Starting phenix.real_space_refine on Wed Nov 15 19:12:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc7_4499/11_2023/6qc7_4499_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc7_4499/11_2023/6qc7_4499.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc7_4499/11_2023/6qc7_4499_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc7_4499/11_2023/6qc7_4499_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc7_4499/11_2023/6qc7_4499_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc7_4499/11_2023/6qc7_4499.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc7_4499/11_2023/6qc7_4499.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc7_4499/11_2023/6qc7_4499_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc7_4499/11_2023/6qc7_4499_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 12 5.49 5 S 462 5.16 5 C 42105 2.51 5 N 11027 2.21 5 O 11718 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "V1 PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V1 ARG 32": "NH1" <-> "NH2" Residue "V1 ARG 237": "NH1" <-> "NH2" Residue "V1 ARG 423": "NH1" <-> "NH2" Residue "V2 ARG 187": "NH1" <-> "NH2" Residue "V2 PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S2 TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S2 TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S3 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S7 ARG 174": "NH1" <-> "NH2" Residue "S7 ARG 178": "NH1" <-> "NH2" Residue "S8 TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V3 PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S4 ARG 64": "NH1" <-> "NH2" Residue "A9 ARG 97": "NH1" <-> "NH2" Residue "A9 ARG 186": "NH1" <-> "NH2" Residue "A9 ARG 292": "NH1" <-> "NH2" Residue "A2 ARG 33": "NH1" <-> "NH2" Residue "A6 ARG 22": "NH1" <-> "NH2" Residue "AL ARG 106": "NH1" <-> "NH2" Residue "AL PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D3 PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 ARG 195": "NH1" <-> "NH2" Residue "D1 TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 ARG 274": "NH1" <-> "NH2" Residue "D6 PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D6 PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D6 ARG 173": "NH1" <-> "NH2" Residue "D5 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D5 PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D5 TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D5 TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D5 PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D5 TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D4 TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D2 PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AK ARG 19": "NH1" <-> "NH2" Residue "B5 ARG 26": "NH1" <-> "NH2" Residue "BJ TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AJ ARG 95": "NH1" <-> "NH2" Residue "AJ PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AJ ARG 305": "NH1" <-> "NH2" Residue "A3 ARG 46": "NH1" <-> "NH2" Residue "B3 PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C2 ARG 5": "NH1" <-> "NH2" Residue "C2 ARG 120": "NH1" <-> "NH2" Residue "B4 ARG 41": "NH1" <-> "NH2" Residue "AM ARG 26": "NH1" <-> "NH2" Residue "AM ARG 81": "NH1" <-> "NH2" Residue "B9 ARG 92": "NH1" <-> "NH2" Residue "B9 ARG 128": "NH1" <-> "NH2" Residue "B9 ARG 176": "NH1" <-> "NH2" Residue "B8 ARG 70": "NH1" <-> "NH2" Residue "A1 ARG 25": "NH1" <-> "NH2" Residue "A1 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 65353 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: {'CIS': 1, 'PTRANS': 32, 'TRANS': 654} Chain: "S2" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3414 Classifications: {'peptide': 424} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 396} Chain breaks: 1 Chain: "S3" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1726 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "S7" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} Chain: "S8" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 10, 'TRANS': 165} Chain: "V3" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 345 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "S6" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 737 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "S4" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1024 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "A9" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2293 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 14, 'TRANS': 272} Chain breaks: 2 Chain: "A2" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 665 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "A5" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 901 Classifications: {'peptide': 111} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 101} Chain: "A6" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 969 Classifications: {'peptide': 114} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 106} Chain: "A7" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 766 Classifications: {'peptide': 96} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 83} Chain breaks: 1 Chain: "AL" Number of atoms: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1201 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "AA" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 645 Classifications: {'peptide': 80} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 76} Chain: "D3" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 728 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain breaks: 1 Chain: "D1" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2415 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 19, 'TRANS': 279} Chain breaks: 1 Chain: "D6" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1308 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 3, 'TRANS': 164} Chain breaks: 1 Chain: "4L" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 96} Chain: "D5" Number of atoms: 4805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4805 Classifications: {'peptide': 606} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 578} Chain: "D4" Number of atoms: 3646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3646 Classifications: {'peptide': 459} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 437} Chain: "D2" Number of atoms: 2724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2724 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 326} Chain: "AK" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1025 Classifications: {'peptide': 140} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 4, 'TRANS': 132} Chain: "B5" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1156 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 128} Chain: "AB" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 702 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "A8" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1404 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 12, 'TRANS': 156} Chain: "BJ" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1441 Classifications: {'peptide': 171} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "AJ" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2583 Classifications: {'peptide': 319} Link IDs: {'CIS': 6, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 298} Chain: "S5" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 822 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "A3" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 582 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 62} Chain: "B3" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 578 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C2" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 997 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 10, 'TRANS': 106} Chain: "B4" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1059 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 117} Chain: "AM" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1143 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 130} Chain: "B6" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 815 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 12, 'TRANS': 83} Chain breaks: 1 Chain: "B7" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1026 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "B9" Number of atoms: 1515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1515 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 16, 'TRANS': 159} Chain: "B2" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 563 Classifications: {'peptide': 65} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 56} Chain: "B8" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1324 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 135} Chain: "BK" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 853 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 93} Chain: "C1" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 391 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 3, 'TRANS': 42} Chain: "B1" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 449 Classifications: {'peptide': 52} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 49} Chain: "A1" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 577 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "V1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "S1" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S7" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "S8" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A9" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "AA" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Chain: "D1" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "D5" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 138 Unusual residues: {'3PE': 2, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 64 Chain: "AK" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "AB" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2715 SG CYSV1 365 46.259 164.057 147.149 1.00 19.90 S ATOM 3039 SG CYSV1 405 47.910 166.284 153.177 1.00 25.94 S ATOM 2695 SG CYSV1 362 52.057 164.106 148.794 1.00 42.29 S ATOM 2676 SG CYSV1 359 49.069 169.953 147.894 1.00 29.97 S ATOM 4116 SG CYSV2 103 28.225 173.539 152.995 1.00 62.43 S ATOM 4150 SG CYSV2 108 25.560 171.228 155.226 1.00 50.81 S ATOM 4430 SG CYSV2 144 32.247 172.518 156.171 1.00 49.06 S ATOM 4453 SG CYSV2 148 30.201 171.171 158.815 1.00 55.86 S ATOM 5785 SG CYSS1 114 58.675 157.796 129.294 1.00 30.07 S ATOM 5724 SG CYSS1 105 54.233 154.863 125.576 1.00 26.13 S ATOM 5745 SG CYSS1 108 56.661 160.671 123.888 1.00 34.04 S ATOM 6117 SG CYSS1 156 58.681 166.475 136.408 1.00 21.08 S ATOM 6094 SG CYSS1 153 53.163 168.062 133.279 1.00 23.11 S ATOM 6141 SG CYSS1 159 58.097 172.333 134.137 1.00 15.31 S ATOM 6471 SG CYSS1 203 58.840 167.299 130.059 1.00 33.58 S ATOM 5230 SG CYSS1 41 61.307 164.736 143.498 1.00 15.62 S ATOM 5316 SG CYSS1 52 59.850 161.265 142.222 1.00 15.70 S ATOM 5341 SG CYSS1 55 61.719 159.588 147.627 1.00 21.23 S ATOM 5442 SG CYSS1 69 62.671 163.491 147.790 1.00 29.37 S ATOM 16127 SG CYSS7 119 69.051 131.513 102.877 1.00 20.87 S ATOM 16357 SG CYSS7 149 62.966 131.788 104.575 1.00 35.26 S ATOM 15629 SG CYSS7 55 64.560 128.356 99.182 1.00 30.89 S ATOM 15623 SG CYSS7 54 65.910 126.049 104.874 1.00 42.47 S ATOM 17549 SG CYSS8 116 59.630 139.847 104.267 1.00 37.80 S ATOM 17596 SG CYSS8 122 56.481 142.908 108.936 1.00 13.24 S ATOM 17323 SG CYSS8 87 63.053 143.580 108.545 1.00 41.58 S ATOM 17625 SG CYSS8 126 51.598 148.663 112.238 1.00 45.92 S ATOM 17296 SG CYSS8 83 57.989 149.263 110.499 1.00 16.20 S ATOM 17254 SG CYSS8 77 54.068 154.044 109.225 1.00 80.47 S ATOM 17273 SG CYSS8 80 55.266 152.446 115.543 1.00 36.31 S ATOM 18846 SG CYSS6 59 39.945 158.698 117.582 1.00 25.48 S ATOM 19024 SG CYSS6 84 43.641 160.705 117.588 1.00 30.85 S ATOM 19046 SG CYSS6 87 40.851 159.019 115.606 1.00 23.84 S Time building chain proxies: 25.61, per 1000 atoms: 0.39 Number of scatterers: 65353 At special positions: 0 Unit cell: (247.8, 219.8, 203, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 462 16.00 P 12 15.00 O 11718 8.00 N 11027 7.00 C 42105 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYSBJ 76 " - pdb=" SG CYSBJ 83 " distance=2.04 Simple disulfide: pdb=" SG CYSBJ 112 " - pdb=" SG CYSBJ 124 " distance=2.03 Simple disulfide: pdb=" SG CYSS5 32 " - pdb=" SG CYSS5 65 " distance=2.04 Simple disulfide: pdb=" SG CYSS5 42 " - pdb=" SG CYSS5 55 " distance=2.04 Simple disulfide: pdb=" SG CYSB7 58 " - pdb=" SG CYSB7 89 " distance=2.01 Simple disulfide: pdb=" SG CYSB7 68 " - pdb=" SG CYSB7 79 " distance=2.04 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.08 Conformation dependent library (CDL) restraints added in 8.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FESS1 803 " pdb="FE1 FESS1 803 " - pdb=" SG CYSS1 52 " pdb="FE1 FESS1 803 " - pdb=" SG CYSS1 41 " pdb="FE2 FESS1 803 " - pdb=" SG CYSS1 55 " pdb="FE2 FESS1 803 " - pdb=" SG CYSS1 69 " pdb=" FESV2 300 " pdb="FE2 FESV2 300 " - pdb=" SG CYSV2 148 " pdb="FE2 FESV2 300 " - pdb=" SG CYSV2 144 " pdb="FE1 FESV2 300 " - pdb=" SG CYSV2 103 " pdb="FE1 FESV2 300 " - pdb=" SG CYSV2 108 " pdb=" SF4S1 801 " pdb="FE3 SF4S1 801 " - pdb=" NE2 HISS1 101 " pdb="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="FE1 SF4S1 802 " - pdb=" SG CYSS1 156 " pdb="FE4 SF4S1 802 " - pdb=" SG CYSS1 203 " pdb="FE3 SF4S1 802 " - pdb=" SG CYSS1 159 " pdb=" SF4S7 300 " 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="FE2 SF4S7 300 " - pdb=" SG CYSS7 149 " pdb=" SF4S8 201 " pdb="FE3 SF4S8 201 " - pdb=" SG CYSS8 122 " pdb="FE2 SF4S8 201 " - pdb=" SG CYSS8 116 " pdb="FE4 SF4S8 201 " - pdb=" SG CYSS8 87 " pdb="FE1 SF4S8 201 " - pdb=" SG CYSS8 119 " pdb=" SF4S8 202 " pdb="FE4 SF4S8 202 " - pdb=" SG CYSS8 80 " pdb="FE3 SF4S8 202 " - pdb=" SG CYSS8 77 " pdb="FE1 SF4S8 202 " - pdb=" SG CYSS8 126 " pdb="FE2 SF4S8 202 " - pdb=" SG CYSS8 83 " pdb=" SF4V1 500 " pdb="FE1 SF4V1 500 " - pdb=" SG CYSV1 365 " pdb="FE2 SF4V1 500 " - pdb=" SG CYSV1 405 " pdb="FE4 SF4V1 500 " - pdb=" SG CYSV1 359 " pdb="FE3 SF4V1 500 " - pdb=" SG CYSV1 362 " 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 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15198 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 311 helices and 28 sheets defined 48.4% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.03 Creating SS restraints... Processing helix chain 'V1' and resid 33 through 39 Processing helix chain 'V1' and resid 45 through 49 Processing helix chain 'V1' and resid 53 through 63 Processing helix chain 'V1' and resid 75 through 81 Processing helix chain 'V1' and resid 108 through 113 Processing helix chain 'V1' and resid 115 through 128 Processing helix chain 'V1' and resid 143 through 159 Processing helix chain 'V1' and resid 166 through 168 No H-bonds generated for 'chain 'V1' and resid 166 through 168' Processing helix chain 'V1' and resid 185 through 187 No H-bonds generated for 'chain 'V1' and resid 185 through 187' Processing helix chain 'V1' and resid 191 through 196 Processing helix chain 'V1' and resid 225 through 236 Proline residue: V1 232 - end of helix removed outlier: 3.590A 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 283 removed outlier: 3.678A pdb=" N HISV1 283 " --> pdb=" O LEUV1 279 " (cutoff:3.500A) 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 363 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: 3.851A pdb=" N ALAV2 46 " --> pdb=" O LYSV2 43 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VALV2 47 " --> pdb=" O ALAV2 44 " (cutoff:3.500A) removed outlier: 4.515A 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 73 Processing helix chain 'V2' and resid 78 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 178 Processing helix chain 'S1' and resid 26 through 33 Processing helix chain 'S1' and resid 84 through 97 Processing helix chain 'S1' and resid 116 through 122 Processing helix chain 'S1' and resid 159 through 165 Processing helix chain 'S1' and resid 197 through 199 No H-bonds generated for 'chain 'S1' and resid 197 through 199' Processing helix chain 'S1' and resid 265 through 268 No H-bonds generated for 'chain 'S1' and resid 265 through 268' Processing helix chain 'S1' and resid 271 through 274 No H-bonds generated for 'chain 'S1' and resid 271 through 274' Processing helix chain 'S1' and resid 296 through 308 Processing helix chain 'S1' and resid 325 through 338 Processing helix chain 'S1' and resid 359 through 361 No H-bonds generated for 'chain 'S1' and resid 359 through 361' Processing helix chain 'S1' and resid 370 through 373 Processing helix chain 'S1' and resid 389 through 401 Processing helix chain 'S1' and resid 426 through 434 Processing helix chain 'S1' and resid 439 through 444 Processing helix chain 'S1' and resid 463 through 479 Processing helix chain 'S1' and resid 497 through 505 Processing helix chain 'S1' and resid 512 through 516 Processing helix chain 'S1' and resid 534 through 536 No H-bonds generated for 'chain 'S1' and resid 534 through 536' Processing helix chain 'S1' and resid 596 through 606 Processing helix chain 'S1' and resid 616 through 626 Processing helix chain 'S1' and resid 628 through 631 removed outlier: 3.671A pdb=" N VALS1 631 " --> pdb=" O PROS1 628 " (cutoff:3.500A) No H-bonds generated for 'chain 'S1' and resid 628 through 631' Processing helix chain 'S1' and resid 642 through 650 removed outlier: 3.536A pdb=" N LYSS1 650 " --> pdb=" O SERS1 646 " (cutoff:3.500A) Processing helix chain 'S1' and resid 668 through 672 Processing helix chain 'S1' and resid 676 through 679 No H-bonds generated for 'chain 'S1' and resid 676 through 679' Processing helix chain 'S1' and resid 683 through 692 Processing helix chain 'S2' and resid 8 through 13 Processing helix chain 'S2' and resid 25 through 27 No H-bonds generated for 'chain 'S2' and resid 25 through 27' Processing helix chain 'S2' and resid 87 through 92 Processing helix chain 'S2' and resid 99 through 105 Processing helix chain 'S2' and resid 113 through 126 Processing helix chain 'S2' and resid 132 through 161 Processing helix chain 'S2' and resid 164 through 184 removed outlier: 3.829A 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 277 through 280 Processing helix chain 'S2' and resid 293 through 316 Processing helix chain 'S2' and resid 335 through 339 Processing helix chain 'S2' and resid 343 through 353 Processing helix chain 'S2' and resid 394 through 405 removed outlier: 3.911A pdb=" N GLYS2 401 " --> pdb=" O ALAS2 397 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEUS2 402 " --> pdb=" O HISS2 398 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ASPS2 403 " --> pdb=" O LEUS2 399 " (cutoff:3.500A) removed outlier: 6.304A 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 16 through 32 Processing helix chain 'S3' and resid 57 through 64 Processing helix chain 'S3' and resid 125 through 137 removed outlier: 3.733A pdb=" N ASNS3 128 " --> pdb=" O LYSS3 125 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TRPS3 129 " --> pdb=" O ALAS3 126 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYRS3 130 " --> pdb=" O ALAS3 127 " (cutoff:3.500A) removed outlier: 3.527A 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 80 through 82 No H-bonds generated for 'chain 'S7' and resid 80 through 82' Processing helix chain 'S7' and resid 97 through 105 Processing helix chain 'S7' and resid 124 through 126 No H-bonds generated for 'chain 'S7' and resid 124 through 126' Processing helix chain 'S7' and resid 136 through 138 No H-bonds generated for 'chain 'S7' and resid 136 through 138' Processing helix chain 'S7' and resid 153 through 168 Processing helix chain 'S7' and resid 172 through 178 Processing helix chain 'S8' and resid 14 through 26 Processing helix chain 'S8' and resid 28 through 41 Processing helix chain 'S8' and resid 82 through 85 No H-bonds generated for 'chain 'S8' and resid 82 through 85' Processing helix chain 'S8' and resid 121 through 124 No H-bonds generated for 'chain 'S8' and resid 121 through 124' 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 160 Processing helix chain 'S8' and resid 163 through 172 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 42 through 45 No H-bonds generated for 'chain 'S6' and resid 42 through 45' 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 79 through 81 No H-bonds generated for 'chain 'S4' and resid 79 through 81' Processing helix chain 'S4' and resid 89 through 98 Processing helix chain 'S4' and resid 118 through 121 No H-bonds generated for 'chain 'S4' and resid 118 through 121' Processing helix chain 'A9' and resid 30 through 41 Processing helix chain 'A9' and resid 53 through 58 Processing helix chain 'A9' and resid 60 through 62 No H-bonds generated for 'chain 'A9' and resid 60 through 62' Processing helix chain 'A9' and resid 78 through 84 Processing helix chain 'A9' and resid 109 through 122 Proline residue: A9 114 - end of helix removed outlier: 3.664A pdb=" N ILEA9 117 " --> pdb=" O ILEA9 113 " (cutoff:3.500A) Processing helix chain 'A9' and resid 144 through 158 Processing helix chain 'A9' and resid 178 through 183 Processing helix chain 'A9' and resid 207 through 219 Processing helix chain 'A9' and resid 238 through 248 Processing helix chain 'A9' and resid 282 through 289 Processing helix chain 'A9' and resid 300 through 303 No H-bonds generated for 'chain 'A9' and resid 300 through 303' Processing helix chain 'A9' and resid 310 through 317 Processing helix chain 'A2' and resid 27 through 38 Processing helix chain 'A2' and resid 41 through 46 Processing helix chain 'A2' and resid 83 through 93 Processing helix chain 'A5' and resid 19 through 36 Processing helix chain 'A5' and resid 42 through 60 removed outlier: 4.341A pdb=" N ALAA5 60 " --> pdb=" O SERA5 56 " (cutoff:3.500A) Processing helix chain 'A5' and resid 65 through 70 Processing helix chain 'A5' and resid 77 through 94 Processing helix chain 'A6' and resid 24 through 39 Processing helix chain 'A6' and resid 42 through 48 Processing helix chain 'A6' and resid 55 through 68 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 4 through 10 Processing helix chain 'AL' and resid 12 through 15 No H-bonds generated for 'chain 'AL' and resid 12 through 15' Processing helix chain 'AL' and resid 21 through 29 removed outlier: 3.689A pdb=" N ARGAL 25 " --> pdb=" O ARGAL 21 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VALAL 26 " --> pdb=" O GLYAL 22 " (cutoff:3.500A) Processing helix chain 'AL' and resid 84 through 90 Processing helix chain 'AA' and resid 8 through 21 Processing helix chain 'AA' and resid 36 through 40 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 'D3' and resid 2 through 22 Processing helix chain 'D3' and resid 53 through 78 removed outlier: 3.682A pdb=" N LEUD3 57 " --> pdb=" O METD3 53 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VALD3 58 " --> pdb=" O LYSD3 54 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALAD3 59 " --> pdb=" O PHED3 55 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILED3 60 " --> pdb=" O PHED3 56 " (cutoff:3.500A) Proline residue: D3 74 - end of helix removed outlier: 5.897A pdb=" N TRPD3 77 " --> pdb=" O LEUD3 73 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALAD3 78 " --> pdb=" O PROD3 74 " (cutoff:3.500A) Processing helix chain 'D3' and resid 85 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 56 Processing helix chain 'D1' and resid 68 through 83 Proline residue: D1 75 - end of helix Processing helix chain 'D1' and resid 102 through 121 Processing helix chain 'D1' and resid 126 through 142 removed outlier: 4.790A pdb=" N TYRD1 142 " --> pdb=" O GLND1 138 " (cutoff:3.500A) Processing helix chain 'D1' and resid 145 through 154 Processing helix chain 'D1' and resid 163 through 170 removed outlier: 4.728A pdb=" N GLUD1 170 " --> pdb=" O ILED1 166 " (cutoff:3.500A) 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 192 Processing helix chain 'D1' and resid 220 through 241 Processing helix chain 'D1' and resid 252 through 276 removed outlier: 4.430A pdb=" N SERD1 276 " --> pdb=" O TRPD1 272 " (cutoff:3.500A) Processing helix chain 'D1' and resid 282 through 306 Proline residue: D1 295 - end of helix Processing helix chain 'D6' and resid 5 through 21 Processing helix chain 'D6' and resid 26 through 46 Processing helix chain 'D6' and resid 52 through 63 removed outlier: 3.700A pdb=" N LEUD6 58 " --> pdb=" O LEUD6 54 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILED6 59 " --> pdb=" O METD6 55 " (cutoff:3.500A) Processing helix chain 'D6' and resid 65 through 74 Processing helix chain 'D6' and resid 87 through 108 Processing helix chain 'D6' and resid 139 through 148 removed outlier: 3.884A pdb=" N LEUD6 146 " --> pdb=" O GLYD6 142 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYRD6 147 " --> pdb=" O ILED6 143 " (cutoff:3.500A) Processing helix chain 'D6' and resid 152 through 171 Processing helix chain '4L' and resid 3 through 20 Processing helix chain '4L' and resid 26 through 50 Processing helix chain '4L' and resid 59 through 84 Processing helix chain 'D5' and resid 2 through 15 removed outlier: 4.536A 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 56 removed outlier: 4.535A 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 87 No H-bonds generated for 'chain 'D5' and resid 84 through 87' Processing helix chain 'D5' and resid 90 through 107 Processing helix chain 'D5' and resid 114 through 133 Processing helix chain 'D5' and resid 137 through 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 211 through 223 Processing helix chain 'D5' and resid 232 through 238 Processing helix chain 'D5' and resid 241 through 248 Processing helix chain 'D5' and resid 254 through 262 removed outlier: 3.818A pdb=" N PHED5 258 " --> pdb=" O ALAD5 255 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEUD5 259 " --> pdb=" O GLYD5 256 " (cutoff:3.500A) Processing helix chain 'D5' and resid 271 through 291 Processing helix chain 'D5' and resid 298 through 318 Processing helix chain 'D5' and resid 322 through 349 Processing helix chain 'D5' and resid 368 through 379 Processing helix chain 'D5' and resid 387 through 400 removed outlier: 4.703A pdb=" N SERD5 391 " --> pdb=" O THRD5 387 " (cutoff:3.500A) removed outlier: 4.402A 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: 5.735A pdb=" N GLYD5 465 " --> pdb=" O SERD5 461 " (cutoff:3.500A) removed outlier: 5.737A 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 546 removed outlier: 3.674A pdb=" N TYRD5 529 " --> pdb=" O LEUD5 526 " (cutoff:3.500A) Proline residue: D5 530 - end of helix removed outlier: 3.634A pdb=" N METD5 533 " --> pdb=" O PROD5 530 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HISD5 534 " --> pdb=" O THRD5 531 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N THRD5 537 " --> pdb=" O HISD5 534 " (cutoff:3.500A) Proline residue: D5 538 - end of helix removed outlier: 3.508A pdb=" N ASND5 541 " --> pdb=" O PROD5 538 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEUD5 542 " --> pdb=" O TYRD5 539 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N METD5 544 " --> pdb=" O ASND5 541 " (cutoff:3.500A) removed outlier: 3.705A 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 585 through 599 Processing helix chain 'D4' and resid 2 through 16 Proline residue: D4 7 - end of helix removed outlier: 3.761A pdb=" N METD4 12 " --> pdb=" O THRD4 8 " (cutoff:3.500A) Proline residue: D4 13 - end of helix removed outlier: 3.992A pdb=" N TRPD4 16 " --> pdb=" O METD4 12 " (cutoff:3.500A) Processing helix chain 'D4' and resid 23 through 41 removed outlier: 3.952A 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 115 through 135 Proline residue: D4 128 - end of helix removed outlier: 3.840A pdb=" N ILED4 131 " --> pdb=" O VALD4 127 " (cutoff:3.500A) Processing helix chain 'D4' and resid 142 through 156 Processing helix chain 'D4' and resid 159 through 170 Processing helix chain 'D4' and resid 176 through 179 No H-bonds generated for 'chain 'D4' and resid 176 through 179' Processing helix chain 'D4' and resid 190 through 206 Processing helix chain 'D4' and resid 214 through 221 removed outlier: 4.584A pdb=" N LYSD4 218 " --> pdb=" O LEUD4 214 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALAD4 219 " --> pdb=" O TRPD4 215 " (cutoff:3.500A) Processing helix chain 'D4' and resid 225 through 248 removed outlier: 5.079A pdb=" N LEUD4 248 " --> pdb=" O METD4 244 " (cutoff:3.500A) Processing helix chain 'D4' and resid 251 through 257 removed outlier: 4.496A pdb=" N ASPD4 255 " --> pdb=" O ASND4 251 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N PHED4 256 " --> pdb=" O PROD4 252 " (cutoff:3.500A) Processing helix chain 'D4' and resid 259 through 277 removed outlier: 3.608A pdb=" N LEUD4 277 " --> pdb=" O SERD4 273 " (cutoff:3.500A) Processing helix chain 'D4' and resid 282 through 302 removed outlier: 3.937A pdb=" N ILED4 286 " --> pdb=" O LEUD4 282 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALAD4 287 " --> pdb=" O LYSD4 283 " (cutoff:3.500A) Processing helix chain 'D4' and resid 306 through 336 Processing helix chain 'D4' and resid 355 through 366 Processing helix chain 'D4' and resid 373 through 388 Processing helix chain 'D4' and resid 393 through 414 removed outlier: 3.861A pdb=" N THRD4 414 " --> pdb=" O METD4 410 " (cutoff:3.500A) Processing helix chain 'D4' and resid 431 through 449 Proline residue: D4 443 - end of helix Processing helix chain 'D2' and resid 3 through 22 Processing helix chain 'D2' and resid 26 through 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 109 through 111 No H-bonds generated for 'chain 'D2' and resid 109 through 111' 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: 4.076A pdb=" N VALD2 141 " --> pdb=" O ALAD2 137 " (cutoff:3.500A) Proline residue: D2 147 - end of helix Processing helix chain 'D2' and resid 151 through 167 Processing helix chain 'D2' and resid 175 through 192 Processing helix chain 'D2' and resid 198 through 220 Processing helix chain 'D2' and resid 227 through 236 Processing helix chain 'D2' and resid 239 through 251 Processing helix chain 'D2' and resid 261 through 271 Processing helix chain 'D2' and resid 277 through 300 removed outlier: 4.519A pdb=" N LEUD2 290 " --> pdb=" O ALAD2 286 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TYRD2 291 " --> pdb=" O LEUD2 287 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N PHED2 292 " --> pdb=" O LEUD2 288 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N TYRD2 293 " --> pdb=" O ASND2 289 " (cutoff:3.500A) Processing helix chain 'D2' and resid 311 through 314 No H-bonds generated for 'chain 'D2' and resid 311 through 314' Processing helix chain 'D2' and resid 327 through 334 Processing helix chain 'D2' and resid 340 through 345 removed outlier: 3.817A pdb=" N SERD2 344 " --> pdb=" O PROD2 341 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILED2 345 " --> pdb=" O ILED2 342 " (cutoff:3.500A) Processing helix chain 'AK' and resid 2 through 8 Processing helix chain 'AK' and resid 19 through 43 Processing helix chain 'AK' and resid 48 through 80 Processing helix chain 'AK' and resid 87 through 104 Processing helix chain 'AK' and resid 107 through 130 Processing helix chain 'B5' and resid 16 through 46 removed outlier: 4.855A pdb=" N THRB5 32 " --> pdb=" O TYRB5 28 " (cutoff:3.500A) Proline residue: B5 35 - end of helix Processing helix chain 'B5' and resid 70 through 78 Processing helix chain 'B5' and resid 83 through 117 Processing helix chain 'AB' and resid 8 through 20 Processing helix chain 'AB' and resid 44 through 58 Processing helix chain 'AB' and resid 64 through 67 No H-bonds generated for 'chain 'AB' and resid 64 through 67' 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 39 through 48 Processing helix chain 'A8' and resid 56 through 74 Processing helix chain 'A8' and resid 80 through 89 Processing helix chain 'A8' and resid 100 through 113 Processing helix chain 'BJ' and resid 28 through 56 removed outlier: 5.138A 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: 4.469A pdb=" N GLUBJ 86 " --> pdb=" O LEUBJ 82 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 126 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 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: 4.406A pdb=" N CYSAJ 161 " --> pdb=" O LYSAJ 157 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLUAJ 162 " --> pdb=" O VALAJ 158 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 176 through 186 Processing helix chain 'AJ' and resid 189 through 192 No H-bonds generated for 'chain 'AJ' and resid 189 through 192' Processing helix chain 'AJ' and resid 196 through 208 Processing helix chain 'AJ' and resid 210 through 214 Processing helix chain 'AJ' and resid 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 266 through 272 removed outlier: 5.364A pdb=" N TYRAJ 272 " --> pdb=" O GLUAJ 268 " (cutoff:3.500A) 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 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 removed outlier: 3.532A pdb=" N LEUB3 66 " --> pdb=" O PHEB3 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B3' and resid 62 through 66' Processing helix chain 'B3' and resid 70 through 82 removed outlier: 3.768A pdb=" N PHEB3 74 " --> pdb=" O PHEB3 70 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ALAB3 75 " --> pdb=" O LYSB3 71 " (cutoff:3.500A) Processing helix chain 'C2' and resid 16 through 19 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 48 Processing helix chain 'B4' and resid 62 through 71 Processing helix chain 'B4' and resid 73 through 75 No H-bonds generated for 'chain 'B4' and resid 73 through 75' Processing helix chain 'B4' and resid 83 through 93 Processing helix chain 'B4' and resid 95 through 117 Processing helix chain 'AM' and resid 32 through 69 Processing helix chain 'AM' and resid 71 through 96 Processing helix chain 'AM' and resid 130 through 135 Processing helix chain 'AM' and resid 138 through 141 No H-bonds generated for 'chain 'AM' and resid 138 through 141' Processing helix chain 'B6' and resid 5 through 25 Processing helix chain 'B6' and resid 68 through 84 Proline residue: B6 77 - end of helix Processing helix chain 'B6' and resid 87 through 91 Processing helix chain 'B7' and resid 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 48 Processing helix chain 'B9' and resid 56 through 72 Processing helix chain 'B9' and resid 94 through 96 No H-bonds generated for 'chain 'B9' and resid 94 through 96' Processing helix chain 'B9' and resid 108 through 113 Processing helix chain 'B9' and resid 115 through 130 Processing helix chain 'B9' and resid 134 through 142 Processing helix chain 'B9' and resid 167 through 170 No H-bonds generated for 'chain 'B9' and resid 167 through 170' Processing helix chain 'B2' and resid 19 through 41 Processing helix chain 'B8' and resid 5 through 7 No H-bonds generated for 'chain 'B8' and resid 5 through 7' Processing helix chain 'B8' and resid 18 through 26 Processing helix chain 'B8' and resid 60 through 62 No H-bonds generated for 'chain 'B8' and resid 60 through 62' Processing helix chain 'B8' and resid 81 through 83 No H-bonds generated for 'chain 'B8' and resid 81 through 83' Processing helix chain 'B8' and resid 99 through 121 Processing helix chain 'BK' and resid 51 through 63 removed outlier: 4.049A 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 14 through 45 Processing helix chain 'B1' and resid 14 through 33 removed outlier: 3.699A pdb=" N VALB1 18 " --> pdb=" O VALB1 14 " (cutoff:3.500A) Processing helix chain 'A1' and resid 3 through 29 Proline residue: A1 7 - end of helix Proline residue: A1 19 - end of helix Processing helix chain 'A1' and resid 42 through 55 Processing sheet with id= A, first strand: chain 'V1' and resid 220 through 223 removed outlier: 6.558A pdb=" N TYRV1 92 " --> pdb=" O THRV1 221 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ALAV1 223 " --> pdb=" O TYRV1 92 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VALV1 94 " --> pdb=" O ALAV1 223 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ALAV1 133 " --> pdb=" O LEUV1 93 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VALV1 95 " --> pdb=" O ALAV1 133 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYRV1 135 " --> pdb=" O VALV1 95 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ALAV1 97 " --> pdb=" O TYRV1 135 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N TYRV1 137 " --> pdb=" O ALAV1 97 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASPV1 174 " --> pdb=" O ALAV1 134 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILEV1 136 " --> pdb=" O ASPV1 174 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHEV1 176 " --> pdb=" O ILEV1 136 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILEV1 138 " --> pdb=" O PHEV1 176 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VALV1 178 " --> pdb=" O ILEV1 138 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'V1' and resid 253 through 257 Processing sheet with id= C, first strand: chain 'V1' and resid 294 through 298 removed outlier: 6.542A pdb=" N METV1 337 " --> pdb=" O LEUV1 295 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VALV1 297 " --> pdb=" O ILEV1 335 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILEV1 335 " --> pdb=" O VALV1 297 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'V2' and resid 138 through 142 Processing sheet with id= E, first strand: chain 'S1' and resid 16 through 20 removed outlier: 6.738A pdb=" N TRPS1 77 " --> pdb=" O PHES1 12 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'S1' and resid 146 through 148 Processing sheet with id= G, first strand: chain 'S1' and resid 173 through 177 Processing sheet with id= H, first strand: chain 'S1' and resid 223 through 228 Processing sheet with id= I, first strand: chain 'S1' and resid 283 through 286 Processing sheet with id= J, first strand: chain 'S1' and resid 342 through 344 removed outlier: 6.285A pdb=" N VALS1 559 " --> pdb=" O TYRS1 545 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N GLYS1 547 " --> pdb=" O VALS1 559 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEUS1 561 " --> pdb=" O GLYS1 547 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S1' and resid 490 through 492 removed outlier: 7.230A pdb=" N ASNS1 491 " --> pdb=" O PROS1 449 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N VALS1 451 " --> pdb=" O ASNS1 491 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VALS1 376 " --> pdb=" O METS1 450 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VALS1 452 " --> pdb=" O VALS1 376 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEUS1 378 " --> pdb=" O VALS1 452 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYSS1 405 " --> pdb=" O VALS1 377 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N LEUS1 379 " --> pdb=" O LYSS1 405 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALAS1 407 " --> pdb=" O LEUS1 379 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASPS1 420 " --> pdb=" O LEUS1 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'S1' and resid 572 through 574 removed outlier: 3.562A pdb=" N TYRS1 573 " --> pdb=" O GLNS1 581 " (cutoff:3.500A) 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 369 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 173 through 177 Processing sheet with id= Q, first strand: chain 'S7' and resid 85 through 88 removed outlier: 6.464A pdb=" N TYRS7 112 " --> pdb=" O METS7 86 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VALS7 88 " --> pdb=" O TYRS7 112 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VALS7 114 " --> pdb=" O VALS7 88 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILES7 144 " --> pdb=" O SERS7 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'S8' and resid 93 through 96 Processing sheet with id= S, first strand: chain 'S6' and resid 56 through 59 Processing sheet with id= T, first strand: chain 'S4' and resid 103 through 105 removed outlier: 7.053A pdb=" N ALAS4 35 " --> pdb=" O ASPS4 104 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'S4' and resid 64 through 67 removed outlier: 3.671A pdb=" N SERS4 74 " --> pdb=" O TRPS4 65 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASNS4 67 " --> pdb=" O TRPS4 72 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TRPS4 72 " --> pdb=" O ASNS4 67 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A9' and resid 90 through 93 removed outlier: 6.590A pdb=" N GLNA9 44 " --> pdb=" O ALAA9 21 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VALA9 23 " --> pdb=" O GLNA9 44 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILEA9 46 " --> pdb=" O VALA9 23 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILEA9 69 " --> pdb=" O VALA9 47 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'A9' and resid 130 through 134 removed outlier: 6.131A pdb=" N THRA9 164 " --> pdb=" O HISA9 131 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N SERA9 133 " --> pdb=" O THRA9 164 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ILEA9 166 " --> pdb=" O SERA9 133 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'A9' and resid 170 through 172 removed outlier: 3.977A pdb=" N VALA9 205 " --> pdb=" O ASPA9 170 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'A2' and resid 51 through 56 removed outlier: 3.719A pdb=" N ILEA2 18 " --> pdb=" O PROA2 51 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARGA2 67 " --> pdb=" O ARGA2 16 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILEA2 18 " --> pdb=" O TRPA2 65 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRPA2 65 " --> pdb=" O ILEA2 18 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILEA2 20 " --> pdb=" O LYSA2 63 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LYSA2 63 " --> pdb=" O ILEA2 20 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'AL' and resid 40 through 42 Processing sheet with id= AA, first strand: chain 'D5' and resid 61 through 67 Processing sheet with id= AB, first strand: chain 'AJ' and resid 122 through 125 removed outlier: 6.815A pdb=" N VALAJ 168 " --> pdb=" O THRAJ 26 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ASPAJ 28 " --> pdb=" O VALAJ 168 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILEAJ 170 " --> pdb=" O ASPAJ 28 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLUAJ 219 " --> pdb=" O VALAJ 169 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N TYRAJ 171 " --> pdb=" O GLUAJ 219 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LEUAJ 221 " --> pdb=" O TYRAJ 171 " (cutoff:3.500A) 2718 hydrogen bonds defined for protein. 7938 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: 20.63 Time building geometry restraints manager: 21.15 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: 27747 1.42 - 1.64: 38432 1.64 - 1.86: 750 1.86 - 2.08: 0 2.08 - 2.30: 80 Bond restraints: 67009 Sorted by residual: bond pdb=" O2B NDPA9 401 " pdb=" P2B NDPA9 401 " ideal model delta sigma weight residual 1.833 1.620 0.213 3.80e-02 6.93e+02 3.15e+01 bond pdb=" C13 ZMPAA 101 " pdb=" N1 ZMPAA 101 " ideal model delta sigma weight residual 1.451 1.339 0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" C16 ZMPAA 101 " pdb=" N2 ZMPAA 101 " ideal model delta sigma weight residual 1.452 1.341 0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C16 ZMPAB 101 " pdb=" N2 ZMPAB 101 " ideal model delta sigma weight residual 1.452 1.342 0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" O5D NDPA9 401 " pdb=" PN NDPA9 401 " ideal model delta sigma weight residual 1.757 1.576 0.181 3.50e-02 8.16e+02 2.68e+01 ... (remaining 67004 not shown) Histogram of bond angle deviations from ideal: 70.65 - 84.46: 72 84.46 - 98.27: 17 98.27 - 112.08: 32918 112.08 - 125.90: 56291 125.90 - 139.71: 1570 Bond angle restraints: 90868 Sorted by residual: angle pdb=" S1 FESS1 803 " pdb="FE2 FESS1 803 " pdb=" S2 FESS1 803 " ideal model delta sigma weight residual 104.33 91.67 12.66 1.14e+00 7.69e-01 1.23e+02 angle pdb=" S1 FESV2 300 " pdb="FE2 FESV2 300 " pdb=" S2 FESV2 300 " ideal model delta sigma weight residual 104.33 91.82 12.51 1.14e+00 7.69e-01 1.20e+02 angle pdb="FE1 FESV2 300 " pdb=" S2 FESV2 300 " pdb="FE2 FESV2 300 " ideal model delta sigma weight residual 75.66 87.94 -12.28 1.14e+00 7.69e-01 1.16e+02 angle pdb=" PA NDPA9 401 " pdb=" O3 NDPA9 401 " pdb=" PN NDPA9 401 " ideal model delta sigma weight residual 107.74 128.62 -20.88 1.95e+00 2.62e-01 1.14e+02 angle pdb=" S1 FESV2 300 " pdb="FE1 FESV2 300 " pdb=" S2 FESV2 300 " ideal model delta sigma weight residual 104.33 91.57 12.76 1.20e+00 6.94e-01 1.13e+02 ... (remaining 90863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.66: 39384 28.66 - 57.31: 812 57.31 - 85.97: 69 85.97 - 114.63: 3 114.63 - 143.28: 2 Dihedral angle restraints: 40270 sinusoidal: 16714 harmonic: 23556 Sorted by residual: dihedral pdb=" CA PHEB7 30 " pdb=" C PHEB7 30 " pdb=" N PROB7 31 " pdb=" CA PROB7 31 " ideal model delta harmonic sigma weight residual -180.00 -121.49 -58.51 0 5.00e+00 4.00e-02 1.37e+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 -123.37 -56.63 0 5.00e+00 4.00e-02 1.28e+02 dihedral pdb=" CA ILEA7 67 " pdb=" C ILEA7 67 " pdb=" N VALA7 68 " pdb=" CA VALA7 68 " ideal model delta harmonic sigma weight residual 180.00 126.80 53.20 0 5.00e+00 4.00e-02 1.13e+02 ... (remaining 40267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.223: 9963 4.223 - 8.446: 0 8.446 - 12.670: 0 12.670 - 16.893: 0 16.893 - 21.116: 24 Chirality restraints: 9987 Sorted by residual: chirality pdb="FE3 SF4V1 500 " pdb=" S1 SF4V1 500 " pdb=" S2 SF4V1 500 " pdb=" S4 SF4V1 500 " both_signs ideal model delta sigma weight residual False -10.55 10.56 -21.12 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE4 SF4S8 201 " pdb=" S1 SF4S8 201 " pdb=" S2 SF4S8 201 " pdb=" S3 SF4S8 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.56 21.11 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE1 SF4S8 202 " pdb=" S2 SF4S8 202 " pdb=" S3 SF4S8 202 " pdb=" S4 SF4S8 202 " both_signs ideal model delta sigma weight residual False -10.55 10.56 -21.11 2.00e-01 2.50e+01 1.11e+04 ... (remaining 9984 not shown) Planarity restraints: 11478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMNV1 501 " -0.026 2.00e-02 2.50e+03 4.30e-02 8.79e+01 pdb=" C10 FMNV1 501 " -0.051 2.00e-02 2.50e+03 pdb=" C2 FMNV1 501 " 0.034 2.00e-02 2.50e+03 pdb=" C4 FMNV1 501 " -0.010 2.00e-02 2.50e+03 pdb=" C4A FMNV1 501 " -0.038 2.00e-02 2.50e+03 pdb=" C5A FMNV1 501 " -0.020 2.00e-02 2.50e+03 pdb=" C6 FMNV1 501 " 0.025 2.00e-02 2.50e+03 pdb=" C7 FMNV1 501 " 0.036 2.00e-02 2.50e+03 pdb=" C7M FMNV1 501 " 0.030 2.00e-02 2.50e+03 pdb=" C8 FMNV1 501 " 0.016 2.00e-02 2.50e+03 pdb=" C8M FMNV1 501 " 0.059 2.00e-02 2.50e+03 pdb=" C9 FMNV1 501 " -0.030 2.00e-02 2.50e+03 pdb=" C9A FMNV1 501 " -0.047 2.00e-02 2.50e+03 pdb=" N1 FMNV1 501 " -0.014 2.00e-02 2.50e+03 pdb=" N10 FMNV1 501 " -0.062 2.00e-02 2.50e+03 pdb=" N3 FMNV1 501 " 0.026 2.00e-02 2.50e+03 pdb=" N5 FMNV1 501 " -0.024 2.00e-02 2.50e+03 pdb=" O2 FMNV1 501 " 0.116 2.00e-02 2.50e+03 pdb=" O4 FMNV1 501 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VALA7 68 " -0.032 2.00e-02 2.50e+03 6.44e-02 4.15e+01 pdb=" C VALA7 68 " 0.111 2.00e-02 2.50e+03 pdb=" O VALA7 68 " -0.042 2.00e-02 2.50e+03 pdb=" N META7 69 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SERA7 70 " -0.020 2.00e-02 2.50e+03 4.19e-02 1.76e+01 pdb=" C SERA7 70 " 0.072 2.00e-02 2.50e+03 pdb=" O SERA7 70 " -0.028 2.00e-02 2.50e+03 pdb=" N SERA7 71 " -0.024 2.00e-02 2.50e+03 ... (remaining 11475 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 1501 2.68 - 3.24: 62049 3.24 - 3.79: 105268 3.79 - 4.35: 131405 4.35 - 4.90: 211812 Nonbonded interactions: 512035 Sorted by model distance: nonbonded pdb=" CA ALAS3 80 " pdb=" O GLUS3 91 " model vdw 2.126 3.470 nonbonded pdb=" CB SERAB 44 " pdb=" O7 ZMPAB 101 " model vdw 2.202 2.752 nonbonded pdb=" O SERD1 119 " pdb=" OG SERD1 123 " model vdw 2.219 2.440 nonbonded pdb=" O GLNS3 38 " pdb=" CA SERA7 70 " model vdw 2.222 3.470 nonbonded pdb=" OG SERD5 77 " pdb=" OG SERD5 79 " model vdw 2.235 2.440 ... (remaining 512030 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'AA' and (resid 5 through 84 or (resid 101 and (name C10 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C20 or name C21 or name C3 or name C4 or name C5 \ or name C6 or name C7 or name C8 or name C9 or name N1 or name N2 or name O1 or \ name O2 or name O3 or name O4 or name O5 or name O6 or name O7 or name P1 or nam \ e S1 )))) selection = (chain 'AB' and (resid 5 through 84 or resid 101)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.950 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: 0.070 Extract box with map and model: 28.880 Check model and map are aligned: 0.730 Set scattering table: 0.450 Process input model: 144.910 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 186.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.213 67009 Z= 0.423 Angle : 1.203 20.876 90868 Z= 0.630 Chirality : 1.034 21.116 9987 Planarity : 0.008 0.088 11478 Dihedral : 11.600 143.281 25036 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.31 % Favored : 87.62 % Rotamer: Outliers : 0.47 % Allowed : 5.77 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.33 % Twisted Proline : 1.04 % Twisted General : 0.53 % 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: -4.14 (0.07), residues: 7980 helix: -1.96 (0.06), residues: 4144 sheet: -2.13 (0.24), residues: 392 loop : -3.86 (0.09), residues: 3444 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3260 residues out of total 7073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 3227 time to evaluate : 5.831 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 revert: symmetry clash revert: symmetry clash 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: 33 outliers final: 4 residues processed: 3242 average time/residue: 0.6910 time to fit residues: 3707.5653 Evaluate side-chains 1796 residues out of total 7073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1792 time to evaluate : 5.744 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4566 time to fit residues: 11.2527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 664 optimal weight: 0.2980 chunk 596 optimal weight: 0.8980 chunk 330 optimal weight: 7.9990 chunk 203 optimal weight: 2.9990 chunk 402 optimal weight: 0.9990 chunk 318 optimal weight: 20.0000 chunk 616 optimal weight: 5.9990 chunk 238 optimal weight: 2.9990 chunk 375 optimal weight: 4.9990 chunk 459 optimal weight: 0.4980 chunk 714 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V1 261 HIS V1 373 ASN ** V2 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V2 121 GLN ** V2 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 51 ASN S1 365 ASN ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2 50 ASN S2 79 HIS S2 84 HIS S2 135 GLN ** S2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 157 HIS ** S2 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2 316 ASN S2 398 HIS ** S2 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 19 HIS S3 87 GLN S3 88 ASN S3 102 ASN ** S3 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 127 HIS S8 168 ASN S6 16 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN A9 2 HIS A9 103 ASN A9 180 ASN A9 288 HIS A2 47 ASN A2 80 ASN A2 85 GLN A5 36 HIS A5 49 GLN ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 95 GLN A6 25 ASN ** A6 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 125 HIS ** A7 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3 10 ASN ** D1 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 157 ASN ** D1 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 194 ASN ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 304 HIS D6 175 ASN D5 72 GLN D5 115 ASN ** D5 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 248 HIS D5 309 GLN ** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 470 ASN D5 524 ASN D5 534 HIS D5 580 GLN ** D5 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 43 ASN ** D4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 144 ASN ** D4 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 192 ASN ** D4 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2 2 ASN D2 174 GLN D2 186 HIS D2 204 ASN D2 235 ASN D2 316 GLN B5 44 ASN ** B5 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B5 143 ASN ** BJ 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 99 GLN BJ 122 GLN AJ 76 ASN AJ 97 GLN ** AJ 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 204 ASN AJ 251 GLN AJ 271 ASN ** AJ 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S5 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S5 15 HIS S5 26 HIS S5 33 HIS B4 49 GLN B4 51 ASN B4 82 ASN AM 75 GLN B7 91 HIS ** B9 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B8 72 ASN A1 27 HIS Total number of N/Q/H flips: 73 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.265 67009 Z= 0.558 Angle : 1.689 51.134 90868 Z= 1.070 Chirality : 0.305 6.314 9987 Planarity : 0.006 0.075 11478 Dihedral : 8.492 112.854 9034 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 0.24 % Allowed : 4.43 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.33 % Twisted Proline : 0.84 % 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: -2.72 (0.09), residues: 7980 helix: -0.56 (0.07), residues: 4161 sheet: -1.83 (0.26), residues: 360 loop : -3.47 (0.09), residues: 3459 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2386 residues out of total 7073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 2369 time to evaluate : 5.799 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 outliers start: 17 outliers final: 8 residues processed: 2377 average time/residue: 0.6481 time to fit residues: 2607.6686 Evaluate side-chains 1715 residues out of total 7073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1707 time to evaluate : 5.802 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.4901 time to fit residues: 15.5822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 397 optimal weight: 5.9990 chunk 221 optimal weight: 5.9990 chunk 594 optimal weight: 5.9990 chunk 486 optimal weight: 0.0170 chunk 197 optimal weight: 5.9990 chunk 715 optimal weight: 0.0770 chunk 773 optimal weight: 0.8980 chunk 637 optimal weight: 10.0000 chunk 710 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 574 optimal weight: 0.1980 overall best weight: 1.0378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V1 116 HIS V1 373 ASN ** V2 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 214 GLN ** S1 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 198 ASN ** S1 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 640 ASN ** S2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 157 HIS S2 231 ASN S2 398 HIS ** S2 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 88 ASN ** S3 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 162 GLN S8 65 HIS S6 16 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN A9 2 HIS ** A9 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 24 GLN A5 49 GLN ** A5 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 85 ASN A7 20 GLN ** A7 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 17 HIS ** AL 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 10 ASN ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 157 ASN ** D1 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 304 HIS ** D6 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 175 ASN D5 200 GLN D5 226 GLN D5 332 HIS ** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 43 ASN ** D4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN ** B5 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A8 72 GLN A8 76 HIS BJ 77 HIS ** AJ 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 257 HIS AJ 271 ASN S5 6 GLN ** A3 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 60 GLN B6 82 HIS B7 116 GLN ** B9 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B9 75 HIS ** B9 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 58 GLN B8 78 HIS A1 31 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.245 67009 Z= 0.533 Angle : 1.666 50.631 90868 Z= 1.058 Chirality : 0.312 6.367 9987 Planarity : 0.005 0.075 11478 Dihedral : 8.020 92.052 9034 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer: Outliers : 0.20 % Allowed : 4.13 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.34 % Twisted Proline : 0.42 % Twisted General : 0.16 % 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: -2.20 (0.09), residues: 7980 helix: -0.03 (0.08), residues: 4137 sheet: -1.71 (0.26), residues: 385 loop : -3.34 (0.09), residues: 3458 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2199 residues out of total 7073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 2185 time to evaluate : 5.730 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 outliers start: 14 outliers final: 6 residues processed: 2196 average time/residue: 0.6061 time to fit residues: 2272.0219 Evaluate side-chains 1653 residues out of total 7073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1647 time to evaluate : 5.712 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4661 time to fit residues: 13.0113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 707 optimal weight: 7.9990 chunk 538 optimal weight: 5.9990 chunk 371 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 341 optimal weight: 4.9990 chunk 480 optimal weight: 0.9990 chunk 718 optimal weight: 3.9990 chunk 760 optimal weight: 9.9990 chunk 375 optimal weight: 4.9990 chunk 680 optimal weight: 9.9990 chunk 205 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V1 150 GLN V1 373 ASN ** V2 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 157 ASN ** S1 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 336 ASN S1 392 ASN ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 150 HIS S2 157 HIS ** S2 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 38 GLN ** S3 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S3 88 ASN ** S3 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 65 HIS V3 55 ASN ** S6 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S4 29 HIS S4 50 ASN ** A9 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 148 ASN A2 21 HIS A2 80 ASN A5 75 GLN A5 85 ASN ** A7 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 17 HIS ** AL 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AL 69 ASN AL 112 ASN D3 10 ASN ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 304 HIS D5 59 GLN D5 205 ASN ** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4 331 ASN B5 69 HIS A8 72 GLN AJ 151 HIS AJ 264 GLN AJ 271 ASN A3 45 ASN ** B4 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 111 HIS B9 138 GLN A1 31 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.253 67009 Z= 0.571 Angle : 1.695 51.382 90868 Z= 1.073 Chirality : 0.311 6.511 9987 Planarity : 0.006 0.071 11478 Dihedral : 7.854 85.454 9034 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.01 % Allowed : 11.44 % Favored : 88.55 % Rotamer: Outliers : 0.07 % Allowed : 4.40 % Favored : 95.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.34 % Twisted Proline : 0.42 % Twisted General : 0.16 % 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: -2.01 (0.09), residues: 7980 helix: 0.13 (0.08), residues: 4156 sheet: -1.63 (0.25), residues: 393 loop : -3.27 (0.10), residues: 3431 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2001 residues out of total 7073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1996 time to evaluate : 5.832 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 outliers start: 5 outliers final: 2 residues processed: 2001 average time/residue: 0.6001 time to fit residues: 2055.1208 Evaluate side-chains 1548 residues out of total 7073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1546 time to evaluate : 5.806 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4441 time to fit residues: 9.3423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 633 optimal weight: 8.9990 chunk 431 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 566 optimal weight: 0.9990 chunk 313 optimal weight: 10.0000 chunk 649 optimal weight: 10.0000 chunk 525 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 388 optimal weight: 10.0000 chunk 682 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V1 431 GLN V2 9 HIS ** V2 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 198 ASN ** S1 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 392 ASN ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 150 HIS S2 157 HIS ** S2 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2 306 GLN ** S2 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 88 ASN S3 211 GLN ** S7 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S6 16 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN A9 2 HIS ** A9 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 37 HIS A9 115 GLN ** A9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 75 GLN A7 20 GLN AL 17 HIS AL 31 ASN AL 69 ASN AL 112 ASN D3 10 ASN ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 287 HIS D1 304 HIS ** D1 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 400 ASN ** D5 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 204 ASN B5 143 ASN AJ 271 ASN S5 26 HIS A3 10 ASN ** A3 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B7 49 GLN ** B9 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 6 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.242 67009 Z= 0.537 Angle : 1.672 50.691 90868 Z= 1.061 Chirality : 0.311 6.363 9987 Planarity : 0.005 0.067 11478 Dihedral : 7.640 86.232 9034 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.64 % Favored : 89.35 % Rotamer: Outliers : 0.10 % Allowed : 3.46 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.34 % Twisted Proline : 0.42 % Twisted General : 0.16 % 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: -1.79 (0.09), residues: 7980 helix: 0.31 (0.08), residues: 4162 sheet: -1.51 (0.27), residues: 362 loop : -3.16 (0.10), residues: 3456 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2060 residues out of total 7073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 2053 time to evaluate : 5.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 2060 average time/residue: 0.6331 time to fit residues: 2233.7633 Evaluate side-chains 1567 residues out of total 7073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1564 time to evaluate : 5.734 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4720 time to fit residues: 10.4157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 255 optimal weight: 4.9990 chunk 685 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 446 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 761 optimal weight: 10.0000 chunk 632 optimal weight: 4.9990 chunk 352 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 251 optimal weight: 6.9990 chunk 399 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V1 361 GLN V2 9 HIS V2 99 HIS ** V2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 28 GLN S1 336 ASN S1 392 ASN ** S1 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 98 GLN S2 150 HIS S2 157 HIS ** S2 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 67 HIS S3 88 ASN S7 162 GLN ** S8 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V3 55 ASN S6 16 GLN S4 50 ASN ** A9 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 75 GLN A5 85 ASN A6 47 HIS AL 17 HIS ** AL 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 10 ASN ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 32 GLN D1 157 ASN ** D1 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 287 HIS ** D1 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 192 ASN ** D5 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 400 ASN D5 470 ASN ** D5 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 192 ASN D2 174 GLN D2 235 ASN A8 72 GLN AJ 271 ASN A3 45 ASN A3 51 ASN ** B4 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 111 HIS ** B7 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B9 32 HIS ** B8 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.239 67009 Z= 0.553 Angle : 1.688 50.843 90868 Z= 1.069 Chirality : 0.312 6.459 9987 Planarity : 0.005 0.066 11478 Dihedral : 7.576 83.281 9034 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.47 % Favored : 88.53 % Rotamer: Outliers : 0.08 % Allowed : 3.15 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.33 % Twisted Proline : 0.21 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.09), residues: 7980 helix: 0.36 (0.08), residues: 4146 sheet: -1.62 (0.25), residues: 382 loop : -3.13 (0.10), residues: 3452 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1982 residues out of total 7073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1976 time to evaluate : 5.806 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 outliers start: 6 outliers final: 2 residues processed: 1981 average time/residue: 0.6123 time to fit residues: 2087.6603 Evaluate side-chains 1561 residues out of total 7073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1559 time to evaluate : 5.790 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4607 time to fit residues: 9.6284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 734 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 433 optimal weight: 10.0000 chunk 556 optimal weight: 9.9990 chunk 430 optimal weight: 0.8980 chunk 640 optimal weight: 8.9990 chunk 425 optimal weight: 3.9990 chunk 758 optimal weight: 5.9990 chunk 474 optimal weight: 7.9990 chunk 462 optimal weight: 10.0000 chunk 350 optimal weight: 4.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 336 ASN ** S1 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 392 ASN ** S1 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 98 GLN ** S2 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 88 ASN S3 211 GLN S7 106 GLN S7 162 GLN ** S8 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V3 55 ASN S6 16 GLN S4 50 ASN ** A9 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 75 GLN A7 20 GLN ** A7 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 17 HIS ** AL 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 10 ASN ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 32 GLN ** D1 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 248 HIS D5 295 GLN ** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 400 ASN D5 470 ASN ** D5 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 192 ASN ** D4 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 434 ASN ** D2 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2 186 HIS D2 204 ASN D2 235 ASN A8 72 GLN AJ 50 HIS AJ 200 GLN AJ 271 ASN ** B4 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B6 82 HIS ** B7 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 6 HIS ** B2 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B8 55 GLN C1 35 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.5591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.235 67009 Z= 0.588 Angle : 1.715 50.976 90868 Z= 1.080 Chirality : 0.313 6.456 9987 Planarity : 0.006 0.087 11478 Dihedral : 7.726 85.400 9034 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 21.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.14 % Favored : 87.86 % Rotamer: Outliers : 0.04 % Allowed : 2.39 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.34 % Twisted Proline : 0.21 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.09), residues: 7980 helix: 0.28 (0.08), residues: 4137 sheet: -1.62 (0.26), residues: 386 loop : -3.16 (0.10), residues: 3457 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1934 residues out of total 7073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1931 time to evaluate : 5.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 1933 average time/residue: 0.6253 time to fit residues: 2084.5568 Evaluate side-chains 1529 residues out of total 7073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1528 time to evaluate : 5.740 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5575 time to fit residues: 8.7251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 469 optimal weight: 8.9990 chunk 302 optimal weight: 0.6980 chunk 453 optimal weight: 8.9990 chunk 228 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 482 optimal weight: 0.8980 chunk 516 optimal weight: 0.9990 chunk 375 optimal weight: 0.0270 chunk 70 optimal weight: 2.9990 chunk 596 optimal weight: 10.0000 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 392 ASN ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 150 HIS S2 157 HIS S3 88 ASN S7 106 GLN ** S7 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 65 HIS S6 13 HIS ** S6 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN A9 2 HIS ** A9 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 115 GLN ** A9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 75 GLN A6 47 HIS A7 28 GLN AL 17 HIS AL 59 HIS ** AL 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 10 ASN ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 287 HIS ** D1 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 205 ASN ** D5 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 400 ASN ** D5 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4 26 ASN ** D4 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 366 ASN ** D2 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN AJ 200 GLN AJ 271 ASN S5 69 GLN C2 117 HIS B7 84 HIS ** B7 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.5741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.252 67009 Z= 0.535 Angle : 1.680 50.635 90868 Z= 1.062 Chirality : 0.312 6.347 9987 Planarity : 0.005 0.074 11478 Dihedral : 7.389 84.204 9034 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer: Outliers : 0.01 % Allowed : 1.33 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.34 % Twisted Proline : 0.42 % Twisted General : 0.16 % 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: -1.55 (0.09), residues: 7980 helix: 0.51 (0.08), residues: 4132 sheet: -1.29 (0.27), residues: 364 loop : -3.05 (0.10), residues: 3484 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1996 residues out of total 7073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1995 time to evaluate : 5.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1996 average time/residue: 0.5970 time to fit residues: 2047.7816 Evaluate side-chains 1553 residues out of total 7073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1552 time to evaluate : 5.768 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4512 time to fit residues: 8.5671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 690 optimal weight: 1.9990 chunk 726 optimal weight: 3.9990 chunk 663 optimal weight: 0.1980 chunk 706 optimal weight: 0.0670 chunk 425 optimal weight: 0.9990 chunk 307 optimal weight: 3.9990 chunk 555 optimal weight: 4.9990 chunk 216 optimal weight: 5.9990 chunk 638 optimal weight: 3.9990 chunk 668 optimal weight: 0.2980 chunk 704 optimal weight: 2.9990 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V2 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 392 ASN ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 157 HIS S3 88 ASN ** S7 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S7 162 GLN S8 156 ASN S4 50 ASN ** A9 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 75 GLN A6 47 HIS A7 20 GLN AL 17 HIS AL 69 ASN AL 112 ASN D3 10 ASN ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 157 ASN ** D1 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 287 HIS D1 292 ASN D1 304 HIS ** D1 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 204 ASN D2 235 ASN B5 86 ASN ** BJ 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 271 ASN ** B7 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 6 HIS ** B2 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 41 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.5932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.251 67009 Z= 0.533 Angle : 1.680 50.694 90868 Z= 1.061 Chirality : 0.312 6.351 9987 Planarity : 0.005 0.083 11478 Dihedral : 7.193 84.328 9034 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer: Outliers : 0.04 % Allowed : 0.88 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.34 % Twisted Proline : 0.21 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.09), residues: 7980 helix: 0.52 (0.08), residues: 4152 sheet: -1.21 (0.27), residues: 365 loop : -3.00 (0.10), residues: 3463 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1970 residues out of total 7073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1967 time to evaluate : 6.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 1968 average time/residue: 0.6200 time to fit residues: 2109.6267 Evaluate side-chains 1587 residues out of total 7073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1587 time to evaluate : 6.127 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.8235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 464 optimal weight: 8.9990 chunk 747 optimal weight: 0.0770 chunk 456 optimal weight: 5.9990 chunk 354 optimal weight: 7.9990 chunk 519 optimal weight: 7.9990 chunk 784 optimal weight: 4.9990 chunk 721 optimal weight: 0.9980 chunk 624 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 482 optimal weight: 0.8980 chunk 382 optimal weight: 20.0000 overall best weight: 1.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V2 101 GLN ** V2 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 392 ASN ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 157 HIS S3 88 ASN ** S3 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 106 GLN S7 162 GLN S8 65 HIS S8 156 ASN S4 50 ASN ** A9 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 37 HIS ** A9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 75 GLN A6 47 HIS AL 17 HIS AL 59 HIS ** AL 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 10 ASN D1 157 ASN ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 287 HIS D1 317 GLN ** 4L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 524 ASN ** D5 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 331 ASN ** D2 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN ** BJ 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 271 ASN ** C2 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.6045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.245 67009 Z= 0.539 Angle : 1.690 50.712 90868 Z= 1.066 Chirality : 0.312 6.365 9987 Planarity : 0.005 0.071 11478 Dihedral : 7.211 85.566 9034 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 0.03 % Allowed : 0.51 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.34 % Twisted Proline : 0.21 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.09), residues: 7980 helix: 0.51 (0.08), residues: 4151 sheet: -1.16 (0.27), residues: 362 loop : -3.01 (0.10), residues: 3467 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1924 residues out of total 7073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1922 time to evaluate : 6.007 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 outliers start: 2 outliers final: 1 residues processed: 1922 average time/residue: 0.6126 time to fit residues: 2039.1283 Evaluate side-chains 1523 residues out of total 7073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1522 time to evaluate : 5.823 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5616 time to fit residues: 8.7975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 787 random chunks: chunk 495 optimal weight: 1.9990 chunk 665 optimal weight: 9.9990 chunk 191 optimal weight: 8.9990 chunk 575 optimal weight: 1.9990 chunk 92 optimal weight: 0.0870 chunk 173 optimal weight: 8.9990 chunk 625 optimal weight: 8.9990 chunk 261 optimal weight: 8.9990 chunk 642 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V1 200 GLN ** V2 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 392 ASN ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 157 HIS ** S3 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 88 ASN ** S3 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 106 GLN ** S7 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 23 GLN S8 156 ASN S4 50 ASN ** A9 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 75 GLN A6 47 HIS A7 20 GLN ** AL 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 10 ASN D1 157 ASN ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D6 46 ASN ** 4L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4 331 ASN D4 374 ASN ** D2 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 63 GLN ** D2 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN AJ 200 GLN AJ 271 ASN ** B7 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.099976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.089357 restraints weight = 216501.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.091255 restraints weight = 133805.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.092799 restraints weight = 84324.537| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.6142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.244 67009 Z= 0.546 Angle : 1.695 50.725 90868 Z= 1.069 Chirality : 0.312 6.368 9987 Planarity : 0.005 0.069 11478 Dihedral : 7.209 85.089 9034 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 0.03 % Allowed : 0.51 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.34 % Twisted Proline : 0.21 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.09), residues: 7980 helix: 0.49 (0.08), residues: 4161 sheet: -1.13 (0.27), residues: 357 loop : -3.00 (0.10), residues: 3462 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28191.68 seconds wall clock time: 489 minutes 13.88 seconds (29353.88 seconds total)