Starting phenix.real_space_refine on Sun Mar 24 11:27:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4e_17407/03_2024/8p4e_17407_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4e_17407/03_2024/8p4e_17407.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4e_17407/03_2024/8p4e_17407_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4e_17407/03_2024/8p4e_17407_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4e_17407/03_2024/8p4e_17407_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4e_17407/03_2024/8p4e_17407.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4e_17407/03_2024/8p4e_17407.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4e_17407/03_2024/8p4e_17407_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4e_17407/03_2024/8p4e_17407_updated.pdb" } resolution = 3.9 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= 0.001 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 84 5.49 5 Mg 1 5.21 5 S 250 5.16 5 C 25812 2.51 5 N 7192 2.21 5 O 7866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "M PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 234": "OE1" <-> "OE2" Residue "M GLU 252": "OE1" <-> "OE2" Residue "M PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 277": "OD1" <-> "OD2" Residue "M TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 305": "OD1" <-> "OD2" Residue "M ASP 316": "OD1" <-> "OD2" Residue "M PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 343": "OD1" <-> "OD2" Residue "M TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 363": "OD1" <-> "OD2" Residue "M ASP 376": "OD1" <-> "OD2" Residue "M GLU 385": "OE1" <-> "OE2" Residue "M ASP 402": "OD1" <-> "OD2" Residue "M PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 468": "OD1" <-> "OD2" Residue "M PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 556": "OE1" <-> "OE2" Residue "M PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 227": "NH1" <-> "NH2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A ARG 334": "NH1" <-> "NH2" Residue "A PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 924": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 928": "NH1" <-> "NH2" Residue "A ARG 931": "NH1" <-> "NH2" Residue "A ARG 1149": "NH1" <-> "NH2" Residue "A ARG 1153": "NH1" <-> "NH2" Residue "A ARG 1160": "NH1" <-> "NH2" Residue "A ARG 1167": "NH1" <-> "NH2" Residue "A TYR 1176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1213": "NH1" <-> "NH2" Residue "A ARG 1218": "NH1" <-> "NH2" Residue "A ARG 1408": "NH1" <-> "NH2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B ARG 83": "NH1" <-> "NH2" Residue "B TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 834": "NH1" <-> "NH2" Residue "B ARG 886": "NH1" <-> "NH2" Residue "B TYR 1029": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 40": "NH1" <-> "NH2" Residue "I PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 41213 Number of models: 1 Model: "" Number of chains: 24 Chain: "Z" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 397 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "M" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2649 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 18, 'TRANS': 310} Chain breaks: 1 Chain: "A" Number of atoms: 11142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1407, 11142 Classifications: {'peptide': 1407} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 1337} Chain breaks: 5 Chain: "B" Number of atoms: 8928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1116, 8928 Classifications: {'peptide': 1116} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 53, 'TRANS': 1062} Chain breaks: 6 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 2071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2071 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Modifications used: {'COO': 1} 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: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 950 Classifications: {'peptide': 117} Modifications used: {'COO': 1} 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: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 389 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "D" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 998 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 125} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "G" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1305 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 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: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 462 Unusual residues: {'MGT': 1} Classifications: {'RNA': 20, 'undetermined': 1} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 5} Link IDs: {'rna2p': 5, 'rna3p': 14, None: 1} Not linked: pdbres="MGT P 101 " pdbres=" G P 31 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "N" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 538 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain breaks: 1 Chain: "T" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 714 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3814 SG CYS A 111 79.820 13.495 79.663 1.00 52.15 S ATOM 3842 SG CYS A 114 80.492 9.649 81.560 1.00 60.58 S ATOM 3510 SG CYS A 71 65.908 44.656 112.718 1.00 41.25 S ATOM 3532 SG CYS A 74 69.610 46.534 113.136 1.00 35.32 S ATOM 3579 SG CYS A 81 67.422 47.926 110.442 1.00 35.83 S ATOM 22685 SG CYS B1119 82.293 39.715 107.622 1.00 32.24 S ATOM 22707 SG CYS B1122 81.599 37.103 105.178 1.00 35.98 S ATOM 22822 SG CYS B1137 79.363 37.773 108.243 1.00 48.78 S ATOM 23810 SG CYS C 88 52.916 112.776 114.184 1.00 27.25 S ATOM 23823 SG CYS C 90 50.781 109.558 114.461 1.00 37.75 S ATOM 23858 SG CYS C 94 49.382 112.758 113.325 1.00 23.11 S ATOM 23880 SG CYS C 97 50.804 110.919 110.565 1.00 16.65 S ATOM 28821 SG CYS I 17 45.228 27.392 24.003 1.00 39.89 S ATOM 28845 SG CYS I 20 45.045 26.576 27.518 1.00 41.99 S ATOM 29006 SG CYS I 39 48.625 25.952 27.380 1.00 38.99 S ATOM 29031 SG CYS I 42 46.030 23.999 25.030 1.00 43.23 S ATOM 29383 SG CYS I 86 49.026 70.546 15.137 1.00 32.07 S ATOM 29407 SG CYS I 89 45.624 71.910 14.579 1.00 31.64 S ATOM 29646 SG CYS I 119 44.390 69.710 17.205 1.00 38.63 S ATOM 29757 SG CYS J 7 50.945 108.090 79.517 1.00 28.01 S ATOM 29781 SG CYS J 10 53.852 111.855 79.476 1.00 23.57 S ATOM 30045 SG CYS J 44 53.469 109.588 76.811 1.00 23.69 S ATOM 30051 SG CYS J 45 50.077 111.463 78.259 1.00 21.59 S ATOM 31232 SG CYS L 22 18.898 79.732 95.306 1.00 35.66 S ATOM 31349 SG CYS L 36 19.130 78.109 98.513 1.00 37.97 S Time building chain proxies: 20.28, per 1000 atoms: 0.49 Number of scatterers: 41213 At special positions: 0 Unit cell: (148.05, 149.1, 215.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 250 16.00 P 84 15.00 Mg 1 11.99 O 7866 8.00 N 7192 7.00 C 25812 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.29 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 74 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1119 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1122 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1137 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 94 " pdb=" ZN I 200 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 39 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 119 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " Number of angles added : 21 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9288 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 162 helices and 51 sheets defined 30.8% alpha, 14.6% beta 29 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 18.04 Creating SS restraints... Processing helix chain 'M' and resid 247 through 261 Processing helix chain 'M' and resid 280 through 285 Processing helix chain 'M' and resid 372 through 374 No H-bonds generated for 'chain 'M' and resid 372 through 374' Processing helix chain 'M' and resid 377 through 388 Processing helix chain 'M' and resid 390 through 397 Processing helix chain 'M' and resid 403 through 405 No H-bonds generated for 'chain 'M' and resid 403 through 405' Processing helix chain 'M' and resid 418 through 420 No H-bonds generated for 'chain 'M' and resid 418 through 420' Processing helix chain 'M' and resid 462 through 464 No H-bonds generated for 'chain 'M' and resid 462 through 464' Processing helix chain 'M' and resid 507 through 510 Processing helix chain 'M' and resid 539 through 550 removed outlier: 3.686A pdb=" N SER M 548 " --> pdb=" O ALA M 544 " (cutoff:3.500A) Processing helix chain 'M' and resid 555 through 565 removed outlier: 3.617A pdb=" N PHE M 559 " --> pdb=" O LYS M 555 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS M 565 " --> pdb=" O PHE M 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 34 Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 137 through 147 Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 245 through 247 No H-bonds generated for 'chain 'A' and resid 245 through 247' Processing helix chain 'A' and resid 275 through 295 Processing helix chain 'A' and resid 302 through 318 removed outlier: 4.499A pdb=" N LYS A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 382 through 385 No H-bonds generated for 'chain 'A' and resid 382 through 385' Processing helix chain 'A' and resid 399 through 408 Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' 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 489 through 492 No H-bonds generated for 'chain 'A' and resid 489 through 492' Processing helix chain 'A' and resid 509 through 518 Processing helix chain 'A' and resid 539 through 548 Processing helix chain 'A' and resid 557 through 564 Processing helix chain 'A' and resid 588 through 595 Processing helix chain 'A' and resid 642 through 645 No H-bonds generated for 'chain 'A' and resid 642 through 645' Processing helix chain 'A' and resid 652 through 658 Processing helix chain 'A' and resid 663 through 683 removed outlier: 4.069A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 692 No H-bonds generated for 'chain 'A' and resid 690 through 692' Processing helix chain 'A' and resid 696 through 721 Processing helix chain 'A' and resid 733 through 757 Processing helix chain 'A' and resid 765 through 771 Processing helix chain 'A' and resid 778 through 785 Processing helix chain 'A' and resid 817 through 820 No H-bonds generated for 'chain 'A' and resid 817 through 820' Processing helix chain 'A' and resid 833 through 867 removed outlier: 4.105A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 893 No H-bonds generated for 'chain 'A' and resid 891 through 893' Processing helix chain 'A' and resid 913 through 920 Processing helix chain 'A' and resid 927 through 933 Processing helix chain 'A' and resid 936 through 944 Processing helix chain 'A' and resid 947 through 969 Processing helix chain 'A' and resid 983 through 994 Processing helix chain 'A' and resid 1006 through 1019 Processing helix chain 'A' and resid 1028 through 1037 Processing helix chain 'A' and resid 1039 through 1048 Processing helix chain 'A' and resid 1051 through 1056 Processing helix chain 'A' and resid 1062 through 1077 Processing helix chain 'A' and resid 1087 through 1101 Proline residue: A1098 - end of helix removed outlier: 4.156A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1128 Processing helix chain 'A' and resid 1146 through 1149 Processing helix chain 'A' and resid 1151 through 1161 Processing helix chain 'A' and resid 1190 through 1193 Processing helix chain 'A' and resid 1218 through 1223 Processing helix chain 'A' and resid 1228 through 1242 removed outlier: 7.381A pdb=" N ASP A1241 " --> pdb=" O ALA A1237 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ASP A1242 " --> pdb=" O GLY A1238 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1293 Processing helix chain 'A' and resid 1362 through 1368 Processing helix chain 'A' and resid 1372 through 1389 removed outlier: 5.255A pdb=" N ASP A1389 " --> pdb=" O VAL A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1404 Processing helix chain 'A' and resid 1416 through 1421 removed outlier: 4.839A pdb=" N ARG A1421 " --> pdb=" O HIS A1417 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1430 Processing helix chain 'A' and resid 1436 through 1444 Processing helix chain 'A' and resid 1455 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: 4.323A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE B 28 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 61 removed outlier: 5.270A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (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 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 Processing helix chain 'B' and resid 314 through 322 Processing helix chain 'B' and resid 336 through 345 Processing helix chain 'B' and resid 355 through 377 removed outlier: 4.065A pdb=" N GLU B 358 " --> pdb=" O ASP B 355 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR B 359 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS B 360 " --> pdb=" O CYS B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 424 removed outlier: 3.935A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP B 424 " --> pdb=" O GLN B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 434 No H-bonds generated for 'chain 'B' and resid 431 through 434' Processing helix chain 'B' and resid 438 through 449 removed outlier: 4.195A pdb=" N GLY B 443 " --> pdb=" O ILE B 439 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU B 444 " --> pdb=" O ILE B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 481 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 539 through 547 Processing helix chain 'B' and resid 553 through 555 No H-bonds generated for 'chain 'B' and resid 553 through 555' Processing helix chain 'B' and resid 584 through 591 Processing helix chain 'B' and resid 637 through 644 Processing helix chain 'B' and resid 653 through 658 Processing helix chain 'B' and resid 667 through 672 removed outlier: 3.646A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N THR B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 672' Processing helix chain 'B' and resid 679 through 682 No H-bonds generated for 'chain 'B' and resid 679 through 682' Processing helix chain 'B' and resid 700 through 703 Processing helix chain 'B' and resid 719 through 728 Processing helix chain 'B' and resid 763 through 765 No H-bonds generated for 'chain 'B' and resid 763 through 765' Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 969 through 971 No H-bonds generated for 'chain 'B' and resid 969 through 971' Processing helix chain 'B' and resid 978 through 993 Processing helix chain 'B' and resid 1008 through 1018 removed outlier: 3.863A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1088 through 1097 Processing helix chain 'B' and resid 1100 through 1107 Processing helix chain 'B' and resid 1109 through 1112 No H-bonds generated for 'chain 'B' and resid 1109 through 1112' Processing helix chain 'B' and resid 1153 through 1164 Processing helix chain 'C' and resid 28 through 39 Processing helix chain 'C' and resid 61 through 69 Processing helix chain 'C' and resid 85 through 87 No H-bonds generated for 'chain 'C' and resid 85 through 87' 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 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 241 through 270 removed outlier: 3.924A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 24 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 44 Processing helix chain 'E' and resid 84 through 96 removed outlier: 4.421A pdb=" N VAL E 89 " --> pdb=" O LYS E 85 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 121 removed outlier: 3.615A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET E 121 " --> pdb=" O SER E 117 " (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 163 Processing helix chain 'E' and resid 178 through 183 Processing helix chain 'F' and resid 59 through 74 removed outlier: 3.525A pdb=" N GLY F 67 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 98 Processing helix chain 'H' and resid 84 through 87 Processing helix chain 'I' and resid 64 through 67 No H-bonds generated for 'chain 'I' and resid 64 through 67' Processing helix chain 'I' and resid 70 through 74 Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 31 through 38 removed outlier: 3.550A pdb=" N ASP J 36 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 50 removed outlier: 3.966A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 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 50 removed outlier: 5.812A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 113 removed outlier: 3.726A pdb=" N THR K 92 " --> pdb=" O THR K 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 49 Processing helix chain 'D' and resid 59 through 70 Processing helix chain 'D' and resid 77 through 88 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 '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 33 Processing helix chain 'G' and resid 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' 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: 3.647A 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: 3.528A 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 '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= B, first strand: chain 'M' and resid 289 through 294 removed outlier: 3.749A pdb=" N GLY M 439 " --> pdb=" O LYS M 294 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'M' and resid 319 through 321 removed outlier: 6.547A pdb=" N SER M 409 " --> pdb=" O TYR M 359 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ILE M 361 " --> pdb=" O SER M 409 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG M 411 " --> pdb=" O ILE M 361 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'M' and resid 499 through 501 removed outlier: 3.582A pdb=" N ALA M 499 " --> pdb=" O LEU M 489 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY M 487 " --> pdb=" O ILE M 501 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG M 528 " --> pdb=" O GLU M 516 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LYS M 518 " --> pdb=" O PHE M 526 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N PHE M 526 " --> pdb=" O LYS M 518 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'M' and resid 341 through 343 removed outlier: 6.391A pdb=" N ASP M 343 " --> pdb=" O ILE M 364 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ILE M 364 " --> pdb=" O ASP M 343 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 86 through 88 Processing sheet with id= G, first strand: chain 'A' and resid 190 through 194 Processing sheet with id= H, first strand: chain 'A' and resid 362 through 366 removed outlier: 3.528A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 367 through 369 removed outlier: 5.867A pdb=" N PHE A 482 " --> pdb=" O THR A 368 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.722A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.493A pdb=" N GLU A 631 " --> pdb=" O LEU A 635 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 902 through 905 Processing sheet with id= M, first strand: chain 'A' and resid 1243 through 1246 removed outlier: 4.000A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 1308 through 1311 Processing sheet with id= O, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id= P, first strand: chain 'B' and resid 65 through 67 Processing sheet with id= Q, first strand: chain 'B' and resid 91 through 93 removed outlier: 6.605A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 185 through 187 Processing sheet with id= S, first strand: chain 'B' and resid 197 through 200 Processing sheet with id= T, first strand: chain 'B' and resid 205 through 208 removed outlier: 6.829A pdb=" N MET B 239 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N THR B 218 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL B 237 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU B 220 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE B 235 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ARG B 222 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N SER B 233 " --> pdb=" O ARG B 222 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 484 through 486 Processing sheet with id= V, first strand: chain 'B' and resid 530 through 532 Processing sheet with id= W, first strand: chain 'B' and resid 550 through 552 removed outlier: 7.175A pdb=" N ILE B 567 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILE B 576 " --> pdb=" O THR B 565 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR B 565 " --> pdb=" O ILE B 576 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 748 through 751 removed outlier: 5.549A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 1042 through 1048 removed outlier: 4.424A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE B 965 " --> pdb=" O ALA B 781 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 827 through 829 Processing sheet with id= AA, first strand: chain 'B' and resid 934 through 936 removed outlier: 7.292A pdb=" N MET B 796 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN B 948 " --> pdb=" O MET B 796 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 1115 through 1119 Processing sheet with id= AC, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id= AD, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.827A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 99 through 106 removed outlier: 6.061A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 113 through 115 Processing sheet with id= AG, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.578A pdb=" N ILE E 126 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE E 104 " --> pdb=" O ILE E 126 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLU E 128 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N VAL E 106 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE E 130 " --> pdb=" O VAL E 106 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'E' and resid 147 through 150 Processing sheet with id= AI, first strand: chain 'E' and resid 172 through 174 removed outlier: 6.627A pdb=" N LEU E 208 " --> pdb=" O ILE E 173 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'F' and resid 105 through 109 Processing sheet with id= AK, first strand: chain 'H' and resid 139 through 142 removed outlier: 3.848A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE H 99 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N SER H 113 " --> pdb=" O ILE H 99 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLY H 101 " --> pdb=" O ARG H 111 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ARG H 111 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE H 60 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLU H 7 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU H 58 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE H 9 " --> pdb=" O PHE H 56 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE H 56 " --> pdb=" O ILE H 9 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'I' and resid 25 through 28 Processing sheet with id= AM, first strand: chain 'I' and resid 79 through 81 Processing sheet with id= AN, first strand: chain 'K' and resid 19 through 23 Processing sheet with id= AO, first strand: chain 'G' and resid 2 through 13 removed outlier: 6.799A pdb=" N PHE G 77 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N VAL G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'G' and resid 104 through 109 removed outlier: 6.326A pdb=" N GLU G 100 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N VAL G 89 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE G 160 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N THR G 150 " --> pdb=" O PHE G 158 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE G 158 " --> pdb=" O THR G 150 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'G' and resid 118 through 120 Processing sheet with id= AR, first strand: chain 'G' and resid 50 through 54 removed outlier: 6.691A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'O' and resid 426 through 430 removed outlier: 3.908A pdb=" N PHE O 360 " --> pdb=" O TYR O 272 " (cutoff:3.500A) Processing sheet with id= AT, 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= AU, first strand: chain 'O' and resid 611 through 614 Processing sheet with id= AV, first strand: chain 'O' and resid 719 through 723 Processing sheet with id= AW, 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= AX, 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= AY, first strand: chain 'O' and resid 636 through 638 removed outlier: 6.342A 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) 1298 hydrogen bonds defined for protein. 3579 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 130 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 18.67 Time building geometry restraints manager: 16.77 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: 22728 1.47 - 1.73: 19062 1.73 - 2.00: 394 2.00 - 2.26: 2 2.26 - 2.53: 1 Bond restraints: 42187 Sorted by residual: bond pdb=" CE1 HIS O 659 " pdb=" NE2 HIS O 659 " ideal model delta sigma weight residual 1.321 2.526 -1.205 1.00e-02 1.00e+04 1.45e+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 6.94e+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 4.88e+03 bond pdb=" C PRO O 549 " pdb=" N SER O 550 " ideal model delta sigma weight residual 1.332 1.660 -0.328 1.37e-02 5.33e+03 5.73e+02 bond pdb=" C6 MGT P 101 " pdb=" O6 MGT P 101 " ideal model delta sigma weight residual 1.184 1.409 -0.225 2.00e-02 2.50e+03 1.26e+02 ... (remaining 42182 not shown) Histogram of bond angle deviations from ideal: 58.09 - 79.60: 4 79.60 - 101.11: 215 101.11 - 122.63: 51525 122.63 - 144.14: 5598 144.14 - 165.65: 1 Bond angle restraints: 57343 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 65.18 50.53 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 122.98 165.65 -42.67 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 76.05 45.26 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 84.97 23.43 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 107.20 128.79 -21.59 1.00e+00 1.00e+00 4.66e+02 ... (remaining 57338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 24947 35.51 - 71.01: 614 71.01 - 106.52: 49 106.52 - 142.03: 2 142.03 - 177.53: 3 Dihedral angle restraints: 25615 sinusoidal: 11256 harmonic: 14359 Sorted by residual: dihedral pdb=" C5' A P 40 " pdb=" C4' A P 40 " pdb=" C3' A P 40 " pdb=" O3' A P 40 " ideal model delta sinusoidal sigma weight residual 147.00 36.56 110.44 1 8.00e+00 1.56e-02 2.02e+02 dihedral pdb=" CA HIS A1108 " pdb=" C HIS A1108 " pdb=" N TYR A1109 " pdb=" CA TYR A1109 " ideal model delta harmonic sigma weight residual 180.00 129.45 50.55 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA GLU B 629 " pdb=" C GLU B 629 " pdb=" N LYS B 630 " pdb=" CA LYS B 630 " ideal model delta harmonic sigma weight residual -180.00 -133.34 -46.66 0 5.00e+00 4.00e-02 8.71e+01 ... (remaining 25612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.887: 6382 0.887 - 1.774: 0 1.774 - 2.661: 1 2.661 - 3.548: 0 3.548 - 4.436: 1 Chirality restraints: 6384 Sorted by residual: chirality pdb=" C4' A P 40 " pdb=" C5' A P 40 " pdb=" O4' A P 40 " pdb=" C3' A P 40 " both_signs ideal model delta sigma weight residual False -2.50 1.93 -4.44 2.00e-01 2.50e+01 4.92e+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 0.08 2.33 2.00e-01 2.50e+01 1.36e+02 chirality pdb=" CA ASN M 521 " pdb=" N ASN M 521 " pdb=" C ASN M 521 " pdb=" CB ASN M 521 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.36e+01 ... (remaining 6381 not shown) Planarity restraints: 7139 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR O 314 " -0.113 2.00e-02 2.50e+03 7.19e-02 1.03e+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 " 0.054 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 " -0.127 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 5.80e-02 6.72e+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 " 0.045 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 " 0.006 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 5.35e-02 5.01e+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 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE O 791 " 0.058 2.00e-02 2.50e+03 ... (remaining 7136 not shown) Histogram of nonbonded interaction distances: 0.35 - 1.26: 9 1.26 - 2.17: 55 2.17 - 3.08: 27106 3.08 - 3.99: 111354 3.99 - 4.90: 206989 Warning: very small nonbonded interaction distances. Nonbonded interactions: 345513 Sorted by model distance: nonbonded pdb=" CE LYS A 331 " pdb=" C7 DT N 14 " model vdw 0.354 3.860 nonbonded pdb=" CD LYS A 331 " pdb=" C4 DT N 14 " model vdw 0.949 3.660 nonbonded pdb=" OE2 GLU M 495 " pdb=" CB SER A 436 " model vdw 1.038 3.440 nonbonded pdb=" NE2 GLN G 138 " pdb=" N LYS O 654 " model vdw 1.044 3.200 nonbonded pdb=" CD LYS A 331 " pdb=" C5 DT N 14 " model vdw 1.169 3.660 ... (remaining 345508 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 8.140 Check model and map are aligned: 0.550 Set scattering table: 0.350 Process input model: 120.530 Find NCS groups from input model: 1.030 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 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 : 0.013 1.205 42187 Z= 0.869 Angle : 1.284 50.531 57343 Z= 0.788 Chirality : 0.096 4.436 6384 Planarity : 0.009 0.123 7139 Dihedral : 14.489 177.532 16327 Min Nonbonded Distance : 0.354 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.55 % Favored : 94.39 % Rotamer: Outliers : 1.72 % Allowed : 5.58 % Favored : 92.70 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.11 % 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: -2.95 (0.10), residues: 4884 helix: -2.10 (0.10), residues: 1630 sheet: -1.66 (0.17), residues: 794 loop : -1.89 (0.11), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.007 TRP O 622 HIS 0.037 0.003 HIS O 659 PHE 0.086 0.006 PHE O 791 TYR 0.127 0.006 TYR O 314 ARG 0.015 0.001 ARG O 702 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 363 time to evaluate : 4.243 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: M 396 MET cc_start: -0.0494 (mtm) cc_final: -0.0956 (mtm) REVERT: M 474 THR cc_start: 0.8422 (OUTLIER) cc_final: 0.8039 (p) REVERT: M 482 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8042 (mp) REVERT: O 182 MET cc_start: -0.0361 (mmm) cc_final: -0.2632 (mtm) REVERT: O 645 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.3646 (mp) outliers start: 75 outliers final: 12 residues processed: 434 average time/residue: 0.5630 time to fit residues: 394.9052 Evaluate side-chains 236 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 221 time to evaluate : 4.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 362 TYR Chi-restraints excluded: chain M residue 366 LYS Chi-restraints excluded: chain M residue 390 SER Chi-restraints excluded: chain M residue 418 ILE Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 474 THR Chi-restraints excluded: chain M residue 475 ARG Chi-restraints excluded: chain M residue 482 LEU Chi-restraints excluded: chain M residue 485 ASN Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain O residue 645 LEU Chi-restraints excluded: chain O residue 650 LYS Chi-restraints excluded: chain O residue 653 ARG Chi-restraints excluded: chain O residue 655 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 415 optimal weight: 30.0000 chunk 372 optimal weight: 7.9990 chunk 206 optimal weight: 20.0000 chunk 127 optimal weight: 0.8980 chunk 251 optimal weight: 5.9990 chunk 199 optimal weight: 20.0000 chunk 385 optimal weight: 5.9990 chunk 149 optimal weight: 0.7980 chunk 234 optimal weight: 3.9990 chunk 287 optimal weight: 0.9990 chunk 446 optimal weight: 8.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 378 ASN A 72 GLN A 123 ASN ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 ASN A 272 ASN A 273 GLN A 278 HIS A 293 ASN ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN A 387 ASN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 HIS A 507 GLN A 576 GLN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 HIS A 662 HIS A 704 ASN A 780 ASN A 809 HIS A 905 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1032 GLN A1093 GLN A1129 ASN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1244 ASN A1248 ASN ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1332 GLN A1384 HIS A1457 ASN B 111 ASN B 315 ASN B 486 ASN B 518 HIS B 552 ASN B 577 HIS B 639 HIS B 650 ASN B 683 GLN B 699 HIS ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 842 HIS B 980 HIS B1003 ASN B1021 HIS B1040 GLN ** B1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1129 ASN B1133 HIS B1145 GLN C 55 ASN C 232 ASN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN E 168 ASN H 44 ASN H 76 ASN H 87 GLN I 22 ASN I 32 ASN I 41 ASN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN D 135 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 515 HIS O 643 HIS O 667 ASN O 678 GLN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 42187 Z= 0.223 Angle : 0.656 10.400 57343 Z= 0.340 Chirality : 0.044 0.334 6384 Planarity : 0.005 0.073 7139 Dihedral : 14.525 176.629 6405 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.97 % Favored : 95.95 % Rotamer: Outliers : 1.86 % Allowed : 8.56 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.11), residues: 4884 helix: -0.34 (0.12), residues: 1646 sheet: -1.53 (0.16), residues: 841 loop : -1.23 (0.12), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 988 HIS 0.031 0.001 HIS O 659 PHE 0.024 0.002 PHE A 482 TYR 0.019 0.001 TYR B 388 ARG 0.006 0.001 ARG Z 733 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 238 time to evaluate : 5.183 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: M 312 MET cc_start: 0.0475 (mtp) cc_final: -0.0233 (mtm) REVERT: M 396 MET cc_start: -0.0899 (mtm) cc_final: -0.1115 (mtm) REVERT: A 769 MET cc_start: 0.6506 (mtt) cc_final: 0.6177 (mtt) REVERT: F 59 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.7088 (ptpp) REVERT: O 182 MET cc_start: -0.0154 (mmm) cc_final: -0.1851 (mpp) outliers start: 81 outliers final: 16 residues processed: 302 average time/residue: 0.5554 time to fit residues: 286.3644 Evaluate side-chains 228 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 211 time to evaluate : 4.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 745 VAL Chi-restraints excluded: chain M residue 296 ASP Chi-restraints excluded: chain M residue 362 TYR Chi-restraints excluded: chain M residue 481 LEU Chi-restraints excluded: chain M residue 551 ASN Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 1129 ASN Chi-restraints excluded: chain B residue 22 TRP Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain O residue 348 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 248 optimal weight: 8.9990 chunk 138 optimal weight: 0.6980 chunk 371 optimal weight: 10.0000 chunk 304 optimal weight: 6.9990 chunk 123 optimal weight: 8.9990 chunk 447 optimal weight: 6.9990 chunk 483 optimal weight: 3.9990 chunk 398 optimal weight: 5.9990 chunk 443 optimal weight: 20.0000 chunk 152 optimal weight: 20.0000 chunk 359 optimal weight: 20.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 HIS A 677 ASN ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 ASN A1129 ASN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 42187 Z= 0.285 Angle : 0.628 9.311 57343 Z= 0.325 Chirality : 0.042 0.247 6384 Planarity : 0.004 0.066 7139 Dihedral : 14.142 177.945 6375 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.87 % Favored : 95.07 % Rotamer: Outliers : 1.88 % Allowed : 9.36 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.12), residues: 4884 helix: 0.52 (0.13), residues: 1658 sheet: -1.19 (0.17), residues: 827 loop : -0.85 (0.13), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1334 HIS 0.006 0.001 HIS A 465 PHE 0.030 0.001 PHE E 73 TYR 0.017 0.001 TYR A 187 ARG 0.011 0.000 ARG E 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 210 time to evaluate : 4.683 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: M 312 MET cc_start: 0.1168 (mtp) cc_final: 0.0570 (mtm) REVERT: M 396 MET cc_start: -0.0969 (mtm) cc_final: -0.1193 (mtm) REVERT: A 355 MET cc_start: 0.7681 (mmm) cc_final: 0.7228 (mmm) REVERT: A 400 ASP cc_start: 0.6304 (p0) cc_final: 0.5959 (p0) REVERT: B 108 MET cc_start: 0.6170 (OUTLIER) cc_final: 0.5958 (ppp) REVERT: B 550 MET cc_start: 0.8198 (tmm) cc_final: 0.7503 (tmm) REVERT: B 744 MET cc_start: 0.7150 (mmp) cc_final: 0.6930 (mmp) REVERT: F 59 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.7046 (ptpp) REVERT: H 37 MET cc_start: 0.5379 (mtm) cc_final: 0.4999 (mtm) REVERT: O 175 MET cc_start: 0.6721 (pmm) cc_final: 0.6293 (pmm) REVERT: O 182 MET cc_start: 0.0170 (mmm) cc_final: -0.1132 (mpp) REVERT: O 300 MET cc_start: -0.2554 (tpp) cc_final: -0.2886 (tpt) outliers start: 82 outliers final: 31 residues processed: 279 average time/residue: 0.5104 time to fit residues: 242.7548 Evaluate side-chains 233 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 200 time to evaluate : 4.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 739 THR Chi-restraints excluded: chain Z residue 745 VAL Chi-restraints excluded: chain M residue 296 ASP Chi-restraints excluded: chain M residue 362 TYR Chi-restraints excluded: chain M residue 390 SER Chi-restraints excluded: chain M residue 474 THR Chi-restraints excluded: chain M residue 481 LEU Chi-restraints excluded: chain M residue 482 LEU Chi-restraints excluded: chain M residue 503 VAL Chi-restraints excluded: chain M residue 551 ASN Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain B residue 22 TRP Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain O residue 242 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 442 optimal weight: 50.0000 chunk 336 optimal weight: 7.9990 chunk 232 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 213 optimal weight: 10.0000 chunk 300 optimal weight: 10.0000 chunk 449 optimal weight: 30.0000 chunk 475 optimal weight: 30.0000 chunk 234 optimal weight: 3.9990 chunk 425 optimal weight: 50.0000 chunk 128 optimal weight: 4.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 188 GLN ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 108 ASN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN D 48 ASN ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 347 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 42187 Z= 0.374 Angle : 0.671 16.547 57343 Z= 0.343 Chirality : 0.043 0.223 6384 Planarity : 0.004 0.049 7139 Dihedral : 14.108 178.618 6375 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.22 % Favored : 94.76 % Rotamer: Outliers : 2.04 % Allowed : 9.73 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.12), residues: 4884 helix: 0.86 (0.13), residues: 1638 sheet: -1.01 (0.18), residues: 808 loop : -0.68 (0.13), residues: 2438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 203 HIS 0.010 0.001 HIS A 465 PHE 0.032 0.002 PHE G 158 TYR 0.020 0.002 TYR B 766 ARG 0.013 0.001 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 199 time to evaluate : 4.803 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: M 312 MET cc_start: 0.1520 (mtp) cc_final: 0.1053 (mtm) REVERT: M 396 MET cc_start: -0.0745 (mtm) cc_final: -0.0973 (mtm) REVERT: A 400 ASP cc_start: 0.6536 (p0) cc_final: 0.6050 (p0) REVERT: A 769 MET cc_start: 0.6611 (mtt) cc_final: 0.6214 (mtt) REVERT: B 550 MET cc_start: 0.8359 (tmm) cc_final: 0.7443 (tmm) REVERT: F 59 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7149 (ptpp) REVERT: O 182 MET cc_start: 0.0129 (mmm) cc_final: -0.1946 (mtm) outliers start: 89 outliers final: 40 residues processed: 278 average time/residue: 0.5183 time to fit residues: 246.1427 Evaluate side-chains 231 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 190 time to evaluate : 4.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 736 LEU Chi-restraints excluded: chain Z residue 739 THR Chi-restraints excluded: chain Z residue 745 VAL Chi-restraints excluded: chain Z residue 751 THR Chi-restraints excluded: chain M residue 362 TYR Chi-restraints excluded: chain M residue 474 THR Chi-restraints excluded: chain M residue 482 LEU Chi-restraints excluded: chain M residue 503 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain B residue 22 TRP Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 1127 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain O residue 242 ASN Chi-restraints excluded: chain O residue 342 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 396 optimal weight: 9.9990 chunk 269 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 354 optimal weight: 10.0000 chunk 196 optimal weight: 30.0000 chunk 405 optimal weight: 9.9990 chunk 328 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 242 optimal weight: 5.9990 chunk 426 optimal weight: 50.0000 chunk 120 optimal weight: 5.9990 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 ASN ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 GLN H 29 HIS ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 42187 Z= 0.240 Angle : 0.590 10.101 57343 Z= 0.300 Chirality : 0.042 0.313 6384 Planarity : 0.004 0.051 7139 Dihedral : 13.940 178.054 6375 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.81 % Favored : 95.17 % Rotamer: Outliers : 1.74 % Allowed : 10.51 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.12), residues: 4884 helix: 1.08 (0.13), residues: 1646 sheet: -0.79 (0.18), residues: 799 loop : -0.57 (0.13), residues: 2439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 27 HIS 0.007 0.001 HIS A 465 PHE 0.021 0.001 PHE E 73 TYR 0.020 0.001 TYR G 3 ARG 0.005 0.000 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 202 time to evaluate : 4.862 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: M 312 MET cc_start: 0.1464 (mtp) cc_final: 0.1196 (mtm) REVERT: M 396 MET cc_start: -0.0804 (mtm) cc_final: -0.1019 (mtm) REVERT: M 437 MET cc_start: 0.0739 (OUTLIER) cc_final: 0.0189 (tpp) REVERT: M 557 MET cc_start: -0.3495 (ttt) cc_final: -0.3756 (ttp) REVERT: A 400 ASP cc_start: 0.6352 (p0) cc_final: 0.5883 (p0) REVERT: B 550 MET cc_start: 0.8220 (tmm) cc_final: 0.7585 (tmm) REVERT: O 175 MET cc_start: 0.6989 (pmm) cc_final: 0.6503 (pmm) REVERT: O 182 MET cc_start: 0.0097 (mmm) cc_final: -0.1951 (mtm) REVERT: O 721 MET cc_start: 0.6560 (tpp) cc_final: 0.6301 (tpp) outliers start: 76 outliers final: 38 residues processed: 266 average time/residue: 0.5012 time to fit residues: 230.2246 Evaluate side-chains 235 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 196 time to evaluate : 5.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 736 LEU Chi-restraints excluded: chain Z residue 739 THR Chi-restraints excluded: chain Z residue 745 VAL Chi-restraints excluded: chain M residue 362 TYR Chi-restraints excluded: chain M residue 437 MET Chi-restraints excluded: chain M residue 481 LEU Chi-restraints excluded: chain M residue 482 LEU Chi-restraints excluded: chain M residue 503 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1129 ASN Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain B residue 22 TRP Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 1127 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain O residue 242 ASN Chi-restraints excluded: chain O residue 342 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 160 optimal weight: 8.9990 chunk 428 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 279 optimal weight: 20.0000 chunk 117 optimal weight: 0.9980 chunk 476 optimal weight: 20.0000 chunk 395 optimal weight: 7.9990 chunk 220 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 157 optimal weight: 1.9990 chunk 249 optimal weight: 10.0000 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN A 704 ASN ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 GLN A1129 ASN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1236 ASN ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 HIS H 131 ASN ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN D 89 GLN D 135 GLN ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 42187 Z= 0.304 Angle : 0.626 11.759 57343 Z= 0.316 Chirality : 0.042 0.188 6384 Planarity : 0.004 0.042 7139 Dihedral : 13.862 178.368 6375 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.28 % Favored : 94.70 % Rotamer: Outliers : 1.54 % Allowed : 11.31 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: -0.10 (0.12), residues: 4884 helix: 1.03 (0.13), residues: 1664 sheet: -0.71 (0.18), residues: 816 loop : -0.53 (0.13), residues: 2404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 27 HIS 0.008 0.001 HIS A 465 PHE 0.022 0.001 PHE E 73 TYR 0.016 0.001 TYR A 413 ARG 0.005 0.000 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 197 time to evaluate : 4.571 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: M 301 MET cc_start: -0.0639 (tpt) cc_final: -0.1076 (tpt) REVERT: M 346 MET cc_start: 0.2768 (tpt) cc_final: 0.2300 (tpt) REVERT: M 396 MET cc_start: -0.0820 (mtm) cc_final: -0.1068 (mtp) REVERT: M 437 MET cc_start: 0.0207 (OUTLIER) cc_final: -0.0264 (tpp) REVERT: A 400 ASP cc_start: 0.6523 (p0) cc_final: 0.6030 (p0) REVERT: B 550 MET cc_start: 0.8192 (tmm) cc_final: 0.7605 (tmm) REVERT: O 175 MET cc_start: 0.7033 (pmm) cc_final: 0.6541 (pmm) REVERT: O 182 MET cc_start: 0.0117 (mmm) cc_final: -0.1925 (mtm) outliers start: 67 outliers final: 44 residues processed: 254 average time/residue: 0.4963 time to fit residues: 216.8506 Evaluate side-chains 240 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 195 time to evaluate : 4.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 736 LEU Chi-restraints excluded: chain Z residue 739 THR Chi-restraints excluded: chain Z residue 745 VAL Chi-restraints excluded: chain M residue 321 HIS Chi-restraints excluded: chain M residue 362 TYR Chi-restraints excluded: chain M residue 421 SER Chi-restraints excluded: chain M residue 437 MET Chi-restraints excluded: chain M residue 474 THR Chi-restraints excluded: chain M residue 481 LEU Chi-restraints excluded: chain M residue 482 LEU Chi-restraints excluded: chain M residue 501 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain B residue 22 TRP Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 1089 MET Chi-restraints excluded: chain B residue 1127 ILE Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain O residue 342 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 458 optimal weight: 50.0000 chunk 53 optimal weight: 3.9990 chunk 271 optimal weight: 5.9990 chunk 347 optimal weight: 20.0000 chunk 269 optimal weight: 2.9990 chunk 400 optimal weight: 10.0000 chunk 265 optimal weight: 6.9990 chunk 474 optimal weight: 20.0000 chunk 296 optimal weight: 7.9990 chunk 289 optimal weight: 10.0000 chunk 218 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 654 GLN ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN D 48 ASN ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 42187 Z= 0.298 Angle : 0.628 11.366 57343 Z= 0.315 Chirality : 0.042 0.175 6384 Planarity : 0.004 0.043 7139 Dihedral : 13.834 178.281 6375 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.08 % Favored : 94.90 % Rotamer: Outliers : 1.42 % Allowed : 11.70 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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 (0.13), residues: 4884 helix: 1.09 (0.13), residues: 1665 sheet: -0.65 (0.18), residues: 812 loop : -0.44 (0.14), residues: 2407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 27 HIS 0.008 0.001 HIS A 465 PHE 0.023 0.001 PHE A 458 TYR 0.020 0.001 TYR B 766 ARG 0.009 0.000 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 195 time to evaluate : 4.743 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: M 346 MET cc_start: 0.2744 (tpt) cc_final: 0.2399 (tpt) REVERT: M 396 MET cc_start: -0.0597 (mtm) cc_final: -0.0868 (mtp) REVERT: M 437 MET cc_start: 0.0151 (OUTLIER) cc_final: -0.0365 (tpp) REVERT: A 400 ASP cc_start: 0.6582 (p0) cc_final: 0.6113 (p0) REVERT: B 108 MET cc_start: 0.7042 (ppp) cc_final: 0.6456 (ppp) REVERT: B 529 MET cc_start: 0.7669 (mmm) cc_final: 0.7461 (mmm) REVERT: B 550 MET cc_start: 0.8053 (tmm) cc_final: 0.7610 (tmm) REVERT: O 175 MET cc_start: 0.7025 (pmm) cc_final: 0.6513 (pmm) REVERT: O 182 MET cc_start: 0.0152 (mmm) cc_final: -0.1874 (mtm) outliers start: 62 outliers final: 45 residues processed: 248 average time/residue: 0.4983 time to fit residues: 212.2921 Evaluate side-chains 237 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 191 time to evaluate : 4.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 709 THR Chi-restraints excluded: chain Z residue 736 LEU Chi-restraints excluded: chain Z residue 739 THR Chi-restraints excluded: chain Z residue 745 VAL Chi-restraints excluded: chain Z residue 751 THR Chi-restraints excluded: chain M residue 321 HIS Chi-restraints excluded: chain M residue 362 TYR Chi-restraints excluded: chain M residue 437 MET Chi-restraints excluded: chain M residue 474 THR Chi-restraints excluded: chain M residue 481 LEU Chi-restraints excluded: chain M residue 482 LEU Chi-restraints excluded: chain M residue 501 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain B residue 22 TRP Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 1089 MET Chi-restraints excluded: chain B residue 1127 ILE Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain O residue 342 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 293 optimal weight: 10.0000 chunk 189 optimal weight: 0.0970 chunk 283 optimal weight: 8.9990 chunk 142 optimal weight: 50.0000 chunk 93 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 301 optimal weight: 10.0000 chunk 323 optimal weight: 7.9990 chunk 234 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 372 optimal weight: 0.2980 overall best weight: 4.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 HIS ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 ASN ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 GLN I 41 ASN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 42187 Z= 0.268 Angle : 0.624 11.633 57343 Z= 0.311 Chirality : 0.042 0.228 6384 Planarity : 0.004 0.060 7139 Dihedral : 13.792 178.187 6375 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.02 % Favored : 94.96 % Rotamer: Outliers : 1.40 % Allowed : 12.00 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: 0.12 (0.13), residues: 4884 helix: 1.18 (0.13), residues: 1662 sheet: -0.62 (0.18), residues: 812 loop : -0.37 (0.14), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 27 HIS 0.007 0.001 HIS A 465 PHE 0.038 0.001 PHE A 458 TYR 0.016 0.001 TYR E 125 ARG 0.009 0.000 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 193 time to evaluate : 5.235 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: M 396 MET cc_start: -0.0606 (mtm) cc_final: -0.0899 (mtp) REVERT: M 437 MET cc_start: 0.0004 (OUTLIER) cc_final: -0.0403 (tpp) REVERT: A 400 ASP cc_start: 0.6576 (p0) cc_final: 0.6097 (p0) REVERT: B 108 MET cc_start: 0.7084 (ppp) cc_final: 0.6560 (ppp) REVERT: B 550 MET cc_start: 0.7922 (tmm) cc_final: 0.7609 (tmm) REVERT: O 175 MET cc_start: 0.7046 (pmm) cc_final: 0.6614 (pmm) REVERT: O 182 MET cc_start: 0.0172 (mmm) cc_final: -0.1580 (mpp) REVERT: O 240 MET cc_start: 0.6340 (ptm) cc_final: 0.5972 (ptm) REVERT: O 250 MET cc_start: 0.0081 (ppp) cc_final: -0.0535 (ppp) outliers start: 61 outliers final: 48 residues processed: 245 average time/residue: 0.4920 time to fit residues: 210.1498 Evaluate side-chains 240 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 191 time to evaluate : 4.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 709 THR Chi-restraints excluded: chain Z residue 736 LEU Chi-restraints excluded: chain Z residue 739 THR Chi-restraints excluded: chain Z residue 745 VAL Chi-restraints excluded: chain Z residue 751 THR Chi-restraints excluded: chain M residue 321 HIS Chi-restraints excluded: chain M residue 362 TYR Chi-restraints excluded: chain M residue 420 THR Chi-restraints excluded: chain M residue 421 SER Chi-restraints excluded: chain M residue 437 MET Chi-restraints excluded: chain M residue 474 THR Chi-restraints excluded: chain M residue 481 LEU Chi-restraints excluded: chain M residue 482 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain B residue 22 TRP Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 1089 MET Chi-restraints excluded: chain B residue 1127 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain O residue 342 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 431 optimal weight: 7.9990 chunk 454 optimal weight: 0.2980 chunk 414 optimal weight: 50.0000 chunk 441 optimal weight: 20.0000 chunk 265 optimal weight: 10.0000 chunk 192 optimal weight: 3.9990 chunk 346 optimal weight: 8.9990 chunk 135 optimal weight: 0.9990 chunk 399 optimal weight: 20.0000 chunk 417 optimal weight: 10.0000 chunk 440 optimal weight: 0.9980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 ASN ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 42187 Z= 0.199 Angle : 0.615 17.467 57343 Z= 0.302 Chirality : 0.042 0.233 6384 Planarity : 0.004 0.056 7139 Dihedral : 13.713 178.054 6375 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.77 % Favored : 95.21 % Rotamer: Outliers : 1.19 % Allowed : 12.41 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: 0.20 (0.13), residues: 4884 helix: 1.24 (0.13), residues: 1668 sheet: -0.52 (0.18), residues: 803 loop : -0.34 (0.14), residues: 2413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 27 HIS 0.009 0.001 HIS K 69 PHE 0.029 0.001 PHE A 458 TYR 0.017 0.001 TYR E 125 ARG 0.007 0.000 ARG G 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 196 time to evaluate : 4.580 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: M 312 MET cc_start: -0.0588 (pmm) cc_final: -0.0817 (pmm) REVERT: M 396 MET cc_start: -0.0655 (mtm) cc_final: -0.0943 (mtp) REVERT: A 400 ASP cc_start: 0.6546 (p0) cc_final: 0.6064 (p0) REVERT: A 470 MET cc_start: 0.6595 (mtp) cc_final: 0.6320 (mtp) REVERT: B 108 MET cc_start: 0.7065 (ppp) cc_final: 0.6593 (ppp) REVERT: D 39 MET cc_start: 0.7770 (ppp) cc_final: 0.6867 (ppp) REVERT: O 175 MET cc_start: 0.7073 (pmm) cc_final: 0.6639 (pmm) REVERT: O 182 MET cc_start: 0.0122 (mmm) cc_final: -0.1370 (mpp) REVERT: O 250 MET cc_start: 0.0109 (ppp) cc_final: -0.0545 (ppp) REVERT: O 300 MET cc_start: -0.2968 (tpt) cc_final: -0.3315 (tpt) outliers start: 52 outliers final: 42 residues processed: 238 average time/residue: 0.4834 time to fit residues: 200.8166 Evaluate side-chains 235 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 193 time to evaluate : 4.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 736 LEU Chi-restraints excluded: chain Z residue 739 THR Chi-restraints excluded: chain Z residue 745 VAL Chi-restraints excluded: chain Z residue 751 THR Chi-restraints excluded: chain M residue 321 HIS Chi-restraints excluded: chain M residue 362 TYR Chi-restraints excluded: chain M residue 420 THR Chi-restraints excluded: chain M residue 421 SER Chi-restraints excluded: chain M residue 474 THR Chi-restraints excluded: chain M residue 501 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1129 ASN Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain B residue 22 TRP Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 1089 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain O residue 342 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 290 optimal weight: 6.9990 chunk 467 optimal weight: 9.9990 chunk 285 optimal weight: 0.9990 chunk 221 optimal weight: 9.9990 chunk 324 optimal weight: 6.9990 chunk 490 optimal weight: 10.0000 chunk 451 optimal weight: 50.0000 chunk 390 optimal weight: 30.0000 chunk 40 optimal weight: 0.9990 chunk 301 optimal weight: 7.9990 chunk 239 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 ASN ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.185 42187 Z= 0.248 Angle : 0.697 59.194 57343 Z= 0.362 Chirality : 0.043 0.234 6384 Planarity : 0.004 0.060 7139 Dihedral : 13.713 178.054 6375 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.73 % Favored : 95.25 % Rotamer: Outliers : 1.24 % Allowed : 12.62 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.13), residues: 4884 helix: 1.24 (0.13), residues: 1668 sheet: -0.51 (0.18), residues: 803 loop : -0.33 (0.14), residues: 2413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 27 HIS 0.027 0.001 HIS O 833 PHE 0.027 0.001 PHE A 458 TYR 0.022 0.001 TYR B 206 ARG 0.004 0.000 ARG Z 733 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 193 time to evaluate : 6.647 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: M 312 MET cc_start: -0.0609 (pmm) cc_final: -0.0832 (pmm) REVERT: M 396 MET cc_start: -0.0653 (mtm) cc_final: -0.0940 (mtp) REVERT: M 437 MET cc_start: 0.0197 (mmm) cc_final: -0.0263 (tpp) REVERT: A 400 ASP cc_start: 0.6554 (p0) cc_final: 0.6079 (p0) REVERT: B 108 MET cc_start: 0.7066 (ppp) cc_final: 0.6614 (ppp) REVERT: B 200 MET cc_start: 0.6614 (mmm) cc_final: 0.6320 (mmm) REVERT: E 72 MET cc_start: 0.6146 (tpp) cc_final: 0.5835 (tpp) REVERT: D 39 MET cc_start: 0.7765 (ppp) cc_final: 0.6872 (ppp) REVERT: O 175 MET cc_start: 0.7079 (pmm) cc_final: 0.6642 (pmm) REVERT: O 182 MET cc_start: 0.0130 (mmm) cc_final: -0.1369 (mpp) REVERT: O 250 MET cc_start: 0.0108 (ppp) cc_final: -0.0568 (ppp) REVERT: O 300 MET cc_start: -0.2967 (tpt) cc_final: -0.3307 (tpt) outliers start: 54 outliers final: 46 residues processed: 235 average time/residue: 0.5262 time to fit residues: 216.0944 Evaluate side-chains 239 residues out of total 4391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 193 time to evaluate : 4.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 709 THR Chi-restraints excluded: chain Z residue 736 LEU Chi-restraints excluded: chain Z residue 739 THR Chi-restraints excluded: chain Z residue 745 VAL Chi-restraints excluded: chain Z residue 751 THR Chi-restraints excluded: chain M residue 321 HIS Chi-restraints excluded: chain M residue 362 TYR Chi-restraints excluded: chain M residue 420 THR Chi-restraints excluded: chain M residue 421 SER Chi-restraints excluded: chain M residue 474 THR Chi-restraints excluded: chain M residue 501 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1192 TRP Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain B residue 22 TRP Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 1089 MET Chi-restraints excluded: chain B residue 1127 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain O residue 243 MET Chi-restraints excluded: chain O residue 342 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 310 optimal weight: 1.9990 chunk 415 optimal weight: 30.0000 chunk 119 optimal weight: 6.9990 chunk 359 optimal weight: 8.9990 chunk 57 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 390 optimal weight: 30.0000 chunk 163 optimal weight: 6.9990 chunk 401 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 ASN ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.054072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.033781 restraints weight = 315120.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.034312 restraints weight = 174623.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.034736 restraints weight = 115977.447| |-----------------------------------------------------------------------------| r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.185 42187 Z= 0.248 Angle : 0.697 59.194 57343 Z= 0.362 Chirality : 0.043 0.234 6384 Planarity : 0.004 0.060 7139 Dihedral : 13.713 178.054 6375 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.73 % Favored : 95.25 % Rotamer: Outliers : 1.06 % Allowed : 12.78 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.13), residues: 4884 helix: 1.24 (0.13), residues: 1668 sheet: -0.51 (0.18), residues: 803 loop : -0.33 (0.14), residues: 2413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 27 HIS 0.027 0.001 HIS O 833 PHE 0.027 0.001 PHE A 458 TYR 0.022 0.001 TYR B 206 ARG 0.004 0.000 ARG Z 733 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6769.68 seconds wall clock time: 125 minutes 49.17 seconds (7549.17 seconds total)