Starting phenix.real_space_refine (version: dev) on Fri Feb 24 23:40:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc5_4497/02_2023/6qc5_4497_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc5_4497/02_2023/6qc5_4497.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc5_4497/02_2023/6qc5_4497_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc5_4497/02_2023/6qc5_4497_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc5_4497/02_2023/6qc5_4497_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc5_4497/02_2023/6qc5_4497.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc5_4497/02_2023/6qc5_4497.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc5_4497/02_2023/6qc5_4497_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc5_4497/02_2023/6qc5_4497_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 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 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 "S1 TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S3 TYR 110": "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 "S4 ARG 64": "NH1" <-> "NH2" Residue "A9 ARG 97": "NH1" <-> "NH2" Residue "A9 PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A9 ARG 186": "NH1" <-> "NH2" Residue "A9 TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A9 ARG 251": "NH1" <-> "NH2" Residue "A9 ARG 292": "NH1" <-> "NH2" Residue "A2 ARG 33": "NH1" <-> "NH2" Residue "A6 ARG 22": "NH1" <-> "NH2" Residue "AL ARG 106": "NH1" <-> "NH2" Residue "AM ARG 26": "NH1" <-> "NH2" Residue "AM ARG 81": "NH1" <-> "NH2" Residue "D3 ARG 48": "NH1" <-> "NH2" Residue "D3 PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 ARG 195": "NH1" <-> "NH2" Residue "D6 ARG 173": "NH1" <-> "NH2" Residue "D5 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D5 TYR 485": "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 "AJ ARG 95": "NH1" <-> "NH2" Residue "AJ TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AJ ARG 305": "NH1" <-> "NH2" 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 "B9 ARG 92": "NH1" <-> "NH2" Residue "B9 ARG 128": "NH1" <-> "NH2" Residue "B9 ARG 176": "NH1" <-> "NH2" Residue "B8 ARG 70": "NH1" <-> "NH2" Residue "A1 ARG 25": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 65691 Number of models: 1 Model: "" Number of chains: 57 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: {'PTRANS': 32, 'TRANS': 655} 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: {'CIS': 1, 'PTRANS': 28, 'TRANS': 400} 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: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} Chain: "S8" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1415 Classifications: {'peptide': 176} Modifications used: {'COO': 1} 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: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1025 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "A9" Number of atoms: 2512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2512 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} 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: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 82} Chain breaks: 1 Chain: "AL" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1044 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 11, 'TRANS': 111} 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: "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: {'PTRANS': 7, 'TRANS': 131} Chain: "D3" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 923 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "D1" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2529 Classifications: {'peptide': 318} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 295} Chain: "D6" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1345 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 170} 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': 5, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 299} 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': 1, 'PTRANS': 10, 'TRANS': 107} 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: "B6" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 804 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 12, 'TRANS': 82} 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: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 555 Classifications: {'peptide': 64} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 55} 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: "S2" 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: "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: "D5" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 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 44.833 164.311 141.615 1.00 26.73 S ATOM 3039 SG CYSV1 405 46.527 166.671 147.401 1.00 29.36 S ATOM 2695 SG CYSV1 362 50.693 164.916 142.556 1.00 47.26 S ATOM 2676 SG CYSV1 359 47.403 170.430 142.158 1.00 37.89 S ATOM 4116 SG CYSV2 103 26.974 174.290 148.503 1.00103.62 S ATOM 4150 SG CYSV2 108 24.002 171.584 149.946 1.00 80.24 S ATOM 4430 SG CYSV2 144 30.446 172.788 151.655 1.00 67.01 S ATOM 4453 SG CYSV2 148 28.339 171.166 153.955 1.00 72.81 S ATOM 5785 SG CYSS1 114 56.352 158.009 123.557 1.00 37.00 S ATOM 5724 SG CYSS1 105 51.640 155.444 120.011 1.00 63.51 S ATOM 5745 SG CYSS1 108 54.437 161.083 118.288 1.00 40.60 S ATOM 6117 SG CYSS1 156 56.885 167.138 130.408 1.00 45.22 S ATOM 6094 SG CYSS1 153 51.139 168.773 127.542 1.00 48.84 S ATOM 6141 SG CYSS1 159 55.869 173.080 128.124 1.00 24.96 S ATOM 6471 SG CYSS1 203 56.632 167.954 124.121 1.00 67.28 S ATOM 5230 SG CYSS1 41 59.904 165.621 137.165 1.00 25.69 S ATOM 5316 SG CYSS1 52 58.349 162.124 136.135 1.00 20.75 S ATOM 5341 SG CYSS1 55 60.448 160.464 141.305 1.00 27.18 S ATOM 5442 SG CYSS1 69 61.220 164.250 141.696 1.00 29.72 S ATOM 16168 SG CYSS7 119 66.077 132.603 96.391 1.00 60.99 S ATOM 16398 SG CYSS7 149 60.231 132.590 98.369 1.00 43.86 S ATOM 15670 SG CYSS7 55 61.643 129.084 92.923 1.00 53.62 S ATOM 15664 SG CYSS7 54 63.291 126.885 98.428 1.00 40.80 S ATOM 17591 SG CYSS8 116 56.975 140.440 98.541 1.00 66.18 S ATOM 17638 SG CYSS8 122 53.615 143.529 103.072 1.00 23.93 S ATOM 17365 SG CYSS8 87 60.205 144.387 102.722 1.00 59.91 S ATOM 17667 SG CYSS8 126 48.828 149.278 106.401 1.00 45.62 S ATOM 17338 SG CYSS8 83 55.184 149.884 104.715 1.00 21.85 S ATOM 17296 SG CYSS8 77 50.972 154.639 103.562 1.00 18.97 S ATOM 17315 SG CYSS8 80 52.725 152.824 109.796 1.00 42.26 S ATOM 18889 SG CYSS6 59 37.260 159.157 112.198 1.00 35.44 S ATOM 19067 SG CYSS6 84 40.665 161.074 111.932 1.00 34.90 S ATOM 19089 SG CYSS6 87 37.821 159.158 110.585 1.00 32.36 S Time building chain proxies: 26.84, per 1000 atoms: 0.41 Number of scatterers: 65691 At special positions: 0 Unit cell: (243.6, 221.2, 197.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 464 16.00 P 9 15.00 O 11781 8.00 N 11079 7.00 C 42329 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=2.03 Simple disulfide: pdb=" SG CYSA8 35 " - pdb=" SG CYSA8 65 " distance=2.04 Simple disulfide: pdb=" SG CYSA8 45 " - pdb=" SG CYSA8 55 " distance=2.03 Simple disulfide: pdb=" SG CYSA8 77 " - pdb=" SG CYSA8 109 " distance=2.02 Simple disulfide: pdb=" SG CYSA8 87 " - pdb=" SG CYSA8 99 " distance=2.03 Simple disulfide: pdb=" SG CYSBJ 76 " - pdb=" SG CYSBJ 83 " distance=2.03 Simple disulfide: pdb=" SG CYSBJ 112 " - pdb=" SG CYSBJ 124 " distance=2.03 Simple disulfide: pdb=" SG CYSS5 32 " - pdb=" SG CYSS5 65 " distance=2.03 Simple disulfide: pdb=" SG CYSS5 42 " - pdb=" SG CYSS5 55 " distance=2.04 Simple disulfide: pdb=" SG CYSB7 58 " - pdb=" SG CYSB7 89 " distance=2.02 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: 20.19 Conformation dependent library (CDL) restraints added in 6.9 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="FE1 FESV2 300 " - pdb=" SG CYSV2 103 " pdb="FE2 FESV2 300 " - pdb=" SG CYSV2 148 " pdb="FE2 FESV2 300 " - pdb=" SG CYSV2 144 " pdb="FE1 FESV2 300 " - pdb=" SG CYSV2 108 " pdb=" SF4S1 801 " pdb="FE3 SF4S1 801 " - pdb=" NE2 HISS1 101 " pdb="FE4 SF4S1 801 " - pdb=" SG CYSS1 108 " pdb="FE2 SF4S1 801 " - pdb=" SG CYSS1 105 " pdb="FE1 SF4S1 801 " - pdb=" SG CYSS1 114 " pdb=" SF4S1 802 " pdb="FE2 SF4S1 802 " - pdb=" SG CYSS1 153 " pdb="FE4 SF4S1 802 " - pdb=" SG CYSS1 203 " pdb="FE3 SF4S1 802 " - pdb=" SG CYSS1 159 " pdb="FE1 SF4S1 802 " - pdb=" SG CYSS1 156 " pdb=" SF4S7 300 " pdb="FE2 SF4S7 300 " - pdb=" SG CYSS7 149 " pdb="FE1 SF4S7 300 " - pdb=" SG CYSS7 119 " pdb="FE4 SF4S7 300 " - pdb=" SG CYSS7 54 " pdb="FE3 SF4S7 300 " - pdb=" SG CYSS7 55 " pdb=" SF4S8 201 " pdb="FE2 SF4S8 201 " - pdb=" SG CYSS8 116 " pdb="FE3 SF4S8 201 " - pdb=" SG CYSS8 122 " pdb="FE4 SF4S8 201 " - pdb=" SG CYSS8 87 " pdb="FE1 SF4S8 201 " - pdb=" SG CYSS8 119 " pdb="FE2 SF4S8 201 " - pdb=" NE2 HISS8 65 " pdb=" SF4S8 202 " pdb="FE2 SF4S8 202 " - pdb=" SG CYSS8 83 " pdb="FE3 SF4S8 202 " - pdb=" SG CYSS8 77 " pdb="FE4 SF4S8 202 " - pdb=" SG CYSS8 80 " pdb="FE1 SF4S8 202 " - pdb=" SG CYSS8 126 " pdb=" SF4V1 500 " pdb="FE3 SF4V1 500 " - pdb=" SG CYSV1 362 " pdb="FE1 SF4V1 500 " - pdb=" SG CYSV1 365 " 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 87 " pdb="ZN ZNS6 300 " - pdb=" SG CYSS6 59 " pdb="ZN ZNS6 300 " - pdb=" SG CYSS6 84 " Number of angles added : 3 16076 Ramachandran restraints generated. 8038 Oldfield, 0 Emsley, 8038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15298 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 306 helices and 27 sheets defined 48.2% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.89 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 107 through 113 Processing helix chain 'V1' and resid 115 through 128 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 197 Processing helix chain 'V1' and resid 215 through 217 No H-bonds generated for 'chain 'V1' and resid 215 through 217' Processing helix chain 'V1' and resid 225 through 236 Proline residue: V1 232 - end of helix removed outlier: 3.763A pdb=" N CYSV1 235 " --> pdb=" O SERV1 231 " (cutoff:3.500A) Processing helix chain 'V1' and resid 242 through 244 No H-bonds generated for 'chain 'V1' and resid 242 through 244' Processing helix chain 'V1' and resid 276 through 281 Processing helix chain 'V1' and resid 309 through 312 No H-bonds generated for 'chain 'V1' and resid 309 through 312' Processing helix chain 'V1' and resid 319 through 324 Processing helix chain 'V1' and resid 343 through 356 Processing helix chain 'V1' and resid 364 through 380 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 57 removed outlier: 4.040A pdb=" N VALV2 47 " --> pdb=" O ALAV2 44 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEUV2 48 " --> pdb=" O ALAV2 45 " (cutoff:3.500A) Proline residue: V2 49 - end of helix 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 113 through 124 Processing helix chain 'V2' and resid 166 through 177 Processing helix chain 'S1' and resid 13 through 15 No H-bonds generated for 'chain 'S1' and resid 13 through 15' Processing helix chain 'S1' and resid 26 through 32 Processing helix chain 'S1' and resid 84 through 97 Processing helix chain 'S1' and resid 116 through 123 Processing helix chain 'S1' and resid 159 through 165 Processing helix chain 'S1' and resid 196 through 202 removed outlier: 3.582A pdb=" N ILES1 199 " --> pdb=" O SERS1 196 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILES1 200 " --> pdb=" O GLYS1 197 " (cutoff:3.500A) 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 296 through 309 Processing helix chain 'S1' and resid 325 through 338 Processing helix chain 'S1' and resid 359 through 362 Processing helix chain 'S1' and resid 369 through 373 Processing helix chain 'S1' and resid 389 through 402 Processing helix chain 'S1' and resid 426 through 434 Processing helix chain 'S1' and resid 440 through 444 Processing helix chain 'S1' and resid 455 through 459 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 624 Processing helix chain 'S1' and resid 629 through 631 No H-bonds generated for 'chain 'S1' and resid 629 through 631' Processing helix chain 'S1' and resid 642 through 648 Processing helix chain 'S1' and resid 668 through 672 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 14 Processing helix chain 'S2' and resid 87 through 92 Processing helix chain 'S2' and resid 96 through 104 Proline residue: S2 101 - end of helix 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 185 removed outlier: 4.091A pdb=" N PHES2 168 " --> pdb=" O METS2 164 " (cutoff:3.500A) Processing helix chain 'S2' and resid 208 through 228 Processing helix chain 'S2' and resid 233 through 238 Processing helix chain 'S2' and resid 247 through 252 Processing helix chain 'S2' and resid 258 through 262 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 294 through 316 Processing helix chain 'S2' and resid 335 through 340 Processing helix chain 'S2' and resid 342 through 353 Processing helix chain 'S2' and resid 394 through 405 removed outlier: 3.844A pdb=" N GLYS2 401 " --> pdb=" O ALAS2 397 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEUS2 402 " --> pdb=" O HISS2 398 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ASPS2 403 " --> pdb=" O LEUS2 399 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LYSS2 404 " --> pdb=" O ALAS2 400 " (cutoff:3.500A) Processing helix chain 'S2' and resid 411 through 420 Processing helix chain 'S3' and resid 17 through 32 Processing helix chain 'S3' and resid 34 through 36 No H-bonds generated for 'chain 'S3' and resid 34 through 36' 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: 3.670A pdb=" N ASNS3 128 " --> pdb=" O LYSS3 125 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TRPS3 129 " --> pdb=" O ALAS3 126 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYRS3 130 " --> pdb=" O ALAS3 127 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N METS3 137 " --> pdb=" O ILES3 134 " (cutoff:3.500A) Processing helix chain 'S3' and resid 207 through 209 No H-bonds generated for 'chain 'S3' and resid 207 through 209' Processing helix chain 'S7' and resid 25 through 43 Processing helix chain 'S7' and resid 55 through 62 Processing helix chain 'S7' and resid 94 through 104 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 169 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 145 through 147 No H-bonds generated for 'chain 'S8' and resid 145 through 147' Processing helix chain 'S8' and resid 151 through 158 Processing helix chain 'S8' and resid 163 through 170 Processing helix chain 'V3' and resid 43 through 45 No H-bonds generated for 'chain 'V3' and resid 43 through 45' 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 'S6' and resid 41 through 44 No H-bonds generated for 'chain 'S6' and resid 41 through 44' 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 90 through 99 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 60 through 62 No H-bonds generated for 'chain 'A9' and resid 60 through 62' Processing helix chain 'A9' and resid 79 through 84 Processing helix chain 'A9' and resid 109 through 122 Proline residue: A9 114 - end of helix Processing helix chain 'A9' and resid 144 through 158 Processing helix chain 'A9' and resid 178 through 182 Processing helix chain 'A9' and resid 207 through 219 Processing helix chain 'A9' and resid 238 through 248 Processing helix chain 'A9' and resid 281 through 287 Processing helix chain 'A9' and resid 300 through 303 No H-bonds generated for 'chain 'A9' and resid 300 through 303' Processing helix chain 'A9' and resid 311 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 19 through 36 Processing helix chain 'A5' and resid 42 through 59 Processing helix chain 'A5' and resid 64 through 70 Processing helix chain 'A5' and resid 77 through 94 Processing helix chain 'A6' and resid 24 through 48 removed outlier: 3.544A pdb=" N VALA6 42 " --> pdb=" O TRPA6 38 " (cutoff:3.500A) Proline residue: A6 43 - end of helix Processing helix chain 'A6' and resid 55 through 69 removed outlier: 4.490A 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 117 through 122 Processing helix chain 'A7' and resid 5 through 14 Processing helix chain 'A7' and resid 59 through 61 No H-bonds generated for 'chain 'A7' and resid 59 through 61' Processing helix chain 'AL' and resid 24 through 27 No H-bonds generated for 'chain 'AL' and resid 24 through 27' 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 58 Processing helix chain 'AA' and resid 64 through 68 Processing helix chain 'AA' and resid 73 through 83 Processing helix chain 'AM' and resid 31 through 96 Proline residue: AM 72 - end of helix Processing helix chain 'AM' and resid 130 through 136 Processing helix chain 'AM' and resid 138 through 141 No H-bonds generated for 'chain 'AM' and resid 138 through 141' Processing helix chain 'D3' and resid 2 through 22 Processing helix chain 'D3' and resid 57 through 79 Proline residue: D3 74 - end of helix removed outlier: 5.833A pdb=" N TRPD3 77 " --> pdb=" O LEUD3 73 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALAD3 78 " --> pdb=" O PROD3 74 " (cutoff:3.500A) 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 87 Proline residue: D1 75 - end of helix removed outlier: 4.758A pdb=" N TRPD1 86 " --> pdb=" O ALAD1 82 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILED1 87 " --> pdb=" O LEUD1 83 " (cutoff:3.500A) Processing helix chain 'D1' and resid 102 through 123 Processing helix chain 'D1' and resid 127 through 141 Processing helix chain 'D1' and resid 145 through 157 removed outlier: 3.587A pdb=" N METD1 156 " --> pdb=" O SERD1 152 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASND1 157 " --> pdb=" O VALD1 153 " (cutoff:3.500A) Processing helix chain 'D1' and resid 162 through 168 Processing helix chain 'D1' and resid 174 through 177 No H-bonds generated for 'chain 'D1' and resid 174 through 177' Processing helix chain 'D1' and resid 180 through 193 Processing helix chain 'D1' and resid 220 through 241 Processing helix chain 'D1' and resid 253 through 274 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 73 Processing helix chain 'D6' and resid 83 through 85 No H-bonds generated for 'chain 'D6' and resid 83 through 85' Processing helix chain 'D6' and resid 87 through 108 Processing helix chain 'D6' and resid 139 through 144 Processing helix chain 'D6' and resid 151 through 173 removed outlier: 3.543A 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 15 removed outlier: 5.212A pdb=" N LEUD5 15 " --> pdb=" O THRD5 11 " (cutoff:3.500A) Processing helix chain 'D5' and resid 17 through 23 Processing helix chain 'D5' and resid 32 through 57 removed outlier: 4.068A 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 131 Processing helix chain 'D5' and resid 137 through 155 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 247 Processing helix chain 'D5' and resid 255 through 262 removed outlier: 3.679A pdb=" N LEUD5 259 " --> pdb=" O ALAD5 255 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEUD5 260 " --> pdb=" O GLYD5 256 " (cutoff:3.500A) 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 350 Processing helix chain 'D5' and resid 367 through 379 Processing helix chain 'D5' and resid 387 through 400 removed outlier: 4.806A pdb=" N SERD5 391 " --> pdb=" O THRD5 387 " (cutoff:3.500A) removed outlier: 4.491A 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 470 removed outlier: 5.341A pdb=" N GLYD5 465 " --> pdb=" O SERD5 461 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N PHED5 466 " --> pdb=" O LEUD5 462 " (cutoff:3.500A) 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: 3.731A pdb=" N TYRD5 529 " --> pdb=" O LEUD5 526 " (cutoff:3.500A) Proline residue: D5 530 - end of helix removed outlier: 3.694A pdb=" N METD5 533 " --> pdb=" O PROD5 530 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HISD5 534 " --> pdb=" O THRD5 531 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N THRD5 537 " --> pdb=" O HISD5 534 " (cutoff:3.500A) Proline residue: D5 538 - end of helix removed outlier: 4.450A pdb=" N ASND5 541 " --> pdb=" O PROD5 538 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEUD5 542 " --> pdb=" O TYRD5 539 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THRD5 543 " --> pdb=" O METD5 540 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N METD5 544 " --> pdb=" O ASND5 541 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLND5 546 " --> pdb=" O THRD5 543 " (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 584 through 600 Processing helix chain 'D4' and resid 2 through 10 Proline residue: D4 7 - end of helix Processing helix chain 'D4' and resid 12 through 16 removed outlier: 3.776A pdb=" N TRPD4 16 " --> pdb=" O METD4 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'D4' and resid 12 through 16' Processing helix chain 'D4' and resid 23 through 41 removed outlier: 4.367A pdb=" N LEUD4 41 " --> pdb=" O THRD4 37 " (cutoff:3.500A) Processing helix chain 'D4' and resid 60 through 79 Proline residue: D4 64 - end of helix Proline residue: D4 74 - end of helix Processing helix chain 'D4' and resid 89 through 110 Processing helix chain 'D4' and resid 116 through 135 Proline residue: D4 128 - end of helix removed outlier: 3.662A pdb=" N ILED4 131 " --> pdb=" O VALD4 127 " (cutoff:3.500A) Processing helix chain 'D4' and resid 142 through 171 Proline residue: D4 159 - end of helix removed outlier: 4.072A pdb=" N VALD4 162 " --> pdb=" O LEUD4 158 " (cutoff:3.500A) Processing helix chain 'D4' and resid 176 through 181 Processing helix chain 'D4' and resid 191 through 206 Processing helix chain 'D4' and resid 210 through 221 removed outlier: 5.837A pdb=" N LEUD4 214 " --> pdb=" O GLYD4 211 " (cutoff:3.500A) removed outlier: 3.649A 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 246 Processing helix chain 'D4' and resid 252 through 257 removed outlier: 3.803A pdb=" N METD4 257 " --> pdb=" O THRD4 254 " (cutoff:3.500A) Processing helix chain 'D4' and resid 259 through 277 removed outlier: 3.945A pdb=" N LEUD4 277 " --> pdb=" O SERD4 273 " (cutoff:3.500A) Processing helix chain 'D4' and resid 282 through 303 removed outlier: 4.435A pdb=" N ILED4 286 " --> pdb=" O LEUD4 282 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALAD4 287 " --> pdb=" O LYSD4 283 " (cutoff:3.500A) Processing helix chain 'D4' and resid 306 through 337 Processing helix chain 'D4' and resid 355 through 365 Processing helix chain 'D4' and resid 373 through 389 Processing helix chain 'D4' and resid 393 through 414 removed outlier: 3.733A pdb=" N THRD4 414 " --> pdb=" O METD4 410 " (cutoff:3.500A) Processing helix chain 'D4' and resid 431 through 449 removed outlier: 3.598A pdb=" N LEUD4 442 " --> pdb=" O SERD4 438 " (cutoff:3.500A) Proline residue: D4 443 - end of helix Processing helix chain 'D4' and resid 451 through 453 No H-bonds generated for 'chain 'D4' and resid 451 through 453' Processing helix chain 'D2' and resid 3 through 22 Processing helix chain 'D2' and resid 26 through 43 Proline residue: D2 42 - end of helix Processing helix chain 'D2' and resid 50 through 79 Processing helix chain 'D2' and resid 92 through 106 Processing helix chain 'D2' and resid 115 through 120 Processing helix chain 'D2' and resid 124 through 148 Proline residue: D2 138 - end of helix removed outlier: 3.818A 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 170 removed outlier: 3.757A pdb=" N GLYD2 169 " --> pdb=" O GLYD2 165 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEUD2 170 " --> pdb=" O GLYD2 166 " (cutoff:3.500A) Processing helix chain 'D2' and resid 176 through 193 removed outlier: 4.203A pdb=" N VALD2 193 " --> pdb=" O TRPD2 189 " (cutoff:3.500A) 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 removed outlier: 3.729A pdb=" N METD2 265 " --> pdb=" O METD2 261 " (cutoff:3.500A) Processing helix chain 'D2' and resid 277 through 300 removed outlier: 4.867A pdb=" N LEUD2 290 " --> pdb=" O ALAD2 286 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N TYRD2 291 " --> pdb=" O LEUD2 287 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N PHED2 292 " --> pdb=" O LEUD2 288 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N TYRD2 293 " --> pdb=" O ASND2 289 " (cutoff:3.500A) Processing helix chain 'D2' and resid 311 through 316 removed outlier: 4.457A pdb=" N GLND2 316 " --> pdb=" O LYSD2 312 " (cutoff:3.500A) Processing helix chain 'D2' and resid 326 through 334 Processing helix chain 'D2' and resid 340 through 342 No H-bonds generated for 'chain 'D2' and resid 340 through 342' 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 79 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: 5.542A 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 'B5' and resid 130 through 132 No H-bonds generated for 'chain 'B5' and resid 130 through 132' Processing helix chain 'AB' and resid 8 through 20 Processing helix chain 'AB' and resid 44 through 58 Processing helix chain 'AB' and resid 73 through 84 Processing helix chain 'A8' and resid 21 through 26 Processing helix chain 'A8' and resid 28 through 33 Processing helix chain 'A8' and resid 38 through 49 removed outlier: 3.525A pdb=" N GLUA8 48 " --> pdb=" O CYSA8 45 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLUA8 49 " --> pdb=" O ARGA8 46 " (cutoff:3.500A) Processing helix chain 'A8' and resid 56 through 74 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 56 removed outlier: 4.890A 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 116 removed outlier: 5.088A pdb=" N GLUBJ 86 " --> pdb=" O LEUBJ 82 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 125 through 141 Processing helix chain 'BJ' and resid 152 through 171 Processing helix chain 'AJ' and resid 5 through 10 Processing helix chain 'AJ' and resid 36 through 46 Processing helix chain 'AJ' and resid 58 through 61 No H-bonds generated for 'chain 'AJ' and resid 58 through 61' 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 93 through 116 Processing helix chain 'AJ' and resid 128 through 140 Processing helix chain 'AJ' and resid 146 through 162 removed outlier: 4.396A pdb=" N CYSAJ 161 " --> pdb=" O LYSAJ 157 " (cutoff:3.500A) removed outlier: 5.187A 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 207 Processing helix chain 'AJ' and resid 210 through 214 Processing helix chain 'AJ' and resid 231 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 269 through 272 removed outlier: 4.113A pdb=" N TYRAJ 272 " --> pdb=" O VALAJ 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'AJ' and resid 269 through 272' Processing helix chain 'AJ' and resid 286 through 297 Processing helix chain 'AJ' and resid 306 through 308 No H-bonds generated for 'chain 'AJ' and resid 306 through 308' 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 66 Processing helix chain 'S5' and resid 69 through 88 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 66 Processing helix chain 'B3' and resid 69 through 82 removed outlier: 3.862A pdb=" N GLYB3 73 " --> pdb=" O PHEB3 70 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N PHEB3 74 " --> pdb=" O LYSB3 71 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALAB3 75 " --> pdb=" O TRPB3 72 " (cutoff:3.500A) Processing helix chain 'C2' and resid 16 through 18 No H-bonds generated for 'chain 'C2' and resid 16 through 18' 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 50 Processing helix chain 'B4' and resid 62 through 72 Processing helix chain 'B4' and resid 83 through 93 Processing helix chain 'B4' and resid 95 through 117 Processing helix chain 'B6' and resid 5 through 25 Processing helix chain 'B6' and resid 68 through 91 Proline residue: B6 77 - end of helix removed outlier: 3.614A pdb=" N TYRB6 87 " --> pdb=" O TYRB6 83 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HISB6 88 " --> pdb=" O TYRB6 84 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VALB6 89 " --> pdb=" O LEUB6 85 " (cutoff:3.500A) Processing helix chain 'B7' and resid 3 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 removed outlier: 3.625A pdb=" N GLYB9 73 " --> pdb=" O GLUB9 69 " (cutoff:3.500A) 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 141 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 40 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 27 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 51 through 63 removed outlier: 3.559A pdb=" N VALBK 55 " --> pdb=" O PROBK 51 " (cutoff:3.500A) Processing helix chain 'BK' and resid 70 through 78 Processing helix chain 'BK' and resid 86 through 102 Processing helix chain 'C1' and resid 16 through 45 Processing helix chain 'B1' and resid 15 through 33 Processing helix chain 'A1' and resid 2 through 4 No H-bonds generated for 'chain 'A1' and resid 2 through 4' Processing helix chain 'A1' and resid 6 through 31 Proline residue: A1 19 - end of helix removed outlier: 3.889A pdb=" N ASNA1 31 " --> pdb=" O HISA1 27 " (cutoff:3.500A) Processing helix chain 'A1' and resid 42 through 53 Processing sheet with id= A, first strand: chain 'V1' and resid 221 through 224 removed outlier: 6.442A pdb=" N ALAV1 133 " --> pdb=" O LEUV1 93 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VALV1 95 " --> pdb=" O ALAV1 133 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TYRV1 135 " --> pdb=" O VALV1 95 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ALAV1 97 " --> pdb=" O TYRV1 135 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TYRV1 137 " --> pdb=" O ALAV1 97 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASPV1 174 " --> pdb=" O ALAV1 134 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILEV1 136 " --> pdb=" O ASPV1 174 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHEV1 176 " --> pdb=" O ILEV1 136 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ILEV1 138 " --> pdb=" O PHEV1 176 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VALV1 178 " --> pdb=" O ILEV1 138 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'V1' and resid 253 through 258 Processing sheet with id= C, first strand: chain 'V1' and resid 294 through 298 removed outlier: 6.592A pdb=" N METV1 337 " --> pdb=" O LEUV1 295 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VALV1 297 " --> pdb=" O ILEV1 335 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILEV1 335 " --> pdb=" O VALV1 297 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'V2' and resid 137 through 142 removed outlier: 7.301A pdb=" N TYRV2 98 " --> pdb=" O THRV2 138 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N ILEV2 140 " --> pdb=" O TYRV2 98 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILEV2 100 " --> pdb=" O ILEV2 140 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VALV2 142 " --> pdb=" O ILEV2 100 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VALV2 102 " --> pdb=" O VALV2 142 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'S1' and resid 16 through 20 removed outlier: 6.721A 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 282 through 284 Processing sheet with id= J, first strand: chain 'S1' and resid 342 through 345 removed outlier: 6.825A pdb=" N METS1 521 " --> pdb=" O ALAS1 316 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ILES1 318 " --> pdb=" O METS1 521 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHES1 523 " --> pdb=" O ILES1 318 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHES1 542 " --> pdb=" O LEUS1 522 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEUS1 524 " --> pdb=" O PHES1 542 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VALS1 544 " --> pdb=" O LEUS1 524 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VALS1 559 " --> pdb=" O TYRS1 545 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLYS1 547 " --> pdb=" O VALS1 559 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEUS1 561 " --> pdb=" O GLYS1 547 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S1' and resid 406 through 409 removed outlier: 6.553A pdb=" N VALS1 377 " --> pdb=" O ALAS1 407 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILES1 409 " --> pdb=" O VALS1 377 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEUS1 379 " --> pdb=" O ILES1 409 " (cutoff:3.500A) 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 39 through 42 Processing sheet with id= P, first strand: chain 'S3' and resid 172 through 177 Processing sheet with id= Q, first strand: chain 'S7' and resid 85 through 88 removed outlier: 6.249A pdb=" N TYRS7 112 " --> pdb=" O METS7 86 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VALS7 88 " --> pdb=" O TYRS7 112 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VALS7 114 " --> pdb=" O VALS7 88 " (cutoff:3.500A) removed outlier: 6.527A 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 92 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 105 Processing sheet with id= U, first strand: chain 'S4' and resid 64 through 66 Processing sheet with id= V, first strand: chain 'A9' and resid 228 through 230 removed outlier: 6.637A pdb=" N VALA9 91 " --> pdb=" O ILEA9 130 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ILEA9 132 " --> pdb=" O VALA9 91 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASNA9 93 " --> pdb=" O ILEA9 132 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N HISA9 134 " --> pdb=" O ASNA9 93 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLNA9 44 " --> pdb=" O ALAA9 21 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VALA9 23 " --> pdb=" O GLNA9 44 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILEA9 46 " --> pdb=" O VALA9 23 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'A2' and resid 52 through 56 removed outlier: 6.621A pdb=" N ILEA2 18 " --> pdb=" O LEUA2 53 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ARGA2 55 " --> pdb=" O ILEA2 18 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILEA2 20 " --> pdb=" O ARGA2 55 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'AL' and resid 47 through 50 Processing sheet with id= Y, first strand: chain 'D5' and resid 61 through 65 Processing sheet with id= Z, first strand: chain 'D4' and resid 50 through 52 Processing sheet with id= AA, first strand: chain 'AJ' and resid 122 through 125 removed outlier: 6.754A pdb=" N VALAJ 168 " --> pdb=" O THRAJ 26 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ASPAJ 28 " --> pdb=" O VALAJ 168 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ILEAJ 170 " --> pdb=" O ASPAJ 28 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLUAJ 219 " --> pdb=" O VALAJ 169 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N TYRAJ 171 " --> pdb=" O GLUAJ 219 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEUAJ 221 " --> pdb=" O TYRAJ 171 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ASPAJ 173 " --> pdb=" O LEUAJ 221 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TYRAJ 223 " --> pdb=" O ASPAJ 173 " (cutoff:3.500A) 2747 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: 20.74 Time building geometry restraints manager: 22.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 27971 1.42 - 1.64: 38572 1.64 - 1.86: 753 1.86 - 2.08: 0 2.08 - 2.30: 80 Bond restraints: 67376 Sorted by residual: bond pdb=" C16 ZMPAA 101 " pdb=" N2 ZMPAA 101 " ideal model delta sigma weight residual 1.452 1.332 0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" O5D NDPA9 401 " pdb=" PN NDPA9 401 " ideal model delta sigma weight residual 1.757 1.554 0.203 3.50e-02 8.16e+02 3.35e+01 bond pdb=" C16 ZMPAB 101 " pdb=" N2 ZMPAB 101 " ideal model delta sigma weight residual 1.452 1.340 0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C13 ZMPAA 101 " pdb=" N1 ZMPAA 101 " ideal model delta sigma weight residual 1.451 1.341 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" CA PHEV2 191 " pdb=" C PHEV2 191 " ideal model delta sigma weight residual 1.523 1.595 -0.072 1.34e-02 5.57e+03 2.86e+01 ... (remaining 67371 not shown) Histogram of bond angle deviations from ideal: 69.38 - 83.52: 72 83.52 - 97.65: 13 97.65 - 111.79: 31356 111.79 - 125.92: 58371 125.92 - 140.06: 1591 Bond angle restraints: 91403 Sorted by residual: angle pdb=" PA NDPA9 401 " pdb=" O3 NDPA9 401 " pdb=" PN NDPA9 401 " ideal model delta sigma weight residual 107.74 135.63 -27.89 1.95e+00 2.62e-01 2.04e+02 angle pdb=" S1 FESV2 300 " pdb="FE1 FESV2 300 " pdb=" S2 FESV2 300 " ideal model delta sigma weight residual 104.33 92.45 11.88 1.20e+00 6.94e-01 9.80e+01 angle pdb=" S1 FESV2 300 " pdb="FE2 FESV2 300 " pdb=" S2 FESV2 300 " ideal model delta sigma weight residual 104.33 93.31 11.02 1.14e+00 7.69e-01 9.35e+01 angle pdb=" C5B NDPA9 401 " pdb=" O5B NDPA9 401 " pdb=" PA NDPA9 401 " ideal model delta sigma weight residual 103.84 121.83 -17.99 1.91e+00 2.73e-01 8.83e+01 angle pdb=" S1 FESS1 803 " pdb="FE2 FESS1 803 " pdb=" S2 FESS1 803 " ideal model delta sigma weight residual 104.33 93.77 10.56 1.14e+00 7.69e-01 8.59e+01 ... (remaining 91398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.18: 38758 21.18 - 42.36: 1493 42.36 - 63.54: 167 63.54 - 84.72: 53 84.72 - 105.90: 2 Dihedral angle restraints: 40473 sinusoidal: 16758 harmonic: 23715 Sorted by residual: dihedral pdb=" CA PHEAJ 278 " pdb=" C PHEAJ 278 " pdb=" N LEUAJ 279 " pdb=" CA LEUAJ 279 " ideal model delta harmonic sigma weight residual 180.00 124.66 55.34 0 5.00e+00 4.00e-02 1.22e+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 -128.09 -51.91 0 5.00e+00 4.00e-02 1.08e+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 -129.30 -50.70 0 5.00e+00 4.00e-02 1.03e+02 ... (remaining 40470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.211: 10019 4.211 - 8.423: 0 8.423 - 12.634: 0 12.634 - 16.846: 0 16.846 - 21.057: 24 Chirality restraints: 10043 Sorted by residual: chirality pdb="FE1 SF4S1 802 " pdb=" S2 SF4S1 802 " pdb=" S3 SF4S1 802 " pdb=" S4 SF4S1 802 " both_signs ideal model delta sigma weight residual False -10.55 10.50 -21.06 2.00e-01 2.50e+01 1.11e+04 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 -10.49 21.05 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE3 SF4S7 300 " pdb=" S1 SF4S7 300 " pdb=" S2 SF4S7 300 " pdb=" S4 SF4S7 300 " both_signs ideal model delta sigma weight residual False -10.55 10.49 -21.04 2.00e-01 2.50e+01 1.11e+04 ... (remaining 10040 not shown) Planarity restraints: 11558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMNV1 501 " 0.265 2.00e-02 2.50e+03 1.09e-01 5.63e+02 pdb=" C10 FMNV1 501 " 0.004 2.00e-02 2.50e+03 pdb=" C2 FMNV1 501 " -0.113 2.00e-02 2.50e+03 pdb=" C4 FMNV1 501 " 0.032 2.00e-02 2.50e+03 pdb=" C4A FMNV1 501 " 0.054 2.00e-02 2.50e+03 pdb=" C5A FMNV1 501 " 0.090 2.00e-02 2.50e+03 pdb=" C6 FMNV1 501 " 0.057 2.00e-02 2.50e+03 pdb=" C7 FMNV1 501 " -0.037 2.00e-02 2.50e+03 pdb=" C7M FMNV1 501 " -0.202 2.00e-02 2.50e+03 pdb=" C8 FMNV1 501 " -0.041 2.00e-02 2.50e+03 pdb=" C8M FMNV1 501 " -0.072 2.00e-02 2.50e+03 pdb=" C9 FMNV1 501 " -0.002 2.00e-02 2.50e+03 pdb=" C9A FMNV1 501 " 0.054 2.00e-02 2.50e+03 pdb=" N1 FMNV1 501 " -0.071 2.00e-02 2.50e+03 pdb=" N10 FMNV1 501 " 0.041 2.00e-02 2.50e+03 pdb=" N3 FMNV1 501 " -0.059 2.00e-02 2.50e+03 pdb=" N5 FMNV1 501 " 0.106 2.00e-02 2.50e+03 pdb=" O2 FMNV1 501 " -0.207 2.00e-02 2.50e+03 pdb=" O4 FMNV1 501 " 0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1B NDPA9 401 " -0.090 2.00e-02 2.50e+03 3.99e-02 4.38e+01 pdb=" C2A NDPA9 401 " 0.009 2.00e-02 2.50e+03 pdb=" C4A NDPA9 401 " 0.035 2.00e-02 2.50e+03 pdb=" C5A NDPA9 401 " 0.031 2.00e-02 2.50e+03 pdb=" C6A NDPA9 401 " -0.000 2.00e-02 2.50e+03 pdb=" C8A NDPA9 401 " 0.022 2.00e-02 2.50e+03 pdb=" N1A NDPA9 401 " -0.007 2.00e-02 2.50e+03 pdb=" N3A NDPA9 401 " 0.028 2.00e-02 2.50e+03 pdb=" N6A NDPA9 401 " -0.070 2.00e-02 2.50e+03 pdb=" N7A NDPA9 401 " 0.030 2.00e-02 2.50e+03 pdb=" N9A NDPA9 401 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VALS2 73 " -0.027 2.00e-02 2.50e+03 5.31e-02 2.81e+01 pdb=" C VALS2 73 " 0.092 2.00e-02 2.50e+03 pdb=" O VALS2 73 " -0.035 2.00e-02 2.50e+03 pdb=" N ARGS2 74 " -0.031 2.00e-02 2.50e+03 ... (remaining 11555 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 3364 2.71 - 3.26: 66056 3.26 - 3.80: 110371 3.80 - 4.35: 129211 4.35 - 4.90: 210961 Nonbonded interactions: 519963 Sorted by model distance: nonbonded pdb=" CA ALAS3 80 " pdb=" O GLUS3 91 " model vdw 2.162 3.470 nonbonded pdb=" OH TYRD1 114 " pdb=" O LEUD6 61 " model vdw 2.185 2.440 nonbonded pdb=" O GLNS3 38 " pdb=" CA SERA7 70 " model vdw 2.194 3.470 nonbonded pdb=" O GLUV1 101 " pdb=" OG1 THRV1 104 " model vdw 2.212 2.440 nonbonded pdb=" O THRD1 189 " pdb=" OG1 THRD1 193 " model vdw 2.223 2.440 ... (remaining 519958 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 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 9 5.49 5 S 464 5.16 5 C 42329 2.51 5 N 11079 2.21 5 O 11781 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.810 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: 0.060 Extract box with map and model: 30.520 Check model and map are aligned: 0.760 Process input model: 141.390 Find NCS groups from input model: 2.050 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Set scattering table: 0.460 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 183.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 : 0.009 0.203 67376 Z= 0.567 Angle : 1.285 27.888 91403 Z= 0.676 Chirality : 1.028 21.057 10043 Planarity : 0.009 0.109 11558 Dihedral : 11.800 105.901 25139 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.33 % Favored : 87.51 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.28 % Twisted Proline : 1.24 % Twisted General : 0.57 % 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: -4.12 (0.08), residues: 8038 helix: -1.94 (0.06), residues: 4147 sheet: -2.77 (0.24), residues: 339 loop : -3.75 (0.09), residues: 3552 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16076 Ramachandran restraints generated. 8038 Oldfield, 0 Emsley, 8038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16076 Ramachandran restraints generated. 8038 Oldfield, 0 Emsley, 8038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3082 residues out of total 7118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 3031 time to evaluate : 6.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 51 outliers final: 8 residues processed: 3059 average time/residue: 0.6973 time to fit residues: 3568.2946 Evaluate side-chains 1748 residues out of total 7118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1740 time to evaluate : 6.015 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.5065 time to fit residues: 16.0877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 668 optimal weight: 6.9990 chunk 600 optimal weight: 0.8980 chunk 333 optimal weight: 0.2980 chunk 205 optimal weight: 0.9980 chunk 404 optimal weight: 6.9990 chunk 320 optimal weight: 5.9990 chunk 620 optimal weight: 5.9990 chunk 240 optimal weight: 3.9990 chunk 377 optimal weight: 0.9980 chunk 462 optimal weight: 3.9990 chunk 719 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V1 37 GLN V1 165 ASN V1 437 HIS ** V2 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V2 16 ASN V2 99 HIS S1 36 GLN ** S1 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 336 ASN S1 392 ASN S1 546 GLN S1 621 ASN S1 665 GLN S2 50 ASN S2 54 GLN ** S2 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2 84 HIS ** S2 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2 201 GLN ** S2 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2 398 HIS ** S7 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S7 162 GLN ** S8 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V3 44 HIS ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 46 GLN A9 3 HIS A9 58 HIS ** A9 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 115 GLN A9 119 GLN A9 184 ASN A9 288 HIS A2 61 GLN ** A2 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 36 HIS A5 82 GLN A6 47 HIS ** A6 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A7 8 GLN ** A7 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A7 35 GLN ** AL 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 69 ASN ** AL 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 75 GLN D3 26 GLN ** D3 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 171 GLN D1 304 HIS ** 4L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 72 GLN D5 139 GLN D5 205 ASN ** D5 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 446 ASN D5 484 HIS D5 541 ASN D5 580 GLN D4 81 GLN D4 83 HIS ** D4 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 213 HIS D4 374 ASN D4 434 ASN D4 450 ASN D2 63 GLN ** D2 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN ** AK 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 33 ASN ** A8 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 113 GLN ** BJ 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 97 GLN ** AJ 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 204 ASN ** AJ 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 251 GLN ** AJ 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S5 26 HIS ** S5 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3 45 ASN A3 61 ASN A3 68 HIS C2 59 HIS C2 88 HIS B4 47 GLN B4 49 GLN B4 82 ASN B6 82 HIS ** B7 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B7 91 HIS B9 12 GLN B9 17 GLN B9 74 GLN BK 45 HIS BK 86 GLN A1 31 ASN A1 40 HIS Total number of N/Q/H flips: 74 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.307 67376 Z= 0.504 Angle : 1.691 51.194 91403 Z= 1.070 Chirality : 0.307 6.437 10043 Planarity : 0.006 0.077 11558 Dihedral : 8.108 87.048 9050 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.35 % Favored : 89.64 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.28 % Twisted Proline : 0.82 % 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: -2.73 (0.09), residues: 8038 helix: -0.56 (0.07), residues: 4165 sheet: -2.26 (0.25), residues: 361 loop : -3.41 (0.09), residues: 3512 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16076 Ramachandran restraints generated. 8038 Oldfield, 0 Emsley, 8038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16076 Ramachandran restraints generated. 8038 Oldfield, 0 Emsley, 8038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2398 residues out of total 7118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 2376 time to evaluate : 5.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 22 outliers final: 3 residues processed: 2388 average time/residue: 0.6640 time to fit residues: 2711.2185 Evaluate side-chains 1744 residues out of total 7118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1741 time to evaluate : 5.910 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.5292 time to fit residues: 11.0182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 399 optimal weight: 5.9990 chunk 223 optimal weight: 4.9990 chunk 598 optimal weight: 9.9990 chunk 489 optimal weight: 20.0000 chunk 198 optimal weight: 10.0000 chunk 720 optimal weight: 5.9990 chunk 778 optimal weight: 9.9990 chunk 641 optimal weight: 0.9990 chunk 714 optimal weight: 0.9980 chunk 245 optimal weight: 5.9990 chunk 578 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 198 ASN ** S1 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 336 ASN S1 392 ASN ** S2 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 54 GLN S2 190 HIS ** S2 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 90 GLN ** S8 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V3 65 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 46 GLN A9 184 ASN A9 216 ASN A9 234 ASN A9 288 HIS ** A2 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 82 GLN A5 110 GLN A6 57 GLN A7 8 GLN ** A7 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A7 35 GLN ** AL 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 89 ASN D3 26 GLN ** D1 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 51 ASN D4 81 GLN ** D4 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 213 HIS D4 293 HIS D4 424 ASN D4 450 ASN ** D2 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 29 HIS A8 63 ASN A8 103 GLN ** BJ 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 90 GLN ** BJ 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 114 HIS ** AJ 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 184 GLN ** AJ 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S5 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S5 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S5 69 GLN A3 61 ASN ** A3 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 49 GLN B6 25 GLN ** B9 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B9 17 GLN B9 72 HIS B8 28 ASN ** B8 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B8 136 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.281 67376 Z= 0.561 Angle : 1.700 51.397 91403 Z= 1.073 Chirality : 0.312 6.574 10043 Planarity : 0.006 0.074 11558 Dihedral : 7.894 90.000 9050 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.01 % Allowed : 11.52 % Favored : 88.47 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.28 % Twisted Proline : 0.82 % 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: -2.26 (0.09), residues: 8038 helix: -0.09 (0.08), residues: 4161 sheet: -2.09 (0.25), residues: 376 loop : -3.31 (0.10), residues: 3501 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16076 Ramachandran restraints generated. 8038 Oldfield, 0 Emsley, 8038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16076 Ramachandran restraints generated. 8038 Oldfield, 0 Emsley, 8038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2098 residues out of total 7118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 2083 time to evaluate : 6.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 3 residues processed: 2092 average time/residue: 0.6774 time to fit residues: 2430.9872 Evaluate side-chains 1599 residues out of total 7118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1596 time to evaluate : 5.888 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.5404 time to fit residues: 11.0056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 711 optimal weight: 7.9990 chunk 541 optimal weight: 7.9990 chunk 373 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 343 optimal weight: 9.9990 chunk 483 optimal weight: 9.9990 chunk 723 optimal weight: 0.9980 chunk 765 optimal weight: 6.9990 chunk 377 optimal weight: 5.9990 chunk 685 optimal weight: 20.0000 chunk 206 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1 263 ASN V1 373 ASN V1 437 HIS ** V2 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V2 16 ASN V2 37 ASN ** V2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 198 ASN ** S1 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 336 ASN S1 392 ASN ** S1 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A9 37 HIS ** A9 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 184 ASN A9 203 GLN ** A2 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 110 GLN A6 98 GLN A7 20 GLN ** A7 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 26 GLN ** D1 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 304 HIS D6 120 ASN D5 56 HIS ** D5 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 296 ASN D5 354 GLN ** D4 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4 422 HIS D4 450 ASN D2 63 GLN ** D2 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 63 ASN A8 103 GLN ** BJ 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 50 HIS AJ 97 GLN ** AJ 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 153 ASN AJ 184 GLN AJ 200 GLN ** AJ 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S5 26 HIS ** S5 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S5 69 GLN A3 61 ASN ** A3 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 49 GLN ** B6 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B9 72 HIS B9 74 GLN A1 27 HIS Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.258 67376 Z= 0.544 Angle : 1.688 51.214 91403 Z= 1.067 Chirality : 0.311 6.481 10043 Planarity : 0.006 0.077 11558 Dihedral : 7.722 88.759 9050 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.01 % Allowed : 11.20 % Favored : 88.79 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.28 % Twisted Proline : 0.41 % Twisted General : 0.18 % 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: -1.99 (0.09), residues: 8038 helix: 0.19 (0.08), residues: 4105 sheet: -1.92 (0.26), residues: 366 loop : -3.20 (0.10), residues: 3567 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16076 Ramachandran restraints generated. 8038 Oldfield, 0 Emsley, 8038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16076 Ramachandran restraints generated. 8038 Oldfield, 0 Emsley, 8038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2009 residues out of total 7118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1995 time to evaluate : 5.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 3 residues processed: 2005 average time/residue: 0.6388 time to fit residues: 2198.1715 Evaluate side-chains 1567 residues out of total 7118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1564 time to evaluate : 6.086 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4915 time to fit residues: 10.7844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.6278 > 50: distance: 24 - 27: 4.389 distance: 27 - 28: 7.059 distance: 28 - 29: 8.221 distance: 28 - 31: 5.397 distance: 29 - 30: 17.557 distance: 29 - 35: 17.461 distance: 31 - 32: 7.544 distance: 32 - 33: 10.258 distance: 32 - 34: 8.222 distance: 35 - 36: 6.783 distance: 36 - 37: 3.176 distance: 36 - 39: 19.463 distance: 37 - 38: 4.882 distance: 37 - 41: 4.792 distance: 39 - 40: 29.780 distance: 41 - 42: 7.194 distance: 42 - 43: 11.323 distance: 42 - 45: 7.259 distance: 43 - 44: 14.723 distance: 43 - 48: 16.421 distance: 45 - 46: 18.480 distance: 45 - 47: 19.473 distance: 48 - 49: 13.034 distance: 49 - 50: 10.463 distance: 49 - 52: 8.083 distance: 50 - 51: 14.163 distance: 50 - 55: 28.879 distance: 52 - 53: 8.251 distance: 52 - 54: 14.023 distance: 55 - 56: 18.945 distance: 56 - 57: 18.708 distance: 57 - 58: 27.314 distance: 57 - 59: 29.736 distance: 59 - 60: 7.617 distance: 60 - 61: 9.452 distance: 60 - 63: 19.936 distance: 61 - 62: 9.518 distance: 61 - 67: 19.575 distance: 63 - 64: 12.720 distance: 64 - 65: 4.143 distance: 64 - 66: 21.022 distance: 67 - 68: 4.805 distance: 68 - 69: 7.801 distance: 69 - 70: 3.879 distance: 71 - 72: 15.052 distance: 72 - 73: 14.824 distance: 72 - 75: 12.034 distance: 73 - 74: 11.629 distance: 73 - 80: 22.372 distance: 75 - 76: 8.219 distance: 76 - 77: 8.089 distance: 77 - 78: 5.661 distance: 78 - 79: 18.739 distance: 80 - 81: 12.503 distance: 80 - 86: 33.614 distance: 81 - 82: 12.106 distance: 81 - 84: 28.168 distance: 82 - 83: 18.380 distance: 82 - 87: 21.600 distance: 84 - 85: 24.563 distance: 85 - 86: 11.845 distance: 87 - 88: 4.226 distance: 88 - 89: 6.592 distance: 88 - 91: 11.475 distance: 89 - 90: 15.048 distance: 91 - 92: 4.904 distance: 92 - 93: 4.577 distance: 92 - 94: 12.981