483 (p90) REVERT: A 988 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.8075 (mmm) REVERT: A 1191 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.8001 (mp0) REVERT: B 139 PRO cc_start: 0.9078 (Cg_endo) cc_final: 0.8636 (Cg_exo) REVERT: B 351 TYR cc_start: 0.7788 (t80) cc_final: 0.7583 (t80) REVERT: B 440 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7776 (mm-40) REVERT: B 566 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.6859 (tpt) REVERT: B 839 ASP cc_start: 0.7657 (p0) cc_final: 0.7363 (p0) REVERT: B 876 TYR cc_start: 0.8472 (OUTLIER) cc_final: 0.8245 (p90) REVERT: B 988 MET cc_start: 0.8502 (mmp) cc_final: 0.8190 (tpt) REVERT: B 1174 GLN cc_start: 0.6260 (mm110) cc_final: 0.5243 (mt0) REVERT: C 174 MET cc_start: 0.6641 (OUTLIER) cc_final: 0.6017 (tpp) REVERT: C 216 MET cc_start: 0.8215 (mmm) cc_final: 0.7911 (mmm) REVERT: C 267 MET cc_start: 0.8483 (tpp) cc_final: 0.8211 (tpt) REVERT: C 351 TYR cc_start: 0.7855 (t80) cc_final: 0.7255 (t80) REVERT: C 788 ASN cc_start: 0.7681 (p0) cc_final: 0.7475 (p0) REVERT: C 845 HIS cc_start: 0.7783 (t70) cc_final: 0.7434 (t70) REVERT: C 876 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.8154 (p90) REVERT: C 927 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.7539 (mpp) REVERT: C 935 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8125 (mtpp) REVERT: C 1020 ARG cc_start: 0.8065 (mtp-110) cc_final: 0.7826 (mtp180) REVERT: C 1047 VAL cc_start: 0.8233 (OUTLIER) cc_final: 0.7940 (t) REVERT: C 1139 SER cc_start: 0.8788 (t) cc_final: 0.8584 (m) REVERT: C 1173 HIS cc_start: 0.5583 (OUTLIER) cc_final: 0.5208 (t70) REVERT: D 235 PHE cc_start: 0.8768 (t80) cc_final: 0.8487 (t80) REVERT: D 630 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6862 (tp30) outliers start: 72 outliers final: 39 residues processed: 347 average time/residue: 1.4269 time to fit residues: 580.9083 Evaluate side-chains 347 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 292 time to evaluate : 3.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 440 GLN Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 555 ARG Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 566 MET Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 927 MET Chi-restraints excluded: chain C residue 935 LYS Chi-restraints excluded: chain C residue 1010 MET Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1173 HIS Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 630 GLU Chi-restraints excluded: chain D residue 838 LEU Chi-restraints excluded: chain D residue 1010 MET Chi-restraints excluded: chain D residue 1047 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 10 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 321 optimal weight: 3.9990 chunk 355 optimal weight: 1.9990 chunk 252 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 98 optimal weight: 0.0870 chunk 51 optimal weight: 5.9990 chunk 241 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 GLN B1136 GLN B1175 ASN D1136 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.105560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.083204 restraints weight = 64802.101| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.61 r_work: 0.3121 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 29528 Z= 0.126 Angle : 0.589 12.513 40040 Z= 0.283 Chirality : 0.042 0.258 4552 Planarity : 0.004 0.137 5008 Dihedral : 6.116 127.459 3987 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.43 % Favored : 97.48 % Rotamer: Outliers : 2.03 % Allowed : 22.53 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.14), residues: 3532 helix: 1.48 (0.13), residues: 1668 sheet: -1.03 (0.25), residues: 384 loop : 0.42 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 243 HIS 0.006 0.001 HIS A 586 PHE 0.036 0.001 PHE B 275 TYR 0.020 0.001 TYR A 351 ARG 0.013 0.000 ARG C 555 Details of bonding type rmsd hydrogen bonds : bond 0.03281 ( 1362) hydrogen bonds : angle 3.95783 ( 3813) metal coordination : bond 0.00266 ( 16) metal coordination : angle 1.20084 ( 12) SS BOND : bond 0.00045 ( 4) SS BOND : angle 4.05522 ( 8) covalent geometry : bond 0.00305 (29508) covalent geometry : angle 0.58648 (40020) ********************** 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 372 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 308 time to evaluate : 2.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 VAL cc_start: 0.8736 (OUTLIER) cc_final: 0.8437 (p) REVERT: A 139 PRO cc_start: 0.8481 (Cg_endo) cc_final: 0.8070 (Cg_exo) REVERT: A 252 MET cc_start: 0.6721 (tmt) cc_final: 0.6158 (tmm) REVERT: A 289 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8389 (tp) REVERT: A 355 GLU cc_start: 0.8468 (tt0) cc_final: 0.7936 (tt0) REVERT: A 566 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.6667 (tpt) REVERT: A 876 TYR cc_start: 0.8812 (OUTLIER) cc_final: 0.8416 (p90) REVERT: A 1191 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: B 139 PRO cc_start: 0.9089 (Cg_endo) cc_final: 0.8649 (Cg_exo) REVERT: B 351 TYR cc_start: 0.7759 (t80) cc_final: 0.7532 (t80) REVERT: B 440 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7800 (mm-40) REVERT: B 555 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7568 (ttm-80) REVERT: B 566 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.6837 (tpt) REVERT: B 988 MET cc_start: 0.8549 (mmp) cc_final: 0.8284 (tpt) REVERT: C 174 MET cc_start: 0.6776 (OUTLIER) cc_final: 0.6156 (tpp) REVERT: C 216 MET cc_start: 0.8183 (mmm) cc_final: 0.7877 (mmm) REVERT: C 267 MET cc_start: 0.8485 (tpp) cc_final: 0.8204 (tpt) REVERT: C 289 ILE cc_start: 0.8830 (tp) cc_final: 0.8528 (tp) REVERT: C 351 TYR cc_start: 0.7700 (t80) cc_final: 0.7412 (t80) REVERT: C 355 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7744 (mm-30) REVERT: C 845 HIS cc_start: 0.7825 (t70) cc_final: 0.7473 (t70) REVERT: C 876 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.8180 (p90) REVERT: C 927 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.7524 (mpp) REVERT: C 935 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8113 (mtpp) REVERT: C 1047 VAL cc_start: 0.8295 (OUTLIER) cc_final: 0.8005 (t) REVERT: C 1139 SER cc_start: 0.8789 (t) cc_final: 0.8581 (p) REVERT: C 1173 HIS cc_start: 0.5442 (OUTLIER) cc_final: 0.5078 (t70) REVERT: D 235 PHE cc_start: 0.8723 (t80) cc_final: 0.8434 (t80) REVERT: D 630 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6881 (tp30) REVERT: D 908 MET cc_start: 0.7825 (mmt) cc_final: 0.7610 (mmt) outliers start: 64 outliers final: 39 residues processed: 346 average time/residue: 1.3498 time to fit residues: 550.4332 Evaluate side-chains 355 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 300 time to evaluate : 3.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 440 GLN Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 555 ARG Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 566 MET Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 927 MET Chi-restraints excluded: chain C residue 935 LYS Chi-restraints excluded: chain C residue 1010 MET Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1173 HIS Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 630 GLU Chi-restraints excluded: chain D residue 838 LEU Chi-restraints excluded: chain D residue 1010 MET Chi-restraints excluded: chain D residue 1047 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 288 optimal weight: 6.9990 chunk 355 optimal weight: 4.9990 chunk 236 optimal weight: 0.9990 chunk 342 optimal weight: 0.0570 chunk 163 optimal weight: 2.9990 chunk 222 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 287 optimal weight: 3.9990 chunk 295 optimal weight: 0.0370 chunk 103 optimal weight: 9.9990 chunk 266 optimal weight: 0.7980 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 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 GLN B1136 GLN B1159 HIS D1136 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.095915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.073490 restraints weight = 65333.518| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.70 r_work: 0.3125 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 29528 Z= 0.109 Angle : 0.582 12.416 40040 Z= 0.279 Chirality : 0.041 0.258 4552 Planarity : 0.004 0.138 5008 Dihedral : 6.012 126.312 3985 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.12 % Favored : 97.79 % Rotamer: Outliers : 2.15 % Allowed : 22.56 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.14), residues: 3532 helix: 1.54 (0.13), residues: 1668 sheet: -1.00 (0.25), residues: 384 loop : 0.45 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 243 HIS 0.005 0.001 HIS B1159 PHE 0.027 0.001 PHE A 235 TYR 0.023 0.001 TYR D 582 ARG 0.013 0.000 ARG C 555 Details of bonding type rmsd hydrogen bonds : bond 0.03128 ( 1362) hydrogen bonds : angle 3.91232 ( 3813) metal coordination : bond 0.00231 ( 16) metal coordination : angle 1.02561 ( 12) SS BOND : bond 0.00700 ( 4) SS BOND : angle 2.20535 ( 8) covalent geometry : bond 0.00259 (29508) covalent geometry : angle 0.58139 (40020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19169.65 seconds wall clock time: 332 minutes 28.18 seconds (19948.18 seconds total)