Starting phenix.real_space_refine (version: dev) on Fri May 13 20:20:59 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc6_4498/05_2022/6qc6_4498_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc6_4498/05_2022/6qc6_4498.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc6_4498/05_2022/6qc6_4498_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc6_4498/05_2022/6qc6_4498_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc6_4498/05_2022/6qc6_4498_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc6_4498/05_2022/6qc6_4498.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc6_4498/05_2022/6qc6_4498.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc6_4498/05_2022/6qc6_4498_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc6_4498/05_2022/6qc6_4498_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral 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 "V2 PHE 211": "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 "S7 ARG 174": "NH1" <-> "NH2" Residue "S7 ARG 178": "NH1" <-> "NH2" Residue "S8 TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V3 PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S6 TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S4 ARG 64": "NH1" <-> "NH2" Residue "A9 ARG 97": "NH1" <-> "NH2" Residue "A9 PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A9 ARG 186": "NH1" <-> "NH2" Residue "A9 ARG 292": "NH1" <-> "NH2" Residue "A2 ARG 33": "NH1" <-> "NH2" Residue "A6 ARG 22": "NH1" <-> "NH2" Residue "AL PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AL ARG 106": "NH1" <-> "NH2" Residue "AL PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 TYR 142": "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 TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D5 TYR 422": "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 "AJ ARG 95": "NH1" <-> "NH2" Residue "AJ PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AJ TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AJ ARG 305": "NH1" <-> "NH2" Residue "A3 ARG 46": "NH1" <-> "NH2" 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 "BK TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A1 ARG 25": "NH1" <-> "NH2" Residue "A1 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 65344 Number of models: 1 Model: "" Number of chains: 58 Chain: "V1" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3312 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 21, 'TRANS': 408} Chain: "V2" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1647 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 21, 'CIS': 1, 'TRANS': 189} Chain: "S1" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5275 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 32, 'CIS': 3, 'TRANS': 652} 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: {'PTRANS': 9, 'TRANS': 145, 'PCIS': 1} 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: {'PTRANS': 8, 'CIS': 1, 'TRANS': 101} Chain: "A6" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 969 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'CIS': 1, 'TRANS': 106} Chain: "A7" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 11, 'CIS': 1, 'TRANS': 82} 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: {'PTRANS': 2, 'TRANS': 76, 'PCIS': 1} 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: {'PTRANS': 19, 'CIS': 1, 'TRANS': 279, 'PCIS': 3} 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: {'PTRANS': 3, 'CIS': 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: {'PTRANS': 26, 'CIS': 1, '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: {'PTRANS': 20, 'TRANS': 437, 'PCIS': 1} 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: {'PTRANS': 4, 'CIS': 2, 'TRANS': 132, 'PCIS': 1} 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: {'PTRANS': 12, 'CIS': 2, 'TRANS': 156} Chain: "BJ" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1441 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 9, 'CIS': 1, 'TRANS': 159, 'PCIS': 1} Chain: "AJ" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2583 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 13, 'CIS': 6, 'TRANS': 298, 'PCIS': 1} 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: {'PTRANS': 8, 'CIS': 1, 'TRANS': 117, 'PCIS': 1} Chain: "AM" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1143 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "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: {'PTRANS': 7, 'CIS': 1, '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: {'PTRANS': 19, 'CIS': 1, 'TRANS': 135, 'PCIS': 1} Chain: "BK" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 853 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 7, 'TRANS': 93, 'PCIS': 1} 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: {'PTRANS': 1, 'TRANS': 49, 'PCIS': 1} 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: {'SF4': 2, 'FES': 1} 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: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 60 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 40 Chain: "D4" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 68 Unusual residues: {'PC1': 1, '3PE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 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 Chain: "B8" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2715 SG CYSV1 365 48.225 165.422 146.700 1.00 22.71 S ATOM 3039 SG CYSV1 405 49.721 167.960 152.622 1.00 35.26 S ATOM 2695 SG CYSV1 362 53.954 166.134 147.839 1.00 49.95 S ATOM 2676 SG CYSV1 359 50.455 171.732 147.580 1.00 33.25 S ATOM 4116 SG CYSV2 103 30.010 174.921 152.659 1.00 71.72 S ATOM 4150 SG CYSV2 108 27.213 173.005 154.928 1.00 46.44 S ATOM 4430 SG CYSV2 144 33.958 174.100 156.175 1.00 62.59 S ATOM 4453 SG CYSV2 148 31.784 173.020 158.750 1.00 82.67 S ATOM 5785 SG CYSS1 114 60.691 159.297 128.639 1.00 33.03 S ATOM 5724 SG CYSS1 105 55.835 156.808 125.154 1.00 19.49 S ATOM 5745 SG CYSS1 108 58.138 162.746 123.736 1.00 17.62 S ATOM 6117 SG CYSS1 156 60.245 168.535 136.122 1.00 22.66 S ATOM 6094 SG CYSS1 153 54.632 170.309 133.028 1.00 24.73 S ATOM 6141 SG CYSS1 159 59.524 174.471 133.536 1.00 19.06 S ATOM 6471 SG CYSS1 203 60.311 169.197 129.856 1.00 22.00 S ATOM 5230 SG CYSS1 41 62.077 166.678 143.018 1.00 18.85 S ATOM 5316 SG CYSS1 52 61.367 163.079 141.979 1.00 22.33 S ATOM 5341 SG CYSS1 55 63.947 161.723 147.190 1.00 34.48 S ATOM 5442 SG CYSS1 69 64.309 165.580 147.546 1.00 37.88 S ATOM 16127 SG CYSS7 119 71.224 134.140 102.159 1.00 32.66 S ATOM 16357 SG CYSS7 149 65.463 134.346 103.830 1.00 32.00 S ATOM 15629 SG CYSS7 55 66.921 130.562 98.527 1.00 52.61 S ATOM 15623 SG CYSS7 54 68.382 128.334 104.075 1.00 47.74 S ATOM 17549 SG CYSS8 116 61.813 142.180 103.705 1.00 24.05 S ATOM 17596 SG CYSS8 122 58.352 145.026 108.388 1.00 17.04 S ATOM 17323 SG CYSS8 87 64.845 145.759 108.376 1.00 17.94 S ATOM 17625 SG CYSS8 126 53.380 151.017 112.003 1.00 19.83 S ATOM 17296 SG CYSS8 83 59.644 151.245 110.024 1.00 13.82 S ATOM 17254 SG CYSS8 77 55.690 156.160 108.587 1.00 17.08 S ATOM 17273 SG CYSS8 80 57.282 154.793 114.931 1.00 15.00 S ATOM 18846 SG CYSS6 59 41.491 160.874 116.776 1.00 36.24 S ATOM 19024 SG CYSS6 84 45.230 162.488 116.521 1.00 29.73 S ATOM 19046 SG CYSS6 87 42.675 160.703 114.462 1.00 25.07 S Time building chain proxies: 27.23, per 1000 atoms: 0.42 Number of scatterers: 65344 At special positions: 0 Unit cell: (249.2, 222.6, 201.6, 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 11716 8.00 N 11025 7.00 C 42100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYSAK 17 " - pdb=" SG CYSAK 74 " distance=2.03 Simple disulfide: pdb=" SG CYSAK 94 " - pdb=" SG CYSAK 114 " distance=2.03 Simple disulfide: pdb=" SG CYSA8 35 " - pdb=" SG CYSA8 65 " distance=2.04 Simple disulfide: pdb=" SG CYSA8 45 " - pdb=" SG CYSA8 55 " distance=2.04 Simple disulfide: pdb=" SG CYSA8 77 " - pdb=" SG CYSA8 109 " distance=2.02 Simple disulfide: pdb=" SG CYSA8 87 " - pdb=" SG CYSA8 99 " distance=2.03 Simple disulfide: pdb=" SG CYSBJ 76 " - pdb=" SG CYSBJ 83 " distance=2.04 Simple disulfide: pdb=" SG CYSBJ 112 " - pdb=" SG CYSBJ 124 " distance=2.03 Simple disulfide: pdb=" SG CYSS5 32 " - pdb=" SG CYSS5 65 " distance=2.04 Simple disulfide: pdb=" SG CYSS5 42 " - pdb=" SG CYSS5 55 " distance=2.03 Simple disulfide: pdb=" SG CYSB7 58 " - pdb=" SG CYSB7 89 " distance=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.06 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Iron sulfur cluster coordination Iron sulfur cluster coordination pdb=" FESS1 803 " pdb="FE1 FESS1 803 " - pdb=" SG CYSS1 52 " pdb="FE2 FESS1 803 " - pdb=" SG CYSS1 55 " pdb="FE1 FESS1 803 " - pdb=" SG CYSS1 41 " 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="FE1 SF4S1 801 " - pdb=" SG CYSS1 114 " pdb="FE2 SF4S1 801 " - pdb=" SG CYSS1 105 " pdb=" SF4S1 802 " pdb="FE2 SF4S1 802 " - pdb=" SG CYSS1 153 " pdb="FE3 SF4S1 802 " - pdb=" SG CYSS1 159 " pdb="FE1 SF4S1 802 " - pdb=" SG CYSS1 156 " pdb="FE4 SF4S1 802 " - pdb=" SG CYSS1 203 " pdb=" SF4S7 300 " pdb="FE1 SF4S7 300 " - pdb=" SG CYSS7 119 " pdb="FE2 SF4S7 300 " - pdb=" SG CYSS7 149 " pdb="FE3 SF4S7 300 " - pdb=" SG CYSS7 55 " pdb="FE4 SF4S7 300 " - pdb=" SG CYSS7 54 " 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="FE1 SF4S8 202 " - pdb=" SG CYSS8 126 " pdb="FE4 SF4S8 202 " - pdb=" SG CYSS8 80 " pdb="FE2 SF4S8 202 " - pdb=" SG CYSS8 83 " pdb="FE3 SF4S8 202 " - pdb=" SG CYSS8 77 " pdb=" SF4V1 500 " pdb="FE1 SF4V1 500 " - pdb=" SG CYSV1 365 " pdb="FE3 SF4V1 500 " - pdb=" SG CYSV1 362 " pdb="FE2 SF4V1 500 " - pdb=" SG CYSV1 405 " pdb="FE4 SF4V1 500 " - pdb=" SG CYSV1 359 " Number of angles added : 81 Zn2+ tetrahedral coordination 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 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15196 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 299 helices and 28 sheets defined 48.2% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.60 Creating SS restraints... Processing helix chain 'V1' and resid 33 through 38 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 106 through 113 removed outlier: 4.280A pdb=" N ILEV1 110 " --> pdb=" O LYSV1 106 " (cutoff:3.500A) Processing helix chain 'V1' and resid 115 through 127 Processing helix chain 'V1' and resid 143 through 158 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: 3.811A pdb=" N CYSV1 235 " --> pdb=" O SERV1 231 " (cutoff:3.500A) Processing helix chain 'V1' and resid 276 through 281 Processing helix chain 'V1' and resid 291 through 293 No H-bonds generated for 'chain 'V1' and resid 291 through 293' Processing helix chain 'V1' and resid 309 through 314 removed outlier: 4.959A pdb=" N THRV1 314 " --> pdb=" O SERV1 310 " (cutoff:3.500A) Processing helix chain 'V1' and resid 319 through 324 Processing helix chain 'V1' and resid 343 through 356 Processing helix chain 'V1' and resid 363 through 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: 3.920A pdb=" N VALV2 47 " --> pdb=" O ALAV2 44 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEUV2 48 " --> pdb=" O ALAV2 45 " (cutoff:3.500A) Proline residue: V2 49 - end of helix Processing helix chain 'V2' and resid 63 through 72 Processing helix chain 'V2' and resid 77 through 86 Processing helix chain 'V2' and resid 107 through 110 No H-bonds generated for 'chain 'V2' and resid 107 through 110' Processing helix chain 'V2' and resid 113 through 124 Processing helix chain 'V2' and resid 166 through 177 Processing helix chain 'S1' and resid 13 through 15 No H-bonds generated for 'chain 'S1' and resid 13 through 15' Processing helix chain 'S1' and resid 26 through 33 Processing helix chain 'S1' and resid 84 through 97 Processing helix chain 'S1' and resid 116 through 123 Processing helix chain 'S1' and resid 159 through 165 Processing helix chain 'S1' and resid 197 through 202 removed outlier: 3.545A pdb=" N ILES1 200 " --> pdb=" O GLYS1 197 " (cutoff:3.500A) Processing helix chain 'S1' and resid 265 through 268 No H-bonds generated for 'chain 'S1' and resid 265 through 268' Processing helix chain 'S1' and resid 271 through 275 Processing helix chain 'S1' and resid 296 through 309 Processing helix chain 'S1' and resid 325 through 338 Processing helix chain 'S1' and resid 359 through 362 removed outlier: 4.040A pdb=" N TYRS1 362 " --> pdb=" O ARGS1 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'S1' and resid 359 through 362' Processing helix chain 'S1' and resid 369 through 371 No H-bonds generated for 'chain 'S1' and resid 369 through 371' Processing helix chain 'S1' and resid 389 through 401 Processing helix chain 'S1' and resid 426 through 434 Processing helix chain 'S1' and resid 440 through 444 Processing helix chain 'S1' and resid 456 through 458 No H-bonds generated for 'chain 'S1' and resid 456 through 458' Processing helix chain 'S1' and resid 463 through 479 Processing helix chain 'S1' and resid 497 through 504 Processing helix chain 'S1' and resid 512 through 516 Processing helix chain 'S1' and resid 566 through 568 No H-bonds generated for 'chain 'S1' and resid 566 through 568' 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 630 No H-bonds generated for 'chain 'S1' and resid 628 through 630' Processing helix chain 'S1' and resid 642 through 650 removed outlier: 4.174A pdb=" N LYSS1 650 " --> pdb=" O SERS1 646 " (cutoff:3.500A) Processing helix chain 'S1' and resid 668 through 673 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 87 through 92 Processing helix chain 'S2' and resid 96 through 105 Proline residue: S2 101 - end of helix Processing helix chain 'S2' and resid 113 through 126 Processing helix chain 'S2' and resid 132 through 161 Processing helix chain 'S2' and resid 164 through 184 removed outlier: 4.136A 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 257 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: 4.269A pdb=" N GLYS2 401 " --> pdb=" O ALAS2 397 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEUS2 402 " --> pdb=" O HISS2 398 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ASPS2 403 " --> pdb=" O LEUS2 399 " (cutoff:3.500A) removed outlier: 6.176A 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 120 through 122 No H-bonds generated for 'chain 'S3' and resid 120 through 122' Processing helix chain 'S3' and resid 125 through 137 removed outlier: 3.905A pdb=" N ASNS3 128 " --> pdb=" O LYSS3 125 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N TRPS3 129 " --> pdb=" O ALAS3 126 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILES3 134 " --> pdb=" O GLUS3 131 " (cutoff:3.500A) removed outlier: 3.510A 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 70 through 72 No H-bonds generated for 'chain 'S7' and resid 70 through 72' Processing helix chain 'S7' and resid 94 through 105 Proline residue: S7 98 - end of helix Processing helix chain 'S7' and resid 124 through 126 No H-bonds generated for 'chain 'S7' and resid 124 through 126' Processing helix chain 'S7' and resid 153 through 168 Processing helix chain 'S7' and resid 172 through 178 Processing helix chain 'S8' and resid 14 through 26 Processing helix chain 'S8' and resid 28 through 41 Processing helix chain 'S8' and resid 82 through 86 Processing helix chain 'S8' and resid 121 through 125 Processing helix chain 'S8' and resid 151 through 159 Processing helix chain 'S8' and resid 163 through 171 Processing helix chain 'V3' and resid 50 through 57 Processing helix chain 'S6' and resid 24 through 27 No H-bonds generated for 'chain 'S6' and resid 24 through 27' Processing helix chain '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 78 through 81 removed outlier: 4.092A pdb=" N ASNS4 81 " --> pdb=" O PROS4 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'S4' and resid 78 through 81' Processing helix chain 'S4' and resid 89 through 99 Processing helix chain 'S4' and resid 118 through 121 No H-bonds generated for 'chain 'S4' and resid 118 through 121' Processing helix chain 'A9' and resid 30 through 41 Processing helix chain 'A9' and resid 53 through 58 Processing helix chain 'A9' and resid 78 through 84 Processing helix chain 'A9' and resid 112 through 124 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 287 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 35 Processing helix chain 'A5' and resid 43 through 59 Processing helix chain 'A5' and resid 65 through 70 Processing helix chain 'A5' and resid 77 through 94 Processing helix chain 'A6' and resid 24 through 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 118 through 122 Processing helix chain 'A7' and resid 5 through 14 Processing helix chain 'AL' and resid 4 through 15 removed outlier: 3.660A pdb=" N LEUAL 11 " --> pdb=" O LEUAL 7 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLNAL 12 " --> pdb=" O LYSAL 8 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLNAL 13 " --> pdb=" O ARGAL 9 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VALAL 14 " --> pdb=" O GLYAL 10 " (cutoff:3.500A) Processing helix chain 'AL' and resid 21 through 29 removed outlier: 3.606A 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 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 23 Processing helix chain 'D3' and resid 54 through 77 removed outlier: 4.049A pdb=" N VALD3 58 " --> pdb=" O LYSD3 54 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALAD3 59 " --> pdb=" O PHED3 55 " (cutoff:3.500A) Proline residue: D3 74 - end of helix removed outlier: 5.355A pdb=" N TRPD3 77 " --> pdb=" O LEUD3 73 " (cutoff:3.500A) Processing helix chain 'D3' and resid 84 through 107 Processing helix chain 'D1' and resid 2 through 10 Processing helix chain 'D1' and resid 12 through 31 Processing helix chain 'D1' and resid 46 through 57 Processing helix chain 'D1' and resid 68 through 86 Proline residue: D1 75 - end of helix removed outlier: 4.963A pdb=" N TRPD1 86 " --> pdb=" O ALAD1 82 " (cutoff:3.500A) Processing helix chain 'D1' and resid 102 through 123 Processing helix chain 'D1' and resid 126 through 140 Processing helix chain 'D1' and resid 145 through 157 removed outlier: 4.160A pdb=" N METD1 156 " --> pdb=" O SERD1 152 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ASND1 157 " --> pdb=" O VALD1 153 " (cutoff:3.500A) Processing helix chain 'D1' and resid 163 through 168 Processing helix chain 'D1' and resid 174 through 177 No H-bonds generated for 'chain 'D1' and resid 174 through 177' Processing helix chain 'D1' and resid 179 through 193 Processing helix chain 'D1' and resid 220 through 242 Processing helix chain 'D1' and resid 253 through 276 removed outlier: 4.191A pdb=" N SERD1 276 " --> pdb=" O TRPD1 272 " (cutoff:3.500A) Processing helix chain 'D1' and resid 282 through 308 Proline residue: D1 295 - end of helix Proline residue: D1 308 - end of helix Processing helix chain 'D6' and resid 5 through 21 Processing helix chain 'D6' and resid 26 through 46 Processing helix chain 'D6' and resid 52 through 63 removed outlier: 3.755A pdb=" N LEUD6 58 " --> pdb=" O LEUD6 54 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEUD6 61 " --> pdb=" O PHED6 57 " (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 146 removed outlier: 3.609A pdb=" N LEUD6 146 " --> pdb=" O GLYD6 142 " (cutoff:3.500A) Processing helix chain 'D6' and resid 151 through 171 removed outlier: 3.681A pdb=" N ILED6 155 " --> pdb=" O THRD6 151 " (cutoff:3.500A) Processing helix chain '4L' and resid 3 through 20 Processing helix chain '4L' and resid 26 through 51 Processing helix chain '4L' and resid 59 through 84 Processing helix chain 'D5' and resid 2 through 23 removed outlier: 3.914A pdb=" N LEUD5 15 " --> pdb=" O THRD5 11 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THRD5 16 " --> pdb=" O LEUD5 12 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N METD5 17 " --> pdb=" O ILED5 13 " (cutoff:3.500A) Proline residue: D5 18 - end of helix Processing helix chain 'D5' and resid 32 through 56 removed outlier: 4.655A 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 107 removed outlier: 4.503A pdb=" N VALD5 90 " --> pdb=" O SERD5 86 " (cutoff:3.500A) Proline residue: D5 91 - end of helix Processing helix chain 'D5' and resid 114 through 133 Processing helix chain 'D5' and resid 137 through 157 Processing helix chain 'D5' and resid 162 through 193 Processing helix chain 'D5' and resid 198 through 203 Processing helix chain 'D5' and resid 210 through 223 Processing helix chain 'D5' and resid 232 through 238 Processing helix chain 'D5' and resid 241 through 249 Processing helix chain 'D5' and resid 255 through 262 removed outlier: 3.814A pdb=" N LEUD5 259 " --> pdb=" O ALAD5 255 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEUD5 260 " --> pdb=" O GLYD5 256 " (cutoff:3.500A) Processing helix chain 'D5' and resid 271 through 292 Processing helix chain 'D5' and resid 298 through 318 Processing helix chain 'D5' and resid 322 through 349 Processing helix chain 'D5' and resid 367 through 379 Processing helix chain 'D5' and resid 387 through 400 removed outlier: 4.059A pdb=" N SERD5 391 " --> pdb=" O THRD5 387 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYSD5 392 " --> pdb=" O GLYD5 388 " (cutoff:3.500A) Processing helix chain 'D5' and resid 408 through 431 Processing helix chain 'D5' and resid 448 through 470 removed outlier: 5.924A pdb=" N GLYD5 465 " --> pdb=" O SERD5 461 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N PHED5 466 " --> pdb=" O LEUD5 462 " (cutoff:3.500A) Processing helix chain 'D5' and resid 489 through 508 Processing helix chain 'D5' and resid 519 through 524 Processing helix chain 'D5' and resid 526 through 547 removed outlier: 3.813A pdb=" N TYRD5 529 " --> pdb=" O LEUD5 526 " (cutoff:3.500A) Proline residue: D5 530 - end of helix removed outlier: 3.618A pdb=" N METD5 533 " --> pdb=" O PROD5 530 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HISD5 534 " --> pdb=" O THRD5 531 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N THRD5 537 " --> pdb=" O HISD5 534 " (cutoff:3.500A) Proline residue: D5 538 - end of helix removed outlier: 4.124A pdb=" N ASND5 541 " --> pdb=" O PROD5 538 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEUD5 542 " --> pdb=" O TYRD5 539 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N METD5 544 " --> pdb=" O ASND5 541 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SERD5 545 " --> pdb=" O LEUD5 542 " (cutoff:3.500A) removed outlier: 3.749A 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 564 through 577 Processing helix chain 'D5' and resid 585 through 599 Processing helix chain 'D4' and resid 2 through 4 No H-bonds generated for 'chain 'D4' and resid 2 through 4' Processing helix chain 'D4' and resid 6 through 16 Proline residue: D4 13 - end of helix removed outlier: 3.844A pdb=" N TRPD4 16 " --> pdb=" O METD4 12 " (cutoff:3.500A) Processing helix chain 'D4' and resid 23 through 41 removed outlier: 3.945A pdb=" N LEUD4 41 " --> pdb=" O THRD4 37 " (cutoff:3.500A) Processing helix chain 'D4' and resid 62 through 79 Proline residue: D4 74 - end of helix Processing helix chain 'D4' and resid 89 through 110 Processing helix chain 'D4' and resid 115 through 135 Proline residue: D4 128 - end of helix removed outlier: 3.791A pdb=" N ILED4 131 " --> pdb=" O VALD4 127 " (cutoff:3.500A) Processing helix chain 'D4' and resid 142 through 157 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 191 through 206 Processing helix chain 'D4' and resid 210 through 221 removed outlier: 3.578A pdb=" N HISD4 213 " --> pdb=" O TYRD4 210 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LEUD4 214 " --> pdb=" O GLYD4 211 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TRPD4 215 " --> pdb=" O LEUD4 212 " (cutoff:3.500A) Proline residue: D4 217 - end of helix removed outlier: 3.523A pdb=" N VALD4 221 " --> pdb=" O LYSD4 218 " (cutoff:3.500A) Processing helix chain 'D4' and resid 225 through 248 removed outlier: 5.025A pdb=" N LEUD4 248 " --> pdb=" O METD4 244 " (cutoff:3.500A) Processing helix chain 'D4' and resid 251 through 257 removed outlier: 4.217A pdb=" N ASPD4 255 " --> pdb=" O ASND4 251 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N PHED4 256 " --> pdb=" O PROD4 252 " (cutoff:3.500A) Processing helix chain 'D4' and resid 259 through 277 removed outlier: 3.923A pdb=" N LEUD4 277 " --> pdb=" O SERD4 273 " (cutoff:3.500A) Processing helix chain 'D4' and resid 282 through 302 removed outlier: 3.552A pdb=" N ILED4 286 " --> pdb=" O LYSD4 283 " (cutoff:3.500A) Processing helix chain 'D4' and resid 306 through 336 Processing helix chain 'D4' and resid 355 through 366 Processing helix chain 'D4' and resid 373 through 388 Processing helix chain 'D4' and resid 393 through 414 removed outlier: 3.627A pdb=" N THRD4 414 " --> pdb=" O METD4 410 " (cutoff:3.500A) Processing helix chain 'D4' and resid 431 through 449 removed outlier: 3.694A pdb=" N LEUD4 442 " --> pdb=" O SERD4 438 " (cutoff:3.500A) Proline residue: D4 443 - end of helix Processing helix chain 'D2' and resid 3 through 22 Processing helix chain 'D2' and resid 26 through 41 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 113 through 120 removed outlier: 4.536A pdb=" N GLUD2 117 " --> pdb=" O PHED2 113 " (cutoff:3.500A) Processing helix chain 'D2' and resid 124 through 148 Proline residue: D2 138 - end of helix removed outlier: 3.963A pdb=" N VALD2 141 " --> pdb=" O ALAD2 137 " (cutoff:3.500A) Proline residue: D2 147 - end of helix Processing helix chain 'D2' and resid 151 through 167 Processing helix chain 'D2' and resid 175 through 192 Processing helix chain 'D2' and resid 198 through 220 Processing helix chain 'D2' and resid 227 through 236 Processing helix chain 'D2' and resid 239 through 252 Processing helix chain 'D2' and resid 258 through 271 Proline residue: D2 262 - end of helix removed outlier: 4.204A pdb=" N METD2 265 " --> pdb=" O PROD2 262 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLUD2 269 " --> pdb=" O ILED2 266 " (cutoff:3.500A) Processing helix chain 'D2' and resid 277 through 300 removed outlier: 4.254A pdb=" N LEUD2 290 " --> pdb=" O ALAD2 286 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N TYRD2 291 " --> pdb=" O LEUD2 287 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N PHED2 292 " --> pdb=" O LEUD2 288 " (cutoff:3.500A) removed outlier: 4.932A 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: 3.852A pdb=" N SERD2 344 " --> pdb=" O PROD2 341 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILED2 345 " --> pdb=" O ILED2 342 " (cutoff:3.500A) Processing helix chain 'AK' and resid 2 through 10 Processing helix chain 'AK' and resid 19 through 42 Processing helix chain 'AK' and resid 48 through 79 Processing helix chain 'AK' and resid 87 through 104 Processing helix chain 'AK' and resid 108 through 130 Processing helix chain 'B5' and resid 16 through 46 removed outlier: 4.912A pdb=" N THRB5 32 " --> pdb=" O TYRB5 28 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILEB5 34 " --> pdb=" O LEUB5 30 " (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 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 75 Processing helix chain 'A8' and resid 80 through 89 Processing helix chain 'A8' and resid 101 through 113 Processing helix chain 'BJ' and resid 28 through 56 removed outlier: 5.012A pdb=" N ARGBJ 42 " --> pdb=" O LEUBJ 38 " (cutoff:3.500A) Proline residue: BJ 43 - end of helix Processing helix chain 'BJ' and resid 81 through 115 removed outlier: 4.649A pdb=" N GLUBJ 86 " --> pdb=" O LEUBJ 82 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 125 through 141 Processing helix chain 'BJ' and resid 152 through 172 Processing helix chain 'AJ' and resid 5 through 10 Processing helix chain 'AJ' and resid 36 through 44 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 141 Processing helix chain 'AJ' and resid 146 through 162 removed outlier: 3.510A pdb=" N VALAJ 160 " --> pdb=" O LYSAJ 156 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N CYSAJ 161 " --> pdb=" O LYSAJ 157 " (cutoff:3.500A) removed outlier: 4.974A 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 197 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 269 through 272 removed outlier: 3.946A pdb=" N TYRAJ 272 " --> pdb=" O VALAJ 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'AJ' and resid 269 through 272' Processing helix chain 'AJ' and resid 286 through 297 Processing helix chain '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 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: 3.634A 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 73 through 82 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 20 through 22 No H-bonds generated for 'chain 'B4' and resid 20 through 22' Processing helix chain 'B4' and resid 26 through 48 Processing helix chain 'B4' and resid 62 through 71 Processing helix chain 'B4' and resid 83 through 93 Processing helix chain 'B4' and resid 95 through 117 Processing helix chain 'AM' and resid 31 through 69 Processing helix chain 'AM' and resid 71 through 96 Processing helix chain 'AM' and resid 130 through 135 Processing helix chain 'B6' and resid 5 through 24 Processing helix chain 'B6' and resid 68 through 84 Proline residue: B6 77 - end of helix Processing helix chain 'B6' and resid 87 through 91 Processing helix chain 'B7' and resid 2 through 9 Processing helix chain 'B7' and resid 42 through 47 Processing helix chain 'B7' and resid 59 through 71 Processing helix chain 'B7' and resid 81 through 118 Processing helix chain 'B9' and resid 11 through 29 Processing helix chain 'B9' and resid 34 through 47 Processing helix chain 'B9' and resid 57 through 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 42 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 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: 3.987A 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 83 through 102 removed outlier: 6.316A pdb=" N GLUBK 87 " --> pdb=" O ARGBK 84 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TRPBK 88 " --> pdb=" O METBK 85 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLUBK 92 " --> pdb=" O ALABK 89 " (cutoff:3.500A) Processing helix chain 'C1' and resid 14 through 45 Processing helix chain 'B1' and resid 12 through 33 removed outlier: 3.711A pdb=" N LEUB1 15 " --> pdb=" O ILEB1 12 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N VALB1 16 " --> pdb=" O HISB1 13 " (cutoff:3.500A) Proline residue: B1 17 - end of helix Processing helix chain 'A1' and resid 6 through 29 Proline residue: A1 19 - end of helix Processing helix chain 'A1' and resid 42 through 54 Processing sheet with id= A, first strand: chain 'V1' and resid 221 through 223 removed outlier: 6.278A pdb=" N ALAV1 133 " --> pdb=" O LEUV1 93 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VALV1 95 " --> pdb=" O ALAV1 133 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TYRV1 135 " --> pdb=" O VALV1 95 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASPV1 174 " --> pdb=" O ALAV1 134 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILEV1 136 " --> pdb=" O ASPV1 174 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHEV1 176 " --> pdb=" O ILEV1 136 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ILEV1 138 " --> pdb=" O PHEV1 176 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VALV1 178 " --> pdb=" O ILEV1 138 " (cutoff:3.500A) 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: 6.457A pdb=" N METV1 337 " --> pdb=" O LEUV1 295 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VALV1 297 " --> pdb=" O ILEV1 335 " (cutoff:3.500A) removed outlier: 6.577A 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: 6.609A pdb=" N TRPS1 77 " --> pdb=" O PHES1 12 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'S1' and resid 146 through 148 Processing sheet with id= G, first strand: chain 'S1' and resid 173 through 177 Processing sheet with id= H, first strand: chain 'S1' and resid 223 through 228 Processing sheet with id= I, first strand: chain 'S1' and resid 282 through 286 Processing sheet with id= J, first strand: chain 'S1' and resid 342 through 345 removed outlier: 6.565A pdb=" N METS1 521 " --> pdb=" O ALAS1 316 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILES1 318 " --> pdb=" O METS1 521 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHES1 523 " --> pdb=" O ILES1 318 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VALS1 559 " --> pdb=" O TYRS1 545 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N GLYS1 547 " --> pdb=" O VALS1 559 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEUS1 561 " --> pdb=" O GLYS1 547 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S1' and resid 405 through 409 Processing sheet with id= L, first strand: chain 'S2' and resid 47 through 51 Processing sheet with id= M, first strand: chain 'S2' and resid 361 through 368 Processing sheet with id= N, first strand: chain 'S3' and resid 74 through 76 removed outlier: 6.665A pdb=" N LEUS3 48 " --> pdb=" O ARGS3 106 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LYSS3 108 " --> pdb=" O LEUS3 48 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ILES3 50 " --> pdb=" O LYSS3 108 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N TYRS3 110 " --> pdb=" O ILES3 50 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILES3 52 " --> pdb=" O TYRS3 110 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'S3' and resid 172 through 177 Processing sheet with id= P, first strand: chain 'S7' and resid 47 through 49 removed outlier: 7.002A pdb=" N VALS7 85 " --> pdb=" O METS7 48 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TYRS7 112 " --> pdb=" O METS7 86 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VALS7 88 " --> pdb=" O TYRS7 112 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VALS7 114 " --> pdb=" O VALS7 88 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILES7 144 " --> pdb=" O SERS7 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'S8' and resid 92 through 95 Processing sheet with id= R, first strand: chain 'S6' and resid 50 through 52 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: 6.415A pdb=" N ALAS4 35 " --> pdb=" O ASPS4 104 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A9' and resid 90 through 92 removed outlier: 6.342A pdb=" N GLNA9 44 " --> pdb=" O ALAA9 21 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N VALA9 23 " --> pdb=" O GLNA9 44 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILEA9 46 " --> pdb=" O VALA9 23 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ILEA9 69 " --> pdb=" O VALA9 47 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N TYRA9 49 " --> pdb=" O ILEA9 69 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N META9 71 " --> pdb=" O TYRA9 49 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A9' and resid 130 through 134 removed outlier: 6.399A pdb=" N THRA9 164 " --> pdb=" O HISA9 131 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N SERA9 133 " --> pdb=" O THRA9 164 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILEA9 166 " --> pdb=" O SERA9 133 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHEA9 228 " --> pdb=" O LYSA9 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'A9' and resid 170 through 172 removed outlier: 3.546A pdb=" N VALA9 205 " --> pdb=" O ASPA9 170 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A2' and resid 53 through 56 Processing sheet with id= Y, first strand: chain 'AL' and resid 47 through 50 Processing sheet with id= Z, first strand: chain 'D5' and resid 61 through 67 Processing sheet with id= AA, first strand: chain 'D4' and resid 50 through 52 Processing sheet with id= AB, first strand: chain 'AJ' and resid 122 through 125 removed outlier: 6.545A pdb=" N VALAJ 168 " --> pdb=" O THRAJ 26 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ASPAJ 28 " --> pdb=" O VALAJ 168 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILEAJ 170 " --> pdb=" O ASPAJ 28 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLUAJ 219 " --> pdb=" O VALAJ 169 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYRAJ 171 " --> pdb=" O GLUAJ 219 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LEUAJ 221 " --> pdb=" O TYRAJ 171 " (cutoff:3.500A) 2737 hydrogen bonds defined for protein. 7839 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: 18.84 Time building geometry restraints manager: 21.92 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: 27742 1.42 - 1.64: 38428 1.64 - 1.86: 750 1.86 - 2.08: 0 2.08 - 2.31: 80 Bond restraints: 67000 Sorted by residual: 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 3.05e+01 bond pdb=" O2B NDPA9 401 " pdb=" P2B NDPA9 401 " ideal model delta sigma weight residual 1.833 1.624 0.209 3.80e-02 6.93e+02 3.04e+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=" C13 ZMPAA 101 " pdb=" N1 ZMPAA 101 " ideal model delta sigma weight residual 1.452 1.342 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C13 ZMPAB 101 " pdb=" N1 ZMPAB 101 " ideal model delta sigma weight residual 1.452 1.348 0.104 2.00e-02 2.50e+03 2.70e+01 ... (remaining 66995 not shown) Histogram of bond angle deviations from ideal: 69.02 - 84.73: 72 84.73 - 100.44: 116 100.44 - 116.15: 44159 116.15 - 131.86: 46265 131.86 - 147.57: 244 Bond angle restraints: 90856 Sorted by residual: angle pdb=" C VALS3 37 " pdb=" N GLNS3 38 " pdb=" CA GLNS3 38 " ideal model delta sigma weight residual 122.46 147.57 -25.11 1.80e+00 3.09e-01 1.95e+02 angle pdb=" PA NDPA9 401 " pdb=" O3 NDPA9 401 " pdb=" PN NDPA9 401 " ideal model delta sigma weight residual 107.74 130.91 -23.17 1.95e+00 2.62e-01 1.41e+02 angle pdb=" S1 FESS1 803 " pdb="FE2 FESS1 803 " pdb=" S2 FESS1 803 " ideal model delta sigma weight residual 104.33 91.96 12.37 1.14e+00 7.69e-01 1.18e+02 angle pdb=" S1 FESV2 300 " pdb="FE2 FESV2 300 " pdb=" S2 FESV2 300 " ideal model delta sigma weight residual 104.33 92.18 12.15 1.14e+00 7.69e-01 1.14e+02 angle pdb="FE1 FESV2 300 " pdb=" S2 FESV2 300 " pdb="FE2 FESV2 300 " ideal model delta sigma weight residual 75.66 87.74 -12.08 1.14e+00 7.69e-01 1.12e+02 ... (remaining 90851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.29: 39494 30.29 - 60.58: 678 60.58 - 90.86: 52 90.86 - 121.15: 1 121.15 - 151.44: 3 Dihedral angle restraints: 40228 sinusoidal: 16675 harmonic: 23553 Sorted by residual: dihedral pdb=" CA PROB2 56 " pdb=" C PROB2 56 " pdb=" N SERB2 57 " pdb=" CA SERB2 57 " ideal model delta harmonic sigma weight residual -180.00 -121.88 -58.12 0 5.00e+00 4.00e-02 1.35e+02 dihedral pdb=" CA LYSB3 22 " pdb=" C LYSB3 22 " pdb=" N ILEB3 23 " pdb=" CA ILEB3 23 " ideal model delta harmonic sigma weight residual -180.00 -122.82 -57.18 0 5.00e+00 4.00e-02 1.31e+02 dihedral pdb=" CA PHEAJ 278 " pdb=" C PHEAJ 278 " pdb=" N LEUAJ 279 " pdb=" CA LEUAJ 279 " ideal model delta harmonic sigma weight residual 180.00 123.81 56.19 0 5.00e+00 4.00e-02 1.26e+02 ... (remaining 40225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.231: 9964 4.231 - 8.462: 0 8.462 - 12.693: 0 12.693 - 16.925: 0 16.925 - 21.156: 24 Chirality restraints: 9988 Sorted by residual: chirality pdb="FE4 SF4S7 300 " pdb=" S1 SF4S7 300 " pdb=" S2 SF4S7 300 " pdb=" S3 SF4S7 300 " both_signs ideal model delta sigma weight residual False 10.55 -10.60 21.16 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4V1 500 " pdb=" S1 SF4V1 500 " pdb=" S2 SF4V1 500 " pdb=" S3 SF4V1 500 " both_signs ideal model delta sigma weight residual False 10.55 -10.59 21.14 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4S1 802 " pdb=" S1 SF4S1 802 " pdb=" S2 SF4S1 802 " pdb=" S3 SF4S1 802 " both_signs ideal model delta sigma weight residual False 10.55 -10.56 21.12 2.00e-01 2.50e+01 1.12e+04 ... (remaining 9985 not shown) Planarity restraints: 11476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMNV1 501 " 0.004 2.00e-02 2.50e+03 3.16e-02 4.75e+01 pdb=" C10 FMNV1 501 " 0.045 2.00e-02 2.50e+03 pdb=" C2 FMNV1 501 " -0.025 2.00e-02 2.50e+03 pdb=" C4 FMNV1 501 " 0.010 2.00e-02 2.50e+03 pdb=" C4A FMNV1 501 " 0.039 2.00e-02 2.50e+03 pdb=" C5A FMNV1 501 " 0.016 2.00e-02 2.50e+03 pdb=" C6 FMNV1 501 " -0.011 2.00e-02 2.50e+03 pdb=" C7 FMNV1 501 " -0.023 2.00e-02 2.50e+03 pdb=" C7M FMNV1 501 " -0.050 2.00e-02 2.50e+03 pdb=" C8 FMNV1 501 " -0.011 2.00e-02 2.50e+03 pdb=" C8M FMNV1 501 " -0.010 2.00e-02 2.50e+03 pdb=" C9 FMNV1 501 " 0.008 2.00e-02 2.50e+03 pdb=" C9A FMNV1 501 " 0.023 2.00e-02 2.50e+03 pdb=" N1 FMNV1 501 " 0.016 2.00e-02 2.50e+03 pdb=" N10 FMNV1 501 " 0.040 2.00e-02 2.50e+03 pdb=" N3 FMNV1 501 " -0.021 2.00e-02 2.50e+03 pdb=" N5 FMNV1 501 " 0.027 2.00e-02 2.50e+03 pdb=" O2 FMNV1 501 " -0.087 2.00e-02 2.50e+03 pdb=" O4 FMNV1 501 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VALS1 247 " -0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C VALS1 247 " 0.070 2.00e-02 2.50e+03 pdb=" O VALS1 247 " -0.026 2.00e-02 2.50e+03 pdb=" N METS1 248 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PROS5 94 " -0.067 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PROS5 95 " 0.174 5.00e-02 4.00e+02 pdb=" CA PROS5 95 " -0.050 5.00e-02 4.00e+02 pdb=" CD PROS5 95 " -0.057 5.00e-02 4.00e+02 ... (remaining 11473 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 818 2.65 - 3.21: 58455 3.21 - 3.77: 103679 3.77 - 4.34: 134606 4.34 - 4.90: 216097 Nonbonded interactions: 513655 Sorted by model distance: nonbonded pdb=" CA ALAS3 80 " pdb=" O GLUS3 91 " model vdw 2.082 3.470 nonbonded pdb=" OE1 GLUS2 224 " pdb=" OH TYRS8 40 " model vdw 2.250 2.440 nonbonded pdb=" O ILEA9 19 " pdb=" OG SERA9 43 " model vdw 2.251 2.440 nonbonded pdb=" OG1 THRS6 12 " pdb=" O THRS6 14 " model vdw 2.257 2.440 nonbonded pdb=" OE1 GLUS8 138 " pdb=" OG SERAL 80 " model vdw 2.258 2.440 ... (remaining 513650 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'AA' and (resid 5 through 84 or (resid 101 and (name C10 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C20 or name C21 or name C3 or name C4 or name C5 \ or name C6 or name C7 or name C8 or name C9 or name N1 or name N2 or name O1 or \ name O2 or name O3 or name O4 or name O5 or name O6 or name O7 or name P1 or nam \ e S1 )))) selection = (chain 'AB' and (resid 5 through 84 or resid 101)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 12 5.49 5 S 462 5.16 5 C 42100 2.51 5 N 11025 2.21 5 O 11716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.210 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: 0.050 Extract box with map and model: 30.730 Check model and map are aligned: 0.750 Convert atoms to be neutral: 0.430 Process input model: 139.070 Find NCS groups from input model: 2.010 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 179.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 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 : 0.006 0.209 67000 Z= 0.393 Angle : 1.184 25.111 90856 Z= 0.619 Chirality : 1.035 21.156 9988 Planarity : 0.008 0.100 11476 Dihedral : 11.389 151.439 24996 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.29 % Favored : 89.64 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.34 % Twisted Proline : 1.25 % Twisted General : 0.50 % 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: -4.07 (0.08), residues: 7979 helix: -1.94 (0.06), residues: 4189 sheet: -2.14 (0.25), residues: 372 loop : -3.76 (0.09), residues: 3418 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3303 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 3264 time to evaluate : 6.400 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 outliers start: 39 outliers final: 3 residues processed: 3282 average time/residue: 0.6585 time to fit residues: 3594.5230 Evaluate side-chains 1820 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1817 time to evaluate : 6.083 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4581 time to fit residues: 10.6303 ------------------------------------------------------------------------------- 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: 3.9990 chunk 596 optimal weight: 10.0000 chunk 330 optimal weight: 1.9990 chunk 203 optimal weight: 0.0070 chunk 402 optimal weight: 0.8980 chunk 318 optimal weight: 0.0070 chunk 616 optimal weight: 6.9990 chunk 238 optimal weight: 9.9990 chunk 375 optimal weight: 3.9990 chunk 459 optimal weight: 9.9990 chunk 714 optimal weight: 5.9990 overall best weight: 1.3820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1 293 ASN V1 361 GLN V2 42 HIS S1 36 GLN ** S1 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 255 HIS S1 259 ASN S1 365 ASN ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 682 GLN S2 50 ASN S2 79 HIS S2 84 HIS S2 116 GLN S2 135 GLN S2 316 ASN ** S2 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S3 95 ASN S7 38 ASN ** S7 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 150 ASN V3 44 HIS V3 75 HIS ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 29 HIS S4 46 GLN S4 50 ASN A9 3 HIS A9 203 GLN A9 288 HIS A2 61 GLN A5 20 HIS A5 82 GLN A6 107 HIS A6 125 HIS A7 20 GLN ** A7 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A7 50 ASN AL 17 HIS ** AL 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 108 GLN ** D1 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 194 ASN ** D6 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 23 ASN D5 115 ASN ** D5 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 205 ASN ** D5 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 309 GLN ** D5 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D5 534 HIS D4 82 HIS D4 83 HIS D4 88 ASN ** D4 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 293 HIS ** D4 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2 63 GLN D2 232 HIS D2 316 GLN AK 6 HIS AK 78 GLN B5 143 ASN A8 29 HIS A8 162 HIS ** BJ 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 113 GLN AJ 76 ASN AJ 97 GLN ** AJ 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 200 GLN AJ 204 ASN AJ 251 GLN ** S5 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S5 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S5 96 HIS A3 51 ASN A3 68 HIS B4 51 ASN AM 23 ASN AM 53 ASN AM 84 GLN B6 73 HIS ** B7 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B9 168 HIS B2 24 GLN ** BK 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 103 HIS Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.261 67000 Z= 0.568 Angle : 1.692 51.123 90856 Z= 1.069 Chirality : 0.310 6.456 9988 Planarity : 0.007 0.123 11476 Dihedral : 8.092 133.460 8997 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.98 % Favored : 89.99 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.36 % Twisted Proline : 0.63 % Twisted General : 0.23 % 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: -2.67 (0.09), residues: 7979 helix: -0.54 (0.07), residues: 4206 sheet: -1.85 (0.27), residues: 334 loop : -3.44 (0.09), residues: 3439 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2309 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 2293 time to evaluate : 6.192 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 outliers start: 16 outliers final: 5 residues processed: 2304 average time/residue: 0.6178 time to fit residues: 2407.7714 Evaluate side-chains 1661 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1656 time to evaluate : 6.142 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4588 time to fit residues: 12.4167 ------------------------------------------------------------------------------- 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: 0.6980 chunk 221 optimal weight: 5.9990 chunk 594 optimal weight: 10.0000 chunk 486 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 715 optimal weight: 8.9990 chunk 773 optimal weight: 10.0000 chunk 637 optimal weight: 9.9990 chunk 710 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 chunk 574 optimal weight: 9.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V1 293 ASN V1 356 HIS V2 37 ASN ** V2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 119 GLN S1 401 HIS S1 494 HIS S1 682 GLN S2 135 GLN ** S2 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S8 123 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S6 94 GLN S4 44 ASN S4 50 ASN A9 87 HIS A9 288 HIS ** A2 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 80 ASN A5 85 ASN A6 107 HIS ** A7 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A7 50 ASN AL 31 ASN ** AL 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3 10 ASN D1 5 ASN ** D1 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 59 GLN D5 175 ASN ** D5 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D5 400 ASN D5 570 GLN D4 51 ASN D4 440 HIS ** AK 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 78 GLN B5 44 ASN B5 124 GLN ** BJ 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 151 HIS AJ 184 GLN S5 96 HIS B4 49 GLN AM 23 ASN ** B7 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B9 25 HIS B9 32 HIS B9 138 GLN ** B2 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 103 HIS C1 36 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.235 67000 Z= 0.608 Angle : 1.715 50.949 90856 Z= 1.080 Chirality : 0.314 6.478 9988 Planarity : 0.007 0.129 11476 Dihedral : 7.738 128.871 8997 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.09 % Favored : 88.86 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.34 % Twisted Proline : 0.84 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.09), residues: 7979 helix: -0.06 (0.08), residues: 4164 sheet: -1.72 (0.27), residues: 346 loop : -3.23 (0.10), residues: 3469 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2035 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 2022 time to evaluate : 6.050 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 outliers start: 13 outliers final: 3 residues processed: 2031 average time/residue: 0.6004 time to fit residues: 2070.3910 Evaluate side-chains 1534 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1531 time to evaluate : 6.144 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4306 time to fit residues: 10.4940 ------------------------------------------------------------------------------- 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: 3.9990 chunk 371 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 341 optimal weight: 0.9990 chunk 480 optimal weight: 0.9990 chunk 718 optimal weight: 0.9990 chunk 760 optimal weight: 9.9990 chunk 375 optimal weight: 0.8980 chunk 680 optimal weight: 8.9990 chunk 205 optimal weight: 0.0370 overall best weight: 0.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 37 ASN S1 51 ASN ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S3 160 HIS S7 38 ASN ** S7 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 46 GLN S4 50 ASN ** A9 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A9 288 HIS A2 80 ASN A5 20 HIS A5 110 GLN A6 125 HIS ** A7 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A7 50 ASN ** AL 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 400 ASN D4 440 HIS D2 222 ASN D2 235 ASN ** AK 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 44 ASN B5 69 HIS ** BJ 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S5 69 GLN ** S5 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S5 96 HIS A3 68 HIS B3 47 ASN C2 61 GLN B4 49 GLN AM 23 ASN B7 75 ASN ** B9 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B9 50 HIS B2 24 GLN B8 72 ASN BK 86 GLN A1 31 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.247 67000 Z= 0.546 Angle : 1.669 50.705 90856 Z= 1.057 Chirality : 0.311 6.344 9988 Planarity : 0.006 0.109 11476 Dihedral : 7.304 126.275 8997 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.58 % Favored : 90.40 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.37 % Twisted Proline : 0.84 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.09), residues: 7979 helix: 0.27 (0.08), residues: 4145 sheet: -1.55 (0.27), residues: 372 loop : -3.08 (0.10), residues: 3462 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2129 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 2125 time to evaluate : 6.057 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 outliers start: 4 outliers final: 0 residues processed: 2126 average time/residue: 0.5823 time to fit residues: 2118.8207 Evaluate side-chains 1580 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1580 time to evaluate : 6.067 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.2479 ------------------------------------------------------------------------------- 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: 9.9990 chunk 431 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 566 optimal weight: 10.0000 chunk 313 optimal weight: 0.5980 chunk 649 optimal weight: 7.9990 chunk 525 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 388 optimal weight: 5.9990 chunk 682 optimal weight: 7.9990 chunk 191 optimal weight: 6.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1 398 GLN V1 431 GLN V2 37 ASN ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 430 GLN ** S2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 168 ASN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 46 GLN S4 50 ASN A9 37 HIS ** A9 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A9 288 HIS A7 24 GLN A7 50 ASN ** AL 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3 10 ASN ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D5 400 ASN D4 88 ASN ** D4 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 279 GLN D4 440 HIS ** D2 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN ** AK 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 103 ASN AJ 200 GLN S5 96 HIS ** C2 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 49 GLN B4 74 ASN AM 23 ASN ** B9 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1 27 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.235 67000 Z= 0.578 Angle : 1.690 51.010 90856 Z= 1.068 Chirality : 0.311 6.362 9988 Planarity : 0.006 0.116 11476 Dihedral : 7.204 122.386 8997 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.94 % Favored : 89.03 % Rotamer Outliers : 0.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.37 % Twisted Proline : 0.84 % 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: -1.69 (0.09), residues: 7979 helix: 0.38 (0.08), residues: 4146 sheet: -1.55 (0.26), residues: 361 loop : -3.07 (0.10), residues: 3472 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1983 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1982 time to evaluate : 6.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 1983 average time/residue: 0.5770 time to fit residues: 1962.3943 Evaluate side-chains 1519 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1519 time to evaluate : 6.097 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.9506 ------------------------------------------------------------------------------- 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: 0.8980 chunk 685 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 446 optimal weight: 0.9990 chunk 187 optimal weight: 0.8980 chunk 761 optimal weight: 0.0770 chunk 632 optimal weight: 9.9990 chunk 352 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 251 optimal weight: 4.9990 chunk 399 optimal weight: 2.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V1 116 HIS ** V1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 37 ASN ** S1 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 430 GLN S1 444 GLN ** S2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 347 HIS ** S7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN A9 87 HIS ** A9 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 80 ASN A6 101 HIS A7 50 ASN ** AL 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 400 ASN D4 82 HIS ** D4 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 180 GLN ** D4 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 279 GLN D2 48 HIS ** D2 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 172 GLN D2 235 ASN ** AK 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S5 69 GLN C2 61 GLN B4 49 GLN B4 74 ASN AM 23 ASN B9 32 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.245 67000 Z= 0.545 Angle : 1.674 50.636 90856 Z= 1.058 Chirality : 0.312 6.401 9988 Planarity : 0.005 0.085 11476 Dihedral : 7.012 121.660 8997 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.79 % Favored : 90.19 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.37 % Twisted Proline : 0.63 % 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: -1.53 (0.09), residues: 7979 helix: 0.50 (0.08), residues: 4146 sheet: -1.55 (0.26), residues: 379 loop : -2.98 (0.10), residues: 3454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2043 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2041 time to evaluate : 6.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 2043 average time/residue: 0.5923 time to fit residues: 2072.4655 Evaluate side-chains 1535 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1535 time to evaluate : 6.123 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.0190 ------------------------------------------------------------------------------- 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: 4.9990 chunk 85 optimal weight: 6.9990 chunk 433 optimal weight: 0.9990 chunk 556 optimal weight: 9.9990 chunk 430 optimal weight: 1.9990 chunk 640 optimal weight: 0.9980 chunk 425 optimal weight: 9.9990 chunk 758 optimal weight: 9.9990 chunk 474 optimal weight: 0.7980 chunk 462 optimal weight: 4.9990 chunk 350 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 37 ASN S1 259 ASN S1 401 HIS S1 430 GLN ** S2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 38 ASN ** S8 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN ** A9 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 80 ASN A6 101 HIS ** A7 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A7 50 ASN ** AL 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 248 HIS ** D5 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 400 ASN D5 580 GLN ** D4 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 279 GLN ** D2 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN ** AK 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 63 ASN BJ 64 HIS ** BJ 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 103 ASN S5 44 HIS S5 69 GLN B4 49 GLN B4 74 ASN B7 116 GLN B2 24 GLN BK 103 HIS A1 27 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.239 67000 Z= 0.555 Angle : 1.682 50.748 90856 Z= 1.062 Chirality : 0.312 6.415 9988 Planarity : 0.006 0.103 11476 Dihedral : 6.960 120.793 8997 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.52 % Favored : 89.46 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.37 % Twisted Proline : 0.63 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.09), residues: 7979 helix: 0.52 (0.08), residues: 4145 sheet: -1.60 (0.25), residues: 392 loop : -2.95 (0.10), residues: 3442 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1962 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1960 time to evaluate : 6.160 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: 2 outliers final: 1 residues processed: 1961 average time/residue: 0.5867 time to fit residues: 1975.7876 Evaluate side-chains 1524 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1523 time to evaluate : 6.147 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4541 time to fit residues: 8.9251 ------------------------------------------------------------------------------- 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: 6.9990 chunk 302 optimal weight: 1.9990 chunk 453 optimal weight: 0.9980 chunk 228 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 482 optimal weight: 8.9990 chunk 516 optimal weight: 2.9990 chunk 375 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 596 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V1 113 HIS ** V1 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1 373 ASN ** V1 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 37 ASN S1 237 ASN ** S1 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 430 GLN ** S2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN A2 80 ASN A7 50 ASN ** AL 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 69 ASN ** AL 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3 83 ASN ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 400 ASN D4 82 HIS ** D4 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 180 GLN D4 279 GLN ** D2 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 172 GLN D2 235 ASN ** AK 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 63 ASN ** BJ 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 107 GLN S5 44 HIS B3 47 ASN ** C2 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 49 GLN B4 74 ASN AM 75 GLN B7 116 GLN B8 3 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.239 67000 Z= 0.551 Angle : 1.683 50.695 90856 Z= 1.062 Chirality : 0.312 6.385 9988 Planarity : 0.006 0.112 11476 Dihedral : 6.893 121.134 8997 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.40 % Favored : 89.56 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.37 % Twisted Proline : 0.42 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.09), residues: 7979 helix: 0.57 (0.08), residues: 4143 sheet: -1.62 (0.26), residues: 377 loop : -2.90 (0.10), residues: 3459 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1981 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1979 time to evaluate : 6.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 1980 average time/residue: 0.6024 time to fit residues: 2048.3298 Evaluate side-chains 1534 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1534 time to evaluate : 6.075 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.9863 ------------------------------------------------------------------------------- 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: 0.0370 chunk 726 optimal weight: 5.9990 chunk 663 optimal weight: 9.9990 chunk 706 optimal weight: 8.9990 chunk 425 optimal weight: 0.9990 chunk 307 optimal weight: 2.9990 chunk 555 optimal weight: 10.0000 chunk 216 optimal weight: 1.9990 chunk 638 optimal weight: 0.0010 chunk 668 optimal weight: 1.9990 chunk 704 optimal weight: 1.9990 overall best weight: 1.0070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V1 148 ASN V1 373 ASN V1 398 GLN V2 37 ASN S1 336 ASN S1 430 GLN ** S2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN A9 87 HIS ** A9 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 80 ASN A5 82 GLN A7 50 ASN ** AL 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 138 GLN ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 23 ASN ** D5 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 248 HIS ** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 400 ASN ** D4 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 204 ASN D2 235 ASN D2 316 GLN ** AK 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 64 HIS ** BJ 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 103 ASN S5 44 HIS S5 69 GLN C2 61 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.243 67000 Z= 0.547 Angle : 1.687 50.794 90856 Z= 1.062 Chirality : 0.312 6.368 9988 Planarity : 0.006 0.120 11476 Dihedral : 6.808 121.322 8997 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.89 % Favored : 90.09 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.37 % Twisted Proline : 0.42 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.09), residues: 7979 helix: 0.60 (0.08), residues: 4153 sheet: -1.51 (0.26), residues: 369 loop : -2.86 (0.10), residues: 3457 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1982 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1977 time to evaluate : 6.219 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: 5 outliers final: 0 residues processed: 1981 average time/residue: 0.6008 time to fit residues: 2042.4746 Evaluate side-chains 1535 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1535 time to evaluate : 6.325 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.1711 ------------------------------------------------------------------------------- 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: 7.9990 chunk 747 optimal weight: 6.9990 chunk 456 optimal weight: 1.9990 chunk 354 optimal weight: 0.5980 chunk 519 optimal weight: 0.8980 chunk 784 optimal weight: 3.9990 chunk 721 optimal weight: 9.9990 chunk 624 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 482 optimal weight: 8.9990 chunk 382 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V1 373 ASN V2 37 ASN S1 430 GLN ** S2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 38 ASN ** S8 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN ** A9 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 203 GLN A2 80 ASN A7 50 ASN ** AL 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3 83 ASN ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 138 GLN D1 235 ASN D5 23 ASN D5 135 ASN ** D5 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 400 ASN ** D5 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 180 GLN ** D4 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 279 GLN ** D4 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 186 HIS D2 204 ASN D2 235 ASN ** AK 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 74 ASN ** B9 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B8 56 GLN ** B8 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B8 132 GLN A1 27 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.5833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.591 67000 Z= 0.579 Angle : 1.717 72.724 90856 Z= 1.071 Chirality : 0.312 6.365 9988 Planarity : 0.006 0.115 11476 Dihedral : 6.799 121.190 8997 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.90 % Favored : 90.07 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.37 % Twisted Proline : 0.42 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.09), residues: 7979 helix: 0.60 (0.08), residues: 4139 sheet: -1.40 (0.27), residues: 374 loop : -2.82 (0.10), residues: 3466 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15958 Ramachandran restraints generated. 7979 Oldfield, 0 Emsley, 7979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1931 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1928 time to evaluate : 6.324 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: 3 outliers final: 0 residues processed: 1929 average time/residue: 0.5902 time to fit residues: 1961.6671 Evaluate side-chains 1541 residues out of total 7072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1541 time to evaluate : 6.088 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.9582 ------------------------------------------------------------------------------- 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: 2.9990 chunk 191 optimal weight: 5.9990 chunk 575 optimal weight: 8.9990 chunk 92 optimal weight: 0.0370 chunk 173 optimal weight: 9.9990 chunk 625 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 642 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 115 optimal weight: 0.3980 overall best weight: 1.8864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V1 373 ASN V2 37 ASN S1 430 GLN ** S2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 38 ASN ** S8 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN ** A9 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 80 ASN A7 50 ASN ** AL 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3 83 ASN ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 23 ASN ** D5 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 400 ASN ** D4 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN ** AK 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S5 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B7 116 GLN ** B2 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B8 3 HIS BK 103 HIS A1 40 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.096140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.084622 restraints weight = 210125.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.086598 restraints weight = 119702.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.087957 restraints weight = 78618.350| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.5913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.241 67000 Z= 0.556 Angle : 1.693 50.771 90856 Z= 1.065 Chirality : 0.312 6.360 9988 Planarity : 0.006 0.115 11476 Dihedral : 6.775 121.513 8997 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.93 % Favored : 90.05 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.37 % Twisted Proline : 0.42 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.09), residues: 7979 helix: 0.58 (0.08), residues: 4166 sheet: -1.41 (0.27), residues: 374 loop : -2.79 (0.10), residues: 3439 =============================================================================== Job complete usr+sys time: 26796.32 seconds wall clock time: 463 minutes 45.21 seconds (27825.21 seconds total)