Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 26 01:22:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4f_17408/08_2023/8p4f_17408_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4f_17408/08_2023/8p4f_17408.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4f_17408/08_2023/8p4f_17408_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4f_17408/08_2023/8p4f_17408_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4f_17408/08_2023/8p4f_17408_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4f_17408/08_2023/8p4f_17408.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4f_17408/08_2023/8p4f_17408.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4f_17408/08_2023/8p4f_17408_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4f_17408/08_2023/8p4f_17408_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 107 5.49 5 Mg 1 5.21 5 S 259 5.16 5 C 27302 2.51 5 N 7653 2.21 5 O 8356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 51": "NH1" <-> "NH2" Residue "A ARG 67": "NH1" <-> "NH2" Residue "A ARG 448": "NH1" <-> "NH2" Residue "A ARG 958": "NH1" <-> "NH2" Residue "A ARG 1052": "NH1" <-> "NH2" Residue "A ARG 1053": "NH1" <-> "NH2" Residue "A ARG 1408": "NH1" <-> "NH2" Residue "B TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 886": "NH1" <-> "NH2" Residue "B ARG 1131": "NH1" <-> "NH2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "I PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 198": "NH1" <-> "NH2" Residue "Z ARG 555": "NH1" <-> "NH2" Residue "Z ARG 571": "NH1" <-> "NH2" Residue "Z ARG 577": "NH1" <-> "NH2" Residue "Z ARG 582": "NH1" <-> "NH2" Residue "G ARG 16": "NH1" <-> "NH2" Residue "G GLU 100": "OE1" <-> "OE2" Residue "G TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 132": "OD1" <-> "OD2" Residue "G ASP 134": "OD1" <-> "OD2" Residue "O GLU 146": "OE1" <-> "OE2" Residue "O GLU 148": "OE1" <-> "OE2" Residue "O GLU 160": "OE1" <-> "OE2" Residue "O GLU 164": "OE1" <-> "OE2" Residue "O GLU 170": "OE1" <-> "OE2" Residue "O GLU 185": "OE1" <-> "OE2" Residue "O GLU 187": "OE1" <-> "OE2" Residue "O GLU 189": "OE1" <-> "OE2" Residue "O GLU 193": "OE1" <-> "OE2" Residue "O GLU 194": "OE1" <-> "OE2" Residue "O GLU 212": "OE1" <-> "OE2" Residue "O GLU 213": "OE1" <-> "OE2" Residue "O GLU 225": "OE1" <-> "OE2" Residue "O PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 267": "OE1" <-> "OE2" Residue "O GLU 269": "OE1" <-> "OE2" Residue "O GLU 285": "OE1" <-> "OE2" Residue "O TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 311": "OE1" <-> "OE2" Residue "O GLU 319": "OE1" <-> "OE2" Residue "O PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 322": "OE1" <-> "OE2" Residue "O TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 327": "OE1" <-> "OE2" Residue "O GLU 340": "OE1" <-> "OE2" Residue "O PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 370": "OE1" <-> "OE2" Residue "O GLU 373": "OE1" <-> "OE2" Residue "O GLU 377": "OE1" <-> "OE2" Residue "O PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 425": "OE1" <-> "OE2" Residue "O PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 454": "OD1" <-> "OD2" Residue "O TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 484": "OE1" <-> "OE2" Residue "O GLU 491": "OE1" <-> "OE2" Residue "O GLU 501": "OE1" <-> "OE2" Residue "O PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 525": "OE1" <-> "OE2" Residue "O GLU 530": "OE1" <-> "OE2" Residue "O GLU 534": "OE1" <-> "OE2" Residue "O PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 560": "OE1" <-> "OE2" Residue "O GLU 566": "OE1" <-> "OE2" Residue "O PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 583": "OE1" <-> "OE2" Residue "O GLU 599": "OE1" <-> "OE2" Residue "O TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 630": "OE1" <-> "OE2" Residue "O GLU 640": "OE1" <-> "OE2" Residue "O GLU 648": "OE1" <-> "OE2" Residue "O GLU 673": "OE1" <-> "OE2" Residue "O PHE 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 684": "OE1" <-> "OE2" Residue "O PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 705": "OE1" <-> "OE2" Residue "O TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 710": "OE1" <-> "OE2" Residue "O GLU 711": "OE1" <-> "OE2" Residue "O GLU 713": "OE1" <-> "OE2" Residue "O GLU 720": "OE1" <-> "OE2" Residue "O PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 756": "OE1" <-> "OE2" Residue "O PHE 762": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 802": "OE1" <-> "OE2" Residue "O GLU 824": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 43686 Number of models: 1 Model: "" Number of chains: 26 Chain: "P" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 622 Classifications: {'RNA': 29} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 17, 'rna3p_pyr': 8} Link IDs: {'rna2p': 4, 'rna3p': 24} Chain: "A" Number of atoms: 11261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1421, 11261 Classifications: {'peptide': 1421} Link IDs: {'PCIS': 2, 'PTRANS': 68, 'TRANS': 1350} Chain breaks: 4 Chain: "B" Number of atoms: 9142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1147, 9142 Classifications: {'peptide': 1147} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 53, 'TRANS': 1093} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 2079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2079 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 15, 'TRANS': 243} Chain breaks: 1 Chain: "E" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1711 Classifications: {'peptide': 209} Incomplete info: {'backbone_only': 2} Link IDs: {'PTRANS': 11, 'TRANS': 197} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 946 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 379 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "N" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 610 Classifications: {'DNA': 38} Incomplete info: {'p_only': 9} Link IDs: {'rna3p': 37} Unresolved chain links: 9 Chain breaks: 1 Unresolved chain link angles: 39 Unresolved chain link dihedrals: 29 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {' DG:plan': 1, ' DG:plan2': 1, ' DC:plan2': 1, ' DA:plan2': 2, ' DC:plan': 1, ' DT:plan': 5, ' DA:plan': 2} Unresolved non-hydrogen planarities: 101 Chain: "T" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 774 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "Y" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 911 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "Z" Number of atoms: 3894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3894 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 17, 'TRANS': 470} Chain breaks: 3 Chain: "G" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1341 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1008 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "O" Number of atoms: 5643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 5643 Classifications: {'peptide': 695} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 27, 'TRANS': 663} Chain: "P" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'MGT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1086 SG CYS A 71 73.616 71.615 117.804 1.00174.43 S ATOM 1108 SG CYS A 74 77.003 71.714 117.951 1.00166.79 S ATOM 1155 SG CYS A 81 74.842 73.152 115.095 1.00162.13 S ATOM 1390 SG CYS A 111 87.055 39.794 81.979 1.00183.09 S ATOM 1418 SG CYS A 114 88.720 38.471 84.647 1.00182.27 S ATOM 1764 SG CYS A 184 86.209 36.272 82.465 1.00191.04 S ATOM 20595 SG CYS B1119 90.391 64.924 112.279 1.00148.10 S ATOM 20617 SG CYS B1122 88.560 63.624 109.561 1.00143.35 S ATOM 20732 SG CYS B1137 87.279 63.612 112.688 1.00165.79 S ATOM 20753 SG CYS B1140 89.477 60.627 110.822 1.00167.23 S ATOM 26725 SG CYS I 17 52.739 55.222 27.067 1.00155.52 S ATOM 26749 SG CYS I 20 52.005 54.156 30.974 1.00158.58 S ATOM 26910 SG CYS I 39 55.377 53.769 30.694 1.00159.23 S ATOM 26935 SG CYS I 42 53.411 51.662 28.290 1.00157.72 S ATOM 27287 SG CYS I 86 55.600 99.307 19.418 1.00154.36 S ATOM 27311 SG CYS I 89 52.124 100.294 18.297 1.00162.90 S ATOM 27515 SG CYS I 114 53.806 100.005 22.307 1.00146.80 S ATOM 27550 SG CYS I 119 52.501 97.406 20.192 1.00147.95 S ATOM 27660 SG CYS J 7 57.100 135.003 85.471 1.00 75.68 S ATOM 27684 SG CYS J 10 58.624 138.388 86.231 1.00 78.13 S ATOM 27948 SG CYS J 44 59.391 137.446 83.108 1.00 83.70 S ATOM 27954 SG CYS J 45 56.076 138.623 84.092 1.00 86.52 S ATOM 29107 SG CYS L 19 27.934 105.836 101.379 1.00138.04 S ATOM 29126 SG CYS L 22 24.939 107.539 101.745 1.00137.85 S ATOM 29243 SG CYS L 36 26.085 105.317 104.737 1.00146.22 S ATOM 29269 SG CYS L 39 25.156 103.889 101.248 1.00145.80 S ATOM 30940 SG CYS Y 16 33.114 24.951 95.418 1.00484.94 S ATOM 30962 SG CYS Y 19 34.344 25.347 91.802 1.00462.52 S ATOM 31074 SG CYS Y 33 30.815 25.374 92.193 1.00506.45 S ATOM 31096 SG CYS Y 36 32.757 22.048 92.841 1.00521.18 S Time building chain proxies: 20.18, per 1000 atoms: 0.46 Number of scatterers: 43686 At special positions: 0 Unit cell: (155.4, 176.4, 219.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 259 16.00 P 107 15.00 Mg 1 11.99 O 8356 8.00 N 7653 7.00 C 27302 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.69 Conformation dependent library (CDL) restraints added in 5.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb=" ZN Y 201 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 33 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 16 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 36 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 19 " Number of angles added : 39 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9780 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 177 helices and 56 sheets defined 30.4% alpha, 15.0% beta 35 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 17.77 Creating SS restraints... Processing helix chain 'A' and resid 28 through 34 removed outlier: 3.621A pdb=" N LYS A 32 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 109 removed outlier: 3.624A pdb=" N THR A 103 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 108 " --> pdb=" O LYS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 137 through 150 removed outlier: 3.932A pdb=" N LEU A 141 " --> pdb=" O PRO A 137 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 227 removed outlier: 4.068A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 245 through 248 Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 275 through 295 removed outlier: 3.535A pdb=" N ILE A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 318 removed outlier: 3.667A pdb=" N ALA A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU A 305 " --> pdb=" O HIS A 301 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 342 No H-bonds generated for 'chain 'A' and resid 339 through 342' Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 382 through 387 removed outlier: 3.774A pdb=" N ASN A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 408 removed outlier: 3.804A pdb=" N GLU A 404 " --> pdb=" O ASP A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 468 No H-bonds generated for 'chain 'A' and resid 466 through 468' Processing helix chain 'A' and resid 487 through 489 No H-bonds generated for 'chain 'A' and resid 487 through 489' Processing helix chain 'A' and resid 509 through 518 removed outlier: 3.903A pdb=" N GLU A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 515 " --> pdb=" O THR A 511 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 523 No H-bonds generated for 'chain 'A' and resid 521 through 523' Processing helix chain 'A' and resid 539 through 549 removed outlier: 4.081A pdb=" N VAL A 545 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 546 " --> pdb=" O THR A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 566 removed outlier: 3.556A pdb=" N MET A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 563 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET A 565 " --> pdb=" O MET A 561 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 595 removed outlier: 4.113A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 662 through 677 removed outlier: 3.685A pdb=" N LEU A 667 " --> pdb=" O ASP A 663 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 669 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 670 " --> pdb=" O ARG A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 683 No H-bonds generated for 'chain 'A' and resid 680 through 683' Processing helix chain 'A' and resid 689 through 691 No H-bonds generated for 'chain 'A' and resid 689 through 691' Processing helix chain 'A' and resid 698 through 721 removed outlier: 3.530A pdb=" N THR A 705 " --> pdb=" O ASP A 701 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 714 " --> pdb=" O LYS A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 757 removed outlier: 3.649A pdb=" N ASN A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP A 747 " --> pdb=" O ARG A 743 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER A 754 " --> pdb=" O ASP A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 771 Processing helix chain 'A' and resid 778 through 785 removed outlier: 3.626A pdb=" N SER A 782 " --> pdb=" O LYS A 778 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN A 783 " --> pdb=" O ILE A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 868 removed outlier: 3.730A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A 863 " --> pdb=" O TYR A 859 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 865 " --> pdb=" O GLN A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.671A pdb=" N GLU A 917 " --> pdb=" O ASN A 913 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A 918 " --> pdb=" O LYS A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 933 Processing helix chain 'A' and resid 936 through 944 removed outlier: 3.631A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 944 " --> pdb=" O LYS A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 969 removed outlier: 3.538A pdb=" N ARG A 967 " --> pdb=" O ARG A 963 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 968 " --> pdb=" O GLU A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 973 No H-bonds generated for 'chain 'A' and resid 971 through 973' Processing helix chain 'A' and resid 983 through 992 removed outlier: 3.682A pdb=" N LYS A 992 " --> pdb=" O TRP A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1017 removed outlier: 3.736A pdb=" N VAL A1010 " --> pdb=" O PRO A1006 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY A1012 " --> pdb=" O LYS A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1037 removed outlier: 3.566A pdb=" N ALA A1037 " --> pdb=" O ALA A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1048 Processing helix chain 'A' and resid 1051 through 1055 removed outlier: 3.530A pdb=" N ALA A1055 " --> pdb=" O SER A1051 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1051 through 1055' Processing helix chain 'A' and resid 1062 through 1077 removed outlier: 3.545A pdb=" N GLY A1070 " --> pdb=" O ASP A1066 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A1071 " --> pdb=" O TRP A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1101 removed outlier: 3.529A pdb=" N LEU A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A1096 " --> pdb=" O ALA A1092 " (cutoff:3.500A) Proline residue: A1098 - end of helix removed outlier: 4.381A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1129 removed outlier: 3.855A pdb=" N GLU A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1148 No H-bonds generated for 'chain 'A' and resid 1146 through 1148' Processing helix chain 'A' and resid 1151 through 1161 removed outlier: 3.600A pdb=" N ILE A1157 " --> pdb=" O ARG A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1183 No H-bonds generated for 'chain 'A' and resid 1181 through 1183' Processing helix chain 'A' and resid 1188 through 1198 removed outlier: 3.749A pdb=" N VAL A1193 " --> pdb=" O GLN A1190 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU A1198 " --> pdb=" O VAL A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1223 Processing helix chain 'A' and resid 1228 through 1242 removed outlier: 6.456A pdb=" N ASP A1241 " --> pdb=" O ALA A1237 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ASP A1242 " --> pdb=" O GLY A1238 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1266 No H-bonds generated for 'chain 'A' and resid 1263 through 1266' Processing helix chain 'A' and resid 1282 through 1295 removed outlier: 4.175A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1348 removed outlier: 3.758A pdb=" N SER A1348 " --> pdb=" O MET A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1369 removed outlier: 3.588A pdb=" N VAL A1368 " --> pdb=" O GLU A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1371 through 1387 removed outlier: 3.820A pdb=" N GLU A1379 " --> pdb=" O ARG A1375 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1408 removed outlier: 3.637A pdb=" N LEU A1401 " --> pdb=" O HIS A1397 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A1406 " --> pdb=" O CYS A1402 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ARG A1408 " --> pdb=" O THR A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1416 through 1421 Processing helix chain 'A' and resid 1426 through 1429 No H-bonds generated for 'chain 'A' and resid 1426 through 1429' Processing helix chain 'A' and resid 1435 through 1444 removed outlier: 4.224A pdb=" N MET A1440 " --> pdb=" O ASP A1437 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A1441 " --> pdb=" O VAL A1438 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA A1444 " --> pdb=" O GLU A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1454 through 1459 Processing helix chain 'A' and resid 1479 through 1481 No H-bonds generated for 'chain 'A' and resid 1479 through 1481' Processing helix chain 'B' and resid 22 through 36 removed outlier: 3.989A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 31 " --> pdb=" O TRP B 27 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR B 33 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 52 Processing helix chain 'B' and resid 54 through 60 removed outlier: 3.502A pdb=" N ILE B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 115 Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 247 through 252 removed outlier: 3.551A pdb=" N ALA B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 275 Processing helix chain 'B' and resid 281 through 288 Processing helix chain 'B' and resid 295 through 307 Proline residue: B 303 - end of helix removed outlier: 3.674A pdb=" N GLU B 307 " --> pdb=" O PRO B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 324 removed outlier: 4.365A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 344 Processing helix chain 'B' and resid 355 through 377 removed outlier: 3.985A pdb=" N LYS B 361 " --> pdb=" O GLU B 358 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR B 363 " --> pdb=" O LYS B 360 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE B 364 " --> pdb=" O LYS B 361 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 365 " --> pdb=" O ALA B 362 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 372 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 374 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA B 375 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 377 " --> pdb=" O LEU B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 423 removed outlier: 4.307A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 450 Processing helix chain 'B' and resid 475 through 482 removed outlier: 3.985A pdb=" N SER B 480 " --> pdb=" O ALA B 476 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS B 481 " --> pdb=" O SER B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 517 through 519 No H-bonds generated for 'chain 'B' and resid 517 through 519' Processing helix chain 'B' and resid 539 through 548 removed outlier: 3.673A pdb=" N GLU B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 592 Processing helix chain 'B' and resid 637 through 644 Processing helix chain 'B' and resid 653 through 659 removed outlier: 3.766A pdb=" N SER B 659 " --> pdb=" O ASP B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 682 Processing helix chain 'B' and resid 700 through 703 removed outlier: 3.577A pdb=" N ILE B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 700 through 703' Processing helix chain 'B' and resid 714 through 716 No H-bonds generated for 'chain 'B' and resid 714 through 716' Processing helix chain 'B' and resid 719 through 728 removed outlier: 3.662A pdb=" N THR B 723 " --> pdb=" O SER B 719 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN B 725 " --> pdb=" O ARG B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 removed outlier: 3.758A pdb=" N ARG B 803 " --> pdb=" O SER B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 878 Processing helix chain 'B' and resid 951 through 953 No H-bonds generated for 'chain 'B' and resid 951 through 953' Processing helix chain 'B' and resid 969 through 975 Proline residue: B 973 - end of helix Processing helix chain 'B' and resid 979 through 992 removed outlier: 3.540A pdb=" N CYS B 984 " --> pdb=" O HIS B 980 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS B 988 " --> pdb=" O CYS B 984 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL B 989 " --> pdb=" O LEU B 985 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN B 992 " --> pdb=" O LYS B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1018 removed outlier: 3.727A pdb=" N LEU B1014 " --> pdb=" O LYS B1010 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1088 through 1096 removed outlier: 3.560A pdb=" N ALA B1096 " --> pdb=" O ASP B1092 " (cutoff:3.500A) Processing helix chain 'B' and resid 1100 through 1107 removed outlier: 3.577A pdb=" N GLU B1105 " --> pdb=" O GLN B1101 " (cutoff:3.500A) Processing helix chain 'B' and resid 1153 through 1165 removed outlier: 3.515A pdb=" N SER B1164 " --> pdb=" O GLN B1160 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N MET B1165 " --> pdb=" O GLU B1161 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 35 removed outlier: 3.565A pdb=" N ARG C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 70 removed outlier: 3.575A pdb=" N GLY C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 70 " --> pdb=" O HIS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 200 through 202 No H-bonds generated for 'chain 'C' and resid 200 through 202' Processing helix chain 'C' and resid 241 through 270 removed outlier: 3.895A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER C 247 " --> pdb=" O THR C 243 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS C 254 " --> pdb=" O SER C 250 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS C 255 " --> pdb=" O GLY C 251 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR C 261 " --> pdb=" O SER C 257 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU C 266 " --> pdb=" O GLN C 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 23 removed outlier: 3.654A pdb=" N ARG E 14 " --> pdb=" O LEU E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 33 No H-bonds generated for 'chain 'E' and resid 30 through 33' Processing helix chain 'E' and resid 37 through 43 Processing helix chain 'E' and resid 84 through 97 removed outlier: 3.508A pdb=" N VAL E 89 " --> pdb=" O LYS E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 120 removed outlier: 4.148A pdb=" N GLN E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 153 through 162 Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' Processing helix chain 'E' and resid 178 through 182 Processing helix chain 'F' and resid 61 through 73 removed outlier: 3.581A pdb=" N LEU F 66 " --> pdb=" O ARG F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 98 removed outlier: 3.545A pdb=" N LYS F 98 " --> pdb=" O MET F 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 66 No H-bonds generated for 'chain 'I' and resid 64 through 66' Processing helix chain 'I' and resid 70 through 74 Processing helix chain 'J' and resid 18 through 27 removed outlier: 3.788A pdb=" N GLY J 23 " --> pdb=" O GLU J 19 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 37 Processing helix chain 'J' and resid 43 through 50 removed outlier: 4.085A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 59 No H-bonds generated for 'chain 'J' and resid 56 through 59' Processing helix chain 'K' and resid 6 through 8 No H-bonds generated for 'chain 'K' and resid 6 through 8' Processing helix chain 'K' and resid 40 through 52 removed outlier: 3.846A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE K 46 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 112 removed outlier: 3.554A pdb=" N ILE K 91 " --> pdb=" O PHE K 87 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU K 100 " --> pdb=" O SER K 96 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU K 103 " --> pdb=" O SER K 99 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 5 No H-bonds generated for 'chain 'Y' and resid 3 through 5' Processing helix chain 'Y' and resid 25 through 31 Processing helix chain 'Y' and resid 37 through 40 No H-bonds generated for 'chain 'Y' and resid 37 through 40' Processing helix chain 'Y' and resid 46 through 52 Processing helix chain 'Y' and resid 66 through 68 No H-bonds generated for 'chain 'Y' and resid 66 through 68' Processing helix chain 'Y' and resid 70 through 74 Processing helix chain 'Y' and resid 95 through 103 Processing helix chain 'Z' and resid 189 through 202 Processing helix chain 'Z' and resid 232 through 239 Processing helix chain 'Z' and resid 243 through 248 removed outlier: 5.202A pdb=" N LEU Z 247 " --> pdb=" O ASN Z 244 " (cutoff:3.500A) Processing helix chain 'Z' and resid 257 through 259 No H-bonds generated for 'chain 'Z' and resid 257 through 259' Processing helix chain 'Z' and resid 262 through 264 No H-bonds generated for 'chain 'Z' and resid 262 through 264' Processing helix chain 'Z' and resid 342 through 348 Processing helix chain 'Z' and resid 390 through 395 Processing helix chain 'Z' and resid 465 through 467 No H-bonds generated for 'chain 'Z' and resid 465 through 467' Processing helix chain 'Z' and resid 515 through 517 No H-bonds generated for 'chain 'Z' and resid 515 through 517' Processing helix chain 'Z' and resid 572 through 574 No H-bonds generated for 'chain 'Z' and resid 572 through 574' Processing helix chain 'Z' and resid 631 through 634 Processing helix chain 'Z' and resid 640 through 642 No H-bonds generated for 'chain 'Z' and resid 640 through 642' Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 23 through 34 Processing helix chain 'G' and resid 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'D' and resid 17 through 19 No H-bonds generated for 'chain 'D' and resid 17 through 19' Processing helix chain 'D' and resid 34 through 49 Processing helix chain 'D' and resid 59 through 71 Processing helix chain 'D' and resid 77 through 89 Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 108 through 114 Processing helix chain 'D' and resid 116 through 118 No H-bonds generated for 'chain 'D' and resid 116 through 118' Processing helix chain 'D' and resid 124 through 137 Processing helix chain 'O' and resid 170 through 173 removed outlier: 4.400A pdb=" N ASP O 173 " --> pdb=" O GLU O 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 170 through 173' Processing helix chain 'O' and resid 193 through 206 removed outlier: 4.584A pdb=" N PHE O 206 " --> pdb=" O CYS O 202 " (cutoff:3.500A) Processing helix chain 'O' and resid 211 through 221 Processing helix chain 'O' and resid 225 through 227 No H-bonds generated for 'chain 'O' and resid 225 through 227' Processing helix chain 'O' and resid 235 through 246 Processing helix chain 'O' and resid 282 through 291 Processing helix chain 'O' and resid 310 through 312 No H-bonds generated for 'chain 'O' and resid 310 through 312' Processing helix chain 'O' and resid 318 through 320 No H-bonds generated for 'chain 'O' and resid 318 through 320' Processing helix chain 'O' and resid 329 through 331 No H-bonds generated for 'chain 'O' and resid 329 through 331' Processing helix chain 'O' and resid 339 through 353 Processing helix chain 'O' and resid 373 through 394 removed outlier: 5.059A pdb=" N GLU O 377 " --> pdb=" O ASN O 374 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU O 379 " --> pdb=" O GLN O 376 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLN O 382 " --> pdb=" O LEU O 379 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU O 389 " --> pdb=" O CYS O 386 " (cutoff:3.500A) Processing helix chain 'O' and resid 411 through 423 Processing helix chain 'O' and resid 454 through 470 Processing helix chain 'O' and resid 483 through 488 Processing helix chain 'O' and resid 490 through 519 Processing helix chain 'O' and resid 528 through 538 Processing helix chain 'O' and resid 554 through 562 Processing helix chain 'O' and resid 567 through 571 Processing helix chain 'O' and resid 582 through 585 Processing helix chain 'O' and resid 588 through 590 No H-bonds generated for 'chain 'O' and resid 588 through 590' Processing helix chain 'O' and resid 649 through 651 No H-bonds generated for 'chain 'O' and resid 649 through 651' Processing helix chain 'O' and resid 676 through 689 removed outlier: 3.529A pdb=" N LYS O 688 " --> pdb=" O GLU O 684 " (cutoff:3.500A) Processing helix chain 'O' and resid 709 through 718 removed outlier: 5.748A pdb=" N GLU O 713 " --> pdb=" O GLU O 710 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL O 717 " --> pdb=" O LYS O 714 " (cutoff:3.500A) Processing helix chain 'O' and resid 785 through 787 No H-bonds generated for 'chain 'O' and resid 785 through 787' Processing helix chain 'O' and resid 791 through 796 Processing helix chain 'O' and resid 823 through 832 Processing sheet with id= A, first strand: chain 'A' and resid 86 through 89 Processing sheet with id= B, first strand: chain 'A' and resid 190 through 194 removed outlier: 4.578A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 200 " --> pdb=" O ILE A 214 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 362 through 366 removed outlier: 3.872A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 367 through 369 removed outlier: 6.073A pdb=" N PHE A 482 " --> pdb=" O THR A 368 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.707A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 602 through 605 Processing sheet with id= G, first strand: chain 'A' and resid 902 through 905 Processing sheet with id= H, first strand: chain 'A' and resid 1138 through 1142 removed outlier: 3.797A pdb=" N LYS A1306 " --> pdb=" O ASP A1339 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1173 through 1177 removed outlier: 7.356A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1320 through 1322 Processing sheet with id= K, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.675A pdb=" N ASP B 127 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE B 91 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR B 125 " --> pdb=" O ILE B 91 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 97 through 99 Processing sheet with id= M, first strand: chain 'B' and resid 185 through 187 Processing sheet with id= N, first strand: chain 'B' and resid 391 through 394 removed outlier: 4.020A pdb=" N ALA B 196 " --> pdb=" O ARG B 484 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 206 through 208 removed outlier: 6.842A pdb=" N MET B 239 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N THR B 218 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL B 237 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLU B 220 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE B 235 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ARG B 222 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N SER B 233 " --> pdb=" O ARG B 222 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 602 through 605 removed outlier: 3.638A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 622 through 626 removed outlier: 3.566A pdb=" N ARG B 623 " --> pdb=" O ILE B 665 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.216A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 945 through 949 removed outlier: 7.026A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 827 through 829 Processing sheet with id= U, first strand: chain 'B' and resid 1115 through 1119 Processing sheet with id= V, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id= W, first strand: chain 'B' and resid 121 through 126 removed outlier: 3.709A pdb=" N GLY B 150 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 99 through 106 removed outlier: 5.912A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 182 through 186 Processing sheet with id= Z, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.608A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 113 through 116 removed outlier: 3.558A pdb=" N VAL C 151 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 73 through 76 removed outlier: 6.274A pdb=" N ILE E 126 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE E 104 " --> pdb=" O ILE E 126 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N GLU E 128 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL E 106 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE E 130 " --> pdb=" O VAL E 106 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.523A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 105 through 109 Processing sheet with id= AE, first strand: chain 'H' and resid 25 through 31 removed outlier: 3.541A pdb=" N ASP H 38 " --> pdb=" O GLN H 126 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP H 11 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'I' and resid 25 through 29 removed outlier: 3.621A pdb=" N ILE I 34 " --> pdb=" O ASP I 29 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'I' and resid 94 through 97 Processing sheet with id= AH, first strand: chain 'K' and resid 19 through 23 Processing sheet with id= AI, first strand: chain 'L' and resid 16 through 18 Processing sheet with id= AJ, first strand: chain 'Y' and resid 13 through 15 Processing sheet with id= AK, first strand: chain 'Y' and resid 60 through 63 Processing sheet with id= AL, first strand: chain 'Z' and resid 178 through 183 removed outlier: 3.771A pdb=" N SER Z 214 " --> pdb=" O GLU Z 228 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'Z' and resid 278 through 280 removed outlier: 6.017A pdb=" N SER Z 304 " --> pdb=" O ASP Z 294 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N VAL Z 296 " --> pdb=" O THR Z 302 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N THR Z 302 " --> pdb=" O VAL Z 296 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'Z' and resid 352 through 355 Processing sheet with id= AO, first strand: chain 'Z' and resid 425 through 427 Processing sheet with id= AP, first strand: chain 'Z' and resid 477 through 479 removed outlier: 7.200A pdb=" N ILE Z 501 " --> pdb=" O VAL Z 493 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N VAL Z 495 " --> pdb=" O PHE Z 499 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE Z 499 " --> pdb=" O VAL Z 495 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'Z' and resid 567 through 571 removed outlier: 6.195A pdb=" N LEU Z 561 " --> pdb=" O ILE Z 550 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE Z 550 " --> pdb=" O LEU Z 561 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP Z 543 " --> pdb=" O THR Z 546 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLY Z 548 " --> pdb=" O GLN Z 541 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N GLN Z 541 " --> pdb=" O GLY Z 548 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE Z 550 " --> pdb=" O LEU Z 539 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU Z 539 " --> pdb=" O ILE Z 550 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'Z' and resid 585 through 587 Processing sheet with id= AS, first strand: chain 'Z' and resid 643 through 645 removed outlier: 6.654A pdb=" N PHE Z 623 " --> pdb=" O ARG Z 615 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU Z 617 " --> pdb=" O PHE Z 621 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE Z 621 " --> pdb=" O LEU Z 617 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'Z' and resid 750 through 752 removed outlier: 6.816A pdb=" N ARG Z 733 " --> pdb=" O LYS Z 725 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'G' and resid 2 through 13 removed outlier: 3.749A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA G 47 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N PHE G 77 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N VAL G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'G' and resid 142 through 146 removed outlier: 3.517A pdb=" N LEU G 145 " --> pdb=" O VAL G 85 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL G 88 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU G 97 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP G 156 " --> pdb=" O ASP G 153 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'G' and resid 50 through 54 removed outlier: 6.853A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'O' and resid 426 through 430 removed outlier: 3.907A pdb=" N PHE O 360 " --> pdb=" O TYR O 272 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'O' and resid 591 through 596 removed outlier: 3.654A pdb=" N GLY O 747 " --> pdb=" O SER O 596 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'O' and resid 611 through 614 Processing sheet with id= BA, first strand: chain 'O' and resid 719 through 723 Processing sheet with id= BB, first strand: chain 'O' and resid 758 through 763 removed outlier: 3.548A pdb=" N LYS O 768 " --> pdb=" O SER O 763 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'O' and resid 176 through 179 removed outlier: 6.341A pdb=" N GLY O 178 " --> pdb=" O VAL O 477 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL O 477 " --> pdb=" O GLY O 178 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'O' and resid 636 through 638 removed outlier: 6.343A pdb=" N SER O 638 " --> pdb=" O VAL O 663 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N VAL O 663 " --> pdb=" O SER O 638 " (cutoff:3.500A) 1238 hydrogen bonds defined for protein. 3375 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 19.13 Time building geometry restraints manager: 17.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.47: 24573 1.47 - 1.73: 19740 1.73 - 2.00: 410 2.00 - 2.26: 2 2.26 - 2.53: 1 Bond restraints: 44726 Sorted by residual: bond pdb=" CE1 HIS O 659 " pdb=" NE2 HIS O 659 " ideal model delta sigma weight residual 1.321 2.527 -1.206 1.00e-02 1.00e+04 1.46e+04 bond pdb=" ND1 HIS O 659 " pdb=" CE1 HIS O 659 " ideal model delta sigma weight residual 1.321 2.154 -0.833 1.00e-02 1.00e+04 6.93e+03 bond pdb=" CD2 HIS O 659 " pdb=" NE2 HIS O 659 " ideal model delta sigma weight residual 1.374 2.142 -0.768 1.10e-02 8.26e+03 4.87e+03 bond pdb=" C PRO O 549 " pdb=" N SER O 550 " ideal model delta sigma weight residual 1.332 1.661 -0.329 1.37e-02 5.33e+03 5.76e+02 bond pdb=" CA GLY Y 105 " pdb=" C GLY Y 105 " ideal model delta sigma weight residual 1.511 1.685 -0.173 1.40e-02 5.10e+03 1.53e+02 ... (remaining 44721 not shown) Histogram of bond angle deviations from ideal: 46.71 - 70.50: 3 70.50 - 94.30: 5 94.30 - 118.09: 34684 118.09 - 141.88: 26132 141.88 - 165.67: 1 Bond angle restraints: 60825 Sorted by residual: angle pdb=" CA PRO O 549 " pdb=" C PRO O 549 " pdb=" N SER O 550 " ideal model delta sigma weight residual 115.71 65.16 50.55 1.19e+00 7.06e-01 1.80e+03 angle pdb=" O PRO O 549 " pdb=" C PRO O 549 " pdb=" N SER O 550 " ideal model delta sigma weight residual 122.98 165.67 -42.69 1.09e+00 8.42e-01 1.53e+03 angle pdb=" C PRO O 549 " pdb=" N SER O 550 " pdb=" CA SER O 550 " ideal model delta sigma weight residual 121.31 76.04 45.27 1.49e+00 4.50e-01 9.23e+02 angle pdb=" ND1 HIS O 659 " pdb=" CE1 HIS O 659 " pdb=" NE2 HIS O 659 " ideal model delta sigma weight residual 108.40 84.96 23.44 1.00e+00 1.00e+00 5.49e+02 angle pdb=" CG HIS O 659 " pdb=" CD2 HIS O 659 " pdb=" NE2 HIS O 659 " ideal model delta sigma weight residual 107.20 128.81 -21.61 1.00e+00 1.00e+00 4.67e+02 ... (remaining 60820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.94: 26444 33.94 - 67.89: 489 67.89 - 101.83: 31 101.83 - 135.77: 11 135.77 - 169.72: 4 Dihedral angle restraints: 26979 sinusoidal: 11848 harmonic: 15131 Sorted by residual: dihedral pdb=" CA LYS A 910 " pdb=" C LYS A 910 " pdb=" N PRO A 911 " pdb=" CA PRO A 911 " ideal model delta harmonic sigma weight residual 180.00 136.97 43.03 0 5.00e+00 4.00e-02 7.41e+01 dihedral pdb=" O4' U P 39 " pdb=" C1' U P 39 " pdb=" N1 U P 39 " pdb=" C2 U P 39 " ideal model delta sinusoidal sigma weight residual 200.00 66.72 133.28 1 1.50e+01 4.44e-03 7.19e+01 dihedral pdb=" O4' C P 37 " pdb=" C1' C P 37 " pdb=" N1 C P 37 " pdb=" C2 C P 37 " ideal model delta sinusoidal sigma weight residual -160.00 -44.03 -115.97 1 1.50e+01 4.44e-03 6.13e+01 ... (remaining 26976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.907: 6774 0.907 - 1.814: 1 1.814 - 2.722: 1 2.722 - 3.629: 0 3.629 - 4.536: 2 Chirality restraints: 6778 Sorted by residual: chirality pdb=" C1' G P 31 " pdb=" O4' G P 31 " pdb=" C2' G P 31 " pdb=" N9 G P 31 " both_signs ideal model delta sigma weight residual False 2.46 -2.08 4.54 2.00e-01 2.50e+01 5.14e+02 chirality pdb=" C1' C P 33 " pdb=" O4' C P 33 " pdb=" C2' C P 33 " pdb=" N1 C P 33 " both_signs ideal model delta sigma weight residual False 2.47 -2.04 4.51 2.00e-01 2.50e+01 5.08e+02 chirality pdb=" P A P 34 " pdb=" OP1 A P 34 " pdb=" OP2 A P 34 " pdb=" O5' A P 34 " both_signs ideal model delta sigma weight residual True 2.41 0.01 2.40 2.00e-01 2.50e+01 1.44e+02 ... (remaining 6775 not shown) Planarity restraints: 7524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR O 314 " -0.114 2.00e-02 2.50e+03 7.21e-02 1.04e+02 pdb=" CG TYR O 314 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR O 314 " 0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR O 314 " 0.051 2.00e-02 2.50e+03 pdb=" CE1 TYR O 314 " 0.055 2.00e-02 2.50e+03 pdb=" CE2 TYR O 314 " 0.061 2.00e-02 2.50e+03 pdb=" CZ TYR O 314 " 0.015 2.00e-02 2.50e+03 pdb=" OH TYR O 314 " -0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR O 443 " -0.102 2.00e-02 2.50e+03 5.81e-02 6.74e+01 pdb=" CG TYR O 443 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR O 443 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR O 443 " 0.046 2.00e-02 2.50e+03 pdb=" CE1 TYR O 443 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR O 443 " 0.038 2.00e-02 2.50e+03 pdb=" CZ TYR O 443 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR O 443 " -0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE O 791 " 0.086 2.00e-02 2.50e+03 5.34e-02 4.99e+01 pdb=" CG PHE O 791 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE O 791 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 PHE O 791 " -0.055 2.00e-02 2.50e+03 pdb=" CE1 PHE O 791 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE O 791 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE O 791 " 0.057 2.00e-02 2.50e+03 ... (remaining 7521 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 11 2.08 - 2.78: 9550 2.78 - 3.49: 57362 3.49 - 4.19: 106202 4.19 - 4.90: 183015 Nonbonded interactions: 356140 Sorted by model distance: nonbonded pdb=" OP1 A P 23 " pdb=" NH1 ARG O 235 " model vdw 1.370 2.520 nonbonded pdb=" O3' A P 32 " pdb=" P A P 34 " model vdw 1.643 3.400 nonbonded pdb=" O GLU O 311 " pdb=" NZ LYS O 608 " model vdw 1.779 2.520 nonbonded pdb=" OD2 ASP G 141 " pdb=" NZ LYS O 725 " model vdw 1.784 2.520 nonbonded pdb=" OG SER O 317 " pdb=" ND2 ASN O 667 " model vdw 1.810 2.520 ... (remaining 356135 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.65 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 9.640 Check model and map are aligned: 0.630 Set scattering table: 0.360 Process input model: 119.580 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 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 : 0.015 1.206 44726 Z= 0.990 Angle : 1.297 61.287 60825 Z= 0.800 Chirality : 0.109 4.536 6778 Planarity : 0.008 0.123 7524 Dihedral : 12.930 169.715 17199 Min Nonbonded Distance : 1.370 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.24 % Favored : 95.47 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.42 % 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: -2.88 (0.10), residues: 5160 helix: -3.24 (0.09), residues: 1568 sheet: -1.43 (0.15), residues: 828 loop : -1.12 (0.10), residues: 2764 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 4615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 532 time to evaluate : 5.343 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 outliers start: 48 outliers final: 9 residues processed: 578 average time/residue: 0.6161 time to fit residues: 569.9630 Evaluate side-chains 275 residues out of total 4615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 266 time to evaluate : 5.096 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.5277 time to fit residues: 14.7871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 439 optimal weight: 50.0000 chunk 394 optimal weight: 6.9990 chunk 218 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 265 optimal weight: 2.9990 chunk 210 optimal weight: 6.9990 chunk 407 optimal weight: 8.9990 chunk 157 optimal weight: 0.9990 chunk 247 optimal weight: 7.9990 chunk 303 optimal weight: 5.9990 chunk 472 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 301 HIS A 372 ASN ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 GLN A 671 ASN ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 GLN ** A1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1230 GLN ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN B 111 ASN B 265 GLN ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN B 842 HIS B1021 HIS B1097 HIS ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 HIS I 45 GLN K 69 HIS Y 41 GLN Z 519 GLN ** Z 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 625 HIS G 4 HIS G 9 HIS D 38 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN D 48 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 515 HIS O 659 HIS O 667 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.094 44726 Z= 0.285 Angle : 0.738 14.303 60825 Z= 0.387 Chirality : 0.081 4.056 6778 Planarity : 0.005 0.091 7524 Dihedral : 14.207 174.884 6699 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.00 % Favored : 96.92 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.11), residues: 5160 helix: -1.29 (0.12), residues: 1599 sheet: -0.87 (0.16), residues: 875 loop : -0.53 (0.12), residues: 2686 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 4615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 292 time to evaluate : 5.439 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: 48 outliers final: 22 residues processed: 328 average time/residue: 0.5890 time to fit residues: 315.6687 Evaluate side-chains 263 residues out of total 4615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 241 time to evaluate : 4.656 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.4561 time to fit residues: 23.7162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 262 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 393 optimal weight: 50.0000 chunk 321 optimal weight: 8.9990 chunk 130 optimal weight: 0.9980 chunk 473 optimal weight: 0.1980 chunk 511 optimal weight: 10.0000 chunk 421 optimal weight: 30.0000 chunk 469 optimal weight: 7.9990 chunk 161 optimal weight: 10.0000 chunk 379 optimal weight: 8.9990 overall best weight: 4.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 757 GLN ** A1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1220 HIS A1230 GLN ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN B 312 GLN ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1120 ASN C 145 GLN C 260 GLN F 72 GLN I 22 ASN I 84 HIS ** Z 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN D 128 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 44726 Z= 0.279 Angle : 0.672 11.740 60825 Z= 0.349 Chirality : 0.077 3.964 6778 Planarity : 0.004 0.054 7524 Dihedral : 14.105 179.880 6699 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.80 % Favored : 96.12 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.11), residues: 5160 helix: -0.03 (0.13), residues: 1618 sheet: -0.55 (0.16), residues: 857 loop : -0.26 (0.12), residues: 2685 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 4615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 246 time to evaluate : 4.956 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 outliers start: 46 outliers final: 11 residues processed: 282 average time/residue: 0.5822 time to fit residues: 274.6018 Evaluate side-chains 239 residues out of total 4615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 228 time to evaluate : 4.922 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.4237 time to fit residues: 15.2781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 467 optimal weight: 20.0000 chunk 355 optimal weight: 2.9990 chunk 245 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 225 optimal weight: 0.8980 chunk 317 optimal weight: 10.0000 chunk 474 optimal weight: 10.0000 chunk 502 optimal weight: 50.0000 chunk 248 optimal weight: 8.9990 chunk 449 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 539 GLN ** A1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 HIS ** Z 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 643 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.088 44726 Z= 0.358 Angle : 0.716 17.357 60825 Z= 0.363 Chirality : 0.065 3.930 6778 Planarity : 0.004 0.048 7524 Dihedral : 14.042 177.482 6699 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.17 % Favored : 95.74 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.12), residues: 5160 helix: 0.57 (0.13), residues: 1630 sheet: -0.44 (0.17), residues: 857 loop : -0.10 (0.12), residues: 2673 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 4615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 230 time to evaluate : 5.343 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 outliers start: 43 outliers final: 18 residues processed: 256 average time/residue: 0.5813 time to fit residues: 250.4948 Evaluate side-chains 235 residues out of total 4615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 217 time to evaluate : 5.510 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4311 time to fit residues: 21.7510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 418 optimal weight: 1.9990 chunk 285 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 374 optimal weight: 20.0000 chunk 207 optimal weight: 4.9990 chunk 428 optimal weight: 5.9990 chunk 347 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 256 optimal weight: 2.9990 chunk 451 optimal weight: 0.7980 chunk 126 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 ASN A1034 GLN A1042 ASN A1230 GLN ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 ASN Y 95 GLN ** Z 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS O 503 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 44726 Z= 0.192 Angle : 0.612 13.802 60825 Z= 0.310 Chirality : 0.064 3.918 6778 Planarity : 0.004 0.045 7524 Dihedral : 13.932 177.205 6699 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.84 % Favored : 96.05 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.12), residues: 5160 helix: 0.92 (0.13), residues: 1626 sheet: -0.24 (0.17), residues: 847 loop : -0.02 (0.12), residues: 2687 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 4615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 232 time to evaluate : 4.906 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 outliers start: 30 outliers final: 7 residues processed: 255 average time/residue: 0.5756 time to fit residues: 245.6446 Evaluate side-chains 220 residues out of total 4615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 213 time to evaluate : 4.827 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4165 time to fit residues: 11.7831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 169 optimal weight: 0.0770 chunk 452 optimal weight: 30.0000 chunk 99 optimal weight: 5.9990 chunk 295 optimal weight: 0.1980 chunk 124 optimal weight: 3.9990 chunk 503 optimal weight: 50.0000 chunk 417 optimal weight: 30.0000 chunk 232 optimal weight: 10.0000 chunk 41 optimal weight: 0.0980 chunk 166 optimal weight: 9.9990 chunk 264 optimal weight: 0.7980 overall best weight: 1.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 945 ASN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 ASN ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1021 HIS ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 95 GLN Z 519 GLN ** Z 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 347 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 44726 Z= 0.152 Angle : 0.607 13.607 60825 Z= 0.304 Chirality : 0.063 3.867 6778 Planarity : 0.004 0.043 7524 Dihedral : 13.748 177.568 6699 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.64 % Favored : 96.24 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.12), residues: 5160 helix: 1.06 (0.13), residues: 1618 sheet: -0.05 (0.18), residues: 828 loop : 0.04 (0.12), residues: 2714 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 4615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 230 time to evaluate : 4.993 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 outliers start: 32 outliers final: 10 residues processed: 254 average time/residue: 0.6010 time to fit residues: 258.9916 Evaluate side-chains 227 residues out of total 4615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 217 time to evaluate : 4.970 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.4163 time to fit residues: 14.5681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 485 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 286 optimal weight: 4.9990 chunk 367 optimal weight: 0.6980 chunk 284 optimal weight: 0.9990 chunk 423 optimal weight: 10.0000 chunk 280 optimal weight: 7.9990 chunk 501 optimal weight: 3.9990 chunk 313 optimal weight: 8.9990 chunk 305 optimal weight: 2.9990 chunk 231 optimal weight: 9.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 945 ASN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 95 GLN ** Z 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 44726 Z= 0.193 Angle : 0.612 12.598 60825 Z= 0.306 Chirality : 0.061 3.642 6778 Planarity : 0.003 0.042 7524 Dihedral : 13.665 178.370 6699 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.88 % Favored : 96.01 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.12), residues: 5160 helix: 1.24 (0.13), residues: 1622 sheet: -0.08 (0.18), residues: 835 loop : 0.09 (0.13), residues: 2703 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 4615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 219 time to evaluate : 5.143 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 outliers start: 16 outliers final: 6 residues processed: 230 average time/residue: 0.5647 time to fit residues: 222.8663 Evaluate side-chains 223 residues out of total 4615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 217 time to evaluate : 4.781 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4341 time to fit residues: 11.2291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 310 optimal weight: 9.9990 chunk 200 optimal weight: 9.9990 chunk 299 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 97 optimal weight: 0.0470 chunk 318 optimal weight: 5.9990 chunk 341 optimal weight: 10.0000 chunk 247 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 393 optimal weight: 7.9990 overall best weight: 3.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 945 ASN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1230 GLN C 260 GLN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 519 GLN ** Z 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 44726 Z= 0.229 Angle : 0.642 20.597 60825 Z= 0.317 Chirality : 0.043 0.564 6778 Planarity : 0.004 0.041 7524 Dihedral : 13.648 179.602 6699 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.13 % Favored : 95.74 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.12), residues: 5160 helix: 1.26 (0.13), residues: 1628 sheet: -0.14 (0.17), residues: 853 loop : 0.13 (0.13), residues: 2679 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 4615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 215 time to evaluate : 5.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 225 average time/residue: 0.5899 time to fit residues: 226.9413 Evaluate side-chains 215 residues out of total 4615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 210 time to evaluate : 5.318 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.5226 time to fit residues: 11.8218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 455 optimal weight: 0.7980 chunk 480 optimal weight: 10.0000 chunk 438 optimal weight: 40.0000 chunk 467 optimal weight: 20.0000 chunk 281 optimal weight: 7.9990 chunk 203 optimal weight: 9.9990 chunk 366 optimal weight: 20.0000 chunk 143 optimal weight: 0.0670 chunk 422 optimal weight: 20.0000 chunk 441 optimal weight: 8.9990 chunk 465 optimal weight: 6.9990 overall best weight: 4.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 ASN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 945 ASN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN Y 95 GLN Z 519 GLN ** Z 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 44726 Z= 0.272 Angle : 0.655 12.438 60825 Z= 0.326 Chirality : 0.043 0.342 6778 Planarity : 0.004 0.043 7524 Dihedral : 13.644 179.326 6699 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.28 % Favored : 95.58 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.12), residues: 5160 helix: 1.22 (0.13), residues: 1641 sheet: -0.12 (0.17), residues: 848 loop : 0.10 (0.13), residues: 2671 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 4615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 211 time to evaluate : 5.120 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 outliers start: 12 outliers final: 3 residues processed: 220 average time/residue: 0.5794 time to fit residues: 220.9031 Evaluate side-chains 209 residues out of total 4615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 206 time to evaluate : 5.290 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4587 time to fit residues: 9.4404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 306 optimal weight: 0.0670 chunk 493 optimal weight: 20.0000 chunk 301 optimal weight: 0.4980 chunk 234 optimal weight: 0.9990 chunk 343 optimal weight: 10.0000 chunk 518 optimal weight: 1.9990 chunk 476 optimal weight: 50.0000 chunk 412 optimal weight: 40.0000 chunk 42 optimal weight: 1.9990 chunk 318 optimal weight: 5.9990 chunk 252 optimal weight: 7.9990 overall best weight: 1.1124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 945 ASN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 HIS Z 519 GLN ** Z 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.5349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 44726 Z= 0.155 Angle : 0.630 13.429 60825 Z= 0.310 Chirality : 0.043 0.280 6778 Planarity : 0.003 0.044 7524 Dihedral : 13.517 179.516 6699 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.64 % Favored : 96.22 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.12), residues: 5160 helix: 1.25 (0.13), residues: 1628 sheet: -0.08 (0.17), residues: 854 loop : 0.12 (0.13), residues: 2678 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 4615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 216 time to evaluate : 4.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 220 average time/residue: 0.6076 time to fit residues: 230.9194 Evaluate side-chains 209 residues out of total 4615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 207 time to evaluate : 5.277 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.6662 time to fit residues: 8.9855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 327 optimal weight: 6.9990 chunk 439 optimal weight: 30.0000 chunk 126 optimal weight: 20.0000 chunk 380 optimal weight: 50.0000 chunk 60 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 413 optimal weight: 0.8980 chunk 172 optimal weight: 4.9990 chunk 424 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 945 ASN A1093 GLN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 95 GLN Z 519 GLN ** Z 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.051947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.032934 restraints weight = 345650.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.033802 restraints weight = 181125.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.034464 restraints weight = 118216.084| |-----------------------------------------------------------------------------| r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 44726 Z= 0.256 Angle : 0.668 13.921 60825 Z= 0.329 Chirality : 0.042 0.266 6778 Planarity : 0.004 0.043 7524 Dihedral : 13.489 178.383 6699 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.38 % Favored : 95.48 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.12), residues: 5160 helix: 1.30 (0.13), residues: 1638 sheet: -0.14 (0.17), residues: 854 loop : 0.14 (0.13), residues: 2668 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7471.13 seconds wall clock time: 139 minutes 26.58 seconds (8366.58 seconds total)