Starting phenix.real_space_refine (version: dev) on Thu Dec 22 07:09:58 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnc_7531/12_2022/6cnc_7531.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnc_7531/12_2022/6cnc_7531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnc_7531/12_2022/6cnc_7531.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnc_7531/12_2022/6cnc_7531.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnc_7531/12_2022/6cnc_7531.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnc_7531/12_2022/6cnc_7531.pdb" } resolution = 4.1 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= 0.001 sd= 0.009 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 TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 912": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "O PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 184": "NH1" <-> "NH2" Residue "P ARG 262": "NH1" <-> "NH2" Residue "R ARG 14": "NH1" <-> "NH2" Residue "R ARG 294": "NH1" <-> "NH2" Residue "S ARG 413": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 47836 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 11159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1428, 11159 Classifications: {'peptide': 1428} Link IDs: {'PCIS': 1, 'PTRANS': 65, 'TRANS': 1361} Chain breaks: 2 Chain: "B" Number of atoms: 8788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8788 Classifications: {'peptide': 1114} Link IDs: {'PTRANS': 43, 'TRANS': 1070} Chain: "C" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2655 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 20, 'TRANS': 314} Chain: "D" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 977 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain breaks: 2 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 671 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1484 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 12, 'TRANS': 171} Chain breaks: 2 Chain: "H" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1120 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 135} Chain breaks: 1 Chain: "I" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 321 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "J" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 549 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 792 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "L" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 363 Classifications: {'peptide': 46} Link IDs: {'TRANS': 45} Chain: "M" Number of atoms: 1338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1338 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 8, 'TRANS': 155} Chain breaks: 1 Chain: "N" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 845 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain breaks: 1 Chain: "O" Number of atoms: 4329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4329 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 520} Chain breaks: 2 Chain: "P" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2242 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 7, 'TRANS': 269} Chain breaks: 2 Chain: "Q" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 368 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "R" Number of atoms: 4131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4131 Classifications: {'peptide': 522} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 502} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1649 Classifications: {'peptide': 217} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 42} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 43} Unresolved non-hydrogen planarities: 43 Chain: "X" Number of atoms: 1040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1040 Classifications: {'DNA': 51} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 50} Chain breaks: 1 Chain: "Y" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1249 Classifications: {'DNA': 61} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 60} Chain breaks: 1 Chain: "A" 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: "B" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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: "R" 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 492 SG CYS A 67 87.980 70.919 82.172 1.00 0.00 S ATOM 510 SG CYS A 70 90.254 72.409 78.236 1.00 0.00 S ATOM 557 SG CYS A 77 90.541 72.327 81.532 1.00 0.00 S ATOM 795 SG CYS A 107 72.678 116.000 90.508 1.00 0.00 S ATOM 818 SG CYS A 110 69.946 116.426 88.151 1.00 0.00 S ATOM 1184 SG CYS A 154 72.006 119.091 89.929 1.00 0.00 S ATOM 1208 SG CYS A 157 69.333 118.548 91.203 1.00 0.00 S ATOM 19520 SG CYS B1095 91.849 87.071 71.624 1.00 0.00 S ATOM 19543 SG CYS B1098 89.097 89.945 73.879 1.00 0.00 S ATOM 19609 SG CYS B1107 89.775 85.557 74.126 1.00 0.00 S ATOM 19629 SG CYS B1110 87.852 87.410 71.664 1.00 0.00 S ATOM 28652 SG CYS I 5 79.457 121.853 156.027 1.00 0.00 S ATOM 28671 SG CYS I 8 75.573 121.692 156.965 1.00 0.00 S ATOM 28799 SG CYS I 26 78.592 122.714 153.573 1.00 0.00 S ATOM 28822 SG CYS I 29 76.106 120.588 153.861 1.00 0.00 S ATOM 28988 SG CYS J 7 140.206 49.891 126.675 1.00 0.00 S ATOM 29291 SG CYS J 45 143.129 52.729 127.378 1.00 0.00 S ATOM 29297 SG CYS J 46 143.090 49.217 129.031 1.00 0.00 S ATOM 30330 SG CYS L 31 97.880 35.364 125.473 1.00 0.00 S ATOM 30350 SG CYS L 34 99.271 33.628 127.028 1.00 0.00 S ATOM 30454 SG CYS L 48 95.091 34.687 126.389 1.00 0.00 S ATOM 30477 SG CYS L 51 96.362 35.447 129.110 1.00 0.00 S ATOM 39788 SG CYS R 4 104.328 53.250 76.456 1.00 0.00 S ATOM 39811 SG CYS R 7 104.932 50.060 76.751 1.00 0.00 S ATOM 39952 SG CYS R 25 105.011 50.786 79.865 1.00 0.00 S ATOM 39972 SG CYS R 28 106.639 52.441 79.438 1.00 0.00 S Time building chain proxies: 25.44, per 1000 atoms: 0.53 Number of scatterers: 47836 At special positions: 0 Unit cell: (199.42, 169.92, 202.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 7 29.99 S 242 16.00 P 110 15.00 O 9233 8.00 N 8268 7.00 C 29976 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: 20.30 Conformation dependent library (CDL) restraints added in 6.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 70 " pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 154 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 157 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1107 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1095 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1098 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1110 " pdb=" ZN I2000 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 26 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 8 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 5 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 29 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 46 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb=" ZN L2000 " pdb="ZN ZN L2000 " - pdb=" SG CYS L 51 " pdb="ZN ZN L2000 " - pdb=" SG CYS L 34 " pdb="ZN ZN L2000 " - pdb=" SG CYS L 31 " pdb="ZN ZN L2000 " - pdb=" SG CYS L 48 " pdb=" ZN R1001 " pdb="ZN ZN R1001 " - pdb=" SG CYS R 25 " pdb="ZN ZN R1001 " - pdb=" SG CYS R 4 " pdb="ZN ZN R1001 " - pdb=" SG CYS R 7 " pdb="ZN ZN R1001 " - pdb=" SG CYS R 28 " Number of angles added : 33 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10898 Finding SS restraints... Secondary structure from input PDB file: 215 helices and 53 sheets defined 41.5% alpha, 10.2% beta 38 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 12.58 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 72 through 77 removed outlier: 3.599A pdb=" N SER A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 105 removed outlier: 4.723A pdb=" N LYS A 97 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ALA A 98 " --> pdb=" O GLY A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 128 removed outlier: 3.891A pdb=" N ARG A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 147 removed outlier: 3.508A pdb=" N ASP A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 206 removed outlier: 4.318A pdb=" N GLU A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 283 through 302 removed outlier: 3.793A pdb=" N TRP A 294 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 328 removed outlier: 3.549A pdb=" N ILE A 327 " --> pdb=" O VAL A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 409 through 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 412 through 423 removed outlier: 3.996A pdb=" N GLU A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL A 421 " --> pdb=" O GLN A 417 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 removed outlier: 3.785A pdb=" N TYR A 446 " --> pdb=" O ASN A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'A' and resid 504 through 509 removed outlier: 4.025A pdb=" N TYR A 508 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 532 removed outlier: 3.837A pdb=" N ARG A 528 " --> pdb=" O THR A 524 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 540 Processing helix chain 'A' and resid 555 through 566 Processing helix chain 'A' and resid 572 through 584 removed outlier: 4.105A pdb=" N SER A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 615 removed outlier: 4.117A pdb=" N LEU A 613 " --> pdb=" O VAL A 609 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE A 614 " --> pdb=" O PHE A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 686 Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.735A pdb=" N ASN A 692 " --> pdb=" O GLN A 688 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG A 703 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN A 707 " --> pdb=" O ARG A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 718 removed outlier: 3.867A pdb=" N VAL A 717 " --> pdb=" O GLY A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 747 removed outlier: 4.127A pdb=" N GLU A 729 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU A 732 " --> pdb=" O GLU A 728 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE A 733 " --> pdb=" O GLU A 729 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR A 743 " --> pdb=" O ASP A 739 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LYS A 747 " --> pdb=" O THR A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 784 removed outlier: 4.167A pdb=" N SER A 771 " --> pdb=" O GLY A 767 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL A 780 " --> pdb=" O GLU A 776 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 784 " --> pdb=" O VAL A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 796 Processing helix chain 'A' and resid 802 through 810 removed outlier: 4.054A pdb=" N GLN A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET A 809 " --> pdb=" O ASN A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 877 removed outlier: 3.707A pdb=" N PHE A 863 " --> pdb=" O PRO A 859 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 867 " --> pdb=" O PHE A 863 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY A 868 " --> pdb=" O HIS A 864 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ARG A 869 " --> pdb=" O ALA A 865 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL A 877 " --> pdb=" O VAL A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 894 removed outlier: 4.199A pdb=" N GLU A 881 " --> pdb=" O VAL A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 919 removed outlier: 4.005A pdb=" N GLY A 918 " --> pdb=" O THR A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 947 removed outlier: 4.180A pdb=" N ILE A 945 " --> pdb=" O HIS A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 975 removed outlier: 3.671A pdb=" N GLU A 961 " --> pdb=" O TYR A 957 " (cutoff:3.500A) Proline residue: A 969 - end of helix removed outlier: 5.068A pdb=" N ARG A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 975 " --> pdb=" O GLU A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1026 removed outlier: 4.147A pdb=" N ALA A1018 " --> pdb=" O GLY A1014 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A1019 " --> pdb=" O LYS A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1048 removed outlier: 4.086A pdb=" N THR A1047 " --> pdb=" O PRO A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1050 No H-bonds generated for 'chain 'A' and resid 1049 through 1050' Processing helix chain 'A' and resid 1051 through 1060 Processing helix chain 'A' and resid 1064 through 1081 removed outlier: 3.609A pdb=" N PHE A1070 " --> pdb=" O SER A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1099 removed outlier: 3.779A pdb=" N ILE A1097 " --> pdb=" O GLY A1093 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU A1099 " --> pdb=" O GLN A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1132 removed outlier: 3.719A pdb=" N ILE A1126 " --> pdb=" O GLY A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1161 Processing helix chain 'A' and resid 1189 through 1196 removed outlier: 3.558A pdb=" N ILE A1193 " --> pdb=" O ASP A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1213 Processing helix chain 'A' and resid 1254 through 1267 removed outlier: 3.692A pdb=" N TYR A1258 " --> pdb=" O ASN A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1306 Processing helix chain 'A' and resid 1318 through 1324 removed outlier: 3.703A pdb=" N VAL A1322 " --> pdb=" O HIS A1318 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER A1324 " --> pdb=" O LEU A1320 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1345 removed outlier: 3.855A pdb=" N ARG A1337 " --> pdb=" O TYR A1333 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN A1340 " --> pdb=" O ILE A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1351 through 1363 removed outlier: 4.068A pdb=" N ILE A1355 " --> pdb=" O ASP A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1390 removed outlier: 4.284A pdb=" N GLU A1390 " --> pdb=" O LEU A1386 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1402 Processing helix chain 'A' and resid 1410 through 1418 removed outlier: 4.344A pdb=" N ILE A1416 " --> pdb=" O SER A1412 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A1417 " --> pdb=" O GLU A1413 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1428 removed outlier: 4.219A pdb=" N GLY A1426 " --> pdb=" O ILE A1423 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE A1428 " --> pdb=" O THR A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1441 Processing helix chain 'A' and resid 1447 through 1454 removed outlier: 3.695A pdb=" N SER A1452 " --> pdb=" O PHE A1448 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU A1454 " --> pdb=" O SER A1450 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 44 removed outlier: 3.943A pdb=" N LYS B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 4.187A pdb=" N ALA B 50 " --> pdb=" O HIS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 80 removed outlier: 3.806A pdb=" N SER B 64 " --> pdb=" O GLN B 60 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LEU B 73 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS B 74 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 121 Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 267 through 272 Processing helix chain 'B' and resid 278 through 290 removed outlier: 3.925A pdb=" N ILE B 282 " --> pdb=" O SER B 278 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ASN B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 308 removed outlier: 3.739A pdb=" N LYS B 308 " --> pdb=" O TYR B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 331 Processing helix chain 'B' and resid 333 through 337 removed outlier: 3.944A pdb=" N THR B 336 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 362 removed outlier: 3.989A pdb=" N ARG B 355 " --> pdb=" O MET B 351 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 356 " --> pdb=" O MET B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 379 through 403 removed outlier: 3.744A pdb=" N LEU B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.847A pdb=" N LEU B 407 " --> pdb=" O ILE B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 426 removed outlier: 4.046A pdb=" N VAL B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 440 Processing helix chain 'B' and resid 462 through 467 removed outlier: 3.663A pdb=" N ALA B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B 467 " --> pdb=" O TYR B 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 462 through 467' Processing helix chain 'B' and resid 490 through 494 Processing helix chain 'B' and resid 526 through 536 Processing helix chain 'B' and resid 567 through 580 Processing helix chain 'B' and resid 624 through 632 removed outlier: 3.835A pdb=" N ARG B 628 " --> pdb=" O ASP B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 644 removed outlier: 3.683A pdb=" N LYS B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 657 Processing helix chain 'B' and resid 676 through 681 removed outlier: 3.838A pdb=" N THR B 679 " --> pdb=" O GLU B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 688 Processing helix chain 'B' and resid 690 through 694 Processing helix chain 'B' and resid 695 through 706 removed outlier: 3.951A pdb=" N ASN B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 709 No H-bonds generated for 'chain 'B' and resid 707 through 709' Processing helix chain 'B' and resid 716 through 720 removed outlier: 3.615A pdb=" N ARG B 720 " --> pdb=" O GLN B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 745 removed outlier: 4.109A pdb=" N GLU B 742 " --> pdb=" O THR B 738 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU B 743 " --> pdb=" O LYS B 739 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 749 Processing helix chain 'B' and resid 777 through 781 Processing helix chain 'B' and resid 850 through 853 Processing helix chain 'B' and resid 947 through 953 removed outlier: 4.416A pdb=" N SER B 951 " --> pdb=" O HIS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 971 removed outlier: 4.022A pdb=" N ILE B 962 " --> pdb=" O MET B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 992 removed outlier: 3.803A pdb=" N SER B 988 " --> pdb=" O LEU B 984 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LYS B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE B 990 " --> pdb=" O ASP B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 995 No H-bonds generated for 'chain 'B' and resid 993 through 995' Processing helix chain 'B' and resid 1030 through 1035 removed outlier: 3.703A pdb=" N LYS B1034 " --> pdb=" O MET B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1074 removed outlier: 4.088A pdb=" N ASP B1068 " --> pdb=" O GLU B1064 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N CYS B1069 " --> pdb=" O MET B1065 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL B1070 " --> pdb=" O GLU B1066 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1083 removed outlier: 3.601A pdb=" N LEU B1079 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 1123 through 1135 removed outlier: 3.724A pdb=" N MET B1135 " --> pdb=" O GLU B1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 40 Processing helix chain 'C' and resid 62 through 73 Processing helix chain 'C' and resid 93 through 102 removed outlier: 3.865A pdb=" N GLY C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 125 removed outlier: 4.155A pdb=" N GLU C 124 " --> pdb=" O PRO C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 131 Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 174 through 179 removed outlier: 4.006A pdb=" N THR C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE C 179 " --> pdb=" O GLN C 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 174 through 179' Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 241 through 251 removed outlier: 3.861A pdb=" N ARG C 245 " --> pdb=" O GLY C 241 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 283 removed outlier: 3.903A pdb=" N TYR C 282 " --> pdb=" O GLU C 278 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU C 283 " --> pdb=" O VAL C 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 278 through 283' Processing helix chain 'C' and resid 285 through 287 No H-bonds generated for 'chain 'C' and resid 285 through 287' Processing helix chain 'C' and resid 309 through 331 removed outlier: 3.533A pdb=" N ARG C 319 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS C 329 " --> pdb=" O ALA C 325 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS C 331 " --> pdb=" O TYR C 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 27 Processing helix chain 'D' and resid 55 through 72 removed outlier: 3.851A pdb=" N THR D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN D 64 " --> pdb=" O ARG D 60 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU D 66 " --> pdb=" O VAL D 62 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LYS D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 111 removed outlier: 3.530A pdb=" N MET D 107 " --> pdb=" O PHE D 103 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LYS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 123 Processing helix chain 'D' and resid 130 through 136 removed outlier: 3.600A pdb=" N TYR D 135 " --> pdb=" O MET D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 161 removed outlier: 3.512A pdb=" N MET D 153 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 154 " --> pdb=" O ILE D 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 26 removed outlier: 3.849A pdb=" N ARG E 26 " --> pdb=" O MET E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 55 through 59 Processing helix chain 'E' and resid 66 through 72 removed outlier: 3.507A pdb=" N SER E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 103 removed outlier: 3.513A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N HIS E 99 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU E 102 " --> pdb=" O ILE E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 123 removed outlier: 4.127A pdb=" N LEU E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 140 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 168 removed outlier: 3.538A pdb=" N LEU E 164 " --> pdb=" O GLU E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 88 through 103 removed outlier: 3.574A pdb=" N LEU F 94 " --> pdb=" O ARG F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 126 removed outlier: 3.999A pdb=" N ILE F 120 " --> pdb=" O ASP F 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 20 removed outlier: 3.687A pdb=" N GLN G 17 " --> pdb=" O PRO G 14 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N HIS G 19 " --> pdb=" O ASP G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 34 Processing helix chain 'H' and resid 130 through 134 removed outlier: 3.838A pdb=" N ASN H 133 " --> pdb=" O ARG H 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 27 removed outlier: 4.102A pdb=" N GLU J 19 " --> pdb=" O GLY J 15 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 38 removed outlier: 3.519A pdb=" N LEU J 36 " --> pdb=" O GLU J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 52 removed outlier: 4.613A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 Processing helix chain 'K' and resid 69 through 82 removed outlier: 4.560A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR K 78 " --> pdb=" O ASN K 74 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 142 removed outlier: 3.601A pdb=" N LEU K 117 " --> pdb=" O ALA K 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP K 126 " --> pdb=" O LYS K 122 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS K 138 " --> pdb=" O LYS K 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 139 removed outlier: 3.638A pdb=" N ALA M 136 " --> pdb=" O ASN M 132 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU M 139 " --> pdb=" O LYS M 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 196 removed outlier: 3.655A pdb=" N ASP M 187 " --> pdb=" O PHE M 183 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR M 192 " --> pdb=" O ASP M 188 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG M 193 " --> pdb=" O ALA M 189 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN M 195 " --> pdb=" O VAL M 191 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU M 196 " --> pdb=" O THR M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 229 through 240 Processing helix chain 'M' and resid 252 through 261 removed outlier: 3.795A pdb=" N LYS M 256 " --> pdb=" O PHE M 252 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR M 258 " --> pdb=" O GLN M 254 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS M 261 " --> pdb=" O ASP M 257 " (cutoff:3.500A) Processing helix chain 'N' and resid 275 through 296 removed outlier: 3.506A pdb=" N GLU N 281 " --> pdb=" O ALA N 277 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU N 283 " --> pdb=" O GLU N 279 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN N 284 " --> pdb=" O LEU N 280 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS N 293 " --> pdb=" O HIS N 289 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 57 removed outlier: 3.623A pdb=" N LYS O 50 " --> pdb=" O LEU O 46 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS O 54 " --> pdb=" O LYS O 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 72 removed outlier: 3.934A pdb=" N SER O 63 " --> pdb=" O GLU O 59 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL O 64 " --> pdb=" O ARG O 60 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE O 65 " --> pdb=" O ALA O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 84 removed outlier: 4.216A pdb=" N VAL O 80 " --> pdb=" O VAL O 76 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU O 81 " --> pdb=" O ARG O 77 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS O 82 " --> pdb=" O GLU O 78 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP O 84 " --> pdb=" O VAL O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 100 Processing helix chain 'O' and resid 127 through 133 Processing helix chain 'O' and resid 134 through 139 Processing helix chain 'O' and resid 139 through 144 removed outlier: 3.888A pdb=" N GLN O 143 " --> pdb=" O GLU O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 167 removed outlier: 3.795A pdb=" N SER O 165 " --> pdb=" O GLN O 161 " (cutoff:3.500A) Processing helix chain 'O' and resid 170 through 178 Processing helix chain 'O' and resid 183 through 188 Processing helix chain 'O' and resid 204 through 208 removed outlier: 3.764A pdb=" N TYR O 208 " --> pdb=" O LYS O 205 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 220 removed outlier: 3.507A pdb=" N GLN O 216 " --> pdb=" O GLU O 212 " (cutoff:3.500A) Processing helix chain 'O' and resid 233 through 258 removed outlier: 3.573A pdb=" N LYS O 237 " --> pdb=" O SER O 233 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN O 240 " --> pdb=" O LYS O 236 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS O 251 " --> pdb=" O THR O 247 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE O 252 " --> pdb=" O ASP O 248 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE O 253 " --> pdb=" O PHE O 249 " (cutoff:3.500A) Proline residue: O 256 - end of helix Processing helix chain 'O' and resid 259 through 264 removed outlier: 4.104A pdb=" N LEU O 263 " --> pdb=" O LEU O 259 " (cutoff:3.500A) Processing helix chain 'O' and resid 284 through 304 removed outlier: 3.601A pdb=" N GLN O 295 " --> pdb=" O ARG O 291 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR O 302 " --> pdb=" O ASN O 298 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG O 303 " --> pdb=" O LEU O 299 " (cutoff:3.500A) Processing helix chain 'O' and resid 305 through 320 removed outlier: 4.016A pdb=" N ARG O 317 " --> pdb=" O LYS O 313 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU O 318 " --> pdb=" O ILE O 314 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR O 319 " --> pdb=" O ALA O 315 " (cutoff:3.500A) Processing helix chain 'O' and resid 324 through 328 Processing helix chain 'O' and resid 329 through 333 Processing helix chain 'O' and resid 340 through 356 removed outlier: 3.699A pdb=" N GLU O 348 " --> pdb=" O SER O 344 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLU O 353 " --> pdb=" O ALA O 349 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLU O 354 " --> pdb=" O GLU O 350 " (cutoff:3.500A) Processing helix chain 'O' and resid 357 through 360 Processing helix chain 'O' and resid 453 through 458 Processing helix chain 'O' and resid 459 through 463 Processing helix chain 'O' and resid 482 through 489 removed outlier: 3.627A pdb=" N SER O 489 " --> pdb=" O PRO O 485 " (cutoff:3.500A) Processing helix chain 'O' and resid 501 through 514 removed outlier: 3.882A pdb=" N MET O 505 " --> pdb=" O GLY O 501 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG O 506 " --> pdb=" O PRO O 502 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU O 507 " --> pdb=" O SER O 503 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN O 514 " --> pdb=" O CYS O 510 " (cutoff:3.500A) Processing helix chain 'O' and resid 518 through 526 Processing helix chain 'O' and resid 529 through 537 removed outlier: 3.515A pdb=" N ILE O 533 " --> pdb=" O LYS O 529 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER O 535 " --> pdb=" O LYS O 531 " (cutoff:3.500A) Processing helix chain 'O' and resid 537 through 542 removed outlier: 3.687A pdb=" N ARG O 542 " --> pdb=" O ALA O 538 " (cutoff:3.500A) Processing helix chain 'O' and resid 569 through 577 removed outlier: 3.969A pdb=" N MET O 577 " --> pdb=" O SER O 573 " (cutoff:3.500A) Processing helix chain 'O' and resid 578 through 595 removed outlier: 3.659A pdb=" N GLU O 582 " --> pdb=" O ARG O 578 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASN O 584 " --> pdb=" O ASN O 580 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET O 585 " --> pdb=" O LEU O 581 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA O 586 " --> pdb=" O GLU O 582 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN O 587 " --> pdb=" O TRP O 583 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU O 589 " --> pdb=" O MET O 585 " (cutoff:3.500A) Processing helix chain 'O' and resid 599 through 610 removed outlier: 4.044A pdb=" N LYS O 604 " --> pdb=" O SER O 600 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS O 605 " --> pdb=" O THR O 601 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP O 610 " --> pdb=" O ALA O 606 " (cutoff:3.500A) Processing helix chain 'O' and resid 620 through 649 removed outlier: 4.403A pdb=" N LYS O 628 " --> pdb=" O LEU O 624 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N MET O 629 " --> pdb=" O ASN O 625 " (cutoff:3.500A) Processing helix chain 'P' and resid 11 through 25 removed outlier: 3.528A pdb=" N MET P 22 " --> pdb=" O LEU P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 33 through 40 removed outlier: 3.885A pdb=" N GLN P 37 " --> pdb=" O GLN P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 58 Processing helix chain 'P' and resid 76 through 86 Processing helix chain 'P' and resid 87 through 98 removed outlier: 4.303A pdb=" N LEU P 92 " --> pdb=" O ALA P 88 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL P 93 " --> pdb=" O GLU P 89 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER P 95 " --> pdb=" O ALA P 91 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 115 removed outlier: 3.919A pdb=" N ARG P 113 " --> pdb=" O THR P 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 117 through 132 removed outlier: 3.755A pdb=" N VAL P 121 " --> pdb=" O HIS P 117 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU P 122 " --> pdb=" O GLN P 118 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS P 123 " --> pdb=" O HIS P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 175 through 191 removed outlier: 4.079A pdb=" N ILE P 181 " --> pdb=" O SER P 177 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE P 191 " --> pdb=" O SER P 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 209 through 213 Processing helix chain 'P' and resid 219 through 226 removed outlier: 3.969A pdb=" N GLU P 223 " --> pdb=" O GLN P 219 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 250 removed outlier: 3.775A pdb=" N LEU P 247 " --> pdb=" O LEU P 243 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 68 removed outlier: 3.564A pdb=" N LYS Q 57 " --> pdb=" O SER Q 53 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN Q 60 " --> pdb=" O VAL Q 56 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N PHE Q 61 " --> pdb=" O LYS Q 57 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY Q 62 " --> pdb=" O TYR Q 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1084 through 1088 removed outlier: 3.720A pdb=" N UNK Q1088 " --> pdb=" O UNK Q1085 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 94 removed outlier: 3.633A pdb=" N TYR R 92 " --> pdb=" O ARG R 88 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA R 93 " --> pdb=" O ALA R 89 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU R 94 " --> pdb=" O VAL R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 114 removed outlier: 3.650A pdb=" N ASP R 102 " --> pdb=" O GLU R 98 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN R 106 " --> pdb=" O ASP R 102 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TRP R 107 " --> pdb=" O ALA R 103 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA R 113 " --> pdb=" O LYS R 109 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN R 114 " --> pdb=" O LEU R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 137 removed outlier: 3.573A pdb=" N SER R 128 " --> pdb=" O ASN R 124 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA R 133 " --> pdb=" O CYS R 129 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N CYS R 134 " --> pdb=" O LEU R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 142 through 148 removed outlier: 4.075A pdb=" N SER R 148 " --> pdb=" O ILE R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 168 Processing helix chain 'R' and resid 177 through 188 removed outlier: 3.785A pdb=" N PHE R 181 " --> pdb=" O ASP R 177 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLN R 183 " --> pdb=" O SER R 179 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N HIS R 184 " --> pdb=" O LEU R 180 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS R 188 " --> pdb=" O HIS R 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 212 removed outlier: 3.943A pdb=" N LYS R 197 " --> pdb=" O ASP R 193 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU R 205 " --> pdb=" O ASP R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 235 removed outlier: 3.741A pdb=" N ILE R 223 " --> pdb=" O ARG R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 240 through 249 removed outlier: 4.468A pdb=" N VAL R 247 " --> pdb=" O GLU R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 264 removed outlier: 3.762A pdb=" N ASN R 264 " --> pdb=" O ASN R 260 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 272 Processing helix chain 'R' and resid 287 through 296 removed outlier: 3.578A pdb=" N VAL R 291 " --> pdb=" O PRO R 287 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN R 293 " --> pdb=" O SER R 289 " (cutoff:3.500A) Processing helix chain 'R' and resid 407 through 412 Processing helix chain 'R' and resid 454 through 472 removed outlier: 4.064A pdb=" N LEU R 460 " --> pdb=" O ASP R 456 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA R 466 " --> pdb=" O SER R 462 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG R 467 " --> pdb=" O ARG R 463 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE R 468 " --> pdb=" O LYS R 464 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE R 469 " --> pdb=" O TYR R 465 " (cutoff:3.500A) Processing helix chain 'R' and resid 497 through 506 removed outlier: 3.524A pdb=" N LEU R 501 " --> pdb=" O ARG R 497 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE R 503 " --> pdb=" O GLU R 499 " (cutoff:3.500A) Processing helix chain 'R' and resid 545 through 563 removed outlier: 3.592A pdb=" N ILE R 549 " --> pdb=" O GLN R 545 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR R 550 " --> pdb=" O ARG R 546 " (cutoff:3.500A) Proline residue: R 558 - end of helix Processing helix chain 'R' and resid 587 through 594 removed outlier: 3.780A pdb=" N TYR R 591 " --> pdb=" O THR R 587 " (cutoff:3.500A) Processing helix chain 'R' and resid 616 through 632 Processing helix chain 'R' and resid 633 through 650 removed outlier: 4.082A pdb=" N GLU R 646 " --> pdb=" O ARG R 642 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE R 649 " --> pdb=" O GLN R 645 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA R 650 " --> pdb=" O GLU R 646 " (cutoff:3.500A) Processing helix chain 'S' and resid 292 through 314 removed outlier: 3.852A pdb=" N UNK S 296 " --> pdb=" O UNK S 292 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N UNK S 298 " --> pdb=" O UNK S 294 " (cutoff:3.500A) Processing helix chain 'S' and resid 315 through 319 removed outlier: 3.603A pdb=" N UNK S 319 " --> pdb=" O UNK S 316 " (cutoff:3.500A) Processing helix chain 'S' and resid 383 through 392 removed outlier: 4.047A pdb=" N ALA S 387 " --> pdb=" O ARG S 383 " (cutoff:3.500A) Processing helix chain 'S' and resid 421 through 435 removed outlier: 3.713A pdb=" N LYS S 427 " --> pdb=" O GLU S 423 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE S 428 " --> pdb=" O GLU S 424 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA S 431 " --> pdb=" O LYS S 427 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU S 432 " --> pdb=" O PHE S 428 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER S 433 " --> pdb=" O TYR S 429 " (cutoff:3.500A) Processing helix chain 'S' and resid 438 through 446 removed outlier: 3.944A pdb=" N ILE S 442 " --> pdb=" O ASP S 438 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR S 446 " --> pdb=" O ILE S 442 " (cutoff:3.500A) Processing helix chain 'S' and resid 451 through 465 removed outlier: 3.605A pdb=" N LYS S 455 " --> pdb=" O ARG S 451 " (cutoff:3.500A) Processing helix chain 'S' and resid 465 through 475 removed outlier: 3.981A pdb=" N ILE S 469 " --> pdb=" O ARG S 465 " (cutoff:3.500A) Processing helix chain 'S' and resid 480 through 486 Processing helix chain 'S' and resid 494 through 532 removed outlier: 3.615A pdb=" N ALA S 523 " --> pdb=" O ALA S 519 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN S 528 " --> pdb=" O LYS S 524 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG S 532 " --> pdb=" O GLN S 528 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 84 removed outlier: 3.582A pdb=" N LEU A 261 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 178 through 179 removed outlier: 4.597A pdb=" N ILE A 178 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 391 through 395 removed outlier: 3.668A pdb=" N VAL A 392 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A 493 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A 379 " --> pdb=" O MET A 517 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 404 through 407 removed outlier: 4.390A pdb=" N TYR A 432 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 542 through 543 removed outlier: 3.813A pdb=" N GLU A 548 " --> pdb=" O THR A 543 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 653 through 655 removed outlier: 6.650A pdb=" N ILE A 653 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 897 through 898 removed outlier: 7.250A pdb=" N VAL A 904 " --> pdb=" O VAL A 912 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1140 through 1142 Processing sheet with id=AB1, first strand: chain 'A' and resid 1173 through 1178 Processing sheet with id=AB2, first strand: chain 'D' and resid 3 through 9 removed outlier: 12.647A pdb=" N VAL D 3 " --> pdb=" O LEU G 10 " (cutoff:3.500A) removed outlier: 12.530A pdb=" N LEU G 10 " --> pdb=" O VAL D 3 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N GLU D 5 " --> pdb=" O ALA G 8 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ALA G 8 " --> pdb=" O GLU D 5 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ARG D 7 " --> pdb=" O LYS G 6 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LYS G 6 " --> pdb=" O ARG D 7 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY G 57 " --> pdb=" O LYS A1432 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU G 59 " --> pdb=" O VAL A1430 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N VAL A1430 " --> pdb=" O LEU G 59 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.527A pdb=" N LEU B 93 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP B 132 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE B 98 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR B 130 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL B 100 " --> pdb=" O PRO B 128 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLY B 150 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL B 131 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLU B 148 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 197 through 200 removed outlier: 3.749A pdb=" N GLN B 197 " --> pdb=" O GLU B 378 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 206 through 207 removed outlier: 3.522A pdb=" N LYS B 228 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS B 239 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 251 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 472 through 474 Processing sheet with id=AB7, first strand: chain 'B' and resid 555 through 557 removed outlier: 5.966A pdb=" N TYR B 556 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA B 598 " --> pdb=" O ASN B 593 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR B 591 " --> pdb=" O HIS B 600 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 602 " --> pdb=" O SER B 589 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 589 " --> pdb=" O ALA B 602 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 619 through 620 Processing sheet with id=AB9, first strand: chain 'B' and resid 724 through 728 removed outlier: 3.694A pdb=" N VAL B 898 " --> pdb=" O THR B 791 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU B 895 " --> pdb=" O MET B 886 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N MET B 886 " --> pdb=" O LEU B 895 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LYS B 897 " --> pdb=" O VAL B 884 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL B 884 " --> pdb=" O LYS B 897 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU B 899 " --> pdb=" O ASP B 882 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP B 882 " --> pdb=" O LEU B 899 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 753 through 755 removed outlier: 3.774A pdb=" N SER B 913 " --> pdb=" O GLN B1025 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 942 through 944 removed outlier: 6.554A pdb=" N ALA B 758 " --> pdb=" O MET B 944 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE B1018 " --> pdb=" O VAL B 759 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 841 through 843 removed outlier: 4.309A pdb=" N ILE B 843 " --> pdb=" O VAL B 871 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL B 871 " --> pdb=" O ILE B 843 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 846 through 848 Processing sheet with id=AC5, first strand: chain 'B' and resid 932 through 933 Processing sheet with id=AC6, first strand: chain 'B' and resid 976 through 977 Processing sheet with id=AC7, first strand: chain 'B' and resid 1101 through 1102 removed outlier: 3.552A pdb=" N ASP B1093 " --> pdb=" O GLY B1102 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE B1090 " --> pdb=" O ILE B1121 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 12 through 13 removed outlier: 4.107A pdb=" N ILE C 7 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LEU C 291 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N HIS C 297 " --> pdb=" O LEU C 230 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 41 through 47 removed outlier: 3.866A pdb=" N GLU C 41 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE C 57 " --> pdb=" O GLU C 41 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LEU C 47 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLU C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 168 through 169 removed outlier: 3.544A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL L 65 " --> pdb=" O PHE C 85 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 161 through 163 removed outlier: 7.153A pdb=" N VAL C 162 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 257 through 258 Processing sheet with id=AD4, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.802A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLY E 108 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N PHE E 135 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE E 110 " --> pdb=" O PHE E 135 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 152 through 155 removed outlier: 4.199A pdb=" N SER E 202 " --> pdb=" O GLY E 206 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY E 206 " --> pdb=" O SER E 202 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 83 through 85 Processing sheet with id=AD7, first strand: chain 'G' and resid 98 through 99 removed outlier: 4.159A pdb=" N ILE G 108 " --> pdb=" O VAL G 99 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 120 through 121 Processing sheet with id=AD9, first strand: chain 'G' and resid 152 through 155 Processing sheet with id=AE1, first strand: chain 'H' and resid 100 through 107 removed outlier: 5.801A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER H 13 " --> pdb=" O GLU H 27 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 13 through 14 removed outlier: 4.004A pdb=" N LEU I 13 " --> pdb=" O ALA I 25 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA I 25 " --> pdb=" O LEU I 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'K' and resid 47 through 49 removed outlier: 3.580A pdb=" N GLN K 64 " --> pdb=" O LYS K 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 29 through 30 Processing sheet with id=AE5, first strand: chain 'M' and resid 76 through 77 removed outlier: 6.628A pdb=" N LYS M 77 " --> pdb=" O LEU M 170 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL N 306 " --> pdb=" O ILE N 416 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 121 through 123 Processing sheet with id=AE7, first strand: chain 'M' and resid 121 through 123 removed outlier: 3.768A pdb=" N ALA M 177 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN M 89 " --> pdb=" O ALA M 177 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU M 179 " --> pdb=" O GLN M 89 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA M 91 " --> pdb=" O LEU M 179 " (cutoff:3.500A) removed outlier: 11.875A pdb=" N ARG M 93 " --> pdb=" O PRO M 181 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR M 90 " --> pdb=" O ASP N 393 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASP N 393 " --> pdb=" O TYR M 90 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU N 407 " --> pdb=" O SER N 398 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA M 248 " --> pdb=" O LEU N 408 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 363 through 364 Processing sheet with id=AE9, first strand: chain 'O' and resid 74 through 75 removed outlier: 3.578A pdb=" N LEU O 74 " --> pdb=" O TYR O 120 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 200 through 202 Processing sheet with id=AF2, first strand: chain 'O' and resid 549 through 552 Processing sheet with id=AF3, first strand: chain 'P' and resid 61 through 64 Processing sheet with id=AF4, first strand: chain 'P' and resid 134 through 137 removed outlier: 3.679A pdb=" N MET P 149 " --> pdb=" O LYS P 135 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'P' and resid 253 through 256 Processing sheet with id=AF6, first strand: chain 'R' and resid 13 through 15 Processing sheet with id=AF7, first strand: chain 'R' and resid 446 through 452 removed outlier: 4.563A pdb=" N GLY R 451 " --> pdb=" O ILE R 396 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE R 396 " --> pdb=" O GLY R 451 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU R 393 " --> pdb=" O SER R 489 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N SER R 489 " --> pdb=" O LEU R 393 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN R 395 " --> pdb=" O VAL R 487 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N THR R 399 " --> pdb=" O ILE R 483 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ILE R 483 " --> pdb=" O THR R 399 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N THR R 401 " --> pdb=" O PHE R 481 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N PHE R 481 " --> pdb=" O THR R 401 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE R 486 " --> pdb=" O GLY R 542 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY R 542 " --> pdb=" O ILE R 486 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR R 541 " --> pdb=" O VAL R 529 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'R' and resid 420 through 421 removed outlier: 3.847A pdb=" N ASN R 421 " --> pdb=" O PHE R 425 " (cutoff:3.500A) 1572 hydrogen bonds defined for protein. 4368 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 85 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 21.70 Time building geometry restraints manager: 21.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 13829 1.33 - 1.46: 12022 1.46 - 1.59: 22448 1.59 - 1.71: 220 1.71 - 1.84: 393 Bond restraints: 48912 Sorted by residual: bond pdb=" C TYR J 63 " pdb=" N ASN J 64 " ideal model delta sigma weight residual 1.329 1.248 0.081 1.21e-02 6.83e+03 4.50e+01 bond pdb=" CA GLU A 502 " pdb=" C GLU A 502 " ideal model delta sigma weight residual 1.523 1.444 0.079 1.35e-02 5.49e+03 3.39e+01 bond pdb=" C THR C 151 " pdb=" N ASP C 152 " ideal model delta sigma weight residual 1.332 1.252 0.080 1.44e-02 4.82e+03 3.10e+01 bond pdb=" C ILE F 130 " pdb=" N PRO F 131 " ideal model delta sigma weight residual 1.334 1.207 0.127 2.34e-02 1.83e+03 2.96e+01 bond pdb=" CA ARG B 915 " pdb=" C ARG B 915 " ideal model delta sigma weight residual 1.523 1.596 -0.073 1.34e-02 5.57e+03 2.96e+01 ... (remaining 48907 not shown) Histogram of bond angle deviations from ideal: 96.13 - 103.75: 951 103.75 - 111.37: 20613 111.37 - 118.98: 19482 118.98 - 126.60: 24635 126.60 - 134.22: 835 Bond angle restraints: 66516 Sorted by residual: angle pdb=" N LYS S 489 " pdb=" CA LYS S 489 " pdb=" C LYS S 489 " ideal model delta sigma weight residual 112.68 99.11 13.57 1.33e+00 5.65e-01 1.04e+02 angle pdb=" N LYS C 35 " pdb=" CA LYS C 35 " pdb=" C LYS C 35 " ideal model delta sigma weight residual 111.28 100.84 10.44 1.09e+00 8.42e-01 9.17e+01 angle pdb=" N CYS J 45 " pdb=" CA CYS J 45 " pdb=" C CYS J 45 " ideal model delta sigma weight residual 110.97 100.62 10.35 1.09e+00 8.42e-01 9.01e+01 angle pdb=" N VAL O 491 " pdb=" CA VAL O 491 " pdb=" C VAL O 491 " ideal model delta sigma weight residual 113.42 102.76 10.66 1.17e+00 7.31e-01 8.30e+01 angle pdb=" N HIS B 916 " pdb=" CA HIS B 916 " pdb=" C HIS B 916 " ideal model delta sigma weight residual 113.16 124.36 -11.20 1.24e+00 6.50e-01 8.15e+01 ... (remaining 66511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 28844 35.46 - 70.93: 708 70.93 - 106.39: 52 106.39 - 141.86: 1 141.86 - 177.32: 2 Dihedral angle restraints: 29607 sinusoidal: 12795 harmonic: 16812 Sorted by residual: dihedral pdb=" C ARG B1048 " pdb=" N ARG B1048 " pdb=" CA ARG B1048 " pdb=" CB ARG B1048 " ideal model delta harmonic sigma weight residual -122.60 -139.70 17.10 0 2.50e+00 1.60e-01 4.68e+01 dihedral pdb=" N ARG B1048 " pdb=" C ARG B1048 " pdb=" CA ARG B1048 " pdb=" CB ARG B1048 " ideal model delta harmonic sigma weight residual 122.80 139.07 -16.27 0 2.50e+00 1.60e-01 4.23e+01 dihedral pdb=" CA VAL A1161 " pdb=" C VAL A1161 " pdb=" N GLU A1162 " pdb=" CA GLU A1162 " ideal model delta harmonic sigma weight residual 180.00 150.16 29.84 0 5.00e+00 4.00e-02 3.56e+01 ... (remaining 29604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 7168 0.121 - 0.242: 319 0.242 - 0.363: 33 0.363 - 0.485: 8 0.485 - 0.606: 1 Chirality restraints: 7529 Sorted by residual: chirality pdb=" CA ARG B1048 " pdb=" N ARG B1048 " pdb=" C ARG B1048 " pdb=" CB ARG B1048 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.18e+00 chirality pdb=" CA TRP R 213 " pdb=" N TRP R 213 " pdb=" C TRP R 213 " pdb=" CB TRP R 213 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.82e+00 chirality pdb=" CA ASN G 113 " pdb=" N ASN G 113 " pdb=" C ASN G 113 " pdb=" CB ASN G 113 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.80e+00 ... (remaining 7526 not shown) Planarity restraints: 8164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A1144 " -0.019 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C VAL A1144 " 0.065 2.00e-02 2.50e+03 pdb=" O VAL A1144 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU A1145 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN O 43 " -0.056 5.00e-02 4.00e+02 8.49e-02 1.15e+01 pdb=" N PRO O 44 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO O 44 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO O 44 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 274 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.34e+00 pdb=" C LYS R 274 " -0.053 2.00e-02 2.50e+03 pdb=" O LYS R 274 " 0.020 2.00e-02 2.50e+03 pdb=" N PHE R 275 " 0.018 2.00e-02 2.50e+03 ... (remaining 8161 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 422 2.48 - 3.08: 39396 3.08 - 3.69: 74196 3.69 - 4.29: 106794 4.29 - 4.90: 163572 Nonbonded interactions: 384380 Sorted by model distance: nonbonded pdb=" O PRO B1139 " pdb=" O ARG B1140 " model vdw 1.869 3.040 nonbonded pdb=" O ALA E 181 " pdb=" O ASP E 182 " model vdw 1.912 3.040 nonbonded pdb=" O SER Q 38 " pdb=" O ILE Q 39 " model vdw 1.980 3.040 nonbonded pdb=" O GLN E 179 " pdb=" O ARG E 180 " model vdw 1.985 3.040 nonbonded pdb=" OD1 ASN A 617 " pdb=" N HIS A 618 " model vdw 2.000 2.520 ... (remaining 384375 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: 6 Type Number sf(0) Gaussians Zn 7 6.06 5 P 110 5.49 5 S 242 5.16 5 C 29976 2.51 5 N 8268 2.21 5 O 9233 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: 1.100 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: 9.240 Check model and map are aligned: 0.660 Convert atoms to be neutral: 0.370 Process input model: 135.930 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.127 48912 Z= 0.470 Angle : 1.154 13.569 66516 Z= 0.701 Chirality : 0.061 0.606 7529 Planarity : 0.006 0.085 8164 Dihedral : 13.917 177.324 18709 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 33.65 Ramachandran Plot: Outliers : 1.46 % Allowed : 16.80 % Favored : 81.74 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 1.66 % 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: -5.05 (0.08), residues: 5625 helix: -3.91 (0.07), residues: 1791 sheet: -2.42 (0.18), residues: 593 loop : -3.31 (0.09), residues: 3241 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1222 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1192 time to evaluate : 5.665 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 outliers start: 30 outliers final: 10 residues processed: 1207 average time/residue: 0.6230 time to fit residues: 1217.1682 Evaluate side-chains 637 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 627 time to evaluate : 5.469 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.6180 time to fit residues: 17.6959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 483 optimal weight: 6.9990 chunk 434 optimal weight: 5.9990 chunk 240 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 chunk 292 optimal weight: 6.9990 chunk 232 optimal weight: 0.8980 chunk 449 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 chunk 273 optimal weight: 5.9990 chunk 334 optimal weight: 3.9990 chunk 520 optimal weight: 20.0000 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN A 161 ASN A 315 HIS A 386 ASN ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN A 566 HIS A 589 HIS A 643 ASN A 929 ASN A1385 GLN A1395 HIS B 116 HIS B 140 ASN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 ASN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 HIS ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 HIS B 626 HIS B 693 HIS ** B 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 754 ASN ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 902 GLN B1029 HIS C 87 ASN C 93 GLN C 99 HIS D 64 ASN D 69 ASN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN G 32 ASN H 133 ASN ** M 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 254 GLN N 288 GLN N 377 ASN O 43 ASN O 147 ASN O 193 GLN O 222 HIS ** O 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 337 GLN ** O 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 580 ASN ** O 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 21 GLN P 189 ASN P 219 GLN P 239 ASN P 305 HIS R 35 ASN ** R 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 394 GLN R 414 HIS R 505 HIS S 367 ASN ** S 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 48912 Z= 0.348 Angle : 0.875 12.586 66516 Z= 0.463 Chirality : 0.049 0.342 7529 Planarity : 0.006 0.077 8164 Dihedral : 16.223 179.618 7331 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 23.98 Ramachandran Plot: Outliers : 0.78 % Allowed : 12.00 % Favored : 87.22 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.95 (0.10), residues: 5625 helix: -2.32 (0.10), residues: 1907 sheet: -2.18 (0.18), residues: 656 loop : -2.99 (0.10), residues: 3062 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 908 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 890 time to evaluate : 5.560 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 outliers start: 18 outliers final: 6 residues processed: 904 average time/residue: 0.5657 time to fit residues: 860.5014 Evaluate side-chains 599 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 593 time to evaluate : 6.032 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4095 time to fit residues: 12.5794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 289 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 433 optimal weight: 0.0040 chunk 354 optimal weight: 0.0010 chunk 143 optimal weight: 0.9990 chunk 521 optimal weight: 20.0000 chunk 563 optimal weight: 10.0000 chunk 464 optimal weight: 40.0000 chunk 516 optimal weight: 40.0000 chunk 177 optimal weight: 5.9990 chunk 418 optimal weight: 3.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** A1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 840 GLN ** B 844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 902 GLN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN I 10 ASN M 234 HIS M 254 GLN O 56 HIS O 207 HIS ** O 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 239 ASN R 236 ASN ** S 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 48912 Z= 0.281 Angle : 0.790 13.545 66516 Z= 0.415 Chirality : 0.047 0.301 7529 Planarity : 0.005 0.084 8164 Dihedral : 16.008 174.535 7331 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.82 % Allowed : 11.68 % Favored : 87.50 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.23 (0.10), residues: 5625 helix: -1.39 (0.11), residues: 1944 sheet: -2.00 (0.19), residues: 632 loop : -2.77 (0.10), residues: 3049 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 867 time to evaluate : 6.043 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 outliers start: 5 outliers final: 2 residues processed: 871 average time/residue: 0.5742 time to fit residues: 840.6221 Evaluate side-chains 597 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 595 time to evaluate : 5.458 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4329 time to fit residues: 8.9408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 515 optimal weight: 30.0000 chunk 391 optimal weight: 20.0000 chunk 270 optimal weight: 0.4980 chunk 57 optimal weight: 0.6980 chunk 248 optimal weight: 6.9990 chunk 350 optimal weight: 1.9990 chunk 523 optimal weight: 40.0000 chunk 553 optimal weight: 30.0000 chunk 273 optimal weight: 10.0000 chunk 495 optimal weight: 0.9990 chunk 149 optimal weight: 8.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 643 ASN ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 GLN ** B 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 902 GLN ** B 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN M 234 HIS ** N 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 48912 Z= 0.294 Angle : 0.772 13.212 66516 Z= 0.403 Chirality : 0.046 0.259 7529 Planarity : 0.005 0.071 8164 Dihedral : 15.890 174.888 7331 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 21.21 Ramachandran Plot: Outliers : 0.91 % Allowed : 11.80 % Favored : 87.29 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % 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: -3.00 (0.10), residues: 5625 helix: -1.08 (0.11), residues: 1961 sheet: -1.90 (0.19), residues: 650 loop : -2.72 (0.11), residues: 3014 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 832 time to evaluate : 5.899 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 outliers start: 2 outliers final: 1 residues processed: 833 average time/residue: 0.5791 time to fit residues: 817.8795 Evaluate side-chains 582 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 581 time to evaluate : 5.556 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4128 time to fit residues: 8.3887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 461 optimal weight: 7.9990 chunk 314 optimal weight: 0.0770 chunk 8 optimal weight: 1.9990 chunk 412 optimal weight: 0.9980 chunk 228 optimal weight: 1.9990 chunk 472 optimal weight: 4.9990 chunk 382 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 282 optimal weight: 0.7980 chunk 497 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS A 315 HIS A 455 ASN A 509 ASN ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 643 ASN A 944 ASN ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 GLN ** B 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 754 ASN ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 902 GLN ** B 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 HIS ** N 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 117 HIS P 239 ASN P 305 HIS ** R 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 48912 Z= 0.230 Angle : 0.747 14.194 66516 Z= 0.389 Chirality : 0.046 0.259 7529 Planarity : 0.005 0.065 8164 Dihedral : 15.809 175.480 7331 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.92 % Allowed : 11.36 % Favored : 87.72 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % 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: -2.77 (0.11), residues: 5625 helix: -0.85 (0.11), residues: 1967 sheet: -1.71 (0.20), residues: 633 loop : -2.63 (0.11), residues: 3025 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 848 time to evaluate : 5.605 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 outliers start: 2 outliers final: 1 residues processed: 850 average time/residue: 0.5749 time to fit residues: 829.8764 Evaluate side-chains 599 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 598 time to evaluate : 5.568 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4410 time to fit residues: 8.6619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 186 optimal weight: 3.9990 chunk 498 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 325 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 554 optimal weight: 6.9990 chunk 460 optimal weight: 9.9990 chunk 256 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 291 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 643 ASN A 931 GLN A 944 ASN ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1395 HIS ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 GLN ** B 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 840 GLN ** B 844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 865 GLN B 893 GLN ** B 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN O 244 ASN O 298 ASN O 332 GLN ** O 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 117 HIS ** P 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 499 ASN ** S 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.068 48912 Z= 0.424 Angle : 0.830 12.836 66516 Z= 0.434 Chirality : 0.049 0.300 7529 Planarity : 0.006 0.064 8164 Dihedral : 15.809 176.040 7331 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 22.96 Ramachandran Plot: Outliers : 0.92 % Allowed : 12.91 % Favored : 86.17 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % 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: -2.87 (0.11), residues: 5625 helix: -0.89 (0.11), residues: 1972 sheet: -1.83 (0.19), residues: 665 loop : -2.72 (0.11), residues: 2988 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 760 time to evaluate : 5.643 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 outliers start: 1 outliers final: 1 residues processed: 761 average time/residue: 0.5622 time to fit residues: 725.2849 Evaluate side-chains 548 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 547 time to evaluate : 5.497 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4160 time to fit residues: 8.2592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 534 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 315 optimal weight: 1.9990 chunk 404 optimal weight: 9.9990 chunk 313 optimal weight: 8.9990 chunk 466 optimal weight: 4.9990 chunk 309 optimal weight: 0.9990 chunk 552 optimal weight: 0.0670 chunk 345 optimal weight: 6.9990 chunk 336 optimal weight: 0.4980 chunk 254 optimal weight: 0.0980 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN A 944 ASN ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 GLN ** B 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 754 ASN ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 902 GLN ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 HIS D 64 ASN ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 ASN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 86 HIS M 89 GLN ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 HIS ** N 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 288 GLN O 332 GLN ** O 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 184 HIS ** S 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.089 48912 Z= 0.213 Angle : 0.748 15.268 66516 Z= 0.386 Chirality : 0.046 0.250 7529 Planarity : 0.005 0.104 8164 Dihedral : 15.732 175.745 7331 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.94 % Allowed : 11.34 % Favored : 87.72 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % 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: -2.62 (0.11), residues: 5625 helix: -0.68 (0.11), residues: 1980 sheet: -1.55 (0.20), residues: 625 loop : -2.61 (0.11), residues: 3020 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 808 time to evaluate : 5.679 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 outliers start: 0 outliers final: 0 residues processed: 808 average time/residue: 0.5617 time to fit residues: 778.1018 Evaluate side-chains 570 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 570 time to evaluate : 5.526 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.3921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 341 optimal weight: 0.7980 chunk 220 optimal weight: 0.7980 chunk 329 optimal weight: 6.9990 chunk 166 optimal weight: 0.0770 chunk 108 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 351 optimal weight: 1.9990 chunk 376 optimal weight: 0.5980 chunk 273 optimal weight: 0.0020 chunk 51 optimal weight: 3.9990 chunk 434 optimal weight: 4.9990 overall best weight: 0.4546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN A 944 ASN A1395 HIS B 144 HIS ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 GLN B 902 GLN B 928 GLN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 HIS M 242 ASN ** N 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 100 GLN ** O 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 117 HIS P 239 ASN ** R 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 124 ASN ** S 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 48912 Z= 0.201 Angle : 0.743 15.207 66516 Z= 0.382 Chirality : 0.046 0.253 7529 Planarity : 0.005 0.096 8164 Dihedral : 15.631 176.022 7331 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.94 % Allowed : 11.36 % Favored : 87.70 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % 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: -2.57 (0.11), residues: 5625 helix: -0.59 (0.12), residues: 1993 sheet: -1.63 (0.19), residues: 698 loop : -2.60 (0.11), residues: 2934 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 791 time to evaluate : 6.025 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 outliers start: 1 outliers final: 0 residues processed: 791 average time/residue: 0.5589 time to fit residues: 762.8415 Evaluate side-chains 581 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 581 time to evaluate : 5.497 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.4717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 502 optimal weight: 0.9990 chunk 529 optimal weight: 0.9980 chunk 482 optimal weight: 4.9990 chunk 514 optimal weight: 0.4980 chunk 528 optimal weight: 0.2980 chunk 309 optimal weight: 0.0170 chunk 224 optimal weight: 10.0000 chunk 404 optimal weight: 9.9990 chunk 157 optimal weight: 0.6980 chunk 465 optimal weight: 30.0000 chunk 486 optimal weight: 9.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN A 944 ASN A1318 HIS A1395 HIS ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 902 GLN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 242 ASN ** N 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 48912 Z= 0.195 Angle : 0.736 13.803 66516 Z= 0.377 Chirality : 0.045 0.279 7529 Planarity : 0.005 0.073 8164 Dihedral : 15.553 176.000 7331 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.94 % Allowed : 10.97 % Favored : 88.09 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % 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: -2.47 (0.11), residues: 5625 helix: -0.48 (0.12), residues: 1981 sheet: -1.52 (0.19), residues: 708 loop : -2.57 (0.11), residues: 2936 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 793 time to evaluate : 6.079 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 outliers start: 1 outliers final: 0 residues processed: 793 average time/residue: 0.5612 time to fit residues: 760.0299 Evaluate side-chains 585 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 585 time to evaluate : 5.626 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.5784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 512 optimal weight: 30.0000 chunk 337 optimal weight: 20.0000 chunk 544 optimal weight: 30.0000 chunk 332 optimal weight: 3.9990 chunk 258 optimal weight: 0.6980 chunk 378 optimal weight: 6.9990 chunk 570 optimal weight: 10.0000 chunk 525 optimal weight: 40.0000 chunk 454 optimal weight: 3.9990 chunk 47 optimal weight: 0.0070 chunk 351 optimal weight: 2.9990 overall best weight: 2.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN A 944 ASN ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 GLN B 840 GLN B 902 GLN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 ASN ** I 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 242 ASN ** N 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 332 GLN ** O 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 117 HIS ** P 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 384 HIS ** S 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 48912 Z= 0.286 Angle : 0.755 14.074 66516 Z= 0.390 Chirality : 0.046 0.338 7529 Planarity : 0.005 0.076 8164 Dihedral : 15.526 176.000 7331 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 1.00 % Allowed : 11.79 % Favored : 87.22 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % 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: -2.48 (0.11), residues: 5625 helix: -0.48 (0.12), residues: 1995 sheet: -1.56 (0.19), residues: 711 loop : -2.59 (0.11), residues: 2919 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 722 time to evaluate : 5.661 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: 1 outliers final: 0 residues processed: 722 average time/residue: 0.5704 time to fit residues: 708.8759 Evaluate side-chains 539 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 539 time to evaluate : 5.545 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.6335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 278 optimal weight: 0.2980 chunk 361 optimal weight: 0.8980 chunk 484 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 chunk 419 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 455 optimal weight: 6.9990 chunk 190 optimal weight: 4.9990 chunk 467 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN A 944 ASN ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 840 GLN B 902 GLN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 242 ASN ** N 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 128 HIS ** O 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.120450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.088124 restraints weight = 125842.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.087576 restraints weight = 75724.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.088089 restraints weight = 58890.844| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.5421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.106 48912 Z= 0.204 Angle : 0.735 14.840 66516 Z= 0.377 Chirality : 0.045 0.270 7529 Planarity : 0.005 0.187 8164 Dihedral : 15.494 175.760 7331 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.98 % Allowed : 11.24 % Favored : 87.79 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % 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: -2.37 (0.11), residues: 5625 helix: -0.36 (0.12), residues: 1984 sheet: -1.45 (0.19), residues: 691 loop : -2.55 (0.11), residues: 2950 =============================================================================== Job complete usr+sys time: 12439.78 seconds wall clock time: 223 minutes 42.92 seconds (13422.92 seconds total)