Starting phenix.real_space_refine (version: dev) on Tue May 17 17:03:40 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fyw_3378/05_2022/5fyw_3378.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fyw_3378/05_2022/5fyw_3378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fyw_3378/05_2022/5fyw_3378.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fyw_3378/05_2022/5fyw_3378.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fyw_3378/05_2022/5fyw_3378.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fyw_3378/05_2022/5fyw_3378.pdb" } resolution = 4.35 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 ------------------------------------------------------------------------------- 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= -0.000 sd= 0.004 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B PHE 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 41710 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 10997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1398, 10997 Classifications: {'peptide': 1398} Link IDs: {'PTRANS': 62, 'TRANS': 1333, 'PCIS': 2} Chain breaks: 5 Chain: "B" Number of atoms: 9203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1157, 9203 Classifications: {'peptide': 1157} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 51, 'TRANS': 1105} Chain breaks: 8 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2061 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 11, 'TRANS': 250} Chain: "D" Number of atoms: 1253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1253 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain breaks: 1 Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 200, 'PCIS': 1} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 162, 'PCIS': 1} Chain: "H" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1089 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain breaks: 1 Chain: "I" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "L" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1785 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 919 Inner-chain residues flagged as termini: ['pdbres=" DG N 60 "'] Classifications: {'DNA': 47} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 46} Unresolved chain link angles: 45 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen chiralities: 46 Chain: "O" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1416 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 171, 'PCIS': 2} Chain: "Q" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1144 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 141, 'PCIS': 1} Chain breaks: 3 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 9, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "R" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1347 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain breaks: 8 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 324 Unresolved non-hydrogen angles: 408 Unresolved non-hydrogen dihedrals: 278 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 178 Chain: "T" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 909 Classifications: {'DNA': 47} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 46} Chain breaks: 1 Unresolved chain link angles: 46 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen chiralities: 46 Chain: "U" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 757 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'TRANS': 91} Chain breaks: 1 Chain: "V" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 782 Classifications: {'peptide': 100} Link IDs: {'TRANS': 99} Chain breaks: 1 Chain: "W" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 835 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 157} Link IDs: {'PTRANS': 7, 'TRANS': 160} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 570 Unresolved non-hydrogen angles: 727 Unresolved non-hydrogen dihedrals: 471 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 15, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 6, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 294 Chain: "X" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 710 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 136} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain breaks: 3 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 506 Unresolved non-hydrogen angles: 639 Unresolved non-hydrogen dihedrals: 434 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 4, 'ASP:plan': 13, 'PHE:plan': 4, 'GLU:plan': 12, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 253 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 2, ' MG': 1} 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} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" 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 813 SG CYS A 107 89.951 126.607 127.521 1.00164.06 S ATOM 837 SG CYS A 110 88.961 128.300 130.243 1.00142.57 S ATOM 1142 SG CYS A 148 92.379 129.765 129.479 1.00179.23 S ATOM 508 SG CYS A 67 48.316 120.643 103.771 1.00107.66 S ATOM 530 SG CYS A 70 48.235 124.884 105.496 1.00105.81 S ATOM 583 SG CYS A 77 49.838 123.276 102.328 1.00116.68 S ATOM 19718 SG CYS B1163 54.738 135.381 114.308 1.00110.90 S ATOM 19736 SG CYS B1166 57.488 132.890 113.966 1.00118.04 S ATOM 19861 SG CYS B1182 54.272 131.067 113.537 1.00120.54 S ATOM 19880 SG CYS B1185 54.880 132.742 116.277 1.00120.04 S ATOM 20847 SG CYS C 86 25.902 125.803 39.755 1.00132.68 S ATOM 20864 SG CYS C 88 26.454 123.091 41.843 1.00140.95 S ATOM 20897 SG CYS C 92 26.596 122.609 38.399 1.00 94.59 S ATOM 20920 SG CYS C 95 29.612 123.984 39.639 1.00 92.85 S ATOM 28410 SG CYS I 7 141.093 106.199 87.944 1.00191.60 S ATOM 28435 SG CYS I 10 138.997 103.830 90.156 1.00209.03 S ATOM 28601 SG CYS I 29 138.587 108.127 90.178 1.00219.81 S ATOM 28625 SG CYS I 32 141.292 105.940 91.471 1.00210.19 S ATOM 28952 SG CYS I 75 134.291 125.025 48.007 1.00167.19 S ATOM 28974 SG CYS I 78 134.853 122.022 45.382 1.00183.43 S ATOM 29190 SG CYS I 103 131.634 121.540 46.749 1.00183.79 S ATOM 29210 SG CYS I 106 134.981 121.362 48.753 1.00188.57 S ATOM 29355 SG CYS J 7 60.577 126.549 33.058 1.00 72.78 S ATOM 29378 SG CYS J 10 59.304 128.837 30.709 1.00 59.38 S ATOM 29658 SG CYS J 45 62.351 130.189 30.592 1.00 71.52 S ATOM 29664 SG CYS J 46 60.948 126.900 28.666 1.00 97.89 S ATOM 30787 SG CYS L 31 54.243 89.117 54.837 1.00150.62 S ATOM 30807 SG CYS L 34 53.518 87.028 52.168 1.00133.37 S ATOM 30911 SG CYS L 48 52.247 86.723 56.174 1.00148.15 S ATOM 30934 SG CYS L 51 55.497 85.871 54.896 1.00145.50 S ATOM 31162 SG CYS M 24 29.267 126.335 87.350 1.00148.82 S ATOM 31184 SG CYS M 27 26.791 125.414 85.082 1.00150.84 S ATOM 31328 SG CYS M 45 29.953 123.670 83.894 1.00165.01 S ATOM 31347 SG CYS M 48 29.131 127.721 84.193 1.00115.83 S Time building chain proxies: 23.06, per 1000 atoms: 0.55 Number of scatterers: 41710 At special positions: 0 Unit cell: (164.7, 216, 167.4, 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 10 29.99 S 218 16.00 P 92 15.00 Mg 1 11.99 O 7985 8.00 N 7325 7.00 C 26079 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 - 3.50 Amino acid : False - 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: 16.89 Conformation dependent library (CDL) restraints added in 6.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN A2453 " pdb="ZN ZN A2453 " - pdb=" SG CYS A 107 " pdb="ZN ZN A2453 " - pdb=" SG CYS A 148 " pdb="ZN ZN A2453 " - pdb=" SG CYS A 110 " pdb=" ZN A2454 " pdb="ZN ZN A2454 " - pdb=" SG CYS A 70 " pdb="ZN ZN A2454 " - pdb=" SG CYS A 77 " pdb="ZN ZN A2454 " - pdb=" SG CYS A 67 " pdb="ZN ZN A2454 " - pdb=" NE2 HIS A 80 " pdb=" ZN B2224 " pdb="ZN ZN B2224 " - pdb=" SG CYS B1182 " pdb="ZN ZN B2224 " - pdb=" SG CYS B1166 " pdb="ZN ZN B2224 " - pdb=" SG CYS B1185 " pdb="ZN ZN B2224 " - pdb=" SG CYS B1163 " pdb=" ZN C1266 " pdb="ZN ZN C1266 " - pdb=" SG CYS C 88 " pdb="ZN ZN C1266 " - pdb=" SG CYS C 92 " pdb="ZN ZN C1266 " - pdb=" SG CYS C 86 " pdb="ZN ZN C1266 " - pdb=" SG CYS C 95 " pdb=" ZN I1118 " pdb="ZN ZN I1118 " - pdb=" SG CYS I 7 " pdb="ZN ZN I1118 " - pdb=" SG CYS I 29 " pdb="ZN ZN I1118 " - pdb=" SG CYS I 32 " pdb="ZN ZN I1118 " - pdb=" SG CYS I 10 " pdb=" ZN I1119 " pdb="ZN ZN I1119 " - pdb=" SG CYS I 106 " pdb="ZN ZN I1119 " - pdb=" SG CYS I 78 " pdb="ZN ZN I1119 " - pdb=" SG CYS I 75 " pdb="ZN ZN I1119 " - pdb=" SG CYS I 103 " pdb=" ZN J1066 " pdb="ZN ZN J1066 " - pdb=" SG CYS J 10 " pdb="ZN ZN J1066 " - pdb=" SG CYS J 46 " pdb="ZN ZN J1066 " - pdb=" SG CYS J 45 " pdb="ZN ZN J1066 " - pdb=" SG CYS J 7 " pdb=" ZN L1071 " pdb="ZN ZN L1071 " - pdb=" SG CYS L 51 " pdb="ZN ZN L1071 " - pdb=" SG CYS L 34 " pdb="ZN ZN L1071 " - pdb=" SG CYS L 31 " pdb="ZN ZN L1071 " - pdb=" SG CYS L 48 " pdb=" ZN M1327 " pdb="ZN ZN M1327 " - pdb=" SG CYS M 48 " pdb="ZN ZN M1327 " - pdb=" SG CYS M 27 " pdb="ZN ZN M1327 " - pdb=" SG CYS M 45 " pdb="ZN ZN M1327 " - pdb=" SG CYS M 24 " Number of angles added : 45 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9778 Finding SS restraints... Secondary structure from input PDB file: 183 helices and 81 sheets defined 42.0% alpha, 22.0% beta 38 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 11.92 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.676A pdb=" N ALA A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 145 removed outlier: 4.062A pdb=" N THR A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 214 removed outlier: 3.644A pdb=" N ILE A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 230 through 234 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 286 through 305 Processing helix chain 'A' and resid 324 through 331 removed outlier: 4.361A pdb=" N GLY A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 342 removed outlier: 4.218A pdb=" N MET A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY A 342 " --> pdb=" O GLY A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.919A pdb=" N ALA A 421 " --> pdb=" O TYR A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 472 through 476 removed outlier: 3.781A pdb=" N SER A 476 " --> pdb=" O SER A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 504 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 525 through 536 removed outlier: 3.622A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.550A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 582 removed outlier: 3.654A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 638 removed outlier: 3.721A pdb=" N ARG A 635 " --> pdb=" O HIS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 661 removed outlier: 3.798A pdb=" N LYS A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 646 " --> pdb=" O CYS A 642 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 669 Processing helix chain 'A' and resid 672 through 699 removed outlier: 3.684A pdb=" N ALA A 686 " --> pdb=" O THR A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 removed outlier: 3.610A pdb=" N ILE A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 798 Processing helix chain 'A' and resid 809 through 846 removed outlier: 3.636A pdb=" N PHE A 815 " --> pdb=" O GLN A 811 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A 827 " --> pdb=" O GLY A 823 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR A 836 " --> pdb=" O ALA A 832 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 840 " --> pdb=" O TYR A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 912 Processing helix chain 'A' and resid 915 through 920 Processing helix chain 'A' and resid 922 through 947 Processing helix chain 'A' and resid 959 through 972 removed outlier: 3.795A pdb=" N ILE A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 996 removed outlier: 3.875A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN A 996 " --> pdb=" O ASP A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1034 removed outlier: 5.345A pdb=" N LEU A1017 " --> pdb=" O ASP A1013 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N PHE A1018 " --> pdb=" O ALA A1014 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR A1028 " --> pdb=" O SER A1024 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ARG A1029 " --> pdb=" O ARG A1025 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ARG A1030 " --> pdb=" O LEU A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1078 removed outlier: 4.004A pdb=" N LEU A1067 " --> pdb=" O MET A1063 " (cutoff:3.500A) Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1096 through 1107 Processing helix chain 'A' and resid 1127 through 1139 removed outlier: 3.877A pdb=" N ALA A1131 " --> pdb=" O ASP A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1146 removed outlier: 3.737A pdb=" N VAL A1146 " --> pdb=" O THR A1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1142 through 1146' Processing helix chain 'A' and resid 1166 through 1175 removed outlier: 3.696A pdb=" N PHE A1174 " --> pdb=" O ILE A1170 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER A1175 " --> pdb=" O GLN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1205 Processing helix chain 'A' and resid 1208 through 1221 Processing helix chain 'A' and resid 1255 through 1269 removed outlier: 4.408A pdb=" N MET A1259 " --> pdb=" O GLU A1255 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN A1265 " --> pdb=" O LYS A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1319 removed outlier: 3.856A pdb=" N VAL A1316 " --> pdb=" O ASN A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1360 removed outlier: 3.683A pdb=" N ILE A1335 " --> pdb=" O SER A1331 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE A1341 " --> pdb=" O GLU A1337 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N GLU A1342 " --> pdb=" O VAL A1338 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A1355 " --> pdb=" O GLU A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1377 removed outlier: 3.969A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1403 removed outlier: 3.933A pdb=" N PHE A1402 " --> pdb=" O MET A1398 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU A1403 " --> pdb=" O ARG A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1415 Processing helix chain 'A' and resid 1423 through 1430 Processing helix chain 'A' and resid 1436 through 1441 removed outlier: 4.409A pdb=" N PHE A1441 " --> pdb=" O THR A1438 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1452 removed outlier: 3.864A pdb=" N LEU A1450 " --> pdb=" O ASP A1446 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A1452 " --> pdb=" O GLU A1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 42 removed outlier: 3.981A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 67 removed outlier: 3.775A pdb=" N LEU B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 179 through 184 removed outlier: 3.576A pdb=" N SER B 182 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU B 183 " --> pdb=" O TYR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 193 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 302 Processing helix chain 'B' and resid 307 through 324 removed outlier: 4.382A pdb=" N LEU B 311 " --> pdb=" O ASP B 307 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 338 removed outlier: 3.651A pdb=" N GLY B 338 " --> pdb=" O ILE B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.735A pdb=" N GLY B 342 " --> pdb=" O THR B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 358 removed outlier: 3.988A pdb=" N GLN B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 390 removed outlier: 3.668A pdb=" N PHE B 376 " --> pdb=" O SER B 372 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE B 377 " --> pdb=" O ARG B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 439 Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 449 through 464 removed outlier: 4.404A pdb=" N ILE B 453 " --> pdb=" O ASN B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 removed outlier: 3.786A pdb=" N SER B 559 " --> pdb=" O ILE B 555 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU B 560 " --> pdb=" O THR B 556 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TRP B 561 " --> pdb=" O PHE B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 668 removed outlier: 3.775A pdb=" N THR B 664 " --> pdb=" O LYS B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.751A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 711 Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 750 through 756 removed outlier: 3.705A pdb=" N ILE B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE B 756 " --> pdb=" O ALA B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 761 Processing helix chain 'B' and resid 763 through 777 removed outlier: 3.515A pdb=" N ASN B 767 " --> pdb=" O GLN B 763 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA B 777 " --> pdb=" O MET B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 788 removed outlier: 4.540A pdb=" N ASN B 786 " --> pdb=" O THR B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 813 removed outlier: 3.700A pdb=" N LYS B 813 " --> pdb=" O GLU B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 927 through 932 Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.382A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1039 removed outlier: 3.640A pdb=" N CYS B1029 " --> pdb=" O HIS B1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.624A pdb=" N HIS B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1103 removed outlier: 3.601A pdb=" N LYS B1102 " --> pdb=" O MET B1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1152 removed outlier: 3.719A pdb=" N LEU B1147 " --> pdb=" O ALA B1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 removed outlier: 3.608A pdb=" N ALA C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 removed outlier: 3.704A pdb=" N GLU C 200 " --> pdb=" O ASP C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 239 through 264 Processing helix chain 'D' and resid 53 through 73 removed outlier: 3.618A pdb=" N ILE D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU D 65 " --> pdb=" O GLU D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 133 removed outlier: 3.720A pdb=" N LEU D 123 " --> pdb=" O ARG D 119 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 152 removed outlier: 3.830A pdb=" N LYS D 142 " --> pdb=" O ASN D 138 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN D 146 " --> pdb=" O LYS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 168 removed outlier: 3.799A pdb=" N ALA D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS D 168 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 removed outlier: 3.521A pdb=" N GLY D 181 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 removed outlier: 3.650A pdb=" N ASN D 199 " --> pdb=" O PRO D 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 196 through 199' Processing helix chain 'D' and resid 203 through 218 removed outlier: 3.553A pdb=" N ILE D 210 " --> pdb=" O GLU D 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 26 Processing helix chain 'E' and resid 31 through 37 Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 75 through 79 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 removed outlier: 3.784A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.805A pdb=" N TYR G 25 " --> pdb=" O ARG G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 115 Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'J' and resid 16 through 29 removed outlier: 4.251A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 40 removed outlier: 3.763A pdb=" N SER J 37 " --> pdb=" O GLY J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 53 removed outlier: 4.068A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.683A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.217A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 111 removed outlier: 3.825A pdb=" N LEU K 111 " --> pdb=" O THR K 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 124 through 140 Processing helix chain 'M' and resid 143 through 158 Processing helix chain 'M' and resid 168 through 183 removed outlier: 3.615A pdb=" N MET M 172 " --> pdb=" O MET M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 196 Processing helix chain 'M' and resid 200 through 217 Processing helix chain 'M' and resid 237 through 247 removed outlier: 3.843A pdb=" N ARG M 241 " --> pdb=" O THR M 237 " (cutoff:3.500A) Processing helix chain 'M' and resid 249 through 267 Processing helix chain 'M' and resid 273 through 289 removed outlier: 3.968A pdb=" N ILE M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 302 Processing helix chain 'M' and resid 305 through 319 removed outlier: 3.680A pdb=" N ILE M 315 " --> pdb=" O SER M 311 " (cutoff:3.500A) Processing helix chain 'M' and resid 320 through 324 removed outlier: 3.613A pdb=" N LEU M 323 " --> pdb=" O ARG M 320 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL M 324 " --> pdb=" O ASP M 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 320 through 324' Processing helix chain 'O' and resid 81 through 89 Processing helix chain 'O' and resid 128 through 147 Processing helix chain 'O' and resid 171 through 179 Processing helix chain 'O' and resid 219 through 237 removed outlier: 3.849A pdb=" N ILE O 223 " --> pdb=" O GLN O 219 " (cutoff:3.500A) Proline residue: O 232 - end of helix Processing helix chain 'Q' and resid 26 through 35 Processing helix chain 'Q' and resid 107 through 114 removed outlier: 4.051A pdb=" N LEU Q 111 " --> pdb=" O PRO Q 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 337 through 346 Processing helix chain 'Q' and resid 405 through 414 Processing helix chain 'R' and resid 74 through 82 Processing helix chain 'R' and resid 233 through 244 removed outlier: 3.923A pdb=" N VAL R 237 " --> pdb=" O TYR R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 267 Processing helix chain 'R' and resid 295 through 310 Processing helix chain 'R' and resid 314 through 323 Processing helix chain 'R' and resid 325 through 336 removed outlier: 3.616A pdb=" N LYS R 335 " --> pdb=" O GLU R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 359 through 370 Processing helix chain 'U' and resid 3 through 28 removed outlier: 4.043A pdb=" N SER U 7 " --> pdb=" O ASN U 3 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU U 23 " --> pdb=" O ASN U 19 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASP U 24 " --> pdb=" O GLU U 20 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 47 Processing helix chain 'V' and resid 8 through 12 Processing helix chain 'V' and resid 13 through 29 Processing helix chain 'V' and resid 35 through 55 Processing helix chain 'W' and resid 6 through 20 Processing helix chain 'W' and resid 22 through 35 removed outlier: 3.719A pdb=" N VAL W 26 " --> pdb=" O GLY W 22 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 47 Processing helix chain 'W' and resid 50 through 64 Proline residue: W 56 - end of helix removed outlier: 3.615A pdb=" N ASP W 64 " --> pdb=" O ARG W 60 " (cutoff:3.500A) Processing helix chain 'W' and resid 90 through 111 removed outlier: 3.546A pdb=" N ALA W 94 " --> pdb=" O LYS W 90 " (cutoff:3.500A) Processing helix chain 'W' and resid 132 through 140 Processing helix chain 'W' and resid 168 through 191 Proline residue: W 181 - end of helix Processing helix chain 'X' and resid 124 through 139 removed outlier: 4.359A pdb=" N LEU X 128 " --> pdb=" O ASP X 124 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU X 129 " --> pdb=" O SER X 125 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 151 Processing helix chain 'X' and resid 156 through 166 removed outlier: 4.184A pdb=" N ILE X 160 " --> pdb=" O ASP X 156 " (cutoff:3.500A) Processing helix chain 'X' and resid 187 through 199 Processing helix chain 'X' and resid 200 through 202 No H-bonds generated for 'chain 'X' and resid 200 through 202' Processing helix chain 'X' and resid 206 through 214 Processing helix chain 'X' and resid 216 through 228 removed outlier: 4.428A pdb=" N THR X 220 " --> pdb=" O GLN X 216 " (cutoff:3.500A) Processing helix chain 'X' and resid 256 through 263 Processing helix chain 'X' and resid 272 through 280 Processing sheet with id= AA, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id= AB, first strand: chain 'A' and resid 82 through 91 removed outlier: 10.072A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 10.013A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'A' and resid 173 through 177 removed outlier: 4.759A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 250 through 252 Processing sheet with id= AE, first strand: chain 'A' and resid 343 through 345 Processing sheet with id= AF, first strand: chain 'A' and resid 455 through 456 removed outlier: 4.069A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'A' and resid 455 through 456 removed outlier: 4.069A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'A' and resid 468 through 470 Processing sheet with id= AI, first strand: chain 'A' and resid 363 through 367 Processing sheet with id= AJ, first strand: chain 'A' and resid 375 through 379 removed outlier: 6.751A pdb=" N LYS A 431 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL A 405 " --> pdb=" O LYS A 431 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLU A 433 " --> pdb=" O LYS A 403 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP A 411 " --> pdb=" O ARG A 407 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.702A pdb=" N LYS A 518 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'A' and resid 540 through 541 Processing sheet with id= AM, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.485A pdb=" N TYR H 102 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N SER H 117 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N PHE H 104 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N TYR H 115 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N GLU H 106 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA H 113 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.734A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'A' and resid 766 through 767 Processing sheet with id= AP, first strand: chain 'A' and resid 769 through 770 Processing sheet with id= AQ, first strand: chain 'A' and resid 849 through 850 removed outlier: 3.544A pdb=" N MET A 849 " --> pdb=" O ARG A 857 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'A' and resid 878 through 882 Processing sheet with id= AS, first strand: chain 'A' and resid 1280 through 1287 removed outlier: 5.447A pdb=" N ARG A1281 " --> pdb=" O ASP A1309 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP A1309 " --> pdb=" O ARG A1281 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.883A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU A1192 " --> pdb=" O ILE A1152 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ILE A1152 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N SER A1150 " --> pdb=" O ARG I 45 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ARG I 45 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE A1152 " --> pdb=" O VAL I 43 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'A' and resid 1290 through 1292 Processing sheet with id= AV, first strand: chain 'A' and resid 1442 through 1444 Processing sheet with id= BA, first strand: chain 'B' and resid 109 through 111 Processing sheet with id= BB, first strand: chain 'B' and resid 149 through 150 removed outlier: 3.675A pdb=" N TYR B 149 " --> pdb=" O GLU B 138 " (cutoff:3.500A) No H-bonds generated for sheet with id= BB Processing sheet with id= BC, first strand: chain 'B' and resid 164 through 171 removed outlier: 5.926A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Processing sheet with id= QA, first strand: chain 'Q' and resid 331 through 333 removed outlier: 4.051A pdb=" N LYS Q 333 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE B 70 " --> pdb=" O LYS Q 333 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N HIS B 110 " --> pdb=" O PRO B 100 " (cutoff:3.500A) Processing sheet with id= QB, first strand: chain 'Q' and resid 331 through 333 removed outlier: 4.051A pdb=" N LYS Q 333 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE B 70 " --> pdb=" O LYS Q 333 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N GLU B 89 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N TYR B 137 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N SER B 91 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ARG B 135 " --> pdb=" O SER B 91 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLY B 93 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N LYS B 133 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE B 95 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ASP B 131 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N VAL B 97 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE B 129 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LYS B 99 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLY B 127 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N SER B 125 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR B 149 " --> pdb=" O THR B 136 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'B' and resid 203 through 205 Processing sheet with id= BE, first strand: chain 'B' and resid 215 through 218 Processing sheet with id= BF, first strand: chain 'B' and resid 224 through 227 removed outlier: 3.752A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'B' and resid 497 through 499 Processing sheet with id= BH, first strand: chain 'B' and resid 544 through 545 Processing sheet with id= BI, first strand: chain 'B' and resid 650 through 651 Processing sheet with id= BJ, first strand: chain 'B' and resid 690 through 694 Processing sheet with id= BK, first strand: chain 'B' and resid 703 through 704 Processing sheet with id= BL, first strand: chain 'B' and resid 703 through 704 Processing sheet with id= BM, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.114A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'B' and resid 793 through 796 removed outlier: 3.515A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'B' and resid 793 through 796 removed outlier: 3.515A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'B' and resid 804 through 805 Processing sheet with id= BQ, first strand: chain 'B' and resid 987 through 989 Processing sheet with id= BR, first strand: chain 'B' and resid 987 through 989 removed outlier: 4.149A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'B' and resid 1069 through 1070 Processing sheet with id= BT, first strand: chain 'B' and resid 873 through 874 Processing sheet with id= BU, first strand: chain 'B' and resid 910 through 912 removed outlier: 6.880A pdb=" N THR B 939 " --> pdb=" O ILE B 911 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id= BW, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id= BX, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id= CA, first strand: chain 'C' and resid 7 through 13 removed outlier: 5.716A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.139A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.814A pdb=" N THR C 111 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LYS C 146 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL C 113 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain 'D' and resid 36 through 38 Processing sheet with id= DB, first strand: chain 'D' and resid 48 through 50 removed outlier: 4.631A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing sheet with id= DC, first strand: chain 'D' and resid 48 through 50 removed outlier: 4.631A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL G 77 " --> pdb=" O LEU G 46 " (cutoff:3.500A) Processing sheet with id= GA, first strand: chain 'G' and resid 60 through 61 Processing sheet with id= EA, first strand: chain 'E' and resid 60 through 62 removed outlier: 3.668A pdb=" N TRP E 79 " --> pdb=" O THR E 107 " (cutoff:3.500A) Processing sheet with id= EB, first strand: chain 'E' and resid 87 through 88 Processing sheet with id= EC, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.577A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id= GB, first strand: chain 'G' and resid 85 through 95 removed outlier: 5.728A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) Processing sheet with id= GC, first strand: chain 'G' and resid 120 through 122 Processing sheet with id= IA, first strand: chain 'I' and resid 15 through 19 Processing sheet with id= IB, first strand: chain 'I' and resid 70 through 71 removed outlier: 3.635A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id= KA, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.565A pdb=" N LYS K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR K 61 " --> pdb=" O LYS K 72 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id= MA, first strand: chain 'M' and resid 34 through 37 removed outlier: 6.328A pdb=" N VAL M 43 " --> pdb=" O LEU M 52 " (cutoff:3.500A) Processing sheet with id= OA, first strand: chain 'O' and resid 92 through 93 removed outlier: 3.586A pdb=" N ILE O 106 " --> pdb=" O THR O 111 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR O 111 " --> pdb=" O ILE O 106 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL O 122 " --> pdb=" O VAL O 74 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL O 74 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N THR O 124 " --> pdb=" O ALA O 72 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ALA O 72 " --> pdb=" O THR O 124 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA O 126 " --> pdb=" O ILE O 70 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU O 67 " --> pdb=" O VAL O 161 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N VAL O 161 " --> pdb=" O LEU O 67 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASN O 69 " --> pdb=" O ASN O 159 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASN O 159 " --> pdb=" O ASN O 69 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL O 71 " --> pdb=" O ILE O 157 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE O 157 " --> pdb=" O VAL O 71 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N THR O 73 " --> pdb=" O PHE O 155 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE O 155 " --> pdb=" O THR O 73 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ILE O 160 " --> pdb=" O GLY O 216 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY O 216 " --> pdb=" O ILE O 160 " (cutoff:3.500A) Processing sheet with id= QC, first strand: chain 'Q' and resid 98 through 105 removed outlier: 4.569A pdb=" N ILE R 104 " --> pdb=" O LEU R 122 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 119 through 126 current: chain 'R' and resid 133 through 138 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 133 through 138 current: chain 'R' and resid 220 through 225 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 220 through 225 current: chain 'R' and resid 64 through 72 removed outlier: 4.386A pdb=" N GLN R 67 " --> pdb=" O VAL Q 378 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 384 through 388 current: chain 'Q' and resid 391 through 398 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 391 through 398 current: chain 'Q' and resid 138 through 141 Processing sheet with id=151, first strand: chain 'Q' and resid 393 through 398 No H-bonds generated for sheet with id=151 Processing sheet with id=144, first strand: chain 'Q' and resid 115 through 121 No H-bonds generated for sheet with id=144 Processing sheet with id=145, first strand: chain 'Q' and resid 138 through 141 No H-bonds generated for sheet with id=145 Processing sheet with id=147, first strand: chain 'Q' and resid 350 through 353 No H-bonds generated for sheet with id=147 Processing sheet with id=148, first strand: chain 'Q' and resid 360 through 365 No H-bonds generated for sheet with id=148 Processing sheet with id= RA, first strand: chain 'R' and resid 338 through 340 Processing sheet with id=156, first strand: chain 'R' and resid 133 through 138 No H-bonds generated for sheet with id=156 Processing sheet with id=157, first strand: chain 'R' and resid 211 through 218 No H-bonds generated for sheet with id=157 Processing sheet with id=158, first strand: chain 'R' and resid 220 through 225 No H-bonds generated for sheet with id=158 Processing sheet with id=159, first strand: chain 'R' and resid 253 through 255 No H-bonds generated for sheet with id=159 Processing sheet with id= UA, first strand: chain 'U' and resid 243 through 254 removed outlier: 6.967A pdb=" N VAL V 105 " --> pdb=" O THR V 86 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR V 86 " --> pdb=" O VAL V 105 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N SER V 107 " --> pdb=" O GLN V 84 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLN V 84 " --> pdb=" O SER V 107 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASP V 109 " --> pdb=" O ASN V 82 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N TRP V 76 " --> pdb=" O PHE V 71 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N PHE V 71 " --> pdb=" O TRP V 76 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE V 78 " --> pdb=" O TYR V 69 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR V 69 " --> pdb=" O PHE V 78 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL V 80 " --> pdb=" O ASP V 67 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ASP V 67 " --> pdb=" O VAL V 80 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASN V 82 " --> pdb=" O ASN V 65 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN V 65 " --> pdb=" O ASN V 82 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP U 273 " --> pdb=" O THR U 268 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR U 268 " --> pdb=" O ASP U 273 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR U 275 " --> pdb=" O VAL U 266 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL U 266 " --> pdb=" O THR U 275 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLN U 277 " --> pdb=" O ASP U 264 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N TRP U 258 " --> pdb=" O ARG U 253 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ARG U 253 " --> pdb=" O TRP U 258 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N CYS U 260 " --> pdb=" O VAL U 251 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL U 251 " --> pdb=" O CYS U 260 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU U 262 " --> pdb=" O ASP U 249 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ASP U 249 " --> pdb=" O LEU U 262 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ASP U 264 " --> pdb=" O LEU U 247 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU U 247 " --> pdb=" O ASP U 264 " (cutoff:3.500A) Processing sheet with id= WA, first strand: chain 'W' and resid 68 through 74 Processing sheet with id= WB, first strand: chain 'W' and resid 122 through 123 Processing sheet with id= XA, first strand: chain 'X' and resid 169 through 171 Processing sheet with id= XB, first strand: chain 'X' and resid 232 through 234 1894 hydrogen bonds defined for protein. 5253 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 22.66 Time building geometry restraints manager: 18.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.20: 1 1.20 - 1.36: 14003 1.36 - 1.52: 19846 1.52 - 1.68: 8387 1.68 - 1.84: 345 Bond restraints: 42582 Sorted by residual: bond pdb=" C ASN H 131 " pdb=" N LEU H 132 " ideal model delta sigma weight residual 1.332 1.035 0.297 1.40e-02 5.10e+03 4.50e+02 bond pdb=" C1' DA T 47 " pdb=" N9 DA T 47 " ideal model delta sigma weight residual 1.460 1.324 0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" P DA T 53 " pdb=" O5' DA T 53 " ideal model delta sigma weight residual 1.600 1.478 0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" ND1 HIS I 46 " pdb=" CE1 HIS I 46 " ideal model delta sigma weight residual 1.321 1.375 -0.054 1.00e-02 1.00e+04 2.89e+01 bond pdb=" ND1 HIS B 932 " pdb=" CE1 HIS B 932 " ideal model delta sigma weight residual 1.321 1.375 -0.054 1.00e-02 1.00e+04 2.89e+01 ... (remaining 42577 not shown) Histogram of bond angle deviations from ideal: 86.76 - 101.59: 250 101.59 - 116.42: 29624 116.42 - 131.25: 27808 131.25 - 146.08: 107 146.08 - 160.91: 2 Bond angle restraints: 57791 Sorted by residual: angle pdb=" C ASN H 131 " pdb=" N LEU H 132 " pdb=" CA LEU H 132 " ideal model delta sigma weight residual 121.54 160.91 -39.37 1.91e+00 2.74e-01 4.25e+02 angle pdb=" N ASN H 131 " pdb=" CA ASN H 131 " pdb=" C ASN H 131 " ideal model delta sigma weight residual 110.80 154.67 -43.87 2.13e+00 2.20e-01 4.24e+02 angle pdb=" O ASN H 131 " pdb=" C ASN H 131 " pdb=" N LEU H 132 " ideal model delta sigma weight residual 122.59 97.34 25.25 1.33e+00 5.65e-01 3.60e+02 angle pdb=" CA ASN H 131 " pdb=" C ASN H 131 " pdb=" N LEU H 132 " ideal model delta sigma weight residual 116.84 138.63 -21.79 1.71e+00 3.42e-01 1.62e+02 angle pdb=" C VAL R 336 " pdb=" CA VAL R 336 " pdb=" CB VAL R 336 " ideal model delta sigma weight residual 111.29 90.60 20.69 1.64e+00 3.72e-01 1.59e+02 ... (remaining 57786 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.98: 24487 20.98 - 41.97: 877 41.97 - 62.95: 328 62.95 - 83.94: 27 83.94 - 104.92: 6 Dihedral angle restraints: 25725 sinusoidal: 10682 harmonic: 15043 Sorted by residual: dihedral pdb=" CA ASN H 131 " pdb=" C ASN H 131 " pdb=" N LEU H 132 " pdb=" CA LEU H 132 " ideal model delta harmonic sigma weight residual -180.00 -121.77 -58.23 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" C VAL R 336 " pdb=" N VAL R 336 " pdb=" CA VAL R 336 " pdb=" CB VAL R 336 " ideal model delta harmonic sigma weight residual -122.00 -93.70 -28.30 0 2.50e+00 1.60e-01 1.28e+02 dihedral pdb=" CA LEU B1175 " pdb=" C LEU B1175 " pdb=" N ASN B1176 " pdb=" CA ASN B1176 " ideal model delta harmonic sigma weight residual 180.00 123.54 56.46 0 5.00e+00 4.00e-02 1.28e+02 ... (remaining 25722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.277: 6535 0.277 - 0.554: 21 0.554 - 0.831: 1 0.831 - 1.108: 1 1.108 - 1.385: 1 Chirality restraints: 6559 Sorted by residual: chirality pdb=" CA ASN H 131 " pdb=" N ASN H 131 " pdb=" C ASN H 131 " pdb=" CB ASN H 131 " both_signs ideal model delta sigma weight residual False 2.51 1.13 1.39 2.00e-01 2.50e+01 4.80e+01 chirality pdb=" CA VAL R 336 " pdb=" N VAL R 336 " pdb=" C VAL R 336 " pdb=" CB VAL R 336 " both_signs ideal model delta sigma weight residual False 2.44 3.28 -0.84 2.00e-01 2.50e+01 1.76e+01 chirality pdb=" C1' DC T 52 " pdb=" O4' DC T 52 " pdb=" C2' DC T 52 " pdb=" N1 DC T 52 " both_signs ideal model delta sigma weight residual False 2.47 1.87 0.60 2.00e-01 2.50e+01 9.05e+00 ... (remaining 6556 not shown) Planarity restraints: 7176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT N 67 " -0.089 2.00e-02 2.50e+03 6.06e-02 9.19e+01 pdb=" N1 DT N 67 " -0.029 2.00e-02 2.50e+03 pdb=" C2 DT N 67 " 0.015 2.00e-02 2.50e+03 pdb=" O2 DT N 67 " 0.070 2.00e-02 2.50e+03 pdb=" N3 DT N 67 " 0.035 2.00e-02 2.50e+03 pdb=" C4 DT N 67 " -0.003 2.00e-02 2.50e+03 pdb=" O4 DT N 67 " -0.121 2.00e-02 2.50e+03 pdb=" C5 DT N 67 " 0.069 2.00e-02 2.50e+03 pdb=" C7 DT N 67 " 0.047 2.00e-02 2.50e+03 pdb=" C6 DT N 67 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT T 45 " 0.057 2.00e-02 2.50e+03 5.29e-02 6.98e+01 pdb=" N1 DT T 45 " 0.023 2.00e-02 2.50e+03 pdb=" C2 DT T 45 " -0.019 2.00e-02 2.50e+03 pdb=" O2 DT T 45 " -0.074 2.00e-02 2.50e+03 pdb=" N3 DT T 45 " -0.029 2.00e-02 2.50e+03 pdb=" C4 DT T 45 " 0.035 2.00e-02 2.50e+03 pdb=" O4 DT T 45 " 0.073 2.00e-02 2.50e+03 pdb=" C5 DT T 45 " 0.019 2.00e-02 2.50e+03 pdb=" C7 DT T 45 " -0.102 2.00e-02 2.50e+03 pdb=" C6 DT T 45 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT N 20 " -0.062 2.00e-02 2.50e+03 4.92e-02 6.06e+01 pdb=" N1 DT N 20 " 0.019 2.00e-02 2.50e+03 pdb=" C2 DT N 20 " 0.019 2.00e-02 2.50e+03 pdb=" O2 DT N 20 " -0.041 2.00e-02 2.50e+03 pdb=" N3 DT N 20 " 0.070 2.00e-02 2.50e+03 pdb=" C4 DT N 20 " 0.016 2.00e-02 2.50e+03 pdb=" O4 DT N 20 " -0.071 2.00e-02 2.50e+03 pdb=" C5 DT N 20 " 0.052 2.00e-02 2.50e+03 pdb=" C7 DT N 20 " -0.050 2.00e-02 2.50e+03 pdb=" C6 DT N 20 " 0.049 2.00e-02 2.50e+03 ... (remaining 7173 not shown) Histogram of nonbonded interaction distances: 0.25 - 1.18: 2 1.18 - 2.11: 36 2.11 - 3.04: 28148 3.04 - 3.97: 107539 3.97 - 4.90: 201928 Warning: very small nonbonded interaction distances. Nonbonded interactions: 337653 Sorted by model distance: nonbonded pdb=" NH2 ARG B 249 " pdb=" CA GLN B 415 " model vdw 0.245 3.550 nonbonded pdb=" O GLY B 867 " pdb=" OE1 GLU M 152 " model vdw 1.021 3.040 nonbonded pdb=" NE2 GLN D 37 " pdb=" NZ LYS G 5 " model vdw 1.244 3.200 nonbonded pdb=" CZ ARG B 249 " pdb=" CA GLN B 415 " model vdw 1.266 3.700 nonbonded pdb=" OE2 GLU B 104 " pdb=" NH1 ARG L 54 " model vdw 1.277 2.520 ... (remaining 337648 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 10 6.06 5 P 92 5.49 5 Mg 1 5.21 5 S 218 5.16 5 C 26079 2.51 5 N 7325 2.21 5 O 7985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 9.940 Check model and map are aligned: 0.590 Convert atoms to be neutral: 0.310 Process input model: 126.920 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 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 : 0.010 0.297 42582 Z= 0.623 Angle : 1.136 43.874 57791 Z= 0.687 Chirality : 0.067 1.385 6559 Planarity : 0.007 0.107 7176 Dihedral : 12.786 104.923 15947 Min Nonbonded Distance : 0.245 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.37 % Favored : 94.10 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.10), residues: 5066 helix: -2.27 (0.10), residues: 1891 sheet: -1.45 (0.15), residues: 910 loop : -1.54 (0.11), residues: 2265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 4585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 1064 time to evaluate : 4.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 5 residues processed: 1090 average time/residue: 0.5782 time to fit residues: 999.1500 Evaluate side-chains 516 residues out of total 4585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 511 time to evaluate : 4.819 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3778 time to fit residues: 10.0173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 436 optimal weight: 20.0000 chunk 391 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 264 optimal weight: 0.6980 chunk 209 optimal weight: 6.9990 chunk 405 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 246 optimal weight: 0.9980 chunk 301 optimal weight: 5.9990 chunk 469 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN A 768 GLN A 786 HIS ** A 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1354 ASN B 60 GLN B 115 GLN B 178 ASN ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 ASN ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1076 HIS ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 ASN D 173 HIS ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 ASN ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 HIS ** M 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 197 HIS O 88 HIS R 223 GLN U 280 GLN V 55 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 42582 Z= 0.244 Angle : 0.712 13.492 57791 Z= 0.382 Chirality : 0.046 0.374 6559 Planarity : 0.005 0.092 7176 Dihedral : 14.071 103.862 6479 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.20 % Favored : 95.56 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.11), residues: 5066 helix: 0.14 (0.11), residues: 1931 sheet: -0.76 (0.16), residues: 882 loop : -1.08 (0.12), residues: 2253 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 4585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 670 time to evaluate : 4.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 1 residues processed: 681 average time/residue: 0.5382 time to fit residues: 602.0457 Evaluate side-chains 444 residues out of total 4585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 443 time to evaluate : 4.943 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4250 time to fit residues: 7.3636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 260 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 390 optimal weight: 0.6980 chunk 319 optimal weight: 0.6980 chunk 129 optimal weight: 7.9990 chunk 470 optimal weight: 20.0000 chunk 508 optimal weight: 0.0770 chunk 418 optimal weight: 20.0000 chunk 466 optimal weight: 8.9990 chunk 160 optimal weight: 0.3980 chunk 377 optimal weight: 8.9990 overall best weight: 1.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN A 256 GLN A 299 HIS A 316 GLN A 736 ASN A1059 HIS A1265 ASN B 215 GLN B 224 GLN B 516 ASN ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 HIS ** B1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN G 10 ASN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 193 GLN M 197 HIS ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 277 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 42582 Z= 0.197 Angle : 0.630 11.302 57791 Z= 0.337 Chirality : 0.043 0.317 6559 Planarity : 0.005 0.111 7176 Dihedral : 13.887 103.879 6479 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.62 % Favored : 95.16 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.11), residues: 5066 helix: 0.99 (0.12), residues: 1949 sheet: -0.50 (0.16), residues: 874 loop : -0.92 (0.13), residues: 2243 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 4585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 613 time to evaluate : 5.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 614 average time/residue: 0.5331 time to fit residues: 541.7231 Evaluate side-chains 444 residues out of total 4585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 444 time to evaluate : 4.987 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 464 optimal weight: 10.0000 chunk 353 optimal weight: 7.9990 chunk 244 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 224 optimal weight: 20.0000 chunk 315 optimal weight: 9.9990 chunk 472 optimal weight: 40.0000 chunk 499 optimal weight: 20.0000 chunk 246 optimal weight: 4.9990 chunk 447 optimal weight: 20.0000 chunk 134 optimal weight: 2.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN A 660 ASN A 736 ASN A 881 GLN A 935 GLN A1009 ASN ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1265 ASN B 516 ASN ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN ** C 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN E 54 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 197 HIS Q 99 ASN ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 42582 Z= 0.283 Angle : 0.656 11.216 57791 Z= 0.349 Chirality : 0.043 0.271 6559 Planarity : 0.005 0.095 7176 Dihedral : 13.931 103.879 6479 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.15 % Favored : 94.63 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.12), residues: 5066 helix: 1.13 (0.12), residues: 1966 sheet: -0.41 (0.17), residues: 874 loop : -0.81 (0.13), residues: 2226 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 4585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 535 time to evaluate : 4.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 535 average time/residue: 0.5398 time to fit residues: 478.6401 Evaluate side-chains 389 residues out of total 4585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 389 time to evaluate : 4.954 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.6594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 416 optimal weight: 7.9990 chunk 283 optimal weight: 10.0000 chunk 7 optimal weight: 0.5980 chunk 372 optimal weight: 0.2980 chunk 206 optimal weight: 1.9990 chunk 426 optimal weight: 30.0000 chunk 345 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 255 optimal weight: 7.9990 chunk 448 optimal weight: 30.0000 chunk 126 optimal weight: 6.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 ASN ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1265 ASN B 325 GLN B 657 HIS ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1178 ASN ** B1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN D 173 HIS ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.095 42582 Z= 0.257 Angle : 0.630 12.372 57791 Z= 0.335 Chirality : 0.042 0.258 6559 Planarity : 0.004 0.075 7176 Dihedral : 13.943 101.882 6479 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.39 % Favored : 94.39 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.12), residues: 5066 helix: 1.21 (0.12), residues: 1981 sheet: -0.35 (0.17), residues: 870 loop : -0.72 (0.13), residues: 2215 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 4585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 521 time to evaluate : 5.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 523 average time/residue: 0.5405 time to fit residues: 471.1496 Evaluate side-chains 373 residues out of total 4585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 372 time to evaluate : 5.488 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4554 time to fit residues: 7.4729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 168 optimal weight: 20.0000 chunk 450 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 293 optimal weight: 0.9980 chunk 123 optimal weight: 0.5980 chunk 500 optimal weight: 30.0000 chunk 415 optimal weight: 5.9990 chunk 231 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 165 optimal weight: 5.9990 chunk 262 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 654 ASN A 736 ASN A 742 ASN A1128 GLN ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1265 ASN B 513 GLN ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 HIS B1178 ASN ** B1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 158 HIS M 303 GLN Q 117 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 42582 Z= 0.191 Angle : 0.601 9.698 57791 Z= 0.318 Chirality : 0.042 0.236 6559 Planarity : 0.005 0.132 7176 Dihedral : 13.861 101.400 6479 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.19 % Favored : 94.59 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.12), residues: 5066 helix: 1.34 (0.12), residues: 1973 sheet: -0.27 (0.17), residues: 859 loop : -0.64 (0.13), residues: 2234 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 4585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 524 time to evaluate : 5.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 525 average time/residue: 0.5519 time to fit residues: 485.4689 Evaluate side-chains 381 residues out of total 4585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 380 time to evaluate : 4.957 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4641 time to fit residues: 7.5593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 482 optimal weight: 30.0000 chunk 56 optimal weight: 10.0000 chunk 285 optimal weight: 20.0000 chunk 365 optimal weight: 10.0000 chunk 283 optimal weight: 8.9990 chunk 421 optimal weight: 20.0000 chunk 279 optimal weight: 0.9980 chunk 498 optimal weight: 0.0030 chunk 311 optimal weight: 0.9980 chunk 303 optimal weight: 20.0000 chunk 230 optimal weight: 0.7980 overall best weight: 2.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 ASN A1265 ASN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1178 ASN ** B1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN D 173 HIS ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 GLN I 22 ASN ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 158 HIS M 300 GLN Q 122 GLN ** Q 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.5370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 42582 Z= 0.203 Angle : 0.601 12.136 57791 Z= 0.317 Chirality : 0.042 0.238 6559 Planarity : 0.004 0.074 7176 Dihedral : 13.797 98.463 6479 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.25 % Favored : 94.53 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.12), residues: 5066 helix: 1.40 (0.12), residues: 1973 sheet: -0.16 (0.17), residues: 865 loop : -0.59 (0.13), residues: 2228 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 4585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 509 time to evaluate : 5.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 511 average time/residue: 0.5294 time to fit residues: 452.9020 Evaluate side-chains 374 residues out of total 4585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 373 time to evaluate : 4.919 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4327 time to fit residues: 7.3440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 308 optimal weight: 10.0000 chunk 198 optimal weight: 3.9990 chunk 297 optimal weight: 5.9990 chunk 150 optimal weight: 0.0670 chunk 97 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 316 optimal weight: 7.9990 chunk 339 optimal weight: 7.9990 chunk 246 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 391 optimal weight: 0.9990 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN A 736 ASN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN D 173 HIS ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 158 HIS ** M 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 369 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 42582 Z= 0.267 Angle : 0.648 11.468 57791 Z= 0.341 Chirality : 0.043 0.359 6559 Planarity : 0.005 0.107 7176 Dihedral : 13.869 96.610 6479 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.67 % Favored : 94.14 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.12), residues: 5066 helix: 1.35 (0.12), residues: 1970 sheet: -0.21 (0.17), residues: 876 loop : -0.69 (0.13), residues: 2220 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 4585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 484 time to evaluate : 5.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 485 average time/residue: 0.5513 time to fit residues: 448.2769 Evaluate side-chains 347 residues out of total 4585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 346 time to evaluate : 4.652 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4470 time to fit residues: 7.4137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 453 optimal weight: 40.0000 chunk 477 optimal weight: 0.9990 chunk 435 optimal weight: 6.9990 chunk 464 optimal weight: 10.0000 chunk 279 optimal weight: 6.9990 chunk 202 optimal weight: 4.9990 chunk 364 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 419 optimal weight: 3.9990 chunk 439 optimal weight: 10.0000 chunk 462 optimal weight: 0.5980 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 ASN A1106 ASN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 158 HIS M 300 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.5891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 42582 Z= 0.225 Angle : 0.630 12.217 57791 Z= 0.330 Chirality : 0.043 0.301 6559 Planarity : 0.004 0.069 7176 Dihedral : 13.837 94.221 6479 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.90 % Favored : 93.92 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.12), residues: 5066 helix: 1.35 (0.12), residues: 1978 sheet: -0.21 (0.17), residues: 879 loop : -0.67 (0.13), residues: 2209 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 4585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 468 time to evaluate : 5.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 469 average time/residue: 0.5360 time to fit residues: 423.3064 Evaluate side-chains 341 residues out of total 4585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 5.060 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.5914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 304 optimal weight: 8.9990 chunk 491 optimal weight: 40.0000 chunk 299 optimal weight: 8.9990 chunk 232 optimal weight: 7.9990 chunk 341 optimal weight: 9.9990 chunk 515 optimal weight: 40.0000 chunk 474 optimal weight: 20.0000 chunk 410 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 316 optimal weight: 4.9990 chunk 251 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** A 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN B 686 ASN ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 ASN I 22 ASN ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 158 HIS M 290 GLN ** M 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 55 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.6324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 42582 Z= 0.412 Angle : 0.776 12.308 57791 Z= 0.409 Chirality : 0.045 0.304 6559 Planarity : 0.006 0.110 7176 Dihedral : 14.135 92.031 6479 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 24.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.67 % Favored : 93.15 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.12), residues: 5066 helix: 0.93 (0.12), residues: 1969 sheet: -0.31 (0.17), residues: 854 loop : -0.90 (0.13), residues: 2243 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 4585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 409 time to evaluate : 5.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 409 average time/residue: 0.5617 time to fit residues: 384.2096 Evaluate side-chains 305 residues out of total 4585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 5.283 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.0520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 325 optimal weight: 4.9990 chunk 436 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 chunk 378 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 410 optimal weight: 8.9990 chunk 171 optimal weight: 5.9990 chunk 421 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 HIS ** B 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 158 HIS M 212 ASN ** M 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 55 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.050897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.037935 restraints weight = 358039.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.039035 restraints weight = 213482.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.039799 restraints weight = 148601.498| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.6624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.075 42582 Z= 0.361 Angle : 0.730 10.494 57791 Z= 0.387 Chirality : 0.045 0.314 6559 Planarity : 0.005 0.097 7176 Dihedral : 14.216 90.331 6479 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 23.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.73 % Favored : 93.09 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.12), residues: 5066 helix: 0.86 (0.12), residues: 1975 sheet: -0.42 (0.17), residues: 859 loop : -1.02 (0.13), residues: 2232 =============================================================================== Job complete usr+sys time: 9024.81 seconds wall clock time: 165 minutes 35.04 seconds (9935.04 seconds total)