Starting phenix.real_space_refine on Tue Jul 7 01:49:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8oev_16837/07_2026/8oev_16837.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oev_16837/07_2026/8oev_16837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8oev_16837/07_2026/8oev_16837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oev_16837/07_2026/8oev_16837.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oev_16837/07_2026/8oev_16837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oev_16837/07_2026/8oev_16837.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8oev_16837/07_2026/8oev_16837.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8oev_16837/07_2026/8oev_16837.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.015 sd= 1.086 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 Zn 8 6.06 5 P 77 5.49 5 Mg 1 5.21 5 S 246 5.16 5 C 26159 2.51 5 N 7319 2.21 5 O 7971 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.07s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 41781 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 11159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1409, 11159 Classifications: {'peptide': 1409} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1340} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 9047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1131, 9047 Classifications: {'peptide': 1131} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1077} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2072 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "D" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 967 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain breaks: 1 Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 626 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "G" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1347 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 932 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 110} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 524 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 367 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 549 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain breaks: 1 Chain: "P" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 280 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 9} Chain: "T" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 769 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1074 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "O" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 792 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "Q" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 696 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 83} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 6744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 825, 6744 Classifications: {'peptide': 825} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 790} Chain breaks: 12 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 472 SG CYS A 71 67.289 100.893 93.030 1.00 55.63 S ATOM 494 SG CYS A 74 70.881 99.521 92.486 1.00 53.41 S ATOM 541 SG CYS A 81 68.946 98.502 95.647 1.00 43.12 S ATOM 776 SG CYS A 111 79.263 137.218 120.584 1.00 79.39 S ATOM 804 SG CYS A 114 81.685 138.258 118.102 1.00 78.95 S ATOM 1117 SG CYS A 154 82.361 138.846 121.780 1.00 89.81 S ATOM 1144 SG CYS A 184 79.673 141.016 119.855 1.00 87.15 S ATOM 19775 SG CYS B1196 84.004 108.949 95.651 1.00 51.07 S ATOM 19797 SG CYS B1199 81.875 109.759 98.666 1.00 50.76 S ATOM 19912 SG CYS B1214 80.349 109.441 95.208 1.00 61.29 S ATOM 19933 SG CYS B1217 82.583 112.492 96.225 1.00 68.34 S ATOM 20900 SG CYS C 88 60.026 33.137 101.346 1.00 42.39 S ATOM 20913 SG CYS C 90 57.778 36.185 100.571 1.00 53.45 S ATOM 20948 SG CYS C 94 56.571 32.678 101.425 1.00 33.19 S ATOM 20970 SG CYS C 97 58.039 34.972 104.157 1.00 29.03 S ATOM 28739 SG CYS I 86 58.646 87.211 193.176 1.00 59.16 S ATOM 28763 SG CYS I 89 55.372 85.719 194.568 1.00 61.10 S ATOM 28967 SG CYS I 114 56.116 85.554 190.838 1.00 49.30 S ATOM 29002 SG CYS I 119 55.282 88.853 192.666 1.00 53.99 S ATOM 28187 SG CYS I 17 50.487 128.400 178.807 1.00 81.19 S ATOM 28211 SG CYS I 20 49.501 128.652 175.048 1.00 82.04 S ATOM 28362 SG CYS I 39 52.981 129.471 175.989 1.00 89.78 S ATOM 28387 SG CYS I 42 50.311 131.771 177.106 1.00 94.48 S ATOM 29112 SG CYS J 7 59.650 41.746 134.541 1.00 10.76 S ATOM 29136 SG CYS J 10 61.273 38.392 133.644 1.00 14.19 S ATOM 29400 SG CYS J 44 62.188 40.377 136.938 1.00 15.14 S ATOM 29406 SG CYS J 45 59.121 38.309 136.461 1.00 16.53 S ATOM 30543 SG CYS L 19 27.199 65.380 116.912 1.00 54.09 S ATOM 30562 SG CYS L 22 24.529 62.807 116.533 1.00 61.21 S ATOM 30673 SG CYS L 36 24.456 65.638 114.231 1.00 63.51 S ATOM 30699 SG CYS L 39 23.786 66.368 117.995 1.00 64.33 S Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N GLY S1173 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY S1173 " occ=0.00 residue: pdb=" N GLY S1227 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY S1227 " occ=0.00 residue: pdb=" N GLY S1235 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY S1235 " occ=0.00 residue: pdb=" N GLY S1238 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY S1238 " occ=0.00 residue: pdb=" N GLY S1260 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY S1260 " occ=0.00 Time building chain proxies: 7.48, per 1000 atoms: 0.18 Number of scatterers: 41781 At special positions: 0 Unit cell: (154.35, 164.85, 236.25, 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 8 29.99 S 246 16.00 P 77 15.00 Mg 1 11.99 O 7971 8.00 N 7319 7.00 C 26159 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.30 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 71 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 184 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1199 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1196 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1214 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1217 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 114 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 17 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " Number of angles added : 45 9854 Ramachandran restraints generated. 4927 Oldfield, 0 Emsley, 4927 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9458 Finding SS restraints... Secondary structure from input PDB file: 197 helices and 53 sheets defined 43.4% alpha, 16.5% beta 27 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 4.42 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.639A pdb=" N LYS A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 149 removed outlier: 3.717A pdb=" N ARG A 140 " --> pdb=" O GLN A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 227 Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 274 through 296 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 434 through 438 Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 486 through 490 removed outlier: 3.582A pdb=" N THR A 490 " --> pdb=" O SER A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 539 through 549 Processing helix chain 'A' and resid 556 through 566 removed outlier: 3.852A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 596 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 684 removed outlier: 7.942A pdb=" N HIS A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 9.461A pdb=" N ASP A 663 " --> pdb=" O GLU A 659 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ILE A 664 " --> pdb=" O MET A 660 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 removed outlier: 3.500A pdb=" N ASP A 691 " --> pdb=" O GLY A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 760 removed outlier: 3.547A pdb=" N LEU A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.585A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET A 868 " --> pdb=" O LEU A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.811A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1019 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1078 Processing helix chain 'A' and resid 1086 through 1101 Proline residue: A1098 - end of helix removed outlier: 3.933A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1144 through 1149 Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.502A pdb=" N ALA A1154 " --> pdb=" O ASP A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1197 Processing helix chain 'A' and resid 1217 through 1224 removed outlier: 3.510A pdb=" N MET A1221 " --> pdb=" O ASP A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1240 removed outlier: 3.502A pdb=" N ILE A1231 " --> pdb=" O THR A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1294 Processing helix chain 'A' and resid 1314 through 1318 removed outlier: 3.910A pdb=" N LYS A1317 " --> pdb=" O THR A1314 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS A1318 " --> pdb=" O ASP A1315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1314 through 1318' Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1361 through 1370 Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 3.914A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1433 Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.668A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1469 Processing helix chain 'A' and resid 1478 through 1483 removed outlier: 3.549A pdb=" N LYS A1481 " --> pdb=" O GLU A1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 114 Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 130 through 139 Processing helix chain 'B' and resid 186 through 193 Processing helix chain 'B' and resid 244 through 251 Processing helix chain 'B' and resid 346 through 354 Processing helix chain 'B' and resid 357 through 366 Processing helix chain 'B' and resid 371 through 385 removed outlier: 3.728A pdb=" N MET B 375 " --> pdb=" O ASP B 371 " (cutoff:3.500A) Proline residue: B 380 - end of helix Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 408 through 422 Processing helix chain 'B' and resid 434 through 454 removed outlier: 3.768A pdb=" N LYS B 438 " --> pdb=" O CYS B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 472 through 502 Processing helix chain 'B' and resid 507 through 512 Processing helix chain 'B' and resid 514 through 528 Processing helix chain 'B' and resid 551 through 560 Processing helix chain 'B' and resid 579 through 583 Processing helix chain 'B' and resid 615 through 624 Processing helix chain 'B' and resid 634 through 638 Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 713 through 721 Processing helix chain 'B' and resid 722 through 727 Processing helix chain 'B' and resid 729 through 736 Processing helix chain 'B' and resid 744 through 748 Processing helix chain 'B' and resid 776 through 781 removed outlier: 3.576A pdb=" N LEU B 781 " --> pdb=" O SER B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 787 removed outlier: 3.741A pdb=" N ILE B 787 " --> pdb=" O CYS B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 794 Processing helix chain 'B' and resid 795 through 806 Processing helix chain 'B' and resid 838 through 843 Processing helix chain 'B' and resid 875 through 880 Processing helix chain 'B' and resid 1046 through 1049 Processing helix chain 'B' and resid 1054 through 1071 removed outlier: 3.804A pdb=" N LEU B1058 " --> pdb=" O THR B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1094 Processing helix chain 'B' and resid 1131 through 1135 Processing helix chain 'B' and resid 1154 through 1158 Processing helix chain 'B' and resid 1164 through 1175 Processing helix chain 'B' and resid 1176 through 1185 Processing helix chain 'B' and resid 1230 through 1242 Processing helix chain 'C' and resid 27 through 41 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 129 through 133 removed outlier: 3.698A pdb=" N ARG C 133 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 270 Processing helix chain 'D' and resid 77 through 91 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 118 through 133 removed outlier: 3.581A pdb=" N LYS D 133 " --> pdb=" O LEU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 157 Processing helix chain 'D' and resid 165 through 180 removed outlier: 4.008A pdb=" N LEU D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN D 170 " --> pdb=" O ASP D 166 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN D 171 " --> pdb=" O GLU D 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 24 Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.730A pdb=" N ASP E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 55 through 59 removed outlier: 3.515A pdb=" N THR E 59 " --> pdb=" O THR E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 97 Processing helix chain 'E' and resid 111 through 122 Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 137 through 142 removed outlier: 6.309A pdb=" N THR E 140 " --> pdb=" O ILE E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 163 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.604A pdb=" N PHE G 18 " --> pdb=" O PRO G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.686A pdb=" N GLU G 35 " --> pdb=" O PHE G 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 88 removed outlier: 3.566A pdb=" N ASP H 86 " --> pdb=" O SER H 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 68 removed outlier: 3.550A pdb=" N GLN I 67 " --> pdb=" O GLU I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.760A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 107 removed outlier: 3.928A pdb=" N GLU I 105 " --> pdb=" O ALA I 102 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP I 106 " --> pdb=" O ARG I 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.742A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.766A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 Processing helix chain 'K' and resid 82 through 115 Processing helix chain 'M' and resid 576 through 588 Processing helix chain 'M' and resid 589 through 592 Processing helix chain 'M' and resid 599 through 609 Proline residue: M 605 - end of helix Processing helix chain 'M' and resid 611 through 622 Processing helix chain 'M' and resid 625 through 641 removed outlier: 3.695A pdb=" N ASP M 630 " --> pdb=" O ILE M 626 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN M 631 " --> pdb=" O GLU M 627 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU M 632 " --> pdb=" O GLU M 628 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS M 634 " --> pdb=" O ASP M 630 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL M 635 " --> pdb=" O GLN M 631 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS M 636 " --> pdb=" O LEU M 632 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG M 639 " --> pdb=" O VAL M 635 " (cutoff:3.500A) Processing helix chain 'M' and resid 651 through 680 removed outlier: 3.565A pdb=" N PHE M 676 " --> pdb=" O LYS M 672 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N HIS M 678 " --> pdb=" O ILE M 674 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 44 Processing helix chain 'O' and resid 54 through 58 removed outlier: 3.731A pdb=" N THR O 57 " --> pdb=" O GLU O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 66 through 84 Processing helix chain 'O' and resid 98 through 110 removed outlier: 4.252A pdb=" N GLU O 102 " --> pdb=" O GLU O 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 36 removed outlier: 3.847A pdb=" N LEU Q 27 " --> pdb=" O THR Q 23 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS Q 28 " --> pdb=" O VAL Q 24 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE Q 34 " --> pdb=" O ILE Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 42 Processing helix chain 'S' and resid 285 through 292 Processing helix chain 'S' and resid 295 through 300 Processing helix chain 'S' and resid 311 through 325 Processing helix chain 'S' and resid 354 through 368 Processing helix chain 'S' and resid 372 through 379 removed outlier: 3.553A pdb=" N TYR S 379 " --> pdb=" O PHE S 375 " (cutoff:3.500A) Processing helix chain 'S' and resid 380 through 385 removed outlier: 3.880A pdb=" N VAL S 384 " --> pdb=" O ARG S 380 " (cutoff:3.500A) Processing helix chain 'S' and resid 389 through 427 Processing helix chain 'S' and resid 444 through 454 removed outlier: 3.913A pdb=" N MET S 448 " --> pdb=" O ASP S 444 " (cutoff:3.500A) Processing helix chain 'S' and resid 460 through 471 WARNING: missing atoms! Processing helix chain 'S' and resid 475 through 480 removed outlier: 3.896A pdb=" N GLN S 479 " --> pdb=" O ILE S 475 " (cutoff:3.500A) Processing helix chain 'S' and resid 523 through 530 Processing helix chain 'S' and resid 532 through 538 Processing helix chain 'S' and resid 542 through 553 Processing helix chain 'S' and resid 565 through 572 removed outlier: 3.986A pdb=" N ASP S 572 " --> pdb=" O GLU S 568 " (cutoff:3.500A) Processing helix chain 'S' and resid 580 through 598 Processing helix chain 'S' and resid 599 through 613 Processing helix chain 'S' and resid 621 through 627 Processing helix chain 'S' and resid 634 through 638 removed outlier: 3.602A pdb=" N LYS S 638 " --> pdb=" O TYR S 635 " (cutoff:3.500A) Processing helix chain 'S' and resid 646 through 648 No H-bonds generated for 'chain 'S' and resid 646 through 648' Processing helix chain 'S' and resid 651 through 663 Processing helix chain 'S' and resid 685 through 693 removed outlier: 3.589A pdb=" N ILE S 689 " --> pdb=" O TYR S 685 " (cutoff:3.500A) Processing helix chain 'S' and resid 699 through 720 Processing helix chain 'S' and resid 720 through 754 Processing helix chain 'S' and resid 825 through 843 removed outlier: 4.032A pdb=" N ALA S 830 " --> pdb=" O ARG S 826 " (cutoff:3.500A) Processing helix chain 'S' and resid 856 through 861 Processing helix chain 'S' and resid 861 through 866 removed outlier: 4.034A pdb=" N ARG S 866 " --> pdb=" O GLU S 862 " (cutoff:3.500A) Processing helix chain 'S' and resid 867 through 870 Processing helix chain 'S' and resid 887 through 896 Processing helix chain 'S' and resid 896 through 903 Processing helix chain 'S' and resid 907 through 922 Processing helix chain 'S' and resid 922 through 931 removed outlier: 3.702A pdb=" N GLU S 926 " --> pdb=" O ASP S 922 " (cutoff:3.500A) Processing helix chain 'S' and resid 933 through 939 Processing helix chain 'S' and resid 945 through 949 removed outlier: 3.775A pdb=" N VAL S 949 " --> pdb=" O GLN S 946 " (cutoff:3.500A) Processing helix chain 'S' and resid 950 through 970 Processing helix chain 'S' and resid 973 through 977 Processing helix chain 'S' and resid 979 through 989 removed outlier: 3.633A pdb=" N SER S 982 " --> pdb=" O HIS S 979 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ALA S 984 " --> pdb=" O TYR S 981 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN S 987 " --> pdb=" O ALA S 984 " (cutoff:3.500A) Processing helix chain 'S' and resid 995 through 1008 Processing helix chain 'S' and resid 1013 through 1021 Processing helix chain 'S' and resid 1024 through 1032 Processing helix chain 'S' and resid 1051 through 1056 Processing helix chain 'S' and resid 1059 through 1061 No H-bonds generated for 'chain 'S' and resid 1059 through 1061' Processing helix chain 'S' and resid 1062 through 1072 removed outlier: 3.528A pdb=" N ALA S1066 " --> pdb=" O THR S1062 " (cutoff:3.500A) Processing helix chain 'S' and resid 1086 through 1089 Processing helix chain 'S' and resid 1090 through 1095 removed outlier: 3.711A pdb=" N ASN S1095 " --> pdb=" O GLU S1091 " (cutoff:3.500A) Processing helix chain 'S' and resid 1103 through 1114 Processing helix chain 'S' and resid 1119 through 1132 Processing helix chain 'S' and resid 1145 through 1155 Processing helix chain 'S' and resid 1241 through 1245 Processing helix chain 'S' and resid 1282 through 1287 removed outlier: 3.793A pdb=" N MET S1287 " --> pdb=" O THR S1283 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 removed outlier: 4.496A pdb=" N ARG B1227 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 95 removed outlier: 6.469A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 10.387A pdb=" N LYS A 92 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 10.356A pdb=" N ILE A 249 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 194 removed outlier: 4.301A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.653A pdb=" N LEU B1161 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1137 through 1139 removed outlier: 7.798A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 393 removed outlier: 6.572A pdb=" N LYS A 445 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE A 419 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLU A 447 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA9, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.125A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.473A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB3, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AB4, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB5, first strand: chain 'A' and resid 1307 through 1310 removed outlier: 4.225A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 6.723A pdb=" N THR A1164 " --> pdb=" O LEU A1298 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1244 through 1248 removed outlier: 4.207A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AB9, first strand: chain 'A' and resid 1408 through 1409 removed outlier: 7.317A pdb=" N ARG E 172 " --> pdb=" O GLY A1409 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1471 through 1475 Processing sheet with id=AC2, first strand: chain 'B' and resid 142 through 145 removed outlier: 5.431A pdb=" N TYR B 161 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE B 210 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU B 163 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR B 208 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N PHE B 165 " --> pdb=" O THR B 206 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR B 206 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN B 167 " --> pdb=" O ASP B 204 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ALA B 199 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS B 228 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU B 201 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE B 205 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLN B 222 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LYS B 207 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N GLN B 220 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL B 209 " --> pdb=" O GLN B 218 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLN B 218 " --> pdb=" O VAL B 209 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 142 through 145 removed outlier: 4.009A pdb=" N LYS M 688 " --> pdb=" O ILE B 168 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 174 through 176 Processing sheet with id=AC5, first strand: chain 'B' and resid 262 through 264 Processing sheet with id=AC6, first strand: chain 'B' and resid 468 through 471 Processing sheet with id=AC7, first strand: chain 'B' and resid 283 through 285 removed outlier: 3.771A pdb=" N TYR B 294 " --> pdb=" O MET B 316 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 608 through 609 Processing sheet with id=AC9, first strand: chain 'B' and resid 608 through 609 Processing sheet with id=AD1, first strand: chain 'B' and resid 628 through 629 removed outlier: 5.513A pdb=" N TRP B 650 " --> pdb=" O VAL B 646 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL B 646 " --> pdb=" O TRP B 650 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY B 652 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LYS B 643 " --> pdb=" O ILE B 689 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ILE B 691 " --> pdb=" O LYS B 643 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHE B 645 " --> pdb=" O ILE B 691 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 824 through 828 removed outlier: 6.629A pdb=" N PHE B 995 " --> pdb=" O VAL B 986 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL B 986 " --> pdb=" O PHE B 995 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LYS B 997 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL B 984 " --> pdb=" O LYS B 997 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG B 999 " --> pdb=" O ASP B 982 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 824 through 828 removed outlier: 6.629A pdb=" N PHE B 995 " --> pdb=" O VAL B 986 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL B 986 " --> pdb=" O PHE B 995 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LYS B 997 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL B 984 " --> pdb=" O LYS B 997 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG B 999 " --> pdb=" O ASP B 982 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N VAL B 984 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 836 through 837 Processing sheet with id=AD5, first strand: chain 'B' and resid 1102 through 1103 removed outlier: 7.323A pdb=" N VAL B 871 " --> pdb=" O GLY B1023 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLN B1025 " --> pdb=" O VAL B 871 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N MET B 873 " --> pdb=" O GLN B1025 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE B1119 " --> pdb=" O ILE B 859 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 904 through 906 removed outlier: 6.851A pdb=" N GLN B 915 " --> pdb=" O ASP B 968 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 942 through 944 Processing sheet with id=AD8, first strand: chain 'B' and resid 1204 through 1206 Processing sheet with id=AD9, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.292A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ARG C 228 " --> pdb=" O TYR C 186 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TYR C 186 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.411A pdb=" N GLU C 158 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA C 54 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ARG C 160 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ILE C 52 " --> pdb=" O ARG C 160 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG C 162 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL C 50 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TYR C 164 " --> pdb=" O ASP C 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AE3, first strand: chain 'D' and resid 72 through 73 removed outlier: 3.607A pdb=" N GLU D 72 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE G 5 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA G 74 " --> pdb=" O ILE G 5 " (cutoff:3.500A) removed outlier: 11.171A pdb=" N LEU G 67 " --> pdb=" O ILE G 54 " (cutoff:3.500A) removed outlier: 10.344A pdb=" N ILE G 54 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ASP G 52 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LYS G 71 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR G 50 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LYS G 73 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL G 48 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 72 through 73 removed outlier: 3.607A pdb=" N GLU D 72 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE G 5 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA G 74 " --> pdb=" O ILE G 5 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 26 through 27 removed outlier: 4.536A pdb=" N ALA E 63 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 83 through 86 removed outlier: 6.702A pdb=" N ILE G 160 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N THR G 150 " --> pdb=" O PHE G 158 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N PHE G 158 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 117 through 120 removed outlier: 3.620A pdb=" N CYS G 127 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR G 128 " --> pdb=" O ILE G 137 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 25 through 29 Processing sheet with id=AE9, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF1, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.444A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 60 through 61 removed outlier: 3.780A pdb=" N THR Q 13 " --> pdb=" O GLU O 28 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ALA Q 73 " --> pdb=" O MET Q 6 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ARG Q 8 " --> pdb=" O ALA Q 73 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N VAL Q 75 " --> pdb=" O ARG Q 8 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA Q 78 " --> pdb=" O ARG Q 43 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'S' and resid 640 through 644 removed outlier: 5.394A pdb=" N LYS S 641 " --> pdb=" O ILE S 618 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE S 618 " --> pdb=" O LYS S 641 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 807 through 810 removed outlier: 4.159A pdb=" N ASP S 807 " --> pdb=" O LEU S 798 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE S 795 " --> pdb=" O ALA S 785 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA S 785 " --> pdb=" O PHE S 795 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY S 852 " --> pdb=" O VAL S 885 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'S' and resid 971 through 972 removed outlier: 5.772A pdb=" N VAL S 971 " --> pdb=" O LYS S1036 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'S' and resid 1166 through 1167 Processing sheet with id=AF7, first strand: chain 'S' and resid 1170 through 1171 Processing sheet with id=AF8, first strand: chain 'S' and resid 1269 through 1270 removed outlier: 3.750A pdb=" N LYS S1269 " --> pdb=" O ASP S1278 " (cutoff:3.500A) 1824 hydrogen bonds defined for protein. 5043 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 10.32 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8772 1.33 - 1.45: 9559 1.45 - 1.57: 23855 1.57 - 1.69: 150 1.69 - 1.82: 388 Bond restraints: 42724 Sorted by residual: bond pdb=" C1' DC T 5 " pdb=" N1 DC T 5 " ideal model delta sigma weight residual 1.468 1.523 -0.055 1.40e-02 5.10e+03 1.53e+01 bond pdb=" C ILE B1049 " pdb=" N PRO B1050 " ideal model delta sigma weight residual 1.335 1.384 -0.049 1.30e-02 5.92e+03 1.41e+01 bond pdb=" C3' DC T 33 " pdb=" O3' DC T 33 " ideal model delta sigma weight residual 1.435 1.483 -0.048 1.30e-02 5.92e+03 1.35e+01 bond pdb=" C3' DG N 29 " pdb=" C2' DG N 29 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.25e+01 bond pdb=" N ILE D 157 " pdb=" CA ILE D 157 " ideal model delta sigma weight residual 1.461 1.504 -0.043 1.23e-02 6.61e+03 1.24e+01 ... (remaining 42719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 56876 2.46 - 4.91: 978 4.91 - 7.37: 123 7.37 - 9.83: 29 9.83 - 12.29: 5 Bond angle restraints: 58011 Sorted by residual: angle pdb=" C VAL A 538 " pdb=" N GLN A 539 " pdb=" CA GLN A 539 " ideal model delta sigma weight residual 121.54 133.83 -12.29 1.91e+00 2.74e-01 4.14e+01 angle pdb=" C HIS Q 10 " pdb=" N LYS Q 11 " pdb=" CA LYS Q 11 " ideal model delta sigma weight residual 126.32 136.66 -10.34 1.74e+00 3.30e-01 3.53e+01 angle pdb=" N PRO D 147 " pdb=" CA PRO D 147 " pdb=" C PRO D 147 " ideal model delta sigma weight residual 111.34 102.25 9.09 1.55e+00 4.16e-01 3.44e+01 angle pdb=" N THR S 414 " pdb=" CA THR S 414 " pdb=" C THR S 414 " ideal model delta sigma weight residual 111.28 104.93 6.35 1.09e+00 8.42e-01 3.39e+01 angle pdb=" C PHE O 52 " pdb=" N ALA O 53 " pdb=" CA ALA O 53 " ideal model delta sigma weight residual 121.54 131.53 -9.99 1.91e+00 2.74e-01 2.74e+01 ... (remaining 58006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.11: 25282 35.11 - 70.22: 634 70.22 - 105.33: 39 105.33 - 140.44: 0 140.44 - 175.55: 1 Dihedral angle restraints: 25956 sinusoidal: 11361 harmonic: 14595 Sorted by residual: dihedral pdb=" CA ASN G 124 " pdb=" C ASN G 124 " pdb=" N PRO G 125 " pdb=" CA PRO G 125 " ideal model delta harmonic sigma weight residual 180.00 146.86 33.14 0 5.00e+00 4.00e-02 4.39e+01 dihedral pdb=" CA ILE O 90 " pdb=" C ILE O 90 " pdb=" N PRO O 91 " pdb=" CA PRO O 91 " ideal model delta harmonic sigma weight residual 180.00 -151.00 -29.00 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA MET O 45 " pdb=" C MET O 45 " pdb=" N LEU O 46 " pdb=" CA LEU O 46 " ideal model delta harmonic sigma weight residual 180.00 152.57 27.43 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 25953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 6080 0.102 - 0.205: 361 0.205 - 0.307: 19 0.307 - 0.409: 4 0.409 - 0.512: 1 Chirality restraints: 6465 Sorted by residual: chirality pdb=" CB ILE A 621 " pdb=" CA ILE A 621 " pdb=" CG1 ILE A 621 " pdb=" CG2 ILE A 621 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.51 2.00e-01 2.50e+01 6.55e+00 chirality pdb=" CG LEU A 831 " pdb=" CB LEU A 831 " pdb=" CD1 LEU A 831 " pdb=" CD2 LEU A 831 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" CG LEU L 52 " pdb=" CB LEU L 52 " pdb=" CD1 LEU L 52 " pdb=" CD2 LEU L 52 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.31e+00 ... (remaining 6462 not shown) Planarity restraints: 7244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 157 " 0.029 2.00e-02 2.50e+03 5.52e-02 3.05e+01 pdb=" C ILE D 157 " -0.096 2.00e-02 2.50e+03 pdb=" O ILE D 157 " 0.033 2.00e-02 2.50e+03 pdb=" N PRO D 158 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 539 " 0.028 2.00e-02 2.50e+03 5.46e-02 2.98e+01 pdb=" C GLN A 539 " -0.095 2.00e-02 2.50e+03 pdb=" O GLN A 539 " 0.034 2.00e-02 2.50e+03 pdb=" N ASP A 540 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG S 415 " 0.333 9.50e-02 1.11e+02 1.49e-01 1.37e+01 pdb=" NE ARG S 415 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG S 415 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG S 415 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG S 415 " 0.011 2.00e-02 2.50e+03 ... (remaining 7241 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 380 2.58 - 3.16: 33167 3.16 - 3.74: 68988 3.74 - 4.32: 98235 4.32 - 4.90: 156409 Nonbonded interactions: 357179 Sorted by model distance: nonbonded pdb=" O THR S 815 " pdb=" CD LYS S 829 " model vdw 2.005 3.440 nonbonded pdb=" CG2 VAL G 171 " pdb=" CB ALA S 518 " model vdw 2.068 3.880 nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG A2001 " model vdw 2.086 2.170 nonbonded pdb=" O3' U P 46 " pdb="MG MG A2001 " model vdw 2.127 2.170 nonbonded pdb=" OD1 ASP A 499 " pdb="MG MG A2001 " model vdw 2.135 2.170 ... (remaining 357174 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=0.99 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: 5.420 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: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 42.700 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 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 : 0.005 0.070 42756 Z= 0.257 Angle : 0.813 12.287 58056 Z= 0.478 Chirality : 0.053 0.512 6465 Planarity : 0.006 0.149 7244 Dihedral : 15.384 175.550 16498 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.11), residues: 4927 helix: -0.42 (0.11), residues: 1906 sheet: -0.39 (0.19), residues: 663 loop : -0.77 (0.12), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG A1153 TYR 0.059 0.002 TYR B 829 PHE 0.046 0.002 PHE A 431 TRP 0.028 0.002 TRP A 479 HIS 0.011 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.26 (42724) covalent geometry : angle 0.80481 / 0.48 (58011) hydrogen bonds : bond 0.15390 / 10.10 ( 1860) hydrogen bonds : angle 6.90836 / 4.90 ( 5179) metal coordination : bond 0.00625 / 0.43 ( 32) metal coordination : angle 4.23455 / 2.74 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9854 Ramachandran restraints generated. 4927 Oldfield, 0 Emsley, 4927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9854 Ramachandran restraints generated. 4927 Oldfield, 0 Emsley, 4927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 4439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 683 time to evaluate : 1.299 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: symmetry clash REVERT: A 266 MET cc_start: 0.4024 (mtp) cc_final: 0.3631 (mtp) REVERT: A 959 MET cc_start: 0.8503 (mtt) cc_final: 0.8220 (mtp) REVERT: B 339 TYR cc_start: 0.7428 (m-80) cc_final: 0.7115 (m-80) REVERT: B 967 ARG cc_start: 0.7030 (ptm-80) cc_final: 0.6534 (ttt180) REVERT: B 1158 ASP cc_start: 0.7257 (t0) cc_final: 0.7024 (t0) REVERT: B 1249 MET cc_start: 0.8474 (mmt) cc_final: 0.8072 (mmt) REVERT: I 14 ILE cc_start: 0.8051 (mm) cc_final: 0.7683 (tp) REVERT: I 56 ASN cc_start: 0.7205 (m-40) cc_final: 0.6777 (m110) REVERT: I 109 ARG cc_start: 0.8065 (ttm-80) cc_final: 0.7807 (ttm-80) REVERT: J 19 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7628 (mp0) outliers start: 0 outliers final: 2 residues processed: 683 average time/residue: 0.8291 time to fit residues: 672.2000 Evaluate side-chains 420 residues out of total 4439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 418 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain M residue 621 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 0.9990 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 494 optimal weight: 0.2980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 HIS A1093 GLN A1146 GLN A1384 HIS B 175 HIS B 188 ASN B 396 ASN B 533 GLN B1084 ASN C 217 GLN E 98 ASN I 50 ASN K 89 ASN K 113 GLN M 580 GLN ** M 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 675 GLN S 465 ASN S 517 GLN S 608 GLN S 701 GLN ** S 813 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.141040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.101858 restraints weight = 100358.382| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.25 r_work: 0.3058 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 42756 Z= 0.169 Angle : 0.656 11.620 58056 Z= 0.346 Chirality : 0.045 0.277 6465 Planarity : 0.005 0.124 7244 Dihedral : 11.357 175.416 6293 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.81 % Allowed : 9.94 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.12), residues: 4927 helix: 0.31 (0.12), residues: 1935 sheet: -0.31 (0.20), residues: 634 loop : -0.62 (0.13), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 110 TYR 0.028 0.001 TYR G 128 PHE 0.023 0.002 PHE A 112 TRP 0.016 0.002 TRP B 104 HIS 0.009 0.001 HIS A1310 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (42724) covalent geometry : angle 0.64813 / 0.35 (58011) hydrogen bonds : bond 0.05057 / 3.31 ( 1860) hydrogen bonds : angle 5.57499 / 3.95 ( 5179) metal coordination : bond 0.00641 / 0.45 ( 32) metal coordination : angle 3.70418 / 2.52 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9854 Ramachandran restraints generated. 4927 Oldfield, 0 Emsley, 4927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9854 Ramachandran restraints generated. 4927 Oldfield, 0 Emsley, 4927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 4439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 440 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 MET cc_start: 0.8823 (mtm) cc_final: 0.8601 (mtm) REVERT: A 441 GLN cc_start: 0.8314 (mt0) cc_final: 0.7814 (mt0) REVERT: A 1248 ASN cc_start: 0.7197 (t0) cc_final: 0.6351 (m-40) REVERT: A 1293 LEU cc_start: 0.8897 (mm) cc_final: 0.8614 (mt) REVERT: B 166 GLU cc_start: 0.7548 (tp30) cc_final: 0.7290 (tp30) REVERT: B 339 TYR cc_start: 0.7718 (m-10) cc_final: 0.7385 (m-80) REVERT: B 990 GLN cc_start: 0.8389 (mm-40) cc_final: 0.7975 (tp40) REVERT: B 1158 ASP cc_start: 0.8270 (t0) cc_final: 0.7836 (t0) REVERT: B 1165 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7786 (mt-10) REVERT: B 1249 MET cc_start: 0.8772 (mmt) cc_final: 0.8378 (mmt) REVERT: C 78 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8768 (tp) REVERT: C 265 HIS cc_start: 0.7873 (t70) cc_final: 0.7596 (m170) REVERT: D 76 ASN cc_start: 0.8764 (m110) cc_final: 0.8125 (t0) REVERT: F 80 MET cc_start: 0.8838 (mmm) cc_final: 0.8548 (mmm) REVERT: F 82 GLU cc_start: 0.7567 (pp20) cc_final: 0.6945 (pp20) REVERT: G 41 LYS cc_start: 0.8976 (tppt) cc_final: 0.8585 (tppt) REVERT: G 146 LYS cc_start: 0.9216 (tppp) cc_final: 0.8960 (tppp) REVERT: G 151 ARG cc_start: 0.7716 (tmm160) cc_final: 0.7436 (tmm160) REVERT: I 15 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7474 (mtt180) REVERT: I 56 ASN cc_start: 0.7471 (m-40) cc_final: 0.7258 (m110) REVERT: J 36 ASP cc_start: 0.8773 (m-30) cc_final: 0.8467 (m-30) REVERT: J 58 LYS cc_start: 0.8916 (tptt) cc_final: 0.8582 (tppt) REVERT: K 48 SER cc_start: 0.9323 (p) cc_final: 0.9117 (m) REVERT: L 25 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: L 28 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8710 (mm) REVERT: M 574 MET cc_start: 0.3956 (OUTLIER) cc_final: 0.2855 (mmm) REVERT: M 575 MET cc_start: 0.4518 (mpp) cc_final: 0.4282 (ptp) REVERT: M 580 GLN cc_start: 0.6371 (mt0) cc_final: 0.6165 (mt0) REVERT: M 614 GLN cc_start: 0.8835 (mt0) cc_final: 0.8607 (pt0) REVERT: M 640 ASP cc_start: 0.7564 (m-30) cc_final: 0.7320 (m-30) REVERT: M 652 TRP cc_start: 0.7905 (m-90) cc_final: 0.7698 (m-10) REVERT: M 672 LYS cc_start: 0.9000 (mtmt) cc_final: 0.8650 (mtmt) REVERT: O 45 MET cc_start: 0.1515 (ppp) cc_final: 0.0621 (ptp) REVERT: S 366 MET cc_start: 0.8932 (mpp) cc_final: 0.8505 (mpp) REVERT: S 420 MET cc_start: 0.8413 (tpp) cc_final: 0.8152 (tpt) outliers start: 80 outliers final: 22 residues processed: 482 average time/residue: 0.7501 time to fit residues: 436.0379 Evaluate side-chains 419 residues out of total 4439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 392 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 726 ASN Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 1220 LYS Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 46 GLN Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 25 GLU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain M residue 574 MET Chi-restraints excluded: chain M residue 621 TYR Chi-restraints excluded: chain M residue 629 THR Chi-restraints excluded: chain S residue 592 VAL Chi-restraints excluded: chain S residue 723 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 425 optimal weight: 0.6980 chunk 219 optimal weight: 9.9990 chunk 392 optimal weight: 9.9990 chunk 457 optimal weight: 9.9990 chunk 398 optimal weight: 2.9990 chunk 356 optimal weight: 20.0000 chunk 271 optimal weight: 1.9990 chunk 297 optimal weight: 7.9990 chunk 379 optimal weight: 50.0000 chunk 315 optimal weight: 2.9990 chunk 415 optimal weight: 8.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 HIS A 671 ASN A 723 ASN A1310 HIS B 826 HIS B1045 ASN B1084 ASN C 6 GLN C 111 GLN C 260 GLN D 80 HIS D 135 HIS I 45 GLN M 675 GLN ** S 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 701 GLN ** S 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 983 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.137759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.098071 restraints weight = 100281.554| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.24 r_work: 0.2980 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.113 42756 Z= 0.297 Angle : 0.691 13.488 58056 Z= 0.360 Chirality : 0.048 0.292 6465 Planarity : 0.005 0.080 7244 Dihedral : 11.393 172.973 6291 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.26 % Allowed : 11.66 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.12), residues: 4927 helix: 0.44 (0.12), residues: 1960 sheet: -0.46 (0.19), residues: 644 loop : -0.53 (0.13), residues: 2323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 81 TYR 0.024 0.002 TYR M 600 PHE 0.029 0.002 PHE C 63 TRP 0.023 0.002 TRP B 104 HIS 0.012 0.001 HIS A1310 Details of bonding type rmsd/Z covalent geometry : bond 0.00684 / 0.30 (42724) covalent geometry : angle 0.68129 / 0.36 (58011) hydrogen bonds : bond 0.04882 / 3.19 ( 1860) hydrogen bonds : angle 5.30741 / 3.76 ( 5179) metal coordination : bond 0.01180 / 0.79 ( 32) metal coordination : angle 4.27655 / 2.92 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9854 Ramachandran restraints generated. 4927 Oldfield, 0 Emsley, 4927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9854 Ramachandran restraints generated. 4927 Oldfield, 0 Emsley, 4927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 4439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 422 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.8334 (pm20) cc_final: 0.8087 (pm20) REVERT: A 199 TYR cc_start: 0.8286 (m-80) cc_final: 0.7744 (m-80) REVERT: A 248 MET cc_start: 0.9006 (mtm) cc_final: 0.8683 (mtm) REVERT: A 441 GLN cc_start: 0.8246 (mt0) cc_final: 0.7744 (mt0) REVERT: A 940 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8313 (mtmt) REVERT: A 1196 TYR cc_start: 0.7104 (m-80) cc_final: 0.6883 (m-80) REVERT: A 1248 ASN cc_start: 0.7277 (t0) cc_final: 0.6383 (m-40) REVERT: A 1279 MET cc_start: 0.5452 (tpp) cc_final: 0.4819 (ppp) REVERT: A 1293 LEU cc_start: 0.9034 (mm) cc_final: 0.8802 (mt) REVERT: A 1334 TRP cc_start: 0.8808 (m100) cc_final: 0.8586 (m100) REVERT: B 166 GLU cc_start: 0.7563 (tp30) cc_final: 0.7314 (tp30) REVERT: B 222 GLN cc_start: 0.8397 (mm-40) cc_final: 0.8167 (pt0) REVERT: B 339 TYR cc_start: 0.7802 (m-10) cc_final: 0.7518 (m-80) REVERT: B 493 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7840 (ptm-80) REVERT: B 1158 ASP cc_start: 0.8448 (t0) cc_final: 0.8005 (t0) REVERT: B 1249 MET cc_start: 0.8858 (mmt) cc_final: 0.8426 (mmt) REVERT: C 78 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8879 (tp) REVERT: F 82 GLU cc_start: 0.7811 (pp20) cc_final: 0.7330 (pp20) REVERT: F 96 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8687 (mt-10) REVERT: G 41 LYS cc_start: 0.9121 (tppt) cc_final: 0.8822 (tttt) REVERT: G 146 LYS cc_start: 0.9268 (tppp) cc_final: 0.8956 (tppp) REVERT: G 151 ARG cc_start: 0.7763 (tmm160) cc_final: 0.7420 (OUTLIER) REVERT: I 15 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7492 (mtt180) REVERT: I 56 ASN cc_start: 0.7868 (m-40) cc_final: 0.7257 (m-40) REVERT: I 64 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6823 (mm-30) REVERT: I 93 GLU cc_start: 0.8390 (tt0) cc_final: 0.8133 (tt0) REVERT: J 36 ASP cc_start: 0.8881 (m-30) cc_final: 0.8543 (m-30) REVERT: J 58 LYS cc_start: 0.8930 (tptt) cc_final: 0.8584 (tppt) REVERT: K 48 SER cc_start: 0.9365 (p) cc_final: 0.9125 (m) REVERT: L 25 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7937 (mp0) REVERT: L 28 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8837 (mm) REVERT: L 29 LYS cc_start: 0.7924 (pttt) cc_final: 0.7701 (mptt) REVERT: M 574 MET cc_start: 0.4776 (OUTLIER) cc_final: 0.4073 (mmm) REVERT: M 614 GLN cc_start: 0.8779 (mt0) cc_final: 0.8568 (pt0) REVERT: M 652 TRP cc_start: 0.7931 (m-90) cc_final: 0.7635 (m100) REVERT: M 660 GLN cc_start: 0.8598 (tp40) cc_final: 0.8390 (tp40) REVERT: O 45 MET cc_start: 0.1513 (OUTLIER) cc_final: 0.0629 (ptt) REVERT: S 366 MET cc_start: 0.8792 (mpp) cc_final: 0.8352 (mpp) REVERT: S 420 MET cc_start: 0.8490 (tpp) cc_final: 0.8235 (tpt) outliers start: 100 outliers final: 35 residues processed: 484 average time/residue: 0.7507 time to fit residues: 437.9687 Evaluate side-chains 436 residues out of total 4439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 394 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 940 LYS Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 515 ARG Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 1186 GLU Chi-restraints excluded: chain B residue 1220 LYS Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain H residue 74 GLU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 46 GLN Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 25 GLU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain M residue 574 MET Chi-restraints excluded: chain M residue 621 TYR Chi-restraints excluded: chain O residue 45 MET Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain S residue 584 VAL Chi-restraints excluded: chain S residue 592 VAL Chi-restraints excluded: chain S residue 1017 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 3 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 318 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 234 optimal weight: 0.7980 chunk 403 optimal weight: 40.0000 chunk 71 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 375 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 434 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1171 GLN C 51 GLN C 111 GLN E 133 GLN E 169 GLN ** G 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 GLN ** M 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 675 GLN ** S 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.140230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.101125 restraints weight = 99922.198| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.22 r_work: 0.3038 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 42756 Z= 0.135 Angle : 0.592 9.832 58056 Z= 0.309 Chirality : 0.043 0.269 6465 Planarity : 0.004 0.054 7244 Dihedral : 11.331 174.933 6291 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.92 % Allowed : 13.29 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.12), residues: 4927 helix: 0.79 (0.12), residues: 1926 sheet: -0.37 (0.20), residues: 645 loop : -0.41 (0.13), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 583 TYR 0.020 0.001 TYR M 600 PHE 0.023 0.001 PHE A 112 TRP 0.017 0.001 TRP A1192 HIS 0.010 0.001 HIS A1310 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (42724) covalent geometry : angle 0.58486 / 0.31 (58011) hydrogen bonds : bond 0.03984 / 2.60 ( 1860) hydrogen bonds : angle 5.04789 / 3.57 ( 5179) metal coordination : bond 0.00535 / 0.38 ( 32) metal coordination : angle 3.45224 / 2.34 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9854 Ramachandran restraints generated. 4927 Oldfield, 0 Emsley, 4927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9854 Ramachandran restraints generated. 4927 Oldfield, 0 Emsley, 4927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 4439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 421 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8059 (mtm-85) cc_final: 0.7844 (mtt-85) REVERT: A 248 MET cc_start: 0.9015 (mtm) cc_final: 0.8744 (mtm) REVERT: A 441 GLN cc_start: 0.8174 (mt0) cc_final: 0.7744 (mt0) REVERT: A 1248 ASN cc_start: 0.7126 (t0) cc_final: 0.6372 (m-40) REVERT: A 1279 MET cc_start: 0.5478 (tpp) cc_final: 0.5050 (ppp) REVERT: A 1293 LEU cc_start: 0.8901 (mm) cc_final: 0.8651 (mt) REVERT: B 166 GLU cc_start: 0.7392 (tp30) cc_final: 0.7101 (tp30) REVERT: B 222 GLN cc_start: 0.8385 (mm-40) cc_final: 0.8138 (pt0) REVERT: B 339 TYR cc_start: 0.7919 (m-10) cc_final: 0.7611 (m-80) REVERT: B 386 PHE cc_start: 0.8365 (p90) cc_final: 0.8015 (t80) REVERT: B 726 ASN cc_start: 0.8285 (m110) cc_final: 0.7816 (p0) REVERT: B 990 GLN cc_start: 0.8335 (mm-40) cc_final: 0.8073 (tp40) REVERT: B 1158 ASP cc_start: 0.8438 (t0) cc_final: 0.7970 (t0) REVERT: C 78 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8839 (tp) REVERT: C 265 HIS cc_start: 0.7981 (t70) cc_final: 0.7706 (m170) REVERT: D 119 ARG cc_start: 0.9116 (ptm-80) cc_final: 0.8718 (ttp80) REVERT: F 82 GLU cc_start: 0.7755 (pp20) cc_final: 0.7490 (pp20) REVERT: F 86 GLU cc_start: 0.7890 (pm20) cc_final: 0.7686 (pm20) REVERT: G 41 LYS cc_start: 0.8899 (tppt) cc_final: 0.8436 (tppt) REVERT: G 111 HIS cc_start: 0.8537 (OUTLIER) cc_final: 0.8330 (p-80) REVERT: G 146 LYS cc_start: 0.9255 (tppp) cc_final: 0.8931 (tppp) REVERT: G 164 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8472 (mpm) REVERT: I 56 ASN cc_start: 0.8354 (m-40) cc_final: 0.7673 (m-40) REVERT: J 36 ASP cc_start: 0.8906 (m-30) cc_final: 0.8556 (m-30) REVERT: K 48 SER cc_start: 0.9374 (p) cc_final: 0.9166 (m) REVERT: L 21 GLU cc_start: 0.8142 (tt0) cc_final: 0.7928 (pt0) REVERT: L 25 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: L 27 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7470 (tt0) REVERT: L 28 ILE cc_start: 0.9110 (mm) cc_final: 0.8837 (mm) REVERT: L 29 LYS cc_start: 0.7986 (pttt) cc_final: 0.7783 (pptt) REVERT: M 614 GLN cc_start: 0.8836 (mt0) cc_final: 0.8519 (pt0) REVERT: M 652 TRP cc_start: 0.7917 (m-90) cc_final: 0.7652 (m100) REVERT: M 660 GLN cc_start: 0.8581 (tp40) cc_final: 0.8230 (tp40) REVERT: O 45 MET cc_start: 0.1681 (OUTLIER) cc_final: 0.0744 (ptt) REVERT: Q 74 THR cc_start: 0.3603 (OUTLIER) cc_final: 0.3246 (p) outliers start: 85 outliers final: 30 residues processed: 470 average time/residue: 0.7364 time to fit residues: 419.5964 Evaluate side-chains 435 residues out of total 4439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 398 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 1186 GLU Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 46 GLN Chi-restraints excluded: chain I residue 52 CYS Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 25 GLU Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain M residue 621 TYR Chi-restraints excluded: chain M residue 665 GLN Chi-restraints excluded: chain O residue 45 MET Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain S residue 584 VAL Chi-restraints excluded: chain S residue 1017 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 221 optimal weight: 7.9990 chunk 308 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 327 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 59 optimal weight: 0.0060 chunk 332 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 302 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 531 ASN ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1310 HIS B 659 GLN C 111 GLN E 169 GLN G 93 ASN I 45 GLN M 580 GLN M 588 ASN M 675 GLN ** S 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 701 GLN ** S 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.139599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.100406 restraints weight = 99531.832| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.21 r_work: 0.3026 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 42756 Z= 0.161 Angle : 0.595 10.493 58056 Z= 0.308 Chirality : 0.044 0.367 6465 Planarity : 0.004 0.054 7244 Dihedral : 11.305 172.797 6291 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.10 % Allowed : 13.87 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.12), residues: 4927 helix: 0.88 (0.12), residues: 1934 sheet: -0.29 (0.20), residues: 640 loop : -0.37 (0.13), residues: 2353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 556 TYR 0.017 0.001 TYR B 237 PHE 0.020 0.001 PHE A 234 TRP 0.015 0.001 TRP B 104 HIS 0.009 0.001 HIS A1310 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (42724) covalent geometry : angle 0.58747 / 0.31 (58011) hydrogen bonds : bond 0.03961 / 2.59 ( 1860) hydrogen bonds : angle 4.97759 / 3.52 ( 5179) metal coordination : bond 0.00646 / 0.45 ( 32) metal coordination : angle 3.53547 / 2.43 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9854 Ramachandran restraints generated. 4927 Oldfield, 0 Emsley, 4927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9854 Ramachandran restraints generated. 4927 Oldfield, 0 Emsley, 4927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 4439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 416 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR S 471 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 199 TYR cc_start: 0.8244 (m-80) cc_final: 0.7685 (m-10) REVERT: A 248 MET cc_start: 0.8994 (mtm) cc_final: 0.8775 (mtm) REVERT: A 441 GLN cc_start: 0.8186 (mt0) cc_final: 0.7746 (mt0) REVERT: A 1248 ASN cc_start: 0.7012 (t0) cc_final: 0.6243 (m-40) REVERT: A 1279 MET cc_start: 0.5543 (tpp) cc_final: 0.5136 (ppp) REVERT: A 1293 LEU cc_start: 0.8918 (mm) cc_final: 0.8698 (mt) REVERT: B 166 GLU cc_start: 0.7424 (tp30) cc_final: 0.7140 (tp30) REVERT: B 246 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.7080 (mmt-90) REVERT: B 339 TYR cc_start: 0.7967 (m-10) cc_final: 0.7622 (m-80) REVERT: B 386 PHE cc_start: 0.8382 (p90) cc_final: 0.7980 (t80) REVERT: B 726 ASN cc_start: 0.8295 (m110) cc_final: 0.7977 (p0) REVERT: B 1158 ASP cc_start: 0.8459 (t0) cc_final: 0.7994 (t0) REVERT: C 78 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8862 (tp) REVERT: C 265 HIS cc_start: 0.8005 (t70) cc_final: 0.7746 (m170) REVERT: D 126 ARG cc_start: 0.8640 (ttm-80) cc_final: 0.8302 (ttt180) REVERT: F 82 GLU cc_start: 0.7905 (pp20) cc_final: 0.7483 (pp20) REVERT: F 84 GLU cc_start: 0.7856 (mp0) cc_final: 0.7545 (mp0) REVERT: G 35 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7690 (mt-10) REVERT: G 41 LYS cc_start: 0.9033 (tppt) cc_final: 0.8473 (tppt) REVERT: G 101 ILE cc_start: 0.9344 (OUTLIER) cc_final: 0.8819 (pp) REVERT: G 111 HIS cc_start: 0.8627 (p-80) cc_final: 0.8384 (p-80) REVERT: G 146 LYS cc_start: 0.9250 (tppp) cc_final: 0.8906 (tppp) REVERT: I 23 MET cc_start: 0.8411 (ttt) cc_final: 0.7967 (ttp) REVERT: I 56 ASN cc_start: 0.8462 (m-40) cc_final: 0.7846 (m-40) REVERT: I 57 LYS cc_start: 0.7967 (mmtt) cc_final: 0.7588 (mmmt) REVERT: I 93 GLU cc_start: 0.8382 (tt0) cc_final: 0.8150 (tt0) REVERT: J 36 ASP cc_start: 0.8928 (m-30) cc_final: 0.8686 (m-30) REVERT: L 27 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: L 28 ILE cc_start: 0.9099 (mm) cc_final: 0.8862 (mm) REVERT: L 29 LYS cc_start: 0.8013 (pttt) cc_final: 0.7750 (mptt) REVERT: M 614 GLN cc_start: 0.8844 (mt0) cc_final: 0.8500 (pt0) REVERT: M 652 TRP cc_start: 0.7946 (m-90) cc_final: 0.7657 (m100) REVERT: M 660 GLN cc_start: 0.8567 (tp40) cc_final: 0.8156 (tp40) REVERT: O 45 MET cc_start: 0.0935 (OUTLIER) cc_final: -0.0104 (ptt) REVERT: S 405 GLN cc_start: 0.8415 (tm-30) cc_final: 0.8107 (tm-30) REVERT: S 862 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8143 (tp30) outliers start: 93 outliers final: 44 residues processed: 476 average time/residue: 0.7084 time to fit residues: 409.6310 Evaluate side-chains 449 residues out of total 4439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 398 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 805 MET Chi-restraints excluded: chain B residue 1186 GLU Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 46 GLN Chi-restraints excluded: chain I residue 52 CYS Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain M residue 621 TYR Chi-restraints excluded: chain M residue 665 GLN Chi-restraints excluded: chain O residue 45 MET Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain S residue 327 THR Chi-restraints excluded: chain S residue 471 TYR Chi-restraints excluded: chain S residue 584 VAL Chi-restraints excluded: chain S residue 862 GLU Chi-restraints excluded: chain S residue 1017 LEU Chi-restraints excluded: chain S residue 1160 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 182 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 297 optimal weight: 0.0030 chunk 453 optimal weight: 5.9990 chunk 172 optimal weight: 7.9990 chunk 355 optimal weight: 6.9990 chunk 195 optimal weight: 2.9990 chunk 415 optimal weight: 7.9990 chunk 250 optimal weight: 0.0670 chunk 386 optimal weight: 5.9990 overall best weight: 1.1932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1194 ASN A1310 HIS B 659 GLN C 111 GLN E 169 GLN H 131 ASN I 45 GLN M 580 GLN M 675 GLN ** S 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.139965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.100680 restraints weight = 100060.210| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.24 r_work: 0.3029 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 42756 Z= 0.148 Angle : 0.594 10.306 58056 Z= 0.306 Chirality : 0.043 0.275 6465 Planarity : 0.004 0.053 7244 Dihedral : 11.277 172.436 6291 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.06 % Allowed : 14.62 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.12), residues: 4927 helix: 0.95 (0.12), residues: 1936 sheet: -0.28 (0.20), residues: 651 loop : -0.37 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 67 TYR 0.018 0.001 TYR S 740 PHE 0.025 0.001 PHE A 112 TRP 0.015 0.001 TRP B 104 HIS 0.010 0.001 HIS A1310 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (42724) covalent geometry : angle 0.58686 / 0.31 (58011) hydrogen bonds : bond 0.03829 / 2.51 ( 1860) hydrogen bonds : angle 4.90526 / 3.47 ( 5179) metal coordination : bond 0.00608 / 0.43 ( 32) metal coordination : angle 3.41839 / 2.35 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9854 Ramachandran restraints generated. 4927 Oldfield, 0 Emsley, 4927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9854 Ramachandran restraints generated. 4927 Oldfield, 0 Emsley, 4927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 4439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 412 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.8377 (pm20) cc_final: 0.8053 (pm20) REVERT: A 199 TYR cc_start: 0.8198 (m-80) cc_final: 0.7626 (m-10) REVERT: A 248 MET cc_start: 0.9071 (mtm) cc_final: 0.8843 (mtm) REVERT: A 441 GLN cc_start: 0.8157 (mt0) cc_final: 0.7690 (mt0) REVERT: A 1248 ASN cc_start: 0.6939 (t0) cc_final: 0.6202 (m-40) REVERT: A 1279 MET cc_start: 0.5594 (tpp) cc_final: 0.5188 (ppp) REVERT: A 1293 LEU cc_start: 0.8902 (mm) cc_final: 0.8685 (mt) REVERT: B 166 GLU cc_start: 0.7292 (tp30) cc_final: 0.7007 (tp30) REVERT: B 246 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.7200 (mmt-90) REVERT: B 339 TYR cc_start: 0.8015 (m-10) cc_final: 0.7702 (m-80) REVERT: B 386 PHE cc_start: 0.8449 (p90) cc_final: 0.8049 (t80) REVERT: B 726 ASN cc_start: 0.8299 (m110) cc_final: 0.8051 (OUTLIER) REVERT: B 1158 ASP cc_start: 0.8492 (t0) cc_final: 0.8019 (t0) REVERT: C 78 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8840 (tp) REVERT: C 265 HIS cc_start: 0.7956 (t70) cc_final: 0.7677 (m170) REVERT: D 126 ARG cc_start: 0.8734 (ttm-80) cc_final: 0.8388 (ttt90) REVERT: F 82 GLU cc_start: 0.7976 (pp20) cc_final: 0.7450 (pp20) REVERT: F 84 GLU cc_start: 0.7991 (mp0) cc_final: 0.7667 (mp0) REVERT: G 35 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7686 (mt-10) REVERT: G 101 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.8847 (pp) REVERT: G 111 HIS cc_start: 0.8579 (p-80) cc_final: 0.8346 (p-80) REVERT: G 146 LYS cc_start: 0.9272 (tppp) cc_final: 0.8907 (tppp) REVERT: G 164 MET cc_start: 0.8375 (mpm) cc_final: 0.8090 (mpm) REVERT: I 15 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7545 (mtt180) REVERT: I 23 MET cc_start: 0.8344 (ttt) cc_final: 0.7942 (ttp) REVERT: I 56 ASN cc_start: 0.8495 (m-40) cc_final: 0.7876 (m-40) REVERT: I 57 LYS cc_start: 0.8004 (mmtt) cc_final: 0.7698 (mmmt) REVERT: I 93 GLU cc_start: 0.8336 (tt0) cc_final: 0.8087 (tt0) REVERT: I 118 HIS cc_start: 0.7564 (OUTLIER) cc_final: 0.7329 (t-170) REVERT: J 36 ASP cc_start: 0.8963 (m-30) cc_final: 0.8733 (m-30) REVERT: L 28 ILE cc_start: 0.9108 (mm) cc_final: 0.8891 (mm) REVERT: L 29 LYS cc_start: 0.8049 (pttt) cc_final: 0.7757 (mptt) REVERT: M 574 MET cc_start: 0.4613 (mmm) cc_final: 0.4321 (mmp) REVERT: M 575 MET cc_start: 0.3797 (ptp) cc_final: 0.2772 (ptp) REVERT: M 614 GLN cc_start: 0.8835 (mt0) cc_final: 0.8542 (pt0) REVERT: M 652 TRP cc_start: 0.7943 (m-90) cc_final: 0.7583 (m100) REVERT: M 660 GLN cc_start: 0.8566 (tp40) cc_final: 0.8122 (tp40) REVERT: O 45 MET cc_start: 0.0945 (OUTLIER) cc_final: -0.0098 (ptt) REVERT: Q 74 THR cc_start: 0.3838 (OUTLIER) cc_final: 0.3424 (p) REVERT: S 405 GLN cc_start: 0.8423 (tm-30) cc_final: 0.8115 (tm-30) REVERT: S 862 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8121 (tp30) outliers start: 91 outliers final: 39 residues processed: 469 average time/residue: 0.6997 time to fit residues: 399.6302 Evaluate side-chains 445 residues out of total 4439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 398 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 805 MET Chi-restraints excluded: chain B residue 1186 GLU Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 46 GLN Chi-restraints excluded: chain I residue 52 CYS Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 118 HIS Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain M residue 621 TYR Chi-restraints excluded: chain O residue 45 MET Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain S residue 327 THR Chi-restraints excluded: chain S residue 584 VAL Chi-restraints excluded: chain S residue 862 GLU Chi-restraints excluded: chain S residue 1017 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 160 optimal weight: 1.9990 chunk 404 optimal weight: 40.0000 chunk 376 optimal weight: 0.0000 chunk 97 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 208 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 382 optimal weight: 50.0000 chunk 100 optimal weight: 0.8980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1310 HIS B 659 GLN C 111 GLN E 169 GLN G 138 GLN H 131 ASN I 45 GLN M 580 GLN M 675 GLN ** S 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.140463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.101334 restraints weight = 99731.710| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.25 r_work: 0.3042 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 42756 Z= 0.129 Angle : 0.592 10.523 58056 Z= 0.304 Chirality : 0.043 0.275 6465 Planarity : 0.004 0.053 7244 Dihedral : 11.244 172.259 6291 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.69 % Allowed : 15.45 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.12), residues: 4927 helix: 1.01 (0.12), residues: 1939 sheet: -0.25 (0.20), residues: 641 loop : -0.36 (0.13), residues: 2347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 67 TYR 0.017 0.001 TYR S 740 PHE 0.019 0.001 PHE A 234 TRP 0.014 0.001 TRP B 104 HIS 0.009 0.001 HIS A1310 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (42724) covalent geometry : angle 0.58541 / 0.30 (58011) hydrogen bonds : bond 0.03677 / 2.40 ( 1860) hydrogen bonds : angle 4.84294 / 3.42 ( 5179) metal coordination : bond 0.00498 / 0.36 ( 32) metal coordination : angle 3.26262 / 2.22 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9854 Ramachandran restraints generated. 4927 Oldfield, 0 Emsley, 4927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9854 Ramachandran restraints generated. 4927 Oldfield, 0 Emsley, 4927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 4439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 413 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR S 471 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 66 GLU cc_start: 0.8345 (pm20) cc_final: 0.8082 (pm20) REVERT: A 112 PHE cc_start: 0.7680 (t80) cc_final: 0.7133 (t80) REVERT: A 220 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8372 (ttt90) REVERT: A 441 GLN cc_start: 0.8097 (mt0) cc_final: 0.7639 (mt0) REVERT: A 1248 ASN cc_start: 0.6880 (t0) cc_final: 0.6149 (m-40) REVERT: A 1279 MET cc_start: 0.5565 (tpp) cc_final: 0.5172 (ppp) REVERT: A 1293 LEU cc_start: 0.8895 (mm) cc_final: 0.8678 (mt) REVERT: B 166 GLU cc_start: 0.7384 (tp30) cc_final: 0.7021 (tp30) REVERT: B 186 MET cc_start: 0.8906 (tpp) cc_final: 0.8695 (mmm) REVERT: B 246 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.7180 (mmt-90) REVERT: B 339 TYR cc_start: 0.7998 (m-10) cc_final: 0.7641 (m-80) REVERT: B 346 ILE cc_start: 0.8845 (tp) cc_final: 0.8642 (pp) REVERT: B 386 PHE cc_start: 0.8448 (p90) cc_final: 0.8093 (t80) REVERT: B 498 LYS cc_start: 0.8034 (mttt) cc_final: 0.7698 (ttpp) REVERT: B 1158 ASP cc_start: 0.8502 (t0) cc_final: 0.8046 (t0) REVERT: B 1249 MET cc_start: 0.8895 (mmt) cc_final: 0.8589 (mmm) REVERT: C 78 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8817 (tp) REVERT: C 265 HIS cc_start: 0.7971 (t70) cc_final: 0.7700 (m170) REVERT: D 126 ARG cc_start: 0.8743 (ttm-80) cc_final: 0.8363 (ttt180) REVERT: D 132 LYS cc_start: 0.9075 (mmpt) cc_final: 0.8848 (mmtm) REVERT: F 82 GLU cc_start: 0.7975 (pp20) cc_final: 0.7402 (pp20) REVERT: F 84 GLU cc_start: 0.8050 (mp0) cc_final: 0.7733 (mp0) REVERT: G 101 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.8810 (pp) REVERT: G 111 HIS cc_start: 0.8580 (p-80) cc_final: 0.8377 (p-80) REVERT: G 146 LYS cc_start: 0.9268 (tppp) cc_final: 0.8900 (tppp) REVERT: G 164 MET cc_start: 0.8405 (mpm) cc_final: 0.8048 (mpm) REVERT: I 15 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7575 (mtt180) REVERT: I 23 MET cc_start: 0.8218 (ttt) cc_final: 0.7838 (ttp) REVERT: I 45 GLN cc_start: 0.8790 (mt0) cc_final: 0.7989 (mp-120) REVERT: I 56 ASN cc_start: 0.8619 (m-40) cc_final: 0.8007 (m-40) REVERT: I 57 LYS cc_start: 0.8080 (mmtt) cc_final: 0.7757 (mmmt) REVERT: I 93 GLU cc_start: 0.8338 (tt0) cc_final: 0.8088 (tt0) REVERT: I 118 HIS cc_start: 0.7625 (t-170) cc_final: 0.7237 (t-90) REVERT: J 36 ASP cc_start: 0.8963 (m-30) cc_final: 0.8732 (m-30) REVERT: L 28 ILE cc_start: 0.9109 (mm) cc_final: 0.8894 (mm) REVERT: L 29 LYS cc_start: 0.8067 (pttt) cc_final: 0.7709 (mptt) REVERT: M 574 MET cc_start: 0.4441 (mmm) cc_final: 0.4145 (mmp) REVERT: M 575 MET cc_start: 0.3784 (ptp) cc_final: 0.2690 (ptp) REVERT: M 614 GLN cc_start: 0.8835 (mt0) cc_final: 0.8588 (pt0) REVERT: M 652 TRP cc_start: 0.7944 (m-90) cc_final: 0.7732 (m100) REVERT: M 660 GLN cc_start: 0.8564 (tp40) cc_final: 0.8117 (tp40) REVERT: O 45 MET cc_start: 0.0832 (OUTLIER) cc_final: -0.0260 (ptt) REVERT: Q 74 THR cc_start: 0.3590 (OUTLIER) cc_final: 0.3167 (p) REVERT: S 405 GLN cc_start: 0.8422 (tm-30) cc_final: 0.8101 (tm-30) REVERT: S 862 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8099 (tp30) outliers start: 75 outliers final: 33 residues processed: 459 average time/residue: 0.7078 time to fit residues: 394.4927 Evaluate side-chains 437 residues out of total 4439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 396 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 1186 GLU Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 46 GLN Chi-restraints excluded: chain I residue 52 CYS Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain M residue 621 TYR Chi-restraints excluded: chain O residue 45 MET Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain S residue 471 TYR Chi-restraints excluded: chain S residue 584 VAL Chi-restraints excluded: chain S residue 848 VAL Chi-restraints excluded: chain S residue 862 GLU Chi-restraints excluded: chain S residue 1017 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 41 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 404 optimal weight: 0.5980 chunk 165 optimal weight: 6.9990 chunk 33 optimal weight: 0.3980 chunk 149 optimal weight: 0.0020 chunk 205 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1310 HIS B 659 GLN C 111 GLN E 169 GLN H 131 ASN ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 588 ASN M 675 GLN ** S 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.140664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.101869 restraints weight = 99745.866| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.52 r_work: 0.3034 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 42756 Z= 0.127 Angle : 0.598 11.834 58056 Z= 0.306 Chirality : 0.043 0.279 6465 Planarity : 0.004 0.054 7244 Dihedral : 11.213 171.661 6291 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.65 % Allowed : 15.75 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.12), residues: 4927 helix: 1.06 (0.12), residues: 1945 sheet: -0.22 (0.20), residues: 646 loop : -0.35 (0.13), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1218 TYR 0.016 0.001 TYR S 740 PHE 0.028 0.001 PHE A1284 TRP 0.014 0.001 TRP A1192 HIS 0.009 0.001 HIS A1310 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (42724) covalent geometry : angle 0.59154 / 0.31 (58011) hydrogen bonds : bond 0.03607 / 2.35 ( 1860) hydrogen bonds : angle 4.79558 / 3.39 ( 5179) metal coordination : bond 0.00580 / 0.42 ( 32) metal coordination : angle 3.31317 / 2.23 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9854 Ramachandran restraints generated. 4927 Oldfield, 0 Emsley, 4927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9854 Ramachandran restraints generated. 4927 Oldfield, 0 Emsley, 4927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 4439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 403 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.8334 (pm20) cc_final: 0.8035 (pm20) REVERT: A 441 GLN cc_start: 0.8107 (mt0) cc_final: 0.7616 (mt0) REVERT: A 1248 ASN cc_start: 0.6868 (t0) cc_final: 0.6111 (m-40) REVERT: A 1279 MET cc_start: 0.5540 (tpp) cc_final: 0.5079 (ppp) REVERT: A 1293 LEU cc_start: 0.8889 (mm) cc_final: 0.8670 (mt) REVERT: B 166 GLU cc_start: 0.7543 (tp30) cc_final: 0.7158 (tp30) REVERT: B 186 MET cc_start: 0.8906 (tpp) cc_final: 0.8683 (mmm) REVERT: B 246 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.7209 (mmt-90) REVERT: B 339 TYR cc_start: 0.7983 (m-10) cc_final: 0.7633 (m-80) REVERT: B 386 PHE cc_start: 0.8498 (p90) cc_final: 0.8129 (t80) REVERT: B 498 LYS cc_start: 0.8086 (mttt) cc_final: 0.7747 (ttpp) REVERT: B 787 ILE cc_start: 0.9516 (OUTLIER) cc_final: 0.9056 (mt) REVERT: B 1158 ASP cc_start: 0.8508 (t0) cc_final: 0.8032 (t0) REVERT: B 1249 MET cc_start: 0.8872 (mmt) cc_final: 0.8620 (mmm) REVERT: C 78 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8821 (tp) REVERT: C 145 GLN cc_start: 0.6880 (pm20) cc_final: 0.6641 (pm20) REVERT: C 265 HIS cc_start: 0.7967 (t70) cc_final: 0.7646 (m170) REVERT: D 126 ARG cc_start: 0.8785 (ttm-80) cc_final: 0.8410 (ttt90) REVERT: F 82 GLU cc_start: 0.8018 (pp20) cc_final: 0.7404 (pp20) REVERT: F 84 GLU cc_start: 0.8117 (mp0) cc_final: 0.7799 (mp0) REVERT: G 35 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: G 78 ARG cc_start: 0.9224 (tpt90) cc_final: 0.8628 (mmm160) REVERT: G 146 LYS cc_start: 0.9282 (tppp) cc_final: 0.8910 (tppp) REVERT: G 151 ARG cc_start: 0.6903 (tmm160) cc_final: 0.6642 (tmm160) REVERT: G 164 MET cc_start: 0.8492 (mpm) cc_final: 0.8169 (mpm) REVERT: I 15 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7668 (mtt180) REVERT: I 23 MET cc_start: 0.8182 (ttt) cc_final: 0.7788 (ttp) REVERT: I 45 GLN cc_start: 0.8789 (mt0) cc_final: 0.7989 (mp-120) REVERT: I 56 ASN cc_start: 0.8666 (m-40) cc_final: 0.8023 (m-40) REVERT: I 57 LYS cc_start: 0.8093 (mmtt) cc_final: 0.7797 (mmmt) REVERT: I 93 GLU cc_start: 0.8346 (tt0) cc_final: 0.8087 (tt0) REVERT: I 118 HIS cc_start: 0.7647 (t-170) cc_final: 0.7280 (t-90) REVERT: J 36 ASP cc_start: 0.8977 (m-30) cc_final: 0.8723 (m-30) REVERT: L 28 ILE cc_start: 0.9117 (mm) cc_final: 0.8904 (mm) REVERT: L 29 LYS cc_start: 0.8088 (pttt) cc_final: 0.7714 (mptt) REVERT: M 614 GLN cc_start: 0.8855 (mt0) cc_final: 0.8551 (pt0) REVERT: M 652 TRP cc_start: 0.7971 (m-90) cc_final: 0.7730 (m100) REVERT: M 660 GLN cc_start: 0.8563 (tp40) cc_final: 0.8110 (tp40) REVERT: O 45 MET cc_start: 0.1006 (OUTLIER) cc_final: -0.0088 (ptt) REVERT: Q 74 THR cc_start: 0.3552 (OUTLIER) cc_final: 0.3209 (p) REVERT: S 405 GLN cc_start: 0.8472 (tm-30) cc_final: 0.8145 (tm-30) outliers start: 73 outliers final: 32 residues processed: 449 average time/residue: 0.7032 time to fit residues: 385.1578 Evaluate side-chains 433 residues out of total 4439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 394 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 1186 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 46 GLN Chi-restraints excluded: chain I residue 52 CYS Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain M residue 621 TYR Chi-restraints excluded: chain O residue 45 MET Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain S residue 327 THR Chi-restraints excluded: chain S residue 584 VAL Chi-restraints excluded: chain S residue 848 VAL Chi-restraints excluded: chain S residue 1017 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 194 optimal weight: 0.6980 chunk 338 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 401 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 424 optimal weight: 6.9990 chunk 235 optimal weight: 1.9990 chunk 375 optimal weight: 1.9990 chunk 152 optimal weight: 0.4980 chunk 353 optimal weight: 0.4980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1310 HIS B 100 GLN B 659 GLN C 66 HIS C 111 GLN H 131 ASN M 580 GLN M 675 GLN ** S 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 424 GLN ** S 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.140396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.101360 restraints weight = 100084.903| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.24 r_work: 0.3040 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 42756 Z= 0.145 Angle : 0.614 12.461 58056 Z= 0.313 Chirality : 0.044 0.282 6465 Planarity : 0.004 0.053 7244 Dihedral : 11.205 170.827 6291 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.33 % Allowed : 16.15 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.12), residues: 4927 helix: 1.06 (0.12), residues: 1950 sheet: -0.23 (0.20), residues: 653 loop : -0.35 (0.13), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 515 TYR 0.017 0.001 TYR B 237 PHE 0.024 0.001 PHE A 112 TRP 0.015 0.001 TRP B 104 HIS 0.005 0.001 HIS B1047 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (42724) covalent geometry : angle 0.60756 / 0.31 (58011) hydrogen bonds : bond 0.03646 / 2.36 ( 1860) hydrogen bonds : angle 4.80760 / 3.40 ( 5179) metal coordination : bond 0.00652 / 0.46 ( 32) metal coordination : angle 3.34075 / 2.25 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9854 Ramachandran restraints generated. 4927 Oldfield, 0 Emsley, 4927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9854 Ramachandran restraints generated. 4927 Oldfield, 0 Emsley, 4927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 4439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 400 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.8343 (pm20) cc_final: 0.8056 (pm20) REVERT: A 441 GLN cc_start: 0.8112 (mt0) cc_final: 0.7632 (mt0) REVERT: A 1248 ASN cc_start: 0.6878 (t0) cc_final: 0.6120 (m-40) REVERT: A 1279 MET cc_start: 0.5625 (tpp) cc_final: 0.5159 (ppp) REVERT: A 1293 LEU cc_start: 0.8908 (mm) cc_final: 0.8680 (mt) REVERT: B 166 GLU cc_start: 0.7490 (tp30) cc_final: 0.7111 (tp30) REVERT: B 186 MET cc_start: 0.8922 (tpp) cc_final: 0.8701 (mmm) REVERT: B 246 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.7206 (mmt-90) REVERT: B 339 TYR cc_start: 0.7992 (m-10) cc_final: 0.7653 (m-80) REVERT: B 386 PHE cc_start: 0.8501 (p90) cc_final: 0.8119 (t80) REVERT: B 498 LYS cc_start: 0.8113 (mttt) cc_final: 0.7775 (ttpp) REVERT: B 787 ILE cc_start: 0.9518 (OUTLIER) cc_final: 0.9055 (mt) REVERT: B 1158 ASP cc_start: 0.8521 (t0) cc_final: 0.8032 (t0) REVERT: B 1249 MET cc_start: 0.8886 (mmt) cc_final: 0.8645 (mmm) REVERT: C 78 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8836 (tp) REVERT: C 145 GLN cc_start: 0.6871 (pm20) cc_final: 0.6638 (pm20) REVERT: C 265 HIS cc_start: 0.7971 (t70) cc_final: 0.7677 (m170) REVERT: D 126 ARG cc_start: 0.8732 (ttm-80) cc_final: 0.8347 (ttt90) REVERT: F 82 GLU cc_start: 0.8043 (pp20) cc_final: 0.7429 (pp20) REVERT: F 84 GLU cc_start: 0.8206 (mp0) cc_final: 0.7902 (mp0) REVERT: G 35 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7594 (mt-10) REVERT: G 78 ARG cc_start: 0.9165 (tpt90) cc_final: 0.8582 (mmm160) REVERT: G 129 LYS cc_start: 0.8812 (ttmm) cc_final: 0.8552 (mtpm) REVERT: G 146 LYS cc_start: 0.9284 (tppp) cc_final: 0.8919 (tppp) REVERT: G 151 ARG cc_start: 0.6982 (tmm160) cc_final: 0.6725 (tmm160) REVERT: G 164 MET cc_start: 0.8510 (mpm) cc_final: 0.8290 (mpm) REVERT: I 15 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7664 (mtt180) REVERT: I 23 MET cc_start: 0.8139 (ttt) cc_final: 0.7774 (ttp) REVERT: I 45 GLN cc_start: 0.8751 (mt0) cc_final: 0.7990 (mp-120) REVERT: I 56 ASN cc_start: 0.8702 (m-40) cc_final: 0.8087 (m-40) REVERT: I 57 LYS cc_start: 0.8097 (mmtt) cc_final: 0.7810 (mmmt) REVERT: I 93 GLU cc_start: 0.8345 (tt0) cc_final: 0.8086 (tt0) REVERT: I 118 HIS cc_start: 0.7629 (t-170) cc_final: 0.7217 (t-90) REVERT: J 36 ASP cc_start: 0.8974 (m-30) cc_final: 0.8720 (m-30) REVERT: L 23 HIS cc_start: 0.8337 (m90) cc_final: 0.7980 (t70) REVERT: L 28 ILE cc_start: 0.9109 (mm) cc_final: 0.8908 (mm) REVERT: L 29 LYS cc_start: 0.8120 (pttt) cc_final: 0.7785 (mptt) REVERT: M 614 GLN cc_start: 0.8846 (mt0) cc_final: 0.8562 (pt0) REVERT: M 652 TRP cc_start: 0.7995 (m-90) cc_final: 0.7770 (m100) REVERT: M 660 GLN cc_start: 0.8574 (tp40) cc_final: 0.8118 (tp40) REVERT: O 45 MET cc_start: 0.0867 (OUTLIER) cc_final: -0.0354 (ptt) REVERT: Q 74 THR cc_start: 0.3324 (OUTLIER) cc_final: 0.2988 (p) REVERT: S 405 GLN cc_start: 0.8437 (tm-30) cc_final: 0.8103 (tm-30) REVERT: S 862 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8088 (tp30) outliers start: 59 outliers final: 32 residues processed: 437 average time/residue: 0.7370 time to fit residues: 389.7070 Evaluate side-chains 432 residues out of total 4439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 392 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 1186 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 46 GLN Chi-restraints excluded: chain I residue 52 CYS Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain M residue 621 TYR Chi-restraints excluded: chain O residue 45 MET Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain S residue 327 THR Chi-restraints excluded: chain S residue 848 VAL Chi-restraints excluded: chain S residue 862 GLU Chi-restraints excluded: chain S residue 1017 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 423 optimal weight: 5.9990 chunk 451 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 387 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 349 optimal weight: 8.9990 chunk 344 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 192 optimal weight: 0.0570 chunk 10 optimal weight: 4.9990 chunk 444 optimal weight: 9.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1310 HIS B 659 GLN C 111 GLN H 131 ASN M 675 GLN ** S 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.138833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.099357 restraints weight = 99847.646| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.24 r_work: 0.2997 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 42756 Z= 0.239 Angle : 0.674 14.304 58056 Z= 0.344 Chirality : 0.046 0.288 6465 Planarity : 0.004 0.054 7244 Dihedral : 11.272 169.840 6291 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.17 % Allowed : 16.45 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.12), residues: 4927 helix: 0.91 (0.12), residues: 1974 sheet: -0.35 (0.19), residues: 671 loop : -0.36 (0.13), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1218 TYR 0.021 0.002 TYR F 115 PHE 0.034 0.002 PHE Q 15 TRP 0.018 0.002 TRP B 104 HIS 0.010 0.001 HIS A1310 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.24 (42724) covalent geometry : angle 0.66531 / 0.34 (58011) hydrogen bonds : bond 0.04076 / 2.65 ( 1860) hydrogen bonds : angle 4.95952 / 3.51 ( 5179) metal coordination : bond 0.01013 / 0.70 ( 32) metal coordination : angle 4.00494 / 2.72 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9854 Ramachandran restraints generated. 4927 Oldfield, 0 Emsley, 4927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9854 Ramachandran restraints generated. 4927 Oldfield, 0 Emsley, 4927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 4439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 400 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.8349 (pm20) cc_final: 0.7951 (pm20) REVERT: A 112 PHE cc_start: 0.7602 (t80) cc_final: 0.7132 (t80) REVERT: A 199 TYR cc_start: 0.8231 (m-80) cc_final: 0.7651 (m-10) REVERT: A 220 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8395 (ttt90) REVERT: A 441 GLN cc_start: 0.8139 (mt0) cc_final: 0.7659 (mt0) REVERT: A 735 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8217 (tt0) REVERT: A 1248 ASN cc_start: 0.6944 (t0) cc_final: 0.6202 (m-40) REVERT: A 1279 MET cc_start: 0.5520 (tpp) cc_final: 0.5041 (ppp) REVERT: A 1293 LEU cc_start: 0.9001 (mm) cc_final: 0.8775 (mt) REVERT: B 166 GLU cc_start: 0.7626 (tp30) cc_final: 0.7282 (tp30) REVERT: B 246 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.7205 (mmt-90) REVERT: B 339 TYR cc_start: 0.7979 (m-10) cc_final: 0.7655 (m-80) REVERT: B 386 PHE cc_start: 0.8529 (p90) cc_final: 0.8077 (t80) REVERT: B 498 LYS cc_start: 0.8116 (mttt) cc_final: 0.7795 (ttpp) REVERT: B 1158 ASP cc_start: 0.8505 (t0) cc_final: 0.8035 (t0) REVERT: B 1218 ARG cc_start: 0.7774 (mmm160) cc_final: 0.7572 (mmt180) REVERT: C 78 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8845 (tp) REVERT: C 145 GLN cc_start: 0.6876 (pm20) cc_final: 0.6644 (pm20) REVERT: F 82 GLU cc_start: 0.7990 (pp20) cc_final: 0.7371 (pp20) REVERT: F 84 GLU cc_start: 0.8196 (mp0) cc_final: 0.7903 (mp0) REVERT: G 35 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7669 (mt-10) REVERT: G 78 ARG cc_start: 0.9171 (tpt90) cc_final: 0.8536 (mmm160) REVERT: G 129 LYS cc_start: 0.8868 (ttmm) cc_final: 0.8559 (mtpt) REVERT: G 146 LYS cc_start: 0.9331 (tppp) cc_final: 0.8960 (tppp) REVERT: G 151 ARG cc_start: 0.7096 (tmm160) cc_final: 0.6845 (tmm160) REVERT: G 164 MET cc_start: 0.8614 (mpm) cc_final: 0.8406 (mpm) REVERT: I 15 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7630 (mtt180) REVERT: I 23 MET cc_start: 0.8321 (ttt) cc_final: 0.7879 (ttp) REVERT: I 45 GLN cc_start: 0.8728 (mt0) cc_final: 0.7965 (mp-120) REVERT: I 56 ASN cc_start: 0.8716 (m-40) cc_final: 0.8090 (m-40) REVERT: I 57 LYS cc_start: 0.8114 (mmtt) cc_final: 0.7836 (mmmt) REVERT: I 93 GLU cc_start: 0.8369 (tt0) cc_final: 0.8100 (tt0) REVERT: I 118 HIS cc_start: 0.7775 (t-170) cc_final: 0.7369 (t-90) REVERT: J 36 ASP cc_start: 0.8970 (m-30) cc_final: 0.8716 (m-30) REVERT: L 27 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7465 (tt0) REVERT: L 28 ILE cc_start: 0.9115 (mm) cc_final: 0.8864 (mm) REVERT: L 29 LYS cc_start: 0.8173 (pttt) cc_final: 0.7910 (pptt) REVERT: M 614 GLN cc_start: 0.8820 (mt0) cc_final: 0.8581 (pt0) REVERT: M 652 TRP cc_start: 0.8061 (m-90) cc_final: 0.7797 (m100) REVERT: M 660 GLN cc_start: 0.8595 (tp40) cc_final: 0.8134 (tp40) REVERT: O 45 MET cc_start: 0.0910 (OUTLIER) cc_final: -0.0271 (ptt) REVERT: Q 15 PHE cc_start: 0.6944 (m-80) cc_final: 0.6401 (m-10) REVERT: S 405 GLN cc_start: 0.8397 (tm-30) cc_final: 0.8079 (tm-30) outliers start: 52 outliers final: 32 residues processed: 432 average time/residue: 0.7324 time to fit residues: 383.3685 Evaluate side-chains 431 residues out of total 4439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 391 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 465 TYR Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 1186 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 46 GLN Chi-restraints excluded: chain I residue 52 CYS Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain M residue 621 TYR Chi-restraints excluded: chain O residue 45 MET Chi-restraints excluded: chain S residue 327 THR Chi-restraints excluded: chain S residue 584 VAL Chi-restraints excluded: chain S residue 848 VAL Chi-restraints excluded: chain S residue 1017 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 375 optimal weight: 1.9990 chunk 471 optimal weight: 0.9990 chunk 140 optimal weight: 0.0770 chunk 312 optimal weight: 3.9990 chunk 176 optimal weight: 0.7980 chunk 358 optimal weight: 0.9980 chunk 307 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 280 optimal weight: 0.9980 chunk 354 optimal weight: 2.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1310 HIS B 659 GLN C 111 GLN H 131 ASN ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 580 GLN M 675 GLN ** S 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.140342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.101318 restraints weight = 100208.243| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.25 r_work: 0.3039 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 42756 Z= 0.130 Angle : 0.632 11.067 58056 Z= 0.321 Chirality : 0.044 0.275 6465 Planarity : 0.004 0.068 7244 Dihedral : 11.240 170.388 6291 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.15 % Allowed : 16.61 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.12), residues: 4927 helix: 0.99 (0.12), residues: 1970 sheet: -0.29 (0.20), residues: 657 loop : -0.31 (0.13), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 515 TYR 0.017 0.001 TYR I 54 PHE 0.022 0.001 PHE A 234 TRP 0.015 0.001 TRP A1334 HIS 0.010 0.001 HIS A1310 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (42724) covalent geometry : angle 0.62413 / 0.32 (58011) hydrogen bonds : bond 0.03668 / 2.38 ( 1860) hydrogen bonds : angle 4.86672 / 3.44 ( 5179) metal coordination : bond 0.00581 / 0.42 ( 32) metal coordination : angle 3.56351 / 2.38 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17249.97 seconds wall clock time: 293 minutes 33.13 seconds (17613.13 seconds total)