Starting phenix.real_space_refine on Sat Dec 9 21:48:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc8_4500/12_2023/6qc8_4500_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc8_4500/12_2023/6qc8_4500.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc8_4500/12_2023/6qc8_4500_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc8_4500/12_2023/6qc8_4500_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc8_4500/12_2023/6qc8_4500_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc8_4500/12_2023/6qc8_4500.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc8_4500/12_2023/6qc8_4500.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc8_4500/12_2023/6qc8_4500_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc8_4500/12_2023/6qc8_4500_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.024 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 Fe 28 7.16 5 Zn 1 6.06 5 P 12 5.49 5 S 462 5.16 5 C 42130 2.51 5 N 11037 2.21 5 O 11724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "V1 PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V1 ARG 32": "NH1" <-> "NH2" Residue "V1 ARG 237": "NH1" <-> "NH2" Residue "V1 ARG 423": "NH1" <-> "NH2" Residue "V2 ARG 187": "NH1" <-> "NH2" Residue "V2 PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S2 TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S2 TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S3 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S7 ARG 174": "NH1" <-> "NH2" Residue "S7 ARG 178": "NH1" <-> "NH2" Residue "S8 TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V3 PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S6 TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S4 ARG 64": "NH1" <-> "NH2" Residue "A9 ARG 97": "NH1" <-> "NH2" Residue "A9 ARG 186": "NH1" <-> "NH2" Residue "A9 ARG 292": "NH1" <-> "NH2" Residue "A2 ARG 33": "NH1" <-> "NH2" Residue "A6 ARG 22": "NH1" <-> "NH2" Residue "AL PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AL ARG 106": "NH1" <-> "NH2" Residue "AL PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 ARG 195": "NH1" <-> "NH2" Residue "D1 ARG 274": "NH1" <-> "NH2" Residue "D6 PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D6 TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D6 ARG 173": "NH1" <-> "NH2" Residue "D5 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D5 TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D5 TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D5 TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D5 PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D4 TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D2 PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AK ARG 19": "NH1" <-> "NH2" Residue "B5 ARG 26": "NH1" <-> "NH2" Residue "A8 PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AJ ARG 95": "NH1" <-> "NH2" Residue "AJ PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AJ TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AJ ARG 305": "NH1" <-> "NH2" Residue "S5 TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A3 ARG 46": "NH1" <-> "NH2" Residue "C2 ARG 5": "NH1" <-> "NH2" Residue "C2 ARG 120": "NH1" <-> "NH2" Residue "B4 ARG 41": "NH1" <-> "NH2" Residue "B4 PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AM ARG 26": "NH1" <-> "NH2" Residue "AM ARG 81": "NH1" <-> "NH2" Residue "B9 ARG 92": "NH1" <-> "NH2" Residue "B9 ARG 128": "NH1" <-> "NH2" Residue "B9 ARG 176": "NH1" <-> "NH2" Residue "B8 ARG 70": "NH1" <-> "NH2" Residue "BK TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A1 ARG 25": "NH1" <-> "NH2" Residue "A1 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 65394 Number of models: 1 Model: "" Number of chains: 58 Chain: "V1" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3312 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 21, 'TRANS': 408} Chain: "V2" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1647 Classifications: {'peptide': 212} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 189} Chain: "S1" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5275 Classifications: {'peptide': 688} Link IDs: {'CIS': 3, 'PTRANS': 32, 'TRANS': 652} Chain: "S2" Number of atoms: 3455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3455 Classifications: {'peptide': 430} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 401} Chain: "S3" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1726 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "S7" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} Chain: "S8" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 10, 'TRANS': 165} Chain: "V3" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 345 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "S6" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 737 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "S4" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1024 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "A9" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2293 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 14, 'TRANS': 272} Chain breaks: 2 Chain: "A2" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 665 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "A5" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 901 Classifications: {'peptide': 111} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 101} Chain: "A6" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 969 Classifications: {'peptide': 114} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 106} Chain: "A7" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 766 Classifications: {'peptide': 96} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 83} Chain breaks: 1 Chain: "AL" Number of atoms: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1201 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "AA" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 645 Classifications: {'peptide': 80} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 76} Chain: "D3" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 728 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain breaks: 1 Chain: "D1" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2415 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 19, 'TRANS': 279} Chain breaks: 1 Chain: "D6" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1308 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 3, 'TRANS': 164} Chain breaks: 1 Chain: "4L" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 96} Chain: "D5" Number of atoms: 4805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4805 Classifications: {'peptide': 606} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 578} Chain: "D4" Number of atoms: 3646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3646 Classifications: {'peptide': 459} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 437} Chain: "D2" Number of atoms: 2724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2724 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 326} Chain: "AK" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1025 Classifications: {'peptide': 140} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 4, 'TRANS': 132} Chain: "B5" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1156 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 128} Chain: "AB" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 702 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "A8" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1404 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 12, 'TRANS': 156} Chain: "BJ" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1441 Classifications: {'peptide': 171} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "AJ" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2583 Classifications: {'peptide': 319} Link IDs: {'CIS': 6, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 298} Chain: "S5" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 822 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "A3" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 582 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 62} Chain: "B3" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 578 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C2" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 997 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 10, 'TRANS': 106} Chain: "B4" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1059 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 117} Chain: "AM" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1143 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 130} Chain: "B6" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 815 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 12, 'TRANS': 83} Chain breaks: 1 Chain: "B7" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1026 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "B9" Number of atoms: 1515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1515 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 16, 'TRANS': 159} Chain: "B2" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 563 Classifications: {'peptide': 65} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 56} Chain: "B8" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1324 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 135} Chain: "BK" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 853 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 93} Chain: "C1" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 391 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 3, 'TRANS': 42} Chain: "B1" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 449 Classifications: {'peptide': 52} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 49} Chain: "A1" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 577 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "V1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "S1" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S7" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "S8" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A9" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "AA" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Chain: "D1" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "D5" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 53 Chain: "D4" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "AK" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "AB" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2715 SG CYSV1 365 46.917 163.743 147.093 1.00 22.91 S ATOM 3039 SG CYSV1 405 48.486 165.759 153.173 1.00 27.10 S ATOM 2695 SG CYSV1 362 52.478 163.989 148.493 1.00 46.50 S ATOM 2676 SG CYSV1 359 49.276 169.880 148.262 1.00 54.49 S ATOM 4116 SG CYSV2 103 28.826 173.656 153.700 1.00 57.27 S ATOM 4150 SG CYSV2 108 26.127 171.137 155.734 1.00 35.06 S ATOM 4430 SG CYSV2 144 32.736 172.024 156.659 1.00 33.10 S ATOM 4453 SG CYSV2 148 30.256 170.540 159.189 1.00 41.64 S ATOM 5785 SG CYSS1 114 58.429 157.731 128.992 1.00 17.69 S ATOM 5724 SG CYSS1 105 53.802 154.829 125.577 1.00 29.29 S ATOM 5745 SG CYSS1 108 56.566 160.503 123.655 1.00 21.47 S ATOM 6117 SG CYSS1 156 58.573 166.635 136.287 1.00 31.42 S ATOM 6094 SG CYSS1 153 53.039 167.964 133.237 1.00 38.91 S ATOM 6141 SG CYSS1 159 58.005 172.326 133.379 1.00 18.87 S ATOM 6471 SG CYSS1 203 58.669 167.022 129.894 1.00 41.07 S ATOM 5230 SG CYSS1 41 60.891 164.738 142.953 1.00 28.96 S ATOM 5316 SG CYSS1 52 60.050 161.092 142.399 1.00 12.49 S ATOM 5341 SG CYSS1 55 62.955 160.033 147.266 1.00 21.52 S ATOM 5442 SG CYSS1 69 63.615 163.990 147.341 1.00 22.22 S ATOM 16168 SG CYSS7 119 68.579 131.751 102.204 1.00 24.19 S ATOM 16398 SG CYSS7 149 62.723 131.513 104.320 1.00 29.17 S ATOM 15670 SG CYSS7 55 64.164 128.260 98.761 1.00 58.64 S ATOM 15664 SG CYSS7 54 66.017 126.057 104.262 1.00 37.30 S ATOM 17590 SG CYSS8 116 59.044 139.740 104.099 1.00 37.71 S ATOM 17637 SG CYSS8 122 55.948 142.757 108.973 1.00 24.31 S ATOM 17364 SG CYSS8 87 62.444 143.303 108.280 1.00 55.11 S ATOM 17666 SG CYSS8 126 51.191 148.347 112.399 1.00 59.15 S ATOM 17337 SG CYSS8 83 57.381 148.880 110.218 1.00 34.53 S ATOM 17295 SG CYSS8 77 53.142 153.805 109.262 1.00 22.30 S ATOM 17314 SG CYSS8 80 55.139 152.094 115.292 1.00 22.28 S ATOM 18887 SG CYSS6 59 39.027 158.147 117.875 1.00 24.01 S ATOM 19065 SG CYSS6 84 42.870 159.940 117.461 1.00 14.95 S ATOM 19087 SG CYSS6 87 40.438 158.146 115.259 1.00 16.27 S Time building chain proxies: 25.13, per 1000 atoms: 0.38 Number of scatterers: 65394 At special positions: 0 Unit cell: (247.8, 221.2, 203, 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 1 29.99 Fe 28 26.01 S 462 16.00 P 12 15.00 O 11724 8.00 N 11037 7.00 C 42130 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYSAK 17 " - pdb=" SG CYSAK 74 " distance=2.03 Simple disulfide: pdb=" SG CYSAK 94 " - pdb=" SG CYSAK 114 " distance=2.05 Simple disulfide: pdb=" SG CYSA8 35 " - pdb=" SG CYSA8 65 " distance=2.05 Simple disulfide: pdb=" SG CYSA8 45 " - pdb=" SG CYSA8 55 " distance=2.04 Simple disulfide: pdb=" SG CYSA8 77 " - pdb=" SG CYSA8 109 " distance=2.04 Simple disulfide: pdb=" SG CYSA8 87 " - pdb=" SG CYSA8 99 " distance=2.02 Simple disulfide: pdb=" SG CYSBJ 76 " - pdb=" SG CYSBJ 83 " distance=2.04 Simple disulfide: pdb=" SG CYSBJ 112 " - pdb=" SG CYSBJ 124 " distance=2.03 Simple disulfide: pdb=" SG CYSS5 32 " - pdb=" SG CYSS5 65 " distance=2.04 Simple disulfide: pdb=" SG CYSS5 42 " - pdb=" SG CYSS5 55 " distance=2.03 Simple disulfide: pdb=" SG CYSB7 58 " - pdb=" SG CYSB7 89 " distance=2.04 Simple disulfide: pdb=" SG CYSB7 68 " - pdb=" SG CYSB7 79 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.31 Conformation dependent library (CDL) restraints added in 8.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FESS1 803 " pdb="FE1 FESS1 803 " - pdb=" SG CYSS1 52 " pdb="FE1 FESS1 803 " - pdb=" SG CYSS1 41 " pdb="FE2 FESS1 803 " - pdb=" SG CYSS1 55 " pdb="FE2 FESS1 803 " - pdb=" SG CYSS1 69 " pdb=" FESV2 300 " pdb="FE2 FESV2 300 " - pdb=" SG CYSV2 148 " pdb="FE2 FESV2 300 " - pdb=" SG CYSV2 144 " pdb="FE1 FESV2 300 " - pdb=" SG CYSV2 103 " pdb="FE1 FESV2 300 " - pdb=" SG CYSV2 108 " pdb=" SF4S1 801 " pdb="FE3 SF4S1 801 " - pdb=" NE2 HISS1 101 " pdb="FE1 SF4S1 801 " - pdb=" SG CYSS1 114 " pdb="FE4 SF4S1 801 " - pdb=" SG CYSS1 108 " pdb="FE2 SF4S1 801 " - pdb=" SG CYSS1 105 " pdb=" SF4S1 802 " pdb="FE2 SF4S1 802 " - pdb=" SG CYSS1 153 " pdb="FE3 SF4S1 802 " - pdb=" SG CYSS1 159 " pdb="FE4 SF4S1 802 " - pdb=" SG CYSS1 203 " pdb="FE1 SF4S1 802 " - pdb=" SG CYSS1 156 " pdb=" SF4S7 300 " pdb="FE4 SF4S7 300 " - pdb=" SG CYSS7 54 " pdb="FE1 SF4S7 300 " - pdb=" SG CYSS7 119 " pdb="FE2 SF4S7 300 " - pdb=" SG CYSS7 149 " pdb="FE3 SF4S7 300 " - pdb=" SG CYSS7 55 " pdb=" SF4S8 201 " pdb="FE2 SF4S8 201 " - pdb=" SG CYSS8 116 " pdb="FE4 SF4S8 201 " - pdb=" SG CYSS8 87 " pdb="FE3 SF4S8 201 " - pdb=" SG CYSS8 122 " pdb="FE1 SF4S8 201 " - pdb=" SG CYSS8 119 " pdb=" SF4S8 202 " pdb="FE4 SF4S8 202 " - pdb=" SG CYSS8 80 " pdb="FE1 SF4S8 202 " - pdb=" SG CYSS8 126 " pdb="FE2 SF4S8 202 " - pdb=" SG CYSS8 83 " pdb="FE3 SF4S8 202 " - pdb=" SG CYSS8 77 " pdb=" SF4V1 500 " pdb="FE1 SF4V1 500 " - pdb=" SG CYSV1 365 " pdb="FE3 SF4V1 500 " - pdb=" SG CYSV1 362 " pdb="FE2 SF4V1 500 " - pdb=" SG CYSV1 405 " pdb="FE4 SF4V1 500 " - pdb=" SG CYSV1 359 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZNS6 300 " pdb="ZN ZNS6 300 " - pdb=" NE2 HISS6 68 " pdb="ZN ZNS6 300 " - pdb=" SG CYSS6 84 " pdb="ZN ZNS6 300 " - pdb=" SG CYSS6 59 " pdb="ZN ZNS6 300 " - pdb=" SG CYSS6 87 " Number of angles added : 3 15976 Ramachandran restraints generated. 7988 Oldfield, 0 Emsley, 7988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15208 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 301 helices and 26 sheets defined 48.2% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.15 Creating SS restraints... Processing helix chain 'V1' and resid 33 through 39 Processing helix chain 'V1' and resid 45 through 49 Processing helix chain 'V1' and resid 53 through 63 Processing helix chain 'V1' and resid 75 through 81 Processing helix chain 'V1' and resid 108 through 113 Processing helix chain 'V1' and resid 115 through 129 removed outlier: 3.564A pdb=" N METV1 129 " --> pdb=" O GLYV1 125 " (cutoff:3.500A) Processing helix chain 'V1' and resid 143 through 158 Processing helix chain 'V1' and resid 166 through 168 No H-bonds generated for 'chain 'V1' and resid 166 through 168' Processing helix chain 'V1' and resid 185 through 187 No H-bonds generated for 'chain 'V1' and resid 185 through 187' Processing helix chain 'V1' and resid 191 through 196 Processing helix chain 'V1' and resid 225 through 236 Proline residue: V1 232 - end of helix removed outlier: 3.652A pdb=" N CYSV1 235 " --> pdb=" O SERV1 231 " (cutoff:3.500A) Processing helix chain 'V1' and resid 276 through 283 Processing helix chain 'V1' and resid 309 through 314 removed outlier: 4.504A pdb=" N THRV1 314 " --> pdb=" O SERV1 310 " (cutoff:3.500A) Processing helix chain 'V1' and resid 319 through 324 Processing helix chain 'V1' and resid 343 through 356 Processing helix chain 'V1' and resid 363 through 381 Processing helix chain 'V1' and resid 386 through 399 Processing helix chain 'V1' and resid 407 through 421 Proline residue: V1 414 - end of helix Processing helix chain 'V1' and resid 423 through 437 Processing helix chain 'V2' and resid 25 through 37 Processing helix chain 'V2' and resid 43 through 45 No H-bonds generated for 'chain 'V2' and resid 43 through 45' Processing helix chain 'V2' and resid 47 through 57 Processing helix chain 'V2' and resid 63 through 72 Processing helix chain 'V2' and resid 77 through 86 Processing helix chain 'V2' and resid 107 through 110 No H-bonds generated for 'chain 'V2' and resid 107 through 110' Processing helix chain 'V2' and resid 114 through 124 Processing helix chain 'V2' and resid 166 through 178 Processing helix chain 'S1' and resid 26 through 33 Processing helix chain 'S1' and resid 84 through 97 Processing helix chain 'S1' and resid 115 through 123 Processing helix chain 'S1' and resid 159 through 165 Processing helix chain 'S1' and resid 197 through 199 No H-bonds generated for 'chain 'S1' and resid 197 through 199' Processing helix chain 'S1' and resid 265 through 268 No H-bonds generated for 'chain 'S1' and resid 265 through 268' Processing helix chain 'S1' and resid 271 through 275 Processing helix chain 'S1' and resid 296 through 308 Processing helix chain 'S1' and resid 326 through 338 Processing helix chain 'S1' and resid 359 through 361 No H-bonds generated for 'chain 'S1' and resid 359 through 361' Processing helix chain 'S1' and resid 370 through 372 No H-bonds generated for 'chain 'S1' and resid 370 through 372' Processing helix chain 'S1' and resid 389 through 401 Processing helix chain 'S1' and resid 426 through 434 Processing helix chain 'S1' and resid 438 through 444 Processing helix chain 'S1' and resid 463 through 479 Processing helix chain 'S1' and resid 497 through 504 Processing helix chain 'S1' and resid 512 through 516 Processing helix chain 'S1' and resid 596 through 606 Processing helix chain 'S1' and resid 616 through 626 Processing helix chain 'S1' and resid 642 through 648 Processing helix chain 'S1' and resid 668 through 673 Processing helix chain 'S1' and resid 676 through 680 Processing helix chain 'S1' and resid 683 through 692 Processing helix chain 'S2' and resid 8 through 13 Processing helix chain 'S2' and resid 56 through 58 No H-bonds generated for 'chain 'S2' and resid 56 through 58' Processing helix chain 'S2' and resid 87 through 92 Processing helix chain 'S2' and resid 99 through 105 Processing helix chain 'S2' and resid 113 through 126 Processing helix chain 'S2' and resid 132 through 161 Processing helix chain 'S2' and resid 164 through 184 removed outlier: 4.067A pdb=" N PHES2 168 " --> pdb=" O METS2 164 " (cutoff:3.500A) Processing helix chain 'S2' and resid 208 through 229 Processing helix chain 'S2' and resid 233 through 238 Processing helix chain 'S2' and resid 247 through 252 Processing helix chain 'S2' and resid 257 through 262 removed outlier: 3.573A pdb=" N ARGS2 261 " --> pdb=" O VALS2 258 " (cutoff:3.500A) Processing helix chain 'S2' and resid 269 through 272 No H-bonds generated for 'chain 'S2' and resid 269 through 272' Processing helix chain 'S2' and resid 277 through 280 Processing helix chain 'S2' and resid 293 through 316 Processing helix chain 'S2' and resid 335 through 339 Processing helix chain 'S2' and resid 343 through 353 Processing helix chain 'S2' and resid 394 through 405 removed outlier: 3.794A pdb=" N GLYS2 401 " --> pdb=" O ALAS2 397 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEUS2 402 " --> pdb=" O HISS2 398 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASPS2 403 " --> pdb=" O LEUS2 399 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LYSS2 404 " --> pdb=" O ALAS2 400 " (cutoff:3.500A) Processing helix chain 'S2' and resid 411 through 419 Processing helix chain 'S3' and resid 16 through 32 Processing helix chain 'S3' and resid 57 through 64 Processing helix chain 'S3' and resid 120 through 122 No H-bonds generated for 'chain 'S3' and resid 120 through 122' Processing helix chain 'S3' and resid 125 through 137 removed outlier: 3.867A pdb=" N ASNS3 128 " --> pdb=" O LYSS3 125 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TRPS3 129 " --> pdb=" O ALAS3 126 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYRS3 130 " --> pdb=" O ALAS3 127 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N METS3 137 " --> pdb=" O ILES3 134 " (cutoff:3.500A) Processing helix chain 'S7' and resid 25 through 43 Processing helix chain 'S7' and resid 55 through 62 Processing helix chain 'S7' and resid 70 through 72 No H-bonds generated for 'chain 'S7' and resid 70 through 72' Processing helix chain 'S7' and resid 94 through 105 Proline residue: S7 98 - end of helix Processing helix chain 'S7' and resid 124 through 126 No H-bonds generated for 'chain 'S7' and resid 124 through 126' Processing helix chain 'S7' and resid 136 through 138 No H-bonds generated for 'chain 'S7' and resid 136 through 138' Processing helix chain 'S7' and resid 153 through 168 Processing helix chain 'S7' and resid 172 through 178 Processing helix chain 'S8' and resid 14 through 26 Processing helix chain 'S8' and resid 28 through 41 Processing helix chain 'S8' and resid 82 through 86 Processing helix chain 'S8' and resid 121 through 125 Processing helix chain 'S8' and resid 151 through 158 Processing helix chain 'S8' and resid 163 through 171 Processing helix chain 'V3' and resid 50 through 57 Processing helix chain 'S6' and resid 24 through 27 No H-bonds generated for 'chain 'S6' and resid 24 through 27' Processing helix chain 'S4' and resid 19 through 21 No H-bonds generated for 'chain 'S4' and resid 19 through 21' Processing helix chain 'S4' and resid 27 through 31 Processing helix chain 'S4' and resid 89 through 98 Processing helix chain 'S4' and resid 118 through 121 No H-bonds generated for 'chain 'S4' and resid 118 through 121' Processing helix chain 'A9' and resid 30 through 41 Processing helix chain 'A9' and resid 53 through 58 Processing helix chain 'A9' and resid 79 through 84 Processing helix chain 'A9' and resid 112 through 123 removed outlier: 3.788A pdb=" N ALAA9 116 " --> pdb=" O LYSA9 112 " (cutoff:3.500A) Processing helix chain 'A9' and resid 144 through 158 Processing helix chain 'A9' and resid 178 through 183 Processing helix chain 'A9' and resid 207 through 219 Processing helix chain 'A9' and resid 238 through 248 Processing helix chain 'A9' and resid 282 through 289 Processing helix chain 'A9' and resid 310 through 317 Processing helix chain 'A2' and resid 27 through 38 Processing helix chain 'A2' and resid 41 through 46 Processing helix chain 'A2' and resid 83 through 93 Processing helix chain 'A5' and resid 20 through 36 Processing helix chain 'A5' and resid 42 through 59 Processing helix chain 'A5' and resid 65 through 70 Processing helix chain 'A5' and resid 77 through 94 Processing helix chain 'A6' and resid 24 through 48 Proline residue: A6 43 - end of helix Processing helix chain 'A6' and resid 55 through 69 removed outlier: 4.150A pdb=" N ASNA6 69 " --> pdb=" O META6 65 " (cutoff:3.500A) Processing helix chain 'A6' and resid 75 through 93 Processing helix chain 'A6' and resid 99 through 105 Processing helix chain 'A6' and resid 119 through 122 No H-bonds generated for 'chain 'A6' and resid 119 through 122' Processing helix chain 'A7' and resid 5 through 14 Processing helix chain 'AL' and resid 3 through 16 removed outlier: 3.620A pdb=" N LEUAL 7 " --> pdb=" O LEUAL 3 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLNAL 12 " --> pdb=" O LYSAL 8 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLNAL 13 " --> pdb=" O ARGAL 9 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VALAL 14 " --> pdb=" O GLYAL 10 " (cutoff:3.500A) Processing helix chain 'AL' and resid 21 through 29 Processing helix chain 'AL' and resid 84 through 90 Processing helix chain 'AA' and resid 8 through 21 Processing helix chain 'AA' and resid 44 through 57 Processing helix chain 'AA' and resid 64 through 68 Processing helix chain 'AA' and resid 73 through 83 Processing helix chain 'D3' and resid 2 through 23 Processing helix chain 'D3' and resid 53 through 72 removed outlier: 4.477A pdb=" N VALD3 58 " --> pdb=" O LYSD3 54 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ALAD3 59 " --> pdb=" O PHED3 55 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILED3 60 " --> pdb=" O PHED3 56 " (cutoff:3.500A) Processing helix chain 'D3' and resid 75 through 78 No H-bonds generated for 'chain 'D3' and resid 75 through 78' Processing helix chain 'D3' and resid 84 through 107 Processing helix chain 'D1' and resid 2 through 10 Processing helix chain 'D1' and resid 12 through 31 Processing helix chain 'D1' and resid 46 through 57 Processing helix chain 'D1' and resid 68 through 85 Proline residue: D1 75 - end of helix Processing helix chain 'D1' and resid 102 through 122 Processing helix chain 'D1' and resid 126 through 155 removed outlier: 4.830A pdb=" N TYRD1 142 " --> pdb=" O GLND1 138 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLUD1 143 " --> pdb=" O THRD1 139 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VALD1 144 " --> pdb=" O ILED1 140 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N THRD1 145 " --> pdb=" O SERD1 141 " (cutoff:3.500A) Processing helix chain 'D1' and resid 163 through 170 removed outlier: 3.873A pdb=" N GLUD1 170 " --> pdb=" O ILED1 166 " (cutoff:3.500A) Processing helix chain 'D1' and resid 180 through 192 Processing helix chain 'D1' and resid 220 through 242 Processing helix chain 'D1' and resid 252 through 276 removed outlier: 4.043A pdb=" N SERD1 276 " --> pdb=" O TRPD1 272 " (cutoff:3.500A) Processing helix chain 'D1' and resid 282 through 311 Proline residue: D1 295 - end of helix Proline residue: D1 308 - end of helix Processing helix chain 'D6' and resid 5 through 21 Processing helix chain 'D6' and resid 26 through 47 Processing helix chain 'D6' and resid 52 through 59 removed outlier: 3.576A pdb=" N PHED6 57 " --> pdb=" O GLYD6 53 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEUD6 58 " --> pdb=" O LEUD6 54 " (cutoff:3.500A) Processing helix chain 'D6' and resid 65 through 75 Processing helix chain 'D6' and resid 87 through 108 Processing helix chain 'D6' and resid 139 through 148 removed outlier: 4.045A pdb=" N LEUD6 146 " --> pdb=" O GLYD6 142 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N TYRD6 147 " --> pdb=" O ILED6 143 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SERD6 148 " --> pdb=" O ALAD6 144 " (cutoff:3.500A) Processing helix chain 'D6' and resid 151 through 171 removed outlier: 3.695A pdb=" N ILED6 155 " --> pdb=" O THRD6 151 " (cutoff:3.500A) Processing helix chain '4L' and resid 4 through 20 Processing helix chain '4L' and resid 26 through 51 Processing helix chain '4L' and resid 59 through 84 Processing helix chain 'D5' and resid 2 through 23 removed outlier: 4.374A pdb=" N LEUD5 15 " --> pdb=" O THRD5 11 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THRD5 16 " --> pdb=" O LEUD5 12 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N METD5 17 " --> pdb=" O ILED5 13 " (cutoff:3.500A) Proline residue: D5 18 - end of helix Processing helix chain 'D5' and resid 32 through 57 removed outlier: 4.388A pdb=" N ILED5 49 " --> pdb=" O ILED5 45 " (cutoff:3.500A) Proline residue: D5 50 - end of helix Processing helix chain 'D5' and resid 84 through 88 Processing helix chain 'D5' and resid 90 through 107 Processing helix chain 'D5' and resid 114 through 133 Processing helix chain 'D5' and resid 137 through 157 Processing helix chain 'D5' and resid 162 through 193 Processing helix chain 'D5' and resid 198 through 203 Processing helix chain 'D5' and resid 210 through 223 Processing helix chain 'D5' and resid 232 through 238 Processing helix chain 'D5' and resid 241 through 248 Processing helix chain 'D5' and resid 254 through 262 removed outlier: 3.710A pdb=" N PHED5 258 " --> pdb=" O ALAD5 255 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEUD5 259 " --> pdb=" O GLYD5 256 " (cutoff:3.500A) Processing helix chain 'D5' and resid 264 through 268 Processing helix chain 'D5' and resid 271 through 292 Processing helix chain 'D5' and resid 298 through 318 Processing helix chain 'D5' and resid 322 through 349 Processing helix chain 'D5' and resid 368 through 379 Processing helix chain 'D5' and resid 387 through 400 removed outlier: 3.978A pdb=" N SERD5 391 " --> pdb=" O THRD5 387 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYSD5 392 " --> pdb=" O GLYD5 388 " (cutoff:3.500A) Processing helix chain 'D5' and resid 408 through 430 Processing helix chain 'D5' and resid 448 through 460 Processing helix chain 'D5' and resid 464 through 470 Processing helix chain 'D5' and resid 489 through 509 Processing helix chain 'D5' and resid 519 through 524 Processing helix chain 'D5' and resid 526 through 547 removed outlier: 4.084A pdb=" N TYRD5 529 " --> pdb=" O LEUD5 526 " (cutoff:3.500A) Proline residue: D5 530 - end of helix removed outlier: 3.679A pdb=" N METD5 533 " --> pdb=" O PROD5 530 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HISD5 534 " --> pdb=" O THRD5 531 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEUD5 536 " --> pdb=" O METD5 533 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N THRD5 537 " --> pdb=" O HISD5 534 " (cutoff:3.500A) Proline residue: D5 538 - end of helix removed outlier: 3.770A pdb=" N LEUD5 542 " --> pdb=" O TYRD5 539 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SERD5 545 " --> pdb=" O LEUD5 542 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYSD5 547 " --> pdb=" O METD5 544 " (cutoff:3.500A) Processing helix chain 'D5' and resid 555 through 561 Processing helix chain 'D5' and resid 563 through 577 Processing helix chain 'D5' and resid 585 through 599 Processing helix chain 'D4' and resid 2 through 16 Proline residue: D4 7 - end of helix removed outlier: 3.865A pdb=" N METD4 12 " --> pdb=" O THRD4 8 " (cutoff:3.500A) Proline residue: D4 13 - end of helix Processing helix chain 'D4' and resid 23 through 41 removed outlier: 4.086A pdb=" N LEUD4 41 " --> pdb=" O THRD4 37 " (cutoff:3.500A) Processing helix chain 'D4' and resid 63 through 79 Proline residue: D4 74 - end of helix Processing helix chain 'D4' and resid 89 through 110 Processing helix chain 'D4' and resid 115 through 135 Proline residue: D4 128 - end of helix removed outlier: 3.873A pdb=" N ILED4 131 " --> pdb=" O VALD4 127 " (cutoff:3.500A) Processing helix chain 'D4' and resid 142 through 156 Processing helix chain 'D4' and resid 159 through 171 Processing helix chain 'D4' and resid 176 through 179 No H-bonds generated for 'chain 'D4' and resid 176 through 179' Processing helix chain 'D4' and resid 190 through 206 Processing helix chain 'D4' and resid 210 through 221 removed outlier: 5.783A pdb=" N LEUD4 214 " --> pdb=" O GLYD4 211 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TRPD4 215 " --> pdb=" O LEUD4 212 " (cutoff:3.500A) Proline residue: D4 217 - end of helix Processing helix chain 'D4' and resid 225 through 248 removed outlier: 4.758A pdb=" N LEUD4 248 " --> pdb=" O METD4 244 " (cutoff:3.500A) Processing helix chain 'D4' and resid 254 through 257 No H-bonds generated for 'chain 'D4' and resid 254 through 257' Processing helix chain 'D4' and resid 259 through 277 removed outlier: 3.973A pdb=" N LEUD4 277 " --> pdb=" O SERD4 273 " (cutoff:3.500A) Processing helix chain 'D4' and resid 282 through 302 removed outlier: 3.541A pdb=" N ILED4 286 " --> pdb=" O LYSD4 283 " (cutoff:3.500A) Processing helix chain 'D4' and resid 306 through 336 Processing helix chain 'D4' and resid 355 through 366 Processing helix chain 'D4' and resid 373 through 388 Processing helix chain 'D4' and resid 393 through 414 removed outlier: 4.171A pdb=" N THRD4 414 " --> pdb=" O METD4 410 " (cutoff:3.500A) Processing helix chain 'D4' and resid 431 through 449 Proline residue: D4 443 - end of helix Processing helix chain 'D2' and resid 3 through 22 Processing helix chain 'D2' and resid 26 through 40 Processing helix chain 'D2' and resid 50 through 79 Processing helix chain 'D2' and resid 92 through 106 Processing helix chain 'D2' and resid 112 through 119 Proline residue: D2 116 - end of helix Processing helix chain 'D2' and resid 124 through 148 Proline residue: D2 138 - end of helix removed outlier: 3.970A pdb=" N VALD2 141 " --> pdb=" O ALAD2 137 " (cutoff:3.500A) Proline residue: D2 147 - end of helix Processing helix chain 'D2' and resid 151 through 167 Processing helix chain 'D2' and resid 175 through 192 Processing helix chain 'D2' and resid 198 through 220 Processing helix chain 'D2' and resid 227 through 236 Processing helix chain 'D2' and resid 239 through 252 Processing helix chain 'D2' and resid 260 through 271 Processing helix chain 'D2' and resid 277 through 300 removed outlier: 4.246A pdb=" N LEUD2 290 " --> pdb=" O ALAD2 286 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYRD2 291 " --> pdb=" O LEUD2 287 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N PHED2 292 " --> pdb=" O LEUD2 288 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N TYRD2 293 " --> pdb=" O ASND2 289 " (cutoff:3.500A) Processing helix chain 'D2' and resid 311 through 316 removed outlier: 4.355A pdb=" N GLND2 316 " --> pdb=" O LYSD2 312 " (cutoff:3.500A) Processing helix chain 'D2' and resid 327 through 334 Processing helix chain 'D2' and resid 340 through 345 removed outlier: 4.383A pdb=" N SERD2 344 " --> pdb=" O PROD2 341 " (cutoff:3.500A) Processing helix chain 'AK' and resid 2 through 10 Processing helix chain 'AK' and resid 19 through 41 Processing helix chain 'AK' and resid 48 through 80 Processing helix chain 'AK' and resid 87 through 104 Processing helix chain 'AK' and resid 108 through 130 Processing helix chain 'B5' and resid 16 through 32 removed outlier: 5.052A pdb=" N THRB5 32 " --> pdb=" O TYRB5 28 " (cutoff:3.500A) Processing helix chain 'B5' and resid 34 through 46 Processing helix chain 'B5' and resid 70 through 78 Processing helix chain 'B5' and resid 83 through 117 Processing helix chain 'AB' and resid 8 through 21 Processing helix chain 'AB' and resid 27 through 29 No H-bonds generated for 'chain 'AB' and resid 27 through 29' Processing helix chain 'AB' and resid 44 through 58 Processing helix chain 'AB' and resid 64 through 66 No H-bonds generated for 'chain 'AB' and resid 64 through 66' Processing helix chain 'AB' and resid 73 through 83 Processing helix chain 'A8' and resid 21 through 26 Processing helix chain 'A8' and resid 28 through 33 Processing helix chain 'A8' and resid 39 through 48 Processing helix chain 'A8' and resid 56 through 75 Processing helix chain 'A8' and resid 80 through 89 Processing helix chain 'A8' and resid 101 through 113 Processing helix chain 'BJ' and resid 28 through 55 removed outlier: 4.944A pdb=" N ARGBJ 42 " --> pdb=" O LEUBJ 38 " (cutoff:3.500A) Proline residue: BJ 43 - end of helix Processing helix chain 'BJ' and resid 81 through 115 removed outlier: 5.139A pdb=" N GLUBJ 86 " --> pdb=" O LEUBJ 82 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 125 through 142 Processing helix chain 'BJ' and resid 152 through 172 Processing helix chain 'AJ' and resid 5 through 10 Processing helix chain 'AJ' and resid 36 through 46 Processing helix chain 'AJ' and resid 56 through 61 removed outlier: 4.385A pdb=" N ALAAJ 59 " --> pdb=" O ILEAJ 56 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 71 through 74 No H-bonds generated for 'chain 'AJ' and resid 71 through 74' Processing helix chain 'AJ' and resid 79 through 84 Processing helix chain 'AJ' and resid 94 through 116 Processing helix chain 'AJ' and resid 128 through 140 Processing helix chain 'AJ' and resid 146 through 162 removed outlier: 4.159A pdb=" N CYSAJ 161 " --> pdb=" O LYSAJ 157 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLUAJ 162 " --> pdb=" O VALAJ 158 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 176 through 186 Processing helix chain 'AJ' and resid 189 through 192 No H-bonds generated for 'chain 'AJ' and resid 189 through 192' Processing helix chain 'AJ' and resid 196 through 208 Processing helix chain 'AJ' and resid 210 through 214 Processing helix chain 'AJ' and resid 232 through 239 Processing helix chain 'AJ' and resid 247 through 249 No H-bonds generated for 'chain 'AJ' and resid 247 through 249' Processing helix chain 'AJ' and resid 254 through 263 Processing helix chain 'AJ' and resid 267 through 272 removed outlier: 5.010A pdb=" N TYRAJ 272 " --> pdb=" O GLUAJ 268 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 286 through 297 Processing helix chain 'S5' and resid 5 through 8 No H-bonds generated for 'chain 'S5' and resid 5 through 8' Processing helix chain 'S5' and resid 15 through 17 No H-bonds generated for 'chain 'S5' and resid 15 through 17' Processing helix chain 'S5' and resid 33 through 42 Processing helix chain 'S5' and resid 50 through 54 Processing helix chain 'S5' and resid 56 through 67 Processing helix chain 'S5' and resid 69 through 88 Processing helix chain 'A3' and resid 11 through 13 No H-bonds generated for 'chain 'A3' and resid 11 through 13' Processing helix chain 'A3' and resid 16 through 30 Processing helix chain 'A3' and resid 38 through 46 Processing helix chain 'B3' and resid 26 through 38 Processing helix chain 'B3' and resid 49 through 52 No H-bonds generated for 'chain 'B3' and resid 49 through 52' Processing helix chain 'B3' and resid 62 through 68 removed outlier: 3.779A pdb=" N LEUB3 66 " --> pdb=" O PHEB3 62 " (cutoff:3.500A) Processing helix chain 'B3' and resid 70 through 82 removed outlier: 4.101A pdb=" N PHEB3 74 " --> pdb=" O PHEB3 70 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ALAB3 75 " --> pdb=" O LYSB3 71 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALAB3 76 " --> pdb=" O TRPB3 72 " (cutoff:3.500A) Processing helix chain 'C2' and resid 17 through 20 Processing helix chain 'C2' and resid 29 through 48 Processing helix chain 'C2' and resid 58 through 96 Processing helix chain 'B4' and resid 26 through 49 Processing helix chain 'B4' and resid 62 through 72 Processing helix chain 'B4' and resid 83 through 116 removed outlier: 3.519A pdb=" N ILEB4 94 " --> pdb=" O ALAB4 90 " (cutoff:3.500A) Proline residue: B4 96 - end of helix Processing helix chain 'AM' and resid 32 through 69 Processing helix chain 'AM' and resid 71 through 96 Processing helix chain 'AM' and resid 130 through 136 Processing helix chain 'B6' and resid 5 through 25 Processing helix chain 'B6' and resid 68 through 84 Proline residue: B6 77 - end of helix Processing helix chain 'B6' and resid 87 through 91 Processing helix chain 'B7' and resid 2 through 9 Processing helix chain 'B7' and resid 42 through 47 Processing helix chain 'B7' and resid 59 through 71 Processing helix chain 'B7' and resid 81 through 118 Processing helix chain 'B9' and resid 11 through 29 Processing helix chain 'B9' and resid 34 through 47 Processing helix chain 'B9' and resid 57 through 73 Processing helix chain 'B9' and resid 94 through 96 No H-bonds generated for 'chain 'B9' and resid 94 through 96' Processing helix chain 'B9' and resid 108 through 113 Processing helix chain 'B9' and resid 115 through 130 Processing helix chain 'B9' and resid 134 through 142 Processing helix chain 'B9' and resid 167 through 170 No H-bonds generated for 'chain 'B9' and resid 167 through 170' Processing helix chain 'B2' and resid 19 through 41 Processing helix chain 'B8' and resid 5 through 7 No H-bonds generated for 'chain 'B8' and resid 5 through 7' Processing helix chain 'B8' and resid 18 through 26 Processing helix chain 'B8' and resid 60 through 62 No H-bonds generated for 'chain 'B8' and resid 60 through 62' Processing helix chain 'B8' and resid 81 through 84 No H-bonds generated for 'chain 'B8' and resid 81 through 84' Processing helix chain 'B8' and resid 99 through 121 Processing helix chain 'BK' and resid 53 through 63 Processing helix chain 'BK' and resid 70 through 78 Processing helix chain 'BK' and resid 87 through 101 Processing helix chain 'C1' and resid 14 through 45 Processing helix chain 'B1' and resid 15 through 33 Processing helix chain 'A1' and resid 5 through 29 Proline residue: A1 19 - end of helix Processing helix chain 'A1' and resid 42 through 53 Processing helix chain 'A1' and resid 60 through 62 No H-bonds generated for 'chain 'A1' and resid 60 through 62' Processing sheet with id= A, first strand: chain 'V1' and resid 220 through 224 removed outlier: 6.566A pdb=" N TYRV1 92 " --> pdb=" O THRV1 221 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ALAV1 223 " --> pdb=" O TYRV1 92 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VALV1 94 " --> pdb=" O ALAV1 223 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALAV1 133 " --> pdb=" O LEUV1 93 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N VALV1 95 " --> pdb=" O ALAV1 133 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TYRV1 135 " --> pdb=" O VALV1 95 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ALAV1 97 " --> pdb=" O TYRV1 135 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N TYRV1 137 " --> pdb=" O ALAV1 97 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASPV1 174 " --> pdb=" O ALAV1 134 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILEV1 136 " --> pdb=" O ASPV1 174 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHEV1 176 " --> pdb=" O ILEV1 136 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILEV1 138 " --> pdb=" O PHEV1 176 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VALV1 178 " --> pdb=" O ILEV1 138 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'V1' and resid 254 through 258 Processing sheet with id= C, first strand: chain 'V1' and resid 294 through 298 removed outlier: 6.577A pdb=" N METV1 337 " --> pdb=" O LEUV1 295 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VALV1 297 " --> pdb=" O ILEV1 335 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILEV1 335 " --> pdb=" O VALV1 297 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'V2' and resid 138 through 142 Processing sheet with id= E, first strand: chain 'S1' and resid 16 through 20 removed outlier: 6.446A pdb=" N TRPS1 77 " --> pdb=" O PHES1 12 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'S1' and resid 146 through 148 Processing sheet with id= G, first strand: chain 'S1' and resid 173 through 177 Processing sheet with id= H, first strand: chain 'S1' and resid 223 through 228 Processing sheet with id= I, first strand: chain 'S1' and resid 283 through 286 Processing sheet with id= J, first strand: chain 'S1' and resid 342 through 345 removed outlier: 6.433A pdb=" N METS1 521 " --> pdb=" O ALAS1 316 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILES1 318 " --> pdb=" O METS1 521 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N PHES1 523 " --> pdb=" O ILES1 318 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VALS1 559 " --> pdb=" O TYRS1 545 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLYS1 547 " --> pdb=" O VALS1 559 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEUS1 561 " --> pdb=" O GLYS1 547 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S1' and resid 490 through 492 removed outlier: 7.299A pdb=" N ASNS1 491 " --> pdb=" O PROS1 449 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N VALS1 451 " --> pdb=" O ASNS1 491 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VALS1 376 " --> pdb=" O METS1 450 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VALS1 452 " --> pdb=" O VALS1 376 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEUS1 378 " --> pdb=" O VALS1 452 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LYSS1 405 " --> pdb=" O VALS1 377 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEUS1 379 " --> pdb=" O LYSS1 405 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALAS1 407 " --> pdb=" O LEUS1 379 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASPS1 420 " --> pdb=" O LEUS1 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'S1' and resid 572 through 574 Processing sheet with id= M, first strand: chain 'S2' and resid 47 through 51 Processing sheet with id= N, first strand: chain 'S2' and resid 361 through 368 Processing sheet with id= O, first strand: chain 'S3' and resid 74 through 76 removed outlier: 6.784A pdb=" N LEUS3 48 " --> pdb=" O ARGS3 106 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LYSS3 108 " --> pdb=" O LEUS3 48 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILES3 50 " --> pdb=" O LYSS3 108 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N TYRS3 110 " --> pdb=" O ILES3 50 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILES3 52 " --> pdb=" O TYRS3 110 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'S3' and resid 173 through 177 Processing sheet with id= Q, first strand: chain 'S7' and resid 47 through 49 removed outlier: 7.117A pdb=" N VALS7 85 " --> pdb=" O METS7 48 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TYRS7 112 " --> pdb=" O METS7 86 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VALS7 88 " --> pdb=" O TYRS7 112 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VALS7 114 " --> pdb=" O VALS7 88 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILES7 144 " --> pdb=" O SERS7 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'S8' and resid 93 through 96 Processing sheet with id= S, first strand: chain 'S6' and resid 56 through 59 Processing sheet with id= T, first strand: chain 'S4' and resid 102 through 106 Processing sheet with id= U, first strand: chain 'A9' and resid 90 through 92 removed outlier: 6.445A pdb=" N GLNA9 44 " --> pdb=" O ALAA9 21 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VALA9 23 " --> pdb=" O GLNA9 44 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILEA9 46 " --> pdb=" O VALA9 23 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A9' and resid 130 through 134 removed outlier: 6.405A pdb=" N THRA9 164 " --> pdb=" O HISA9 131 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N SERA9 133 " --> pdb=" O THRA9 164 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILEA9 166 " --> pdb=" O SERA9 133 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'A2' and resid 53 through 56 Processing sheet with id= X, first strand: chain 'AL' and resid 40 through 42 Processing sheet with id= Y, first strand: chain 'D5' and resid 61 through 67 Processing sheet with id= Z, first strand: chain 'AJ' and resid 122 through 125 removed outlier: 6.843A pdb=" N VALAJ 168 " --> pdb=" O THRAJ 26 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ASPAJ 28 " --> pdb=" O VALAJ 168 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ILEAJ 170 " --> pdb=" O ASPAJ 28 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLUAJ 219 " --> pdb=" O VALAJ 169 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N TYRAJ 171 " --> pdb=" O GLUAJ 219 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEUAJ 221 " --> pdb=" O TYRAJ 171 " (cutoff:3.500A) 2748 hydrogen bonds defined for protein. 8001 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 19.99 Time building geometry restraints manager: 22.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.42: 27759 1.42 - 1.64: 38465 1.64 - 1.86: 750 1.86 - 2.09: 0 2.09 - 2.31: 80 Bond restraints: 67054 Sorted by residual: bond pdb=" C16 ZMPAA 101 " pdb=" N2 ZMPAA 101 " ideal model delta sigma weight residual 1.452 1.336 0.116 2.00e-02 2.50e+03 3.35e+01 bond pdb=" C16 ZMPAB 101 " pdb=" N2 ZMPAB 101 " ideal model delta sigma weight residual 1.452 1.337 0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" O2B NDPA9 401 " pdb=" P2B NDPA9 401 " ideal model delta sigma weight residual 1.833 1.626 0.207 3.80e-02 6.93e+02 2.97e+01 bond pdb=" C13 ZMPAA 101 " pdb=" N1 ZMPAA 101 " ideal model delta sigma weight residual 1.451 1.342 0.109 2.00e-02 2.50e+03 2.94e+01 bond pdb=" O5D NDPA9 401 " pdb=" PN NDPA9 401 " ideal model delta sigma weight residual 1.757 1.567 0.190 3.50e-02 8.16e+02 2.93e+01 ... (remaining 67049 not shown) Histogram of bond angle deviations from ideal: 69.91 - 83.85: 72 83.85 - 97.80: 20 97.80 - 111.75: 30837 111.75 - 125.69: 58401 125.69 - 139.64: 1602 Bond angle restraints: 90932 Sorted by residual: angle pdb=" S1 FESS1 803 " pdb="FE2 FESS1 803 " pdb=" S2 FESS1 803 " ideal model delta sigma weight residual 104.33 91.88 12.45 1.14e+00 7.69e-01 1.19e+02 angle pdb="FE1 FESS1 803 " pdb=" S2 FESS1 803 " pdb="FE2 FESS1 803 " ideal model delta sigma weight residual 75.66 87.65 -11.99 1.14e+00 7.69e-01 1.11e+02 angle pdb=" S1 FESS1 803 " pdb="FE1 FESS1 803 " pdb=" S2 FESS1 803 " ideal model delta sigma weight residual 104.33 92.12 12.21 1.20e+00 6.94e-01 1.04e+02 angle pdb=" S1 FESV2 300 " pdb="FE2 FESV2 300 " pdb=" S2 FESV2 300 " ideal model delta sigma weight residual 104.33 92.80 11.53 1.14e+00 7.69e-01 1.02e+02 angle pdb="FE1 FESV2 300 " pdb=" S2 FESV2 300 " pdb="FE2 FESV2 300 " ideal model delta sigma weight residual 75.66 87.17 -11.51 1.14e+00 7.69e-01 1.02e+02 ... (remaining 90927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.97: 39444 28.97 - 57.95: 844 57.95 - 86.92: 68 86.92 - 115.89: 2 115.89 - 144.87: 1 Dihedral angle restraints: 40359 sinusoidal: 16786 harmonic: 23573 Sorted by residual: dihedral pdb=" CA HISS2 55 " pdb=" C HISS2 55 " pdb=" N PROS2 56 " pdb=" CA PROS2 56 " ideal model delta harmonic sigma weight residual -180.00 -116.98 -63.02 0 5.00e+00 4.00e-02 1.59e+02 dihedral pdb=" CA METD1 91 " pdb=" C METD1 91 " pdb=" N PROD1 92 " pdb=" CA PROD1 92 " ideal model delta harmonic sigma weight residual -180.00 -123.19 -56.81 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" CA ALAD5 365 " pdb=" C ALAD5 365 " pdb=" N METD5 366 " pdb=" CA METD5 366 " ideal model delta harmonic sigma weight residual -180.00 -124.09 -55.91 0 5.00e+00 4.00e-02 1.25e+02 ... (remaining 40356 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.222: 9968 4.222 - 8.443: 0 8.443 - 12.665: 0 12.665 - 16.886: 0 16.886 - 21.108: 24 Chirality restraints: 9992 Sorted by residual: chirality pdb="FE4 SF4V1 500 " pdb=" S1 SF4V1 500 " pdb=" S2 SF4V1 500 " pdb=" S3 SF4V1 500 " both_signs ideal model delta sigma weight residual False 10.55 -10.55 21.11 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE2 SF4S8 202 " pdb=" S1 SF4S8 202 " pdb=" S3 SF4S8 202 " pdb=" S4 SF4S8 202 " both_signs ideal model delta sigma weight residual False 10.55 -10.54 21.10 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE3 SF4S8 202 " pdb=" S1 SF4S8 202 " pdb=" S2 SF4S8 202 " pdb=" S4 SF4S8 202 " both_signs ideal model delta sigma weight residual False -10.55 10.53 -21.08 2.00e-01 2.50e+01 1.11e+04 ... (remaining 9989 not shown) Planarity restraints: 11488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMNV1 501 " -0.047 2.00e-02 2.50e+03 3.00e-02 4.27e+01 pdb=" C10 FMNV1 501 " 0.057 2.00e-02 2.50e+03 pdb=" C2 FMNV1 501 " -0.006 2.00e-02 2.50e+03 pdb=" C4 FMNV1 501 " 0.012 2.00e-02 2.50e+03 pdb=" C4A FMNV1 501 " 0.042 2.00e-02 2.50e+03 pdb=" C5A FMNV1 501 " -0.011 2.00e-02 2.50e+03 pdb=" C6 FMNV1 501 " -0.036 2.00e-02 2.50e+03 pdb=" C7 FMNV1 501 " -0.025 2.00e-02 2.50e+03 pdb=" C7M FMNV1 501 " -0.011 2.00e-02 2.50e+03 pdb=" C8 FMNV1 501 " -0.003 2.00e-02 2.50e+03 pdb=" C8M FMNV1 501 " 0.013 2.00e-02 2.50e+03 pdb=" C9 FMNV1 501 " 0.009 2.00e-02 2.50e+03 pdb=" C9A FMNV1 501 " 0.009 2.00e-02 2.50e+03 pdb=" N1 FMNV1 501 " 0.033 2.00e-02 2.50e+03 pdb=" N10 FMNV1 501 " 0.036 2.00e-02 2.50e+03 pdb=" N3 FMNV1 501 " -0.007 2.00e-02 2.50e+03 pdb=" N5 FMNV1 501 " 0.009 2.00e-02 2.50e+03 pdb=" O2 FMNV1 501 " -0.068 2.00e-02 2.50e+03 pdb=" O4 FMNV1 501 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHED4 52 " 0.027 2.00e-02 2.50e+03 5.35e-02 2.86e+01 pdb=" C PHED4 52 " -0.093 2.00e-02 2.50e+03 pdb=" O PHED4 52 " 0.034 2.00e-02 2.50e+03 pdb=" N SERD4 53 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SERA7 70 " -0.024 2.00e-02 2.50e+03 4.71e-02 2.22e+01 pdb=" C SERA7 70 " 0.081 2.00e-02 2.50e+03 pdb=" O SERA7 70 " -0.031 2.00e-02 2.50e+03 pdb=" N SERA7 71 " -0.027 2.00e-02 2.50e+03 ... (remaining 11485 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 841 2.64 - 3.20: 58403 3.20 - 3.77: 104476 3.77 - 4.33: 135034 4.33 - 4.90: 215730 Nonbonded interactions: 514484 Sorted by model distance: nonbonded pdb=" CA ALAS3 80 " pdb=" O GLUS3 91 " model vdw 2.069 3.470 nonbonded pdb=" OG1 THRS6 12 " pdb=" O THRS6 14 " model vdw 2.186 2.440 nonbonded pdb=" O GLNS3 38 " pdb=" CA SERA7 70 " model vdw 2.206 3.470 nonbonded pdb=" O SERD1 119 " pdb=" OG SERD1 123 " model vdw 2.230 2.440 nonbonded pdb=" O LYSB6 92 " pdb=" OG1 THRB6 95 " model vdw 2.233 2.440 ... (remaining 514479 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'AA' and (resid 5 through 84 or (resid 101 and (name C10 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C20 or name C21 or name C3 or name C4 or name C5 \ or name C6 or name C7 or name C8 or name C9 or name N1 or name N2 or name O1 or \ name O2 or name O3 or name O4 or name O5 or name O6 or name O7 or name P1 or nam \ e S1 )))) selection = (chain 'AB' and (resid 5 through 84 or resid 101)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.550 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: 0.090 Extract box with map and model: 29.100 Check model and map are aligned: 0.730 Set scattering table: 0.460 Process input model: 148.850 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.240 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: 0.020 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 191.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 : 0.008 0.207 67054 Z= 0.531 Angle : 1.258 19.196 90932 Z= 0.663 Chirality : 1.031 21.108 9992 Planarity : 0.009 0.091 11488 Dihedral : 11.927 144.865 25115 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.91 % Favored : 88.03 % Rotamer: Outliers : 0.57 % Allowed : 6.40 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.36 % Twisted Proline : 1.88 % Twisted General : 0.49 % 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: -4.06 (0.07), residues: 7988 helix: -1.95 (0.06), residues: 4118 sheet: -2.15 (0.24), residues: 374 loop : -3.70 (0.09), residues: 3496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.004 TRPV1 413 HIS 0.018 0.003 HISV2 42 PHE 0.046 0.004 PHES2 171 TYR 0.063 0.003 TYRS7 125 ARG 0.023 0.001 ARGS1 253 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15976 Ramachandran restraints generated. 7988 Oldfield, 0 Emsley, 7988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15976 Ramachandran restraints generated. 7988 Oldfield, 0 Emsley, 7988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3053 residues out of total 7076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 3013 time to evaluate : 5.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 5 residues processed: 3031 average time/residue: 0.6722 time to fit residues: 3368.3621 Evaluate side-chains 1789 residues out of total 7076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1784 time to evaluate : 5.632 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4699 time to fit residues: 12.2000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 665 optimal weight: 4.9990 chunk 597 optimal weight: 10.0000 chunk 331 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 402 optimal weight: 0.9980 chunk 319 optimal weight: 20.0000 chunk 617 optimal weight: 4.9990 chunk 239 optimal weight: 6.9990 chunk 375 optimal weight: 0.7980 chunk 459 optimal weight: 0.0870 chunk 715 optimal weight: 30.0000 overall best weight: 1.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1 113 HIS V1 150 GLN V1 373 ASN V2 9 HIS V2 42 HIS ** V2 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 198 ASN S1 365 ASN S1 392 ASN ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 665 GLN S1 682 GLN S2 3 GLN S2 50 ASN S2 59 HIS S2 135 GLN S2 190 HIS S2 347 HIS S3 88 ASN ** S3 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 6 ASN S8 90 GLN V3 55 ASN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S6 94 GLN ** S4 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 3 HIS A9 37 HIS A9 148 ASN ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 44 ASN A6 98 GLN A6 125 HIS ** A7 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 17 HIS AL 31 ASN ** D3 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D6 175 ASN D5 136 ASN ** D5 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 332 HIS ** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 484 HIS D5 570 GLN D4 43 ASN D4 81 GLN D4 88 ASN D4 168 GLN D4 180 GLN ** D4 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4 434 ASN D4 440 HIS D2 134 GLN ** D2 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 289 ASN D2 316 GLN B5 69 HIS B5 86 ASN ** B5 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 63 ASN A8 105 GLN ** BJ 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 200 GLN AJ 251 GLN S5 33 HIS ** S5 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S5 97 HIS A3 10 ASN ** A3 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 53 ASN AM 75 GLN B6 82 HIS B7 49 GLN B7 81 HIS B7 83 GLN B7 91 HIS B9 32 HIS ** B9 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2 13 GLN BK 45 HIS ** B1 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1 40 HIS Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.275 67054 Z= 0.549 Angle : 1.692 51.597 90932 Z= 1.072 Chirality : 0.308 6.604 9992 Planarity : 0.006 0.089 11488 Dihedral : 8.902 130.662 9106 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 0.23 % Allowed : 4.71 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.37 % Twisted Proline : 0.83 % Twisted General : 0.24 % 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: -2.66 (0.09), residues: 7988 helix: -0.48 (0.07), residues: 4109 sheet: -2.13 (0.24), residues: 371 loop : -3.40 (0.09), residues: 3508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRPD2 234 HIS 0.014 0.001 HISD1 287 PHE 0.029 0.002 PHE4L 66 TYR 0.038 0.002 TYRAK 89 ARG 0.009 0.001 ARGAL 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15976 Ramachandran restraints generated. 7988 Oldfield, 0 Emsley, 7988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15976 Ramachandran restraints generated. 7988 Oldfield, 0 Emsley, 7988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2293 residues out of total 7076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 2277 time to evaluate : 5.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 2 residues processed: 2286 average time/residue: 0.6184 time to fit residues: 2413.7352 Evaluate side-chains 1735 residues out of total 7076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1733 time to evaluate : 5.704 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4510 time to fit residues: 9.3448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 397 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 595 optimal weight: 10.0000 chunk 487 optimal weight: 2.9990 chunk 197 optimal weight: 0.9980 chunk 716 optimal weight: 10.0000 chunk 774 optimal weight: 2.9990 chunk 638 optimal weight: 6.9990 chunk 710 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 575 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 119 GLN ** S1 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 392 ASN ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S3 192 GLN ** S7 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 6 ASN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 46 GLN A9 119 GLN A9 288 HIS ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 44 ASN A7 20 GLN ** A7 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 80 GLN ** D1 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4L 92 ASN ** D5 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 541 ASN D5 570 GLN D4 168 GLN ** D4 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4 304 GLN D4 338 HIS ** D4 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN D2 289 ASN A8 63 ASN ** BJ 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 258 ASN AJ 271 ASN S5 81 GLN S5 97 HIS ** B4 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B6 73 HIS ** B9 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2 21 GLN ** B8 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 51 ASN A1 40 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.238 67054 Z= 0.563 Angle : 1.687 50.981 90932 Z= 1.069 Chirality : 0.310 6.405 9992 Planarity : 0.006 0.110 11488 Dihedral : 8.466 118.045 9106 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.03 % Favored : 88.95 % Rotamer: Outliers : 0.11 % Allowed : 5.24 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.37 % Twisted Proline : 0.83 % Twisted General : 0.24 % 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: -2.11 (0.09), residues: 7988 helix: 0.08 (0.08), residues: 4100 sheet: -1.91 (0.25), residues: 366 loop : -3.27 (0.09), residues: 3522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRPD2 234 HIS 0.014 0.002 HISD4 440 PHE 0.033 0.002 PHED3 55 TYR 0.038 0.002 TYRAK 89 ARG 0.009 0.001 ARGB8 58 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15976 Ramachandran restraints generated. 7988 Oldfield, 0 Emsley, 7988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15976 Ramachandran restraints generated. 7988 Oldfield, 0 Emsley, 7988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2071 residues out of total 7076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 2063 time to evaluate : 5.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 2067 average time/residue: 0.6128 time to fit residues: 2167.6073 Evaluate side-chains 1630 residues out of total 7076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1629 time to evaluate : 5.795 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4661 time to fit residues: 8.5810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 708 optimal weight: 4.9990 chunk 538 optimal weight: 0.9980 chunk 372 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 342 optimal weight: 5.9990 chunk 481 optimal weight: 0.6980 chunk 719 optimal weight: 4.9990 chunk 761 optimal weight: 9.9990 chunk 375 optimal weight: 2.9990 chunk 681 optimal weight: 10.0000 chunk 205 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V1 373 ASN S1 198 ASN ** S1 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 392 ASN ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 6 ASN S8 90 GLN V3 55 ASN ** S6 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A9 288 HIS A2 80 ASN ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 44 ASN ** A7 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4L 50 ASN 4L 92 ASN 4L 97 GLN D5 67 HIS D5 205 ASN ** D5 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 509 HIS ** D5 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 279 GLN ** D4 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2 144 GLN ** D2 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN D2 289 ASN A8 63 ASN ** BJ 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 271 ASN S5 97 HIS ** B4 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B6 73 HIS ** B9 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B8 97 ASN ** B1 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1 40 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.243 67054 Z= 0.543 Angle : 1.673 50.785 90932 Z= 1.062 Chirality : 0.312 6.361 9992 Planarity : 0.006 0.097 11488 Dihedral : 8.208 103.611 9106 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.38 % Favored : 89.61 % Rotamer: Outliers : 0.08 % Allowed : 3.60 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.37 % Twisted Proline : 0.83 % Twisted General : 0.21 % 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: -1.86 (0.09), residues: 7988 helix: 0.30 (0.08), residues: 4124 sheet: -1.92 (0.25), residues: 375 loop : -3.19 (0.10), residues: 3489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRPB3 50 HIS 0.011 0.001 HISD4 440 PHE 0.030 0.002 PHEB8 111 TYR 0.036 0.002 TYRD5 422 ARG 0.009 0.001 ARGV1 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15976 Ramachandran restraints generated. 7988 Oldfield, 0 Emsley, 7988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15976 Ramachandran restraints generated. 7988 Oldfield, 0 Emsley, 7988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2075 residues out of total 7076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 2069 time to evaluate : 5.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 2072 average time/residue: 0.6115 time to fit residues: 2181.9863 Evaluate side-chains 1650 residues out of total 7076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1648 time to evaluate : 5.629 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4565 time to fit residues: 9.3769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 634 optimal weight: 7.9990 chunk 432 optimal weight: 0.3980 chunk 11 optimal weight: 6.9990 chunk 567 optimal weight: 6.9990 chunk 314 optimal weight: 1.9990 chunk 649 optimal weight: 9.9990 chunk 526 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 388 optimal weight: 9.9990 chunk 683 optimal weight: 5.9990 chunk 192 optimal weight: 0.8980 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 392 ASN S1 421 HIS ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 581 GLN ** S3 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 6 ASN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A9 288 HIS A6 44 ASN ** A7 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 59 HIS D3 80 GLN ** D1 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 157 ASN D6 120 ASN 4L 92 ASN D5 115 ASN ** D5 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 309 GLN ** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 43 ASN ** D4 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 279 GLN ** D4 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN ** B5 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 63 ASN ** BJ 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 271 ASN ** S5 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S5 97 HIS ** B4 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B6 73 HIS ** B7 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2 21 GLN ** B1 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.244 67054 Z= 0.566 Angle : 1.691 50.914 90932 Z= 1.070 Chirality : 0.312 6.358 9992 Planarity : 0.006 0.093 11488 Dihedral : 8.148 93.886 9106 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.27 % Favored : 88.71 % Rotamer: Outliers : 0.07 % Allowed : 3.60 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.37 % Twisted Proline : 0.62 % Twisted General : 0.20 % 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: -1.78 (0.09), residues: 7988 helix: 0.37 (0.08), residues: 4114 sheet: -2.04 (0.24), residues: 382 loop : -3.12 (0.10), residues: 3492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRPD2 234 HIS 0.026 0.001 HISAK 18 PHE 0.040 0.002 PHE4L 12 TYR 0.037 0.002 TYRB1 25 ARG 0.010 0.001 ARGB8 58 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15976 Ramachandran restraints generated. 7988 Oldfield, 0 Emsley, 7988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15976 Ramachandran restraints generated. 7988 Oldfield, 0 Emsley, 7988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1971 residues out of total 7076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1966 time to evaluate : 5.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 1967 average time/residue: 0.6352 time to fit residues: 2163.2678 Evaluate side-chains 1569 residues out of total 7076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1569 time to evaluate : 5.678 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.6099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 256 optimal weight: 5.9990 chunk 685 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 447 optimal weight: 0.8980 chunk 188 optimal weight: 3.9990 chunk 762 optimal weight: 0.2980 chunk 632 optimal weight: 9.9990 chunk 353 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 252 optimal weight: 20.0000 chunk 400 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1 373 ASN ** S1 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 198 ASN S1 392 ASN ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 149 ASN ** S3 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 6 ASN ** S8 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V3 55 ASN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN ** A9 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 288 HIS ** A2 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 44 ASN ** A7 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3 80 GLN ** D1 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 157 ASN 4L 92 ASN D5 67 HIS D5 72 GLN ** D5 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 323 HIS ** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 43 ASN D4 168 GLN D4 279 GLN ** D4 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN A8 63 ASN BJ 99 GLN ** BJ 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 200 GLN AJ 271 ASN ** S5 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S5 97 HIS ** C2 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B6 73 HIS ** B7 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 9 HIS ** B1 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.249 67054 Z= 0.533 Angle : 1.674 50.727 90932 Z= 1.060 Chirality : 0.312 6.381 9992 Planarity : 0.005 0.117 11488 Dihedral : 7.951 89.980 9106 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.09 % Favored : 89.90 % Rotamer: Outliers : 0.10 % Allowed : 2.67 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.37 % Twisted Proline : 0.62 % Twisted General : 0.20 % 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: -1.61 (0.09), residues: 7988 helix: 0.49 (0.08), residues: 4124 sheet: -1.93 (0.25), residues: 375 loop : -3.02 (0.10), residues: 3489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRPB3 50 HIS 0.020 0.001 HISAK 18 PHE 0.039 0.002 PHED6 17 TYR 0.039 0.002 TYRB1 25 ARG 0.010 0.001 ARGD5 262 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15976 Ramachandran restraints generated. 7988 Oldfield, 0 Emsley, 7988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15976 Ramachandran restraints generated. 7988 Oldfield, 0 Emsley, 7988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2041 residues out of total 7076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 2034 time to evaluate : 5.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 0 residues processed: 2036 average time/residue: 0.6101 time to fit residues: 2146.1474 Evaluate side-chains 1593 residues out of total 7076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1593 time to evaluate : 5.665 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.6360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 735 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 434 optimal weight: 1.9990 chunk 556 optimal weight: 6.9990 chunk 431 optimal weight: 8.9990 chunk 641 optimal weight: 0.7980 chunk 425 optimal weight: 8.9990 chunk 759 optimal weight: 1.9990 chunk 475 optimal weight: 3.9990 chunk 463 optimal weight: 7.9990 chunk 350 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 214 GLN ** S1 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 198 ASN ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 149 ASN S2 306 GLN ** S3 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 6 ASN ** S8 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S4 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S4 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 103 ASN ** A9 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 44 ASN ** A7 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3 80 GLN ** D1 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 157 ASN D5 72 GLN ** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 51 ASN D4 168 GLN D4 279 GLN ** D2 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN ** A8 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 99 GLN ** BJ 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 21 ASN ** AJ 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S5 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S5 97 HIS ** A3 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B6 73 HIS ** B7 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.239 67054 Z= 0.560 Angle : 1.694 50.754 90932 Z= 1.070 Chirality : 0.312 6.386 9992 Planarity : 0.006 0.097 11488 Dihedral : 7.954 85.099 9106 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.01 % Allowed : 11.33 % Favored : 88.66 % Rotamer: Outliers : 0.03 % Allowed : 2.18 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.37 % Twisted Proline : 0.62 % Twisted General : 0.19 % 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: -1.63 (0.09), residues: 7988 helix: 0.44 (0.08), residues: 4106 sheet: -1.86 (0.25), residues: 380 loop : -2.98 (0.10), residues: 3502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRPD2 234 HIS 0.014 0.001 HISD4 319 PHE 0.044 0.002 PHED6 17 TYR 0.028 0.002 TYRB1 25 ARG 0.016 0.001 ARGAL 106 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15976 Ramachandran restraints generated. 7988 Oldfield, 0 Emsley, 7988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15976 Ramachandran restraints generated. 7988 Oldfield, 0 Emsley, 7988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1946 residues out of total 7076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1944 time to evaluate : 5.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 1946 average time/residue: 0.6013 time to fit residues: 2040.2521 Evaluate side-chains 1560 residues out of total 7076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1560 time to evaluate : 5.693 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.6370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 469 optimal weight: 0.6980 chunk 303 optimal weight: 0.9990 chunk 453 optimal weight: 0.0470 chunk 228 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 chunk 482 optimal weight: 0.9980 chunk 517 optimal weight: 0.8980 chunk 375 optimal weight: 0.9990 chunk 70 optimal weight: 0.0270 chunk 596 optimal weight: 2.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1 373 ASN V2 159 ASN ** S1 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 198 ASN ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 149 ASN S2 306 GLN ** S3 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 90 GLN ** S8 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V3 55 ASN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 46 GLN S4 99 ASN A9 37 HIS ** A9 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 288 HIS ** A2 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 44 ASN ** A7 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3 80 GLN ** D1 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 157 ASN ** D5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 82 HIS D4 168 GLN D4 279 GLN ** D4 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4 425 ASN D2 77 ASN ** D2 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN ** B5 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 64 GLN ** BJ 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S5 26 HIS S5 97 HIS ** A3 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B6 73 HIS ** B7 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.257 67054 Z= 0.534 Angle : 1.682 50.723 90932 Z= 1.062 Chirality : 0.312 6.375 9992 Planarity : 0.005 0.145 11488 Dihedral : 7.775 81.710 9106 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.01 % Allowed : 9.70 % Favored : 90.29 % Rotamer: Outliers : 0.01 % Allowed : 1.41 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.37 % Twisted Proline : 0.62 % Twisted General : 0.19 % 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: -1.50 (0.09), residues: 7988 helix: 0.56 (0.08), residues: 4089 sheet: -1.79 (0.26), residues: 375 loop : -2.92 (0.10), residues: 3524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRPAM 103 HIS 0.009 0.001 HISS5 97 PHE 0.054 0.002 PHE4L 12 TYR 0.035 0.002 TYRD5 422 ARG 0.030 0.001 ARGA5 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15976 Ramachandran restraints generated. 7988 Oldfield, 0 Emsley, 7988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15976 Ramachandran restraints generated. 7988 Oldfield, 0 Emsley, 7988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2015 residues out of total 7076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2014 time to evaluate : 5.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 2015 average time/residue: 0.6171 time to fit residues: 2160.6019 Evaluate side-chains 1608 residues out of total 7076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1608 time to evaluate : 5.687 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.7099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 690 optimal weight: 4.9990 chunk 727 optimal weight: 4.9990 chunk 663 optimal weight: 1.9990 chunk 707 optimal weight: 9.9990 chunk 425 optimal weight: 10.0000 chunk 308 optimal weight: 6.9990 chunk 555 optimal weight: 9.9990 chunk 217 optimal weight: 6.9990 chunk 639 optimal weight: 1.9990 chunk 669 optimal weight: 0.0980 chunk 705 optimal weight: 10.0000 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 27 ASN ** S1 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 198 ASN ** S1 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 135 GLN S2 149 ASN S2 157 HIS S2 306 GLN ** S3 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S4 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN ** A9 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 44 ASN ** A7 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 123 GLN ** D1 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 157 ASN ** D5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 168 GLN D4 279 GLN ** D2 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN AK 78 GLN ** B5 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 133 GLN ** BJ 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 271 ASN ** S5 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S5 97 HIS ** A3 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 32 GLN ** B4 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B6 73 HIS ** B7 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.243 67054 Z= 0.559 Angle : 1.702 50.844 90932 Z= 1.072 Chirality : 0.312 6.453 9992 Planarity : 0.006 0.150 11488 Dihedral : 7.828 82.355 9106 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.01 % Allowed : 11.47 % Favored : 88.52 % Rotamer: Outliers : 0.03 % Allowed : 0.96 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.37 % Twisted Proline : 0.62 % Twisted General : 0.19 % 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: -1.57 (0.09), residues: 7988 helix: 0.47 (0.08), residues: 4091 sheet: -1.74 (0.26), residues: 374 loop : -2.91 (0.10), residues: 3523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRPAM 103 HIS 0.021 0.001 HISS4 29 PHE 0.055 0.002 PHE4L 12 TYR 0.039 0.002 TYRS1 213 ARG 0.020 0.001 ARGA5 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15976 Ramachandran restraints generated. 7988 Oldfield, 0 Emsley, 7988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15976 Ramachandran restraints generated. 7988 Oldfield, 0 Emsley, 7988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1922 residues out of total 7076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1920 time to evaluate : 5.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 1921 average time/residue: 0.6037 time to fit residues: 2016.5663 Evaluate side-chains 1549 residues out of total 7076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1549 time to evaluate : 5.760 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.5706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 464 optimal weight: 9.9990 chunk 748 optimal weight: 4.9990 chunk 456 optimal weight: 3.9990 chunk 355 optimal weight: 0.9990 chunk 520 optimal weight: 0.7980 chunk 785 optimal weight: 0.8980 chunk 722 optimal weight: 1.9990 chunk 625 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 482 optimal weight: 8.9990 chunk 383 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 27 ASN ** S1 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 149 ASN ** S2 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 306 GLN ** S3 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 6 ASN S8 90 GLN ** S8 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 156 ASN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S4 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S4 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 44 ASN A6 98 GLN ** A7 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 123 GLN D3 80 GLN ** D1 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 157 ASN ** D5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 168 GLN D4 279 GLN ** D4 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN ** B5 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 258 ASN AJ 271 ASN S5 97 HIS A3 73 GLN B4 32 GLN ** B4 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B6 73 HIS ** B7 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B9 32 HIS ** B9 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.251 67054 Z= 0.537 Angle : 1.692 50.690 90932 Z= 1.066 Chirality : 0.312 6.411 9992 Planarity : 0.005 0.100 11488 Dihedral : 7.695 78.564 9106 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.01 % Allowed : 9.98 % Favored : 90.01 % Rotamer: Outliers : 0.03 % Allowed : 0.38 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.37 % Twisted Proline : 0.62 % Twisted General : 0.17 % 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: -1.50 (0.09), residues: 7988 helix: 0.54 (0.08), residues: 4082 sheet: -1.70 (0.26), residues: 367 loop : -2.89 (0.10), residues: 3539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRPD2 234 HIS 0.010 0.001 HISD4 319 PHE 0.042 0.002 PHE4L 12 TYR 0.031 0.002 TYRS2 108 ARG 0.013 0.000 ARGB6 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15976 Ramachandran restraints generated. 7988 Oldfield, 0 Emsley, 7988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15976 Ramachandran restraints generated. 7988 Oldfield, 0 Emsley, 7988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1932 residues out of total 7076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1930 time to evaluate : 5.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 1931 average time/residue: 0.5932 time to fit residues: 1992.8745 Evaluate side-chains 1570 residues out of total 7076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1570 time to evaluate : 5.613 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.5229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 496 optimal weight: 1.9990 chunk 665 optimal weight: 3.9990 chunk 191 optimal weight: 0.7980 chunk 576 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 173 optimal weight: 7.9990 chunk 626 optimal weight: 1.9990 chunk 262 optimal weight: 10.0000 chunk 642 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1 373 ASN V2 27 ASN ** S1 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 198 ASN ** S1 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 149 ASN S2 306 GLN ** S3 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S4 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S4 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 44 ASN ** A7 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 123 GLN ** D1 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 157 ASN ** D5 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 168 GLN D4 279 GLN ** D4 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN ** B5 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 204 ASN S5 97 HIS B4 32 GLN ** B4 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B6 73 HIS ** B7 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.102082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.091445 restraints weight = 201179.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.093301 restraints weight = 124616.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.094653 restraints weight = 82169.434| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.5704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.244 67054 Z= 0.550 Angle : 1.696 50.736 90932 Z= 1.069 Chirality : 0.312 6.411 9992 Planarity : 0.006 0.129 11488 Dihedral : 7.667 77.408 9106 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.01 % Allowed : 11.09 % Favored : 88.90 % Rotamer: Outliers : 0.01 % Allowed : 0.47 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.37 % Twisted Proline : 0.62 % Twisted General : 0.19 % 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: -1.51 (0.09), residues: 7988 helix: 0.51 (0.08), residues: 4094 sheet: -1.77 (0.26), residues: 385 loop : -2.87 (0.10), residues: 3509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRPD2 234 HIS 0.011 0.001 HISD4 319 PHE 0.044 0.002 PHED6 17 TYR 0.030 0.002 TYRS7 125 ARG 0.021 0.001 ARGB6 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27404.53 seconds wall clock time: 476 minutes 25.19 seconds (28585.19 seconds total)