Starting phenix.real_space_refine on Tue Sep 15 02:11:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7okx_12969/09_2026/7okx_12969_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7okx_12969/09_2026/7okx_12969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7okx_12969/09_2026/7okx_12969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7okx_12969/09_2026/7okx_12969.map" model { file = "/net/cci-nas-00/data/ceres_data/7okx_12969/09_2026/7okx_12969_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7okx_12969/09_2026/7okx_12969_neut.cif" } resolution = 3.3 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= 0.008 sd= 1.104 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 79 5.49 5 Mg 1 5.21 5 S 207 5.16 5 C 21720 2.51 5 N 6126 2.21 5 O 6693 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 134 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34834 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 11149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1407, 11149 Classifications: {'peptide': 1407} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1338} Chain breaks: 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: "M" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1106 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "N" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 549 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "O" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 832 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "P" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 279 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: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 808 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "Z" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 393 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} 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 71 106.103 99.804 76.836 1.00 53.97 S ATOM 494 SG CYS A 74 104.893 103.027 78.626 1.00 50.43 S ATOM 541 SG CYS A 81 102.525 100.033 78.289 1.00 45.79 S ATOM 776 SG CYS A 111 87.822 108.132 33.971 1.00 65.63 S ATOM 804 SG CYS A 114 89.564 111.243 34.067 1.00 69.86 S ATOM 1117 SG CYS A 154 85.929 111.065 32.597 1.00 76.79 S ATOM 1144 SG CYS A 184 89.002 109.797 30.629 1.00 79.71 S ATOM 19765 SG CYS B1196 99.435 115.827 69.767 1.00 45.35 S ATOM 19787 SG CYS B1199 98.092 113.011 67.501 1.00 49.68 S ATOM 19902 SG CYS B1214 101.349 112.656 68.755 1.00 52.69 S ATOM 19923 SG CYS B1217 100.621 115.424 66.112 1.00 64.76 S ATOM 20890 SG CYS C 88 82.395 76.781 137.385 1.00 49.61 S ATOM 20903 SG CYS C 90 84.974 75.524 134.794 1.00 55.35 S ATOM 20938 SG CYS C 94 83.811 73.444 137.704 1.00 41.65 S ATOM 20960 SG CYS C 97 81.493 74.130 134.702 1.00 37.01 S ATOM 28729 SG CYS I 86 18.615 53.504 55.419 1.00 62.37 S ATOM 28753 SG CYS I 89 18.378 49.699 56.023 1.00 69.05 S ATOM 28957 SG CYS I 114 21.189 51.820 57.576 1.00 51.27 S ATOM 28992 SG CYS I 119 20.976 50.987 53.799 1.00 64.00 S ATOM 28177 SG CYS I 17 46.660 59.906 20.796 1.00 35.13 S ATOM 28201 SG CYS I 20 50.523 60.814 21.919 1.00 34.24 S ATOM 28352 SG CYS I 39 47.946 63.095 21.328 1.00 45.53 S ATOM 28377 SG CYS I 42 49.189 60.611 18.185 1.00 49.82 S ATOM 29102 SG CYS J 7 56.418 66.434 118.021 1.00 15.25 S ATOM 29126 SG CYS J 10 55.558 67.580 121.529 1.00 15.23 S ATOM 29390 SG CYS J 44 52.838 67.603 118.701 1.00 20.26 S ATOM 29396 SG CYS J 45 54.038 64.549 120.540 1.00 21.78 S ATOM 30533 SG CYS L 19 91.731 48.028 99.479 1.00 49.50 S ATOM 30552 SG CYS L 22 92.122 45.106 101.750 1.00 53.06 S ATOM 30663 SG CYS L 36 95.088 46.200 99.877 1.00 57.01 S ATOM 30689 SG CYS L 39 92.267 44.551 97.931 1.00 56.16 S Time building chain proxies: 8.38, per 1000 atoms: 0.24 Number of scatterers: 34834 At special positions: 0 Unit cell: (158.55, 171.15, 160.65, 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 207 16.00 P 79 15.00 Mg 1 11.99 O 6693 8.00 N 6126 7.00 C 21720 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: 3.37 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 81 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 71 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 111 " 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 B1214 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1196 " 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 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " 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 17 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 20 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " 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 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " Number of angles added : 45 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7816 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 49 sheets defined 36.7% alpha, 20.1% beta 27 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 4.73 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 59 through 63 removed outlier: 3.683A pdb=" N GLY A 63 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.594A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 removed outlier: 3.600A pdb=" N VAL A 235 " --> pdb=" O GLU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 274 through 296 removed outlier: 3.571A pdb=" N ASN A 296 " --> pdb=" O ARG A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 319 removed outlier: 3.579A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) 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 386 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' 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 488 through 493 removed outlier: 3.502A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (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 538 through 549 Processing helix chain 'A' and resid 556 through 565 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 661 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.520A pdb=" N ASN A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 759 removed outlier: 3.581A pdb=" N SER A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 772 removed outlier: 3.708A pdb=" N SER A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.704A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 847 " --> pdb=" O GLY A 843 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 3.674A 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 removed outlier: 3.510A pdb=" N ARG A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 934 removed outlier: 4.222A pdb=" N ARG A 932 " --> pdb=" O ARG A 928 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 933 " --> pdb=" O ALA A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 944 removed outlier: 3.728A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1017 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1052 through 1057 Processing helix chain 'A' and resid 1061 through 1080 Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1102 removed outlier: 3.537A pdb=" N MET A1102 " --> pdb=" O ALA A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1144 through 1149 removed outlier: 3.594A pdb=" N SER A1147 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1162 Processing helix chain 'A' and resid 1189 through 1197 Processing helix chain 'A' and resid 1217 through 1223 removed outlier: 3.644A pdb=" N ASP A1223 " --> pdb=" O LYS A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1280 through 1294 Processing helix chain 'A' and resid 1342 through 1348 Processing helix chain 'A' and resid 1361 through 1369 removed outlier: 3.670A pdb=" N ILE A1365 " --> pdb=" O ASP A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1389 removed outlier: 4.504A pdb=" N ASP A1389 " --> pdb=" O VAL A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 3.900A 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 removed outlier: 3.636A pdb=" N PHE A1432 " --> pdb=" O MET A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.844A 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 1479 through 1483 removed outlier: 3.837A pdb=" N TYR A1482 " --> pdb=" O LYS A1479 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A1483 " --> pdb=" O CYS A1480 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1479 through 1483' Processing helix chain 'B' and resid 95 through 97 No H-bonds generated for 'chain 'B' and resid 95 through 97' Processing helix chain 'B' and resid 98 through 114 removed outlier: 3.857A pdb=" N TRP B 104 " --> pdb=" O GLN B 100 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 105 " --> pdb=" O GLU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 removed outlier: 3.803A pdb=" N SER B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) 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 353 Processing helix chain 'B' and resid 357 through 366 Processing helix chain 'B' and resid 371 through 378 removed outlier: 4.086A pdb=" N MET B 377 " --> pdb=" O GLU B 373 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL B 378 " --> pdb=" O MET B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 385 Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 408 through 423 Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.592A pdb=" N VAL B 428 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 454 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 removed outlier: 3.770A pdb=" N GLY B 483 " --> pdb=" O PHE B 479 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP B 501 " --> pdb=" O GLN B 497 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ARG B 502 " --> pdb=" O LYS B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 528 removed outlier: 3.513A pdb=" N SER B 518 " --> pdb=" O THR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 560 Processing helix chain 'B' and resid 573 through 577 Processing helix chain 'B' and resid 579 through 583 Processing helix chain 'B' and resid 615 through 625 removed outlier: 3.793A pdb=" N GLU B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 633 No H-bonds generated for 'chain 'B' and resid 631 through 633' Processing helix chain 'B' and resid 634 through 638 removed outlier: 3.855A pdb=" N ILE B 638 " --> pdb=" O PRO B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 713 through 721 removed outlier: 3.512A pdb=" N ILE B 717 " --> pdb=" O LYS B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 727 removed outlier: 3.640A pdb=" N ASN B 727 " --> pdb=" O ARG B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 736 Processing helix chain 'B' and resid 744 through 748 removed outlier: 3.588A pdb=" N GLU B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 744 through 748' Processing helix chain 'B' and resid 755 through 760 Processing helix chain 'B' and resid 776 through 781 removed outlier: 3.757A pdb=" N ILE B 780 " --> pdb=" O PRO B 777 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 781 " --> pdb=" O SER B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 794 removed outlier: 3.580A pdb=" N ASN B 794 " --> pdb=" O PRO B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 806 Processing helix chain 'B' and resid 838 through 843 removed outlier: 3.755A pdb=" N GLU B 842 " --> pdb=" O ARG B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 875 through 880 Processing helix chain 'B' and resid 921 through 925 removed outlier: 4.004A pdb=" N LYS B 924 " --> pdb=" O ILE B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1049 Processing helix chain 'B' and resid 1054 through 1071 removed outlier: 3.912A 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 1154 through 1158 removed outlier: 3.622A pdb=" N ARG B1157 " --> pdb=" O GLY B1154 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1175 Processing helix chain 'B' and resid 1176 through 1185 Processing helix chain 'B' and resid 1229 through 1241 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.568A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) 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 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 removed outlier: 3.593A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 79 through 84 Processing helix chain 'D' and resid 84 through 92 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 118 through 132 removed outlier: 3.878A pdb=" N LYS D 132 " --> pdb=" O LEU D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 157 Processing helix chain 'D' and resid 158 through 161 removed outlier: 3.522A pdb=" N GLU D 161 " --> pdb=" O PRO D 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 158 through 161' Processing helix chain 'D' and resid 167 through 180 Processing helix chain 'E' and resid 3 through 24 removed outlier: 3.553A pdb=" N TYR E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 121 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 163 Processing helix chain 'E' and resid 166 through 170 removed outlier: 3.698A pdb=" N LEU E 170 " --> pdb=" O GLU E 167 " (cutoff:3.500A) 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 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.643A pdb=" N VAL G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS G 27 " --> pdb=" O LEU G 23 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 118 removed outlier: 3.591A pdb=" N GLU G 118 " --> pdb=" O SER G 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 88 removed outlier: 3.690A pdb=" N ASP H 86 " --> pdb=" O SER H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 132 No H-bonds generated for 'chain 'H' and resid 130 through 132' Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.573A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (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: 3.754A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.648A 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: 3.753A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 52 removed outlier: 4.001A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 115 Processing helix chain 'M' and resid 35 through 48 removed outlier: 3.600A pdb=" N HIS M 48 " --> pdb=" O THR M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 146 removed outlier: 4.231A pdb=" N TYR M 131 " --> pdb=" O THR M 127 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN M 132 " --> pdb=" O ASN M 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 19 through 23 removed outlier: 3.543A pdb=" N PHE O 22 " --> pdb=" O GLY O 19 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 48 removed outlier: 3.703A pdb=" N ARG A 51 " --> pdb=" O GLU A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 95 removed outlier: 6.772A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 10.541A pdb=" N LYS A 92 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 10.468A 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: 3.587A pdb=" N GLU A 201 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 4.457A 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: 3.585A 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: 5.913A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 393 removed outlier: 6.587A pdb=" N LYS A 445 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE A 419 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 6.691A 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: 6.347A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE H 56 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ILE H 9 " --> pdb=" O PHE H 56 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU H 58 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU H 7 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE H 60 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ARG H 111 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLY H 101 " --> pdb=" O ARG H 111 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N SER H 113 " --> pdb=" O ILE H 99 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE H 99 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.657A 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: 3.935A 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: 6.897A pdb=" N THR A1164 " --> pdb=" O LEU A1298 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1243 through 1248 removed outlier: 4.116A pdb=" N ASN A1248 " --> pdb=" O VAL A1256 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL A1256 " --> pdb=" O ASN A1248 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ALA A1171 " --> pdb=" O LYS I 57 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LYS I 57 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR A1173 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL I 55 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE A1175 " --> pdb=" O ILE I 53 " (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: 4.120A pdb=" N GLN E 174 " --> pdb=" O GLY A1409 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 72 through 73 removed outlier: 4.480A pdb=" N GLU D 72 " --> pdb=" O HIS G 4 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.109A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN G 53 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS G 71 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ILE G 51 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LYS G 73 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA G 47 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE G 77 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 142 through 144 removed outlier: 4.488A pdb=" N ASP B 204 " --> pdb=" O GLU B 166 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE B 168 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TYR B 202 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU B 170 " --> pdb=" O PRO B 200 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA B 199 " --> pdb=" O GLY B 227 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLY B 227 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU B 201 " --> pdb=" O PHE B 225 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N PHE B 225 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL B 203 " --> pdb=" O LYS B 223 " (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 removed outlier: 6.413A pdb=" N ALA B 273 " --> pdb=" O ASN B 563 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 282 through 285 removed outlier: 3.650A pdb=" N TYR B 294 " --> pdb=" O MET B 316 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP B 313 " --> pdb=" O THR B 336 " (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: 5.495A pdb=" N TRP B 650 " --> pdb=" O VAL B 646 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL B 646 " --> pdb=" O TRP B 650 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY B 652 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYS B 643 " --> pdb=" O ILE B 689 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ILE B 691 " --> pdb=" O LYS B 643 " (cutoff:3.500A) removed outlier: 6.255A 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: 4.103A pdb=" N LYS B 994 " --> pdb=" O GLU B 895 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE B 995 " --> pdb=" O VAL B 986 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL B 986 " --> pdb=" O PHE B 995 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS B 997 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL B 984 " --> pdb=" O LYS B 997 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ARG B 999 " --> pdb=" O ASP B 982 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL B1003 " --> pdb=" O THR B 978 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N THR B 978 " --> pdb=" O VAL B1003 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 824 through 828 removed outlier: 4.103A pdb=" N LYS B 994 " --> pdb=" O GLU B 895 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE B 995 " --> pdb=" O VAL B 986 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL B 986 " --> pdb=" O PHE B 995 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS B 997 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL B 984 " --> pdb=" O LYS B 997 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ARG B 999 " --> pdb=" O ASP B 982 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL B1003 " --> pdb=" O THR B 978 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N THR B 978 " --> pdb=" O VAL B1003 " (cutoff:3.500A) removed outlier: 5.379A 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: 7.081A pdb=" N VAL B 871 " --> pdb=" O GLY B1023 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLN B1025 " --> pdb=" O VAL B 871 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N MET B 873 " --> pdb=" O GLN B1025 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE B1119 " --> pdb=" O ILE B 859 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 897 through 898 removed outlier: 4.942A pdb=" N GLU B 903 " --> pdb=" O THR B 949 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR B 949 " --> pdb=" O GLU B 903 " (cutoff:3.500A) removed outlier: 6.664A 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 removed outlier: 7.415A pdb=" N THR B 971 " --> pdb=" O ILE B 943 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1192 through 1196 Processing sheet with id=AD9, first strand: chain 'B' and resid 1204 through 1206 Processing sheet with id=AE1, first strand: chain 'C' and resid 8 through 15 removed outlier: 5.838A pdb=" N VAL C 9 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLU C 24 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE C 22 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN C 18 " --> pdb=" O THR C 15 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ARG C 228 " --> pdb=" O TYR C 186 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N TYR C 186 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.985A pdb=" N ARG C 162 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ILE C 52 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N TYR C 164 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL C 50 " --> pdb=" O TYR C 164 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LYS C 166 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ASP C 48 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY C 168 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ALA C 46 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AE4, first strand: chain 'E' and resid 60 through 63 removed outlier: 4.049A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AE6, first strand: chain 'G' and resid 84 through 92 removed outlier: 3.729A pdb=" N VAL G 88 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY G 161 " --> pdb=" O PHE G 107 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 128 through 129 Processing sheet with id=AE8, first strand: chain 'I' and resid 24 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 22 Processing sheet with id=AF2, first strand: chain 'M' and resid 57 through 58 removed outlier: 6.471A pdb=" N ARG O 17 " --> pdb=" O LEU O 99 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 112 through 117 removed outlier: 6.964A pdb=" N CYS M 99 " --> pdb=" O LEU M 115 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N PHE M 117 " --> pdb=" O PHE M 97 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N PHE M 97 " --> pdb=" O PHE M 117 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE O 33 " --> pdb=" O ASP M 98 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N PHE O 30 " --> pdb=" O SER O 104 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N ILE O 106 " --> pdb=" O PHE O 30 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR O 32 " --> pdb=" O ILE O 106 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL O 108 " --> pdb=" O THR O 32 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ARG O 34 " --> pdb=" O VAL O 108 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LYS O 110 " --> pdb=" O ARG O 34 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ASP O 36 " --> pdb=" O LYS O 110 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL O 74 " --> pdb=" O THR O 111 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Z' and resid 742 through 746 removed outlier: 3.691A pdb=" N ASP Z 726 " --> pdb=" O ARG Z 733 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLU Z 735 " --> pdb=" O VAL Z 724 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL Z 724 " --> pdb=" O GLU Z 735 " (cutoff:3.500A) 1385 hydrogen bonds defined for protein. 3828 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 64 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 11.42 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5741 1.32 - 1.44: 9352 1.44 - 1.57: 20067 1.57 - 1.69: 156 1.69 - 1.82: 324 Bond restraints: 35640 Sorted by residual: bond pdb=" C1' DT T 27 " pdb=" N1 DT T 27 " ideal model delta sigma weight residual 1.468 1.524 -0.056 1.40e-02 5.10e+03 1.62e+01 bond pdb=" C PRO J 64 " pdb=" O PRO J 64 " ideal model delta sigma weight residual 1.234 1.192 0.041 1.14e-02 7.69e+03 1.30e+01 bond pdb=" C3' DT T 32 " pdb=" O3' DT T 32 " ideal model delta sigma weight residual 1.435 1.481 -0.046 1.30e-02 5.92e+03 1.25e+01 bond pdb=" C3' DA T 11 " pdb=" C2' DA T 11 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DA N 30 " pdb=" C2' DA N 30 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.55e+00 ... (remaining 35635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 47252 2.16 - 4.31: 1065 4.31 - 6.47: 107 6.47 - 8.63: 39 8.63 - 10.78: 7 Bond angle restraints: 48470 Sorted by residual: angle pdb=" C CYS I 20 " pdb=" N ASN I 21 " pdb=" CA ASN I 21 " ideal model delta sigma weight residual 122.74 130.20 -7.46 1.44e+00 4.82e-01 2.69e+01 angle pdb=" N3 DT N 10 " pdb=" C4 DT N 10 " pdb=" O4 DT N 10 " ideal model delta sigma weight residual 119.90 122.66 -2.76 6.00e-01 2.78e+00 2.11e+01 angle pdb=" N3 DT N 34 " pdb=" C4 DT N 34 " pdb=" O4 DT N 34 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT T 13 " pdb=" C4 DT T 13 " pdb=" O4 DT T 13 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 angle pdb=" C3' DT T 32 " pdb=" O3' DT T 32 " pdb=" P DC T 33 " ideal model delta sigma weight residual 119.70 124.80 -5.10 1.20e+00 6.94e-01 1.80e+01 ... (remaining 48465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.96: 20934 34.96 - 69.91: 684 69.91 - 104.87: 65 104.87 - 139.82: 0 139.82 - 174.78: 1 Dihedral angle restraints: 21684 sinusoidal: 9603 harmonic: 12081 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 180.00 140.84 39.16 0 5.00e+00 4.00e-02 6.13e+01 dihedral pdb=" CA MET G 117 " pdb=" C MET G 117 " pdb=" N GLU G 118 " pdb=" CA GLU G 118 " ideal model delta harmonic sigma weight residual -180.00 -148.86 -31.14 0 5.00e+00 4.00e-02 3.88e+01 dihedral pdb=" CA ASN G 122 " pdb=" C ASN G 122 " pdb=" N SER G 123 " pdb=" CA SER G 123 " ideal model delta harmonic sigma weight residual 180.00 150.09 29.91 0 5.00e+00 4.00e-02 3.58e+01 ... (remaining 21681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 5097 0.103 - 0.206: 322 0.206 - 0.309: 7 0.309 - 0.411: 2 0.411 - 0.514: 1 Chirality restraints: 5429 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 6.61e+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 4.22e+00 chirality pdb=" CB ILE G 147 " pdb=" CA ILE G 147 " pdb=" CG1 ILE G 147 " pdb=" CG2 ILE G 147 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.74e+00 ... (remaining 5426 not shown) Planarity restraints: 6007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 829 " -0.025 2.00e-02 2.50e+03 2.13e-02 9.10e+00 pdb=" CG TYR B 829 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR B 829 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 829 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 829 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 829 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR B 829 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 829 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR M 131 " -0.014 2.00e-02 2.50e+03 2.91e-02 8.44e+00 pdb=" C TYR M 131 " 0.050 2.00e-02 2.50e+03 pdb=" O TYR M 131 " -0.019 2.00e-02 2.50e+03 pdb=" N GLN M 132 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 112 " -0.020 2.00e-02 2.50e+03 2.17e-02 8.24e+00 pdb=" CG PHE A 112 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE A 112 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 112 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A 112 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 112 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 112 " 0.000 2.00e-02 2.50e+03 ... (remaining 6004 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 525 2.65 - 3.22: 29965 3.22 - 3.78: 56819 3.78 - 4.34: 81115 4.34 - 4.90: 130220 Nonbonded interactions: 298644 Sorted by model distance: nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG A2001 " model vdw 2.093 2.170 nonbonded pdb=" ND1 HIS O 31 " pdb=" OG SER O 104 " model vdw 2.097 3.120 nonbonded pdb=" O3' A P 46 " pdb="MG MG A2001 " model vdw 2.106 2.170 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2001 " model vdw 2.107 2.170 nonbonded pdb=" OG SER B 938 " pdb=" OE2 GLU Z 735 " model vdw 2.213 3.040 ... (remaining 298639 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 46.590 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 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 0.092 35672 Z= 0.247 Angle : 0.784 16.514 48515 Z= 0.459 Chirality : 0.052 0.514 5429 Planarity : 0.006 0.064 6007 Dihedral : 16.562 174.779 13868 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.03 % Allowed : 0.46 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.03 % 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: -1.33 (0.12), residues: 4099 helix: -0.84 (0.13), residues: 1369 sheet: -1.07 (0.19), residues: 696 loop : -0.69 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG I 103 TYR 0.052 0.002 TYR B 829 PHE 0.051 0.002 PHE A 112 TRP 0.021 0.002 TRP B 530 HIS 0.013 0.001 HIS B 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.25 (35640) covalent geometry : angle 0.76388 / 0.46 (48470) hydrogen bonds : bond 0.15958 / 10.42 ( 1429) hydrogen bonds : angle 7.30216 / 5.04 ( 3956) metal coordination : bond 0.01111 / 0.79 ( 32) metal coordination : angle 5.87680 / 3.95 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 555 time to evaluate : 1.330 Fit side-chains revert: symmetry clash REVERT: A 220 ARG cc_start: 0.7290 (tpt-90) cc_final: 0.7046 (tpt-90) REVERT: A 407 ARG cc_start: 0.8026 (ttp80) cc_final: 0.7738 (ttp80) REVERT: A 524 MET cc_start: 0.8108 (mmp) cc_final: 0.7860 (mmm) REVERT: A 918 LYS cc_start: 0.8606 (tmtt) cc_final: 0.8340 (tptm) REVERT: B 465 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.8152 (m-80) REVERT: B 471 ASP cc_start: 0.7976 (m-30) cc_final: 0.7753 (m-30) REVERT: B 484 MET cc_start: 0.7864 (mmt) cc_final: 0.7567 (mmt) REVERT: B 497 GLN cc_start: 0.7825 (tp40) cc_final: 0.7478 (tp40) REVERT: B 868 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7470 (mm-30) REVERT: B 869 ASP cc_start: 0.7703 (m-30) cc_final: 0.7265 (m-30) REVERT: B 967 ARG cc_start: 0.7672 (ptm-80) cc_final: 0.7416 (ptt90) REVERT: B 1242 MET cc_start: 0.8765 (mtp) cc_final: 0.8551 (mtp) REVERT: C 154 ARG cc_start: 0.8369 (ttt-90) cc_final: 0.8038 (ttt-90) REVERT: D 66 LYS cc_start: 0.7071 (tppp) cc_final: 0.6838 (ttmt) REVERT: E 172 ARG cc_start: 0.8069 (mtt90) cc_final: 0.7823 (mtt90) REVERT: H 37 MET cc_start: 0.8277 (mmt) cc_final: 0.7589 (mmt) outliers start: 1 outliers final: 0 residues processed: 555 average time/residue: 0.2584 time to fit residues: 225.8929 Evaluate side-chains 483 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 482 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 465 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.8980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 GLN A 441 GLN B 221 HIS B 727 ASN C 217 GLN C 232 ASN D 177 GLN ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 GLN K 89 ASN O 14 HIS O 92 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.148162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.112818 restraints weight = 42728.474| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.09 r_work: 0.2876 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 35672 Z= 0.185 Angle : 0.593 12.911 48515 Z= 0.309 Chirality : 0.045 0.284 5429 Planarity : 0.005 0.051 6007 Dihedral : 13.242 176.505 5466 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.84 % Allowed : 5.98 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.62 (0.13), residues: 4099 helix: 0.13 (0.14), residues: 1383 sheet: -1.05 (0.18), residues: 738 loop : -0.39 (0.14), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 103 TYR 0.021 0.001 TYR B 829 PHE 0.024 0.002 PHE A 112 TRP 0.017 0.002 TRP A1192 HIS 0.006 0.001 HIS Z 737 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (35640) covalent geometry : angle 0.57485 / 0.31 (48470) hydrogen bonds : bond 0.04562 / 2.94 ( 1429) hydrogen bonds : angle 5.51680 / 3.85 ( 3956) metal coordination : bond 0.00787 / 0.56 ( 32) metal coordination : angle 4.84137 / 3.52 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 496 time to evaluate : 1.354 Fit side-chains revert: symmetry clash REVERT: A 220 ARG cc_start: 0.7867 (tpt-90) cc_final: 0.7618 (tpt-90) REVERT: A 918 LYS cc_start: 0.8658 (tmtt) cc_final: 0.8414 (tptm) REVERT: B 465 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.8422 (m-80) REVERT: B 471 ASP cc_start: 0.8660 (m-30) cc_final: 0.8434 (m-30) REVERT: B 869 ASP cc_start: 0.8115 (m-30) cc_final: 0.7656 (m-30) REVERT: B 967 ARG cc_start: 0.7995 (ptm-80) cc_final: 0.7709 (ptt90) REVERT: B 1218 ARG cc_start: 0.7593 (mtm180) cc_final: 0.7095 (mtp-110) REVERT: B 1228 MET cc_start: 0.8847 (ptt) cc_final: 0.8640 (ptt) REVERT: B 1242 MET cc_start: 0.9047 (mtp) cc_final: 0.8843 (mtp) REVERT: C 154 ARG cc_start: 0.8499 (ttt-90) cc_final: 0.8146 (ttt-90) REVERT: E 108 GLN cc_start: 0.7863 (tm-30) cc_final: 0.7521 (tm-30) REVERT: E 172 ARG cc_start: 0.8297 (mtt90) cc_final: 0.7968 (mtt90) REVERT: H 146 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8119 (ttpt) REVERT: I 93 GLU cc_start: 0.8178 (tt0) cc_final: 0.7926 (tt0) outliers start: 31 outliers final: 17 residues processed: 510 average time/residue: 0.2547 time to fit residues: 205.0076 Evaluate side-chains 488 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 469 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 905 ASN Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 465 TYR Chi-restraints excluded: chain B residue 761 GLU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 146 LYS Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain M residue 44 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 39 optimal weight: 0.2980 chunk 160 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 chunk 321 optimal weight: 0.7980 chunk 277 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 218 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 352 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 GLN A 982 ASN A1236 ASN B 221 HIS B 727 ASN H 131 ASN I 45 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.147711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.112230 restraints weight = 42725.001| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.09 r_work: 0.2836 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 35672 Z= 0.159 Angle : 0.550 12.306 48515 Z= 0.285 Chirality : 0.044 0.317 5429 Planarity : 0.004 0.056 6007 Dihedral : 13.120 176.335 5466 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.12 % Allowed : 8.62 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.20 (0.13), residues: 4099 helix: 0.66 (0.14), residues: 1377 sheet: -0.93 (0.19), residues: 710 loop : -0.26 (0.14), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 928 TYR 0.019 0.001 TYR O 35 PHE 0.019 0.001 PHE A 458 TRP 0.014 0.001 TRP A1192 HIS 0.007 0.001 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (35640) covalent geometry : angle 0.53351 / 0.28 (48470) hydrogen bonds : bond 0.03995 / 2.60 ( 1429) hydrogen bonds : angle 5.13917 / 3.60 ( 3956) metal coordination : bond 0.00697 / 0.49 ( 32) metal coordination : angle 4.36427 / 3.21 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 495 time to evaluate : 1.350 Fit side-chains REVERT: A 147 LEU cc_start: 0.8253 (mp) cc_final: 0.7989 (mp) REVERT: A 192 ARG cc_start: 0.6898 (tmm-80) cc_final: 0.6676 (tmm-80) REVERT: A 918 LYS cc_start: 0.8647 (tmtt) cc_final: 0.8410 (tptm) REVERT: A 927 GLU cc_start: 0.7751 (pm20) cc_final: 0.7453 (pm20) REVERT: B 471 ASP cc_start: 0.8613 (m-30) cc_final: 0.8392 (m-30) REVERT: B 510 LEU cc_start: 0.8818 (tt) cc_final: 0.8610 (pp) REVERT: B 869 ASP cc_start: 0.8145 (m-30) cc_final: 0.7727 (m-30) REVERT: B 967 ARG cc_start: 0.7898 (ptm-80) cc_final: 0.7598 (ptt90) REVERT: B 1218 ARG cc_start: 0.7576 (mtm180) cc_final: 0.6932 (mtp-110) REVERT: B 1228 MET cc_start: 0.8908 (ptt) cc_final: 0.8694 (ptt) REVERT: C 154 ARG cc_start: 0.8416 (ttt-90) cc_final: 0.8074 (ttt-90) REVERT: E 108 GLN cc_start: 0.7935 (tm-30) cc_final: 0.7607 (tm-30) REVERT: E 172 ARG cc_start: 0.8262 (mtt90) cc_final: 0.7909 (mtt90) REVERT: H 146 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8103 (ttpt) REVERT: I 93 GLU cc_start: 0.8172 (tt0) cc_final: 0.7845 (tt0) REVERT: O 36 ASP cc_start: 0.8300 (p0) cc_final: 0.8061 (p0) outliers start: 41 outliers final: 29 residues processed: 516 average time/residue: 0.2472 time to fit residues: 202.8717 Evaluate side-chains 498 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 468 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 905 ASN Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 761 GLU Chi-restraints excluded: chain B residue 978 THR Chi-restraints excluded: chain B residue 1213 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 146 LYS Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain O residue 72 MET Chi-restraints excluded: chain O residue 85 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 314 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 221 optimal weight: 2.9990 chunk 402 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 344 optimal weight: 3.9990 chunk 300 optimal weight: 6.9990 chunk 353 optimal weight: 20.0000 chunk 264 optimal weight: 9.9990 chunk 176 optimal weight: 0.8980 chunk 48 optimal weight: 0.0970 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 982 ASN B 221 HIS B 727 ASN D 80 HIS E 132 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.146817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.110994 restraints weight = 42658.087| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.06 r_work: 0.2878 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 35672 Z= 0.206 Angle : 0.567 12.601 48515 Z= 0.292 Chirality : 0.045 0.309 5429 Planarity : 0.004 0.047 6007 Dihedral : 13.074 177.879 5464 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.28 % Allowed : 10.20 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.11 (0.13), residues: 4099 helix: 0.75 (0.14), residues: 1382 sheet: -0.91 (0.19), residues: 723 loop : -0.20 (0.14), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 220 TYR 0.022 0.001 TYR B 237 PHE 0.022 0.002 PHE A 112 TRP 0.013 0.002 TRP B 104 HIS 0.005 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.21 (35640) covalent geometry : angle 0.55012 / 0.29 (48470) hydrogen bonds : bond 0.03984 / 2.60 ( 1429) hydrogen bonds : angle 5.10565 / 3.58 ( 3956) metal coordination : bond 0.00738 / 0.52 ( 32) metal coordination : angle 4.47924 / 3.32 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 476 time to evaluate : 1.377 Fit side-chains revert: symmetry clash REVERT: A 112 PHE cc_start: 0.8609 (t80) cc_final: 0.8231 (t80) REVERT: A 147 LEU cc_start: 0.8267 (mp) cc_final: 0.7945 (mp) REVERT: A 220 ARG cc_start: 0.7954 (tpt-90) cc_final: 0.7701 (tpt-90) REVERT: B 383 ASP cc_start: 0.7736 (m-30) cc_final: 0.7508 (m-30) REVERT: B 471 ASP cc_start: 0.8659 (m-30) cc_final: 0.8442 (m-30) REVERT: B 869 ASP cc_start: 0.8257 (m-30) cc_final: 0.7859 (m-30) REVERT: B 967 ARG cc_start: 0.7966 (ptm-80) cc_final: 0.7646 (ptt90) REVERT: B 1158 ASP cc_start: 0.8123 (t0) cc_final: 0.7822 (t70) REVERT: B 1218 ARG cc_start: 0.7567 (mtm180) cc_final: 0.6977 (mtp-110) REVERT: B 1228 MET cc_start: 0.8939 (ptt) cc_final: 0.8724 (ptt) REVERT: E 108 GLN cc_start: 0.7993 (tm-30) cc_final: 0.7477 (tm-30) REVERT: E 172 ARG cc_start: 0.8250 (mtt90) cc_final: 0.7917 (mtt90) REVERT: H 146 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8173 (ttpt) REVERT: I 93 GLU cc_start: 0.8226 (tt0) cc_final: 0.7911 (tt0) REVERT: O 36 ASP cc_start: 0.8296 (p0) cc_final: 0.8050 (p0) outliers start: 47 outliers final: 36 residues processed: 502 average time/residue: 0.2494 time to fit residues: 199.0877 Evaluate side-chains 496 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 459 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 465 TYR Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 761 GLU Chi-restraints excluded: chain B residue 978 THR Chi-restraints excluded: chain B residue 1213 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 146 LYS Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain K residue 103 GLU Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 72 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 56 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 306 optimal weight: 0.1980 chunk 295 optimal weight: 8.9990 chunk 199 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 42 optimal weight: 0.5980 chunk 191 optimal weight: 2.9990 chunk 157 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 187 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 HIS A 982 ASN A1042 ASN B 221 HIS B 727 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.149481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.114167 restraints weight = 42588.765| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.03 r_work: 0.2888 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 35672 Z= 0.110 Angle : 0.509 10.866 48515 Z= 0.265 Chirality : 0.043 0.311 5429 Planarity : 0.004 0.057 6007 Dihedral : 12.951 176.329 5464 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.33 % Allowed : 11.13 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: 0.14 (0.13), residues: 4099 helix: 1.05 (0.14), residues: 1372 sheet: -0.80 (0.19), residues: 701 loop : -0.12 (0.14), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 928 TYR 0.017 0.001 TYR B 237 PHE 0.019 0.001 PHE A 112 TRP 0.013 0.001 TRP A1192 HIS 0.005 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (35640) covalent geometry : angle 0.49501 / 0.26 (48470) hydrogen bonds : bond 0.03419 / 2.25 ( 1429) hydrogen bonds : angle 4.87406 / 3.43 ( 3956) metal coordination : bond 0.00601 / 0.42 ( 32) metal coordination : angle 3.89595 / 2.88 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 498 time to evaluate : 1.289 Fit side-chains revert: symmetry clash REVERT: A 112 PHE cc_start: 0.8554 (t80) cc_final: 0.8138 (t80) REVERT: A 147 LEU cc_start: 0.8230 (mp) cc_final: 0.7938 (mp) REVERT: A 220 ARG cc_start: 0.7924 (tpt-90) cc_final: 0.7611 (tpt-90) REVERT: A 918 LYS cc_start: 0.8685 (tmtt) cc_final: 0.8469 (tptm) REVERT: A 1447 GLU cc_start: 0.8160 (tt0) cc_final: 0.7814 (mt-10) REVERT: B 383 ASP cc_start: 0.7700 (m-30) cc_final: 0.7483 (m-30) REVERT: B 655 LYS cc_start: 0.8797 (mmtm) cc_final: 0.8160 (tttm) REVERT: B 869 ASP cc_start: 0.8143 (m-30) cc_final: 0.7755 (m-30) REVERT: B 967 ARG cc_start: 0.7846 (ptm-80) cc_final: 0.7497 (ptt90) REVERT: B 1158 ASP cc_start: 0.8083 (t0) cc_final: 0.7770 (t70) REVERT: C 154 ARG cc_start: 0.8378 (ttt-90) cc_final: 0.8016 (ttt-90) REVERT: D 170 GLN cc_start: 0.7361 (tp40) cc_final: 0.6841 (tp40) REVERT: E 108 GLN cc_start: 0.8050 (tm-30) cc_final: 0.7549 (tm-30) REVERT: E 172 ARG cc_start: 0.8181 (mtt90) cc_final: 0.7961 (mtt90) REVERT: G 17 TYR cc_start: 0.9044 (m-80) cc_final: 0.8798 (m-80) REVERT: H 146 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8060 (ttpt) REVERT: I 93 GLU cc_start: 0.8125 (tt0) cc_final: 0.7747 (tt0) REVERT: O 36 ASP cc_start: 0.8238 (p0) cc_final: 0.7964 (p0) outliers start: 49 outliers final: 32 residues processed: 525 average time/residue: 0.2536 time to fit residues: 211.4130 Evaluate side-chains 505 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 472 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain B residue 465 TYR Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 978 THR Chi-restraints excluded: chain B residue 1156 SER Chi-restraints excluded: chain B residue 1213 GLU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 146 LYS Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain O residue 72 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 144 optimal weight: 0.1980 chunk 288 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 314 optimal weight: 2.9990 chunk 341 optimal weight: 0.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 HIS A 982 ASN B 507 ASN B 727 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.145693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.108642 restraints weight = 42567.040| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.23 r_work: 0.2824 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 35672 Z= 0.208 Angle : 0.564 11.854 48515 Z= 0.289 Chirality : 0.045 0.310 5429 Planarity : 0.004 0.049 6007 Dihedral : 12.979 177.977 5464 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.58 % Allowed : 11.81 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: 0.10 (0.13), residues: 4099 helix: 1.00 (0.14), residues: 1377 sheet: -0.83 (0.19), residues: 728 loop : -0.12 (0.14), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 928 TYR 0.022 0.001 TYR B 237 PHE 0.017 0.002 PHE C 63 TRP 0.013 0.002 TRP B 104 HIS 0.006 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (35640) covalent geometry : angle 0.54920 / 0.29 (48470) hydrogen bonds : bond 0.03837 / 2.51 ( 1429) hydrogen bonds : angle 4.96719 / 3.49 ( 3956) metal coordination : bond 0.00695 / 0.49 ( 32) metal coordination : angle 4.28221 / 3.21 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 481 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 ARG cc_start: 0.7987 (mmt90) cc_final: 0.7301 (mmt180) REVERT: A 112 PHE cc_start: 0.8617 (t80) cc_final: 0.8163 (t80) REVERT: A 147 LEU cc_start: 0.8267 (mp) cc_final: 0.7947 (mp) REVERT: A 220 ARG cc_start: 0.7957 (tpt-90) cc_final: 0.7624 (tpt-90) REVERT: B 869 ASP cc_start: 0.8245 (m-30) cc_final: 0.7851 (m-30) REVERT: B 967 ARG cc_start: 0.7922 (ptm-80) cc_final: 0.7575 (ptt90) REVERT: B 1158 ASP cc_start: 0.8027 (t0) cc_final: 0.7797 (t70) REVERT: D 170 GLN cc_start: 0.7292 (tp40) cc_final: 0.6847 (tp40) REVERT: E 108 GLN cc_start: 0.8087 (tm-30) cc_final: 0.7601 (tm-30) REVERT: H 146 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8151 (ttpt) REVERT: I 36 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7204 (pp) REVERT: I 93 GLU cc_start: 0.8103 (tt0) cc_final: 0.7728 (tt0) REVERT: O 36 ASP cc_start: 0.8260 (p0) cc_final: 0.8011 (p0) outliers start: 58 outliers final: 46 residues processed: 520 average time/residue: 0.2446 time to fit residues: 202.5266 Evaluate side-chains 514 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 466 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1407 CYS Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 761 GLU Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 978 THR Chi-restraints excluded: chain B residue 1156 SER Chi-restraints excluded: chain B residue 1213 GLU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 146 LYS Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain K residue 103 GLU Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 72 MET Chi-restraints excluded: chain O residue 85 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 152 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 406 optimal weight: 30.0000 chunk 353 optimal weight: 9.9990 chunk 259 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 411 optimal weight: 9.9990 chunk 146 optimal weight: 2.9990 chunk 399 optimal weight: 0.0000 chunk 373 optimal weight: 0.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 GLN B 727 ASN I 98 GLN M 80 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.145777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.108727 restraints weight = 42750.691| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.24 r_work: 0.2866 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 35672 Z= 0.191 Angle : 0.552 12.013 48515 Z= 0.284 Chirality : 0.045 0.308 5429 Planarity : 0.004 0.053 6007 Dihedral : 12.968 178.563 5464 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.71 % Allowed : 12.38 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: 0.12 (0.13), residues: 4099 helix: 1.01 (0.14), residues: 1379 sheet: -0.80 (0.19), residues: 715 loop : -0.12 (0.14), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 172 TYR 0.023 0.001 TYR B 237 PHE 0.015 0.002 PHE A 112 TRP 0.013 0.002 TRP B 104 HIS 0.005 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (35640) covalent geometry : angle 0.53724 / 0.28 (48470) hydrogen bonds : bond 0.03742 / 2.45 ( 1429) hydrogen bonds : angle 4.95619 / 3.49 ( 3956) metal coordination : bond 0.00670 / 0.47 ( 32) metal coordination : angle 4.22449 / 3.16 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 479 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.8647 (t80) cc_final: 0.8204 (t80) REVERT: A 147 LEU cc_start: 0.8463 (mp) cc_final: 0.8139 (mp) REVERT: A 220 ARG cc_start: 0.7936 (tpt-90) cc_final: 0.7657 (tpt-90) REVERT: B 869 ASP cc_start: 0.8249 (m-30) cc_final: 0.7891 (m-30) REVERT: B 967 ARG cc_start: 0.8042 (ptm-80) cc_final: 0.7749 (ptt90) REVERT: D 170 GLN cc_start: 0.7204 (tp40) cc_final: 0.6752 (tp40) REVERT: E 108 GLN cc_start: 0.7976 (tm-30) cc_final: 0.7534 (tm-30) REVERT: F 86 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7419 (mt-10) REVERT: H 146 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8229 (ttpt) REVERT: I 36 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7376 (pp) REVERT: I 93 GLU cc_start: 0.8134 (tt0) cc_final: 0.7781 (tt0) REVERT: O 36 ASP cc_start: 0.8248 (p0) cc_final: 0.7977 (p0) outliers start: 63 outliers final: 48 residues processed: 519 average time/residue: 0.2407 time to fit residues: 199.7517 Evaluate side-chains 521 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 470 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 465 TYR Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 761 GLU Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 978 THR Chi-restraints excluded: chain B residue 1156 SER Chi-restraints excluded: chain B residue 1182 GLU Chi-restraints excluded: chain B residue 1213 GLU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 146 LYS Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain O residue 72 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 316 optimal weight: 0.6980 chunk 405 optimal weight: 50.0000 chunk 77 optimal weight: 0.3980 chunk 95 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 195 optimal weight: 3.9990 chunk 246 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 114 optimal weight: 30.0000 chunk 7 optimal weight: 30.0000 chunk 348 optimal weight: 0.2980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 GLN A 982 ASN B 727 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.148153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.112597 restraints weight = 42440.265| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.09 r_work: 0.2844 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35672 Z= 0.127 Angle : 0.520 11.066 48515 Z= 0.268 Chirality : 0.043 0.307 5429 Planarity : 0.004 0.052 6007 Dihedral : 12.914 177.626 5464 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.61 % Allowed : 12.65 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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 (0.13), residues: 4099 helix: 1.19 (0.14), residues: 1374 sheet: -0.79 (0.19), residues: 703 loop : -0.09 (0.14), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 166 TYR 0.019 0.001 TYR B 237 PHE 0.020 0.001 PHE O 37 TRP 0.013 0.001 TRP A1192 HIS 0.005 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (35640) covalent geometry : angle 0.50633 / 0.27 (48470) hydrogen bonds : bond 0.03445 / 2.27 ( 1429) hydrogen bonds : angle 4.83752 / 3.41 ( 3956) metal coordination : bond 0.00586 / 0.41 ( 32) metal coordination : angle 3.95029 / 2.95 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 487 time to evaluate : 1.400 Fit side-chains revert: symmetry clash REVERT: A 70 ARG cc_start: 0.7844 (mmt90) cc_final: 0.7278 (mmt180) REVERT: A 112 PHE cc_start: 0.8562 (t80) cc_final: 0.8098 (t80) REVERT: A 147 LEU cc_start: 0.8244 (mp) cc_final: 0.7903 (mp) REVERT: A 220 ARG cc_start: 0.7929 (tpt-90) cc_final: 0.7613 (tpt-90) REVERT: A 1447 GLU cc_start: 0.8180 (tt0) cc_final: 0.7838 (mt-10) REVERT: B 869 ASP cc_start: 0.8258 (m-30) cc_final: 0.7891 (m-30) REVERT: B 967 ARG cc_start: 0.7862 (ptm-80) cc_final: 0.7519 (ptt90) REVERT: C 154 ARG cc_start: 0.8396 (ttt-90) cc_final: 0.8045 (ttt-90) REVERT: D 170 GLN cc_start: 0.7223 (tp40) cc_final: 0.6802 (tp40) REVERT: E 108 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7631 (tm-30) REVERT: F 86 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7465 (mt-10) REVERT: F 100 ARG cc_start: 0.9120 (mmm-85) cc_final: 0.8863 (mtp85) REVERT: G 17 TYR cc_start: 0.9049 (m-80) cc_final: 0.8821 (m-80) REVERT: H 8 ASP cc_start: 0.8770 (t0) cc_final: 0.8437 (t70) REVERT: H 146 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8115 (ttpt) REVERT: I 93 GLU cc_start: 0.8158 (tt0) cc_final: 0.7755 (tt0) REVERT: O 36 ASP cc_start: 0.8293 (p0) cc_final: 0.8029 (p0) outliers start: 59 outliers final: 48 residues processed: 523 average time/residue: 0.2338 time to fit residues: 195.7281 Evaluate side-chains 526 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 476 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1407 CYS Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 465 TYR Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 761 GLU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 978 THR Chi-restraints excluded: chain B residue 1156 SER Chi-restraints excluded: chain B residue 1182 GLU Chi-restraints excluded: chain B residue 1213 GLU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 82 GLU Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 146 LYS Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain K residue 103 GLU Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 72 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 45 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 chunk 327 optimal weight: 2.9990 chunk 167 optimal weight: 0.4980 chunk 361 optimal weight: 0.4980 chunk 412 optimal weight: 8.9990 chunk 386 optimal weight: 1.9990 chunk 227 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 GLN A 441 GLN A 982 ASN B 507 ASN B 727 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.148928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.113653 restraints weight = 42262.315| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.02 r_work: 0.2877 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35672 Z= 0.122 Angle : 0.515 10.602 48515 Z= 0.266 Chirality : 0.043 0.308 5429 Planarity : 0.004 0.053 6007 Dihedral : 12.871 177.804 5464 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.58 % Allowed : 12.92 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: 0.32 (0.13), residues: 4099 helix: 1.26 (0.14), residues: 1374 sheet: -0.73 (0.19), residues: 703 loop : -0.06 (0.14), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 166 TYR 0.017 0.001 TYR B 237 PHE 0.014 0.001 PHE O 37 TRP 0.013 0.001 TRP A1192 HIS 0.005 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (35640) covalent geometry : angle 0.50217 / 0.27 (48470) hydrogen bonds : bond 0.03352 / 2.21 ( 1429) hydrogen bonds : angle 4.76870 / 3.37 ( 3956) metal coordination : bond 0.00585 / 0.41 ( 32) metal coordination : angle 3.77981 / 2.82 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 487 time to evaluate : 1.413 Fit side-chains revert: symmetry clash REVERT: A 112 PHE cc_start: 0.8507 (t80) cc_final: 0.8012 (t80) REVERT: A 147 LEU cc_start: 0.8292 (mp) cc_final: 0.7954 (mp) REVERT: A 220 ARG cc_start: 0.7927 (tpt-90) cc_final: 0.7567 (tpt-90) REVERT: A 918 LYS cc_start: 0.8733 (tmtt) cc_final: 0.8527 (tptm) REVERT: A 1302 GLU cc_start: 0.8461 (mp0) cc_final: 0.8227 (mp0) REVERT: A 1447 GLU cc_start: 0.8156 (tt0) cc_final: 0.7834 (mt-10) REVERT: B 339 TYR cc_start: 0.8357 (m-80) cc_final: 0.8038 (m-80) REVERT: B 869 ASP cc_start: 0.8287 (m-30) cc_final: 0.7918 (m-30) REVERT: B 967 ARG cc_start: 0.7893 (ptm-80) cc_final: 0.7563 (ptt90) REVERT: C 154 ARG cc_start: 0.8397 (ttt-90) cc_final: 0.8046 (ttt-90) REVERT: D 170 GLN cc_start: 0.7260 (tp40) cc_final: 0.6902 (tp40) REVERT: E 108 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7624 (tm-30) REVERT: F 86 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7472 (mt-10) REVERT: F 100 ARG cc_start: 0.9095 (mmm-85) cc_final: 0.8867 (mtp85) REVERT: G 17 TYR cc_start: 0.9041 (m-80) cc_final: 0.8812 (m-80) REVERT: G 117 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6181 (mmt) REVERT: H 8 ASP cc_start: 0.8716 (t0) cc_final: 0.8364 (t70) REVERT: H 146 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8062 (ttpt) REVERT: I 36 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7212 (pp) REVERT: I 93 GLU cc_start: 0.8152 (tt0) cc_final: 0.7863 (tt0) REVERT: L 24 THR cc_start: 0.9068 (p) cc_final: 0.8678 (p) REVERT: M 32 VAL cc_start: 0.9034 (p) cc_final: 0.8811 (m) REVERT: O 36 ASP cc_start: 0.8247 (p0) cc_final: 0.7978 (p0) REVERT: O 84 LYS cc_start: 0.8426 (mtpp) cc_final: 0.8178 (mtpp) outliers start: 58 outliers final: 49 residues processed: 521 average time/residue: 0.2467 time to fit residues: 205.0183 Evaluate side-chains 524 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 471 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 761 GLU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 978 THR Chi-restraints excluded: chain B residue 1156 SER Chi-restraints excluded: chain B residue 1182 GLU Chi-restraints excluded: chain B residue 1213 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 82 GLU Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 146 LYS Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 103 GLU Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 72 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 5 optimal weight: 4.9990 chunk 353 optimal weight: 9.9990 chunk 290 optimal weight: 4.9990 chunk 214 optimal weight: 4.9990 chunk 292 optimal weight: 7.9990 chunk 264 optimal weight: 9.9990 chunk 251 optimal weight: 0.6980 chunk 317 optimal weight: 1.9990 chunk 269 optimal weight: 0.9980 chunk 167 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 GLN A 982 ASN B 727 ASN M 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.148196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.112273 restraints weight = 42667.844| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.15 r_work: 0.2896 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 35672 Z= 0.173 Angle : 0.544 11.356 48515 Z= 0.279 Chirality : 0.044 0.308 5429 Planarity : 0.004 0.053 6007 Dihedral : 12.893 178.690 5464 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.52 % Allowed : 13.17 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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 (0.13), residues: 4099 helix: 1.19 (0.14), residues: 1381 sheet: -0.72 (0.19), residues: 715 loop : -0.04 (0.14), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 166 TYR 0.016 0.001 TYR O 35 PHE 0.016 0.001 PHE O 37 TRP 0.012 0.001 TRP B 104 HIS 0.005 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (35640) covalent geometry : angle 0.53011 / 0.28 (48470) hydrogen bonds : bond 0.03567 / 2.35 ( 1429) hydrogen bonds : angle 4.84371 / 3.42 ( 3956) metal coordination : bond 0.00618 / 0.43 ( 32) metal coordination : angle 3.98702 / 2.99 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8198 Ramachandran restraints generated. 4099 Oldfield, 0 Emsley, 4099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 473 time to evaluate : 1.413 Fit side-chains revert: symmetry clash REVERT: A 112 PHE cc_start: 0.8535 (t80) cc_final: 0.8038 (t80) REVERT: A 147 LEU cc_start: 0.8386 (mp) cc_final: 0.8043 (mp) REVERT: A 220 ARG cc_start: 0.7970 (tpt-90) cc_final: 0.7655 (tpt-90) REVERT: A 1302 GLU cc_start: 0.8544 (mp0) cc_final: 0.8314 (mp0) REVERT: A 1447 GLU cc_start: 0.8241 (tt0) cc_final: 0.7944 (mt-10) REVERT: B 869 ASP cc_start: 0.8356 (m-30) cc_final: 0.7988 (m-30) REVERT: B 967 ARG cc_start: 0.7988 (ptm-80) cc_final: 0.7656 (ptt90) REVERT: C 154 ARG cc_start: 0.8515 (ttt-90) cc_final: 0.8197 (ttt-90) REVERT: D 170 GLN cc_start: 0.7144 (tp40) cc_final: 0.6806 (tp40) REVERT: E 108 GLN cc_start: 0.8138 (tm-30) cc_final: 0.7659 (tm-30) REVERT: F 86 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7477 (mt-10) REVERT: F 100 ARG cc_start: 0.9111 (mmm-85) cc_final: 0.8866 (mtp85) REVERT: G 17 TYR cc_start: 0.8987 (m-80) cc_final: 0.8756 (m-80) REVERT: G 117 MET cc_start: 0.7128 (OUTLIER) cc_final: 0.6203 (mmt) REVERT: H 8 ASP cc_start: 0.8763 (t0) cc_final: 0.8450 (t70) REVERT: H 146 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8170 (ttpt) REVERT: I 36 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7316 (pp) REVERT: I 93 GLU cc_start: 0.8205 (tt0) cc_final: 0.7924 (tt0) REVERT: L 24 THR cc_start: 0.9151 (p) cc_final: 0.8727 (p) REVERT: O 36 ASP cc_start: 0.8247 (p0) cc_final: 0.7981 (p0) outliers start: 56 outliers final: 49 residues processed: 509 average time/residue: 0.2442 time to fit residues: 198.6485 Evaluate side-chains 520 residues out of total 3686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 467 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 465 TYR Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 761 GLU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 978 THR Chi-restraints excluded: chain B residue 1156 SER Chi-restraints excluded: chain B residue 1182 GLU Chi-restraints excluded: chain B residue 1213 GLU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 82 GLU Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 146 LYS Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 103 GLU Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 72 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 365 optimal weight: 0.8980 chunk 237 optimal weight: 0.9980 chunk 234 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 381 optimal weight: 6.9990 chunk 374 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 4 optimal weight: 10.0000 chunk 305 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 982 ASN B 727 ASN B1045 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.150050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.115383 restraints weight = 42615.850| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.98 r_work: 0.2979 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35672 Z= 0.126 Angle : 0.518 10.929 48515 Z= 0.267 Chirality : 0.043 0.309 5429 Planarity : 0.004 0.055 6007 Dihedral : 12.861 178.308 5464 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.55 % Allowed : 13.17 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: 0.35 (0.14), residues: 4099 helix: 1.30 (0.15), residues: 1372 sheet: -0.70 (0.19), residues: 713 loop : -0.05 (0.14), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 172 TYR 0.016 0.001 TYR O 35 PHE 0.014 0.001 PHE O 37 TRP 0.013 0.001 TRP A1192 HIS 0.005 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (35640) covalent geometry : angle 0.50503 / 0.27 (48470) hydrogen bonds : bond 0.03349 / 2.21 ( 1429) hydrogen bonds : angle 4.75969 / 3.36 ( 3956) metal coordination : bond 0.00563 / 0.39 ( 32) metal coordination : angle 3.80605 / 2.85 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9898.84 seconds wall clock time: 170 minutes 14.27 seconds (10214.27 seconds total)