Starting phenix.real_space_refine on Sat Dec 9 21:57:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qa9_4482/12_2023/6qa9_4482_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qa9_4482/12_2023/6qa9_4482.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qa9_4482/12_2023/6qa9_4482_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/6qa9_4482/12_2023/6qa9_4482_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qa9_4482/12_2023/6qa9_4482_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qa9_4482/12_2023/6qa9_4482.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qa9_4482/12_2023/6qa9_4482.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qa9_4482/12_2023/6qa9_4482_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qa9_4482/12_2023/6qa9_4482_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 13 5.49 5 S 462 5.16 5 C 42126 2.51 5 N 11035 2.21 5 O 11738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "V1 PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V1 TYR 26": "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 "S2 TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S2 TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S2 TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S3 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S3 TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S7 ARG 174": "NH1" <-> "NH2" Residue "S7 ARG 178": "NH1" <-> "NH2" Residue "S8 TYR 118": "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 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AL ARG 106": "NH1" <-> "NH2" Residue "AL PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 ARG 195": "NH1" <-> "NH2" Residue "D1 TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D6 PHE 20": "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 "AB PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AJ ARG 95": "NH1" <-> "NH2" Residue "AJ PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AJ TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AJ ARG 305": "NH1" <-> "NH2" Residue "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 "A1 ARG 25": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 65403 Number of models: 1 Model: "" Number of chains: 58 Chain: "V1" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3312 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 21, 'TRANS': 408} Chain: "V2" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1647 Classifications: {'peptide': 212} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 189} Chain: "S1" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5275 Classifications: {'peptide': 688} Link IDs: {'CIS': 2, 'PTRANS': 32, 'TRANS': 653} Chain: "S2" Number of atoms: 3436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3436 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 398} 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: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} Chain: "S8" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1415 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 165} Chain: "V3" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 335 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 3, 'TRANS': 36} Chain: "S6" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 737 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "S4" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1025 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "A9" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2321 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 14, 'TRANS': 275} 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: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 902 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 101} Chain: "A6" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 970 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 106} Chain: "A7" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 752 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 81} Chain breaks: 1 Chain: "AL" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1192 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "AA" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 645 Classifications: {'peptide': 80} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 76} Chain: "D3" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 787 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 1 Chain: "D1" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2390 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 18, 'TRANS': 276} Chain breaks: 2 Chain: "D6" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1308 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 3, 'TRANS': 164} Chain breaks: 1 Chain: "4L" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 96} Chain: "D5" Number of atoms: 4805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4805 Classifications: {'peptide': 606} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 578} Chain: "D4" Number of atoms: 3646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3646 Classifications: {'peptide': 459} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 437} Chain: "D2" Number of atoms: 2724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2724 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 326} Chain: "AK" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1025 Classifications: {'peptide': 140} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 4, 'TRANS': 132} Chain: "B5" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1156 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 128} Chain: "AB" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 702 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "A8" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1404 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 12, 'TRANS': 156} Chain: "BJ" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1441 Classifications: {'peptide': 171} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "AJ" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2583 Classifications: {'peptide': 319} Link IDs: {'CIS': 6, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 298} Chain: "S5" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 822 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "A3" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 582 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 62} Chain: "B3" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 578 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C2" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 997 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 10, 'TRANS': 106} Chain: "B4" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1059 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 117} Chain: "AM" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1143 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'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: {'CIS': 1, 'PTRANS': 7, 'TRANS': 56} Chain: "B8" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1324 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 135} Chain: "BK" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 853 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 93} Chain: "C1" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 391 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 3, 'TRANS': 42} Chain: "B1" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 449 Classifications: {'peptide': 52} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 49} Chain: "A1" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 577 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "V1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "S1" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S7" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "S8" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A9" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "AA" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Chain: "D1" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Chain: "D5" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 Chain: "D4" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 68 Unusual residues: {'3PE': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "A8" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "B9" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2715 SG CYSV1 365 49.835 168.775 74.264 1.00 67.20 S ATOM 2695 SG CYSV1 362 55.239 170.811 74.230 1.00 96.99 S ATOM 4453 SG CYSV2 148 31.395 179.800 77.866 1.00122.48 S ATOM 5785 SG CYSS1 114 63.444 152.211 67.387 1.00 51.74 S ATOM 5745 SG CYSS1 108 60.716 149.362 62.248 1.00 48.62 S ATOM 6117 SG CYSS1 156 61.599 163.017 64.590 1.00 55.89 S ATOM 6094 SG CYSS1 153 55.818 160.718 62.184 1.00 47.26 S ATOM 5230 SG CYSS1 41 63.378 167.682 69.476 1.00 56.39 S ATOM 5316 SG CYSS1 52 63.655 165.341 72.949 1.00 53.66 S ATOM 5341 SG CYSS1 55 65.801 168.323 75.502 1.00 52.31 S ATOM 16149 SG CYSS7 119 78.719 117.200 71.982 1.00 42.48 S ATOM 16379 SG CYSS7 149 73.000 118.201 73.980 1.00 43.58 S ATOM 15651 SG CYSS7 55 75.083 111.883 73.582 1.00 59.36 S ATOM 15645 SG CYSS7 54 77.214 115.359 78.163 1.00 70.37 S ATOM 17619 SG CYSS8 122 64.222 126.803 68.419 1.00 35.83 S ATOM 17346 SG CYSS8 87 70.490 128.138 66.749 1.00 59.47 S ATOM 17648 SG CYSS8 126 58.411 132.741 66.149 1.00 44.30 S ATOM 17319 SG CYSS8 83 64.531 131.767 63.956 1.00 37.12 S ATOM 18860 SG CYSS6 59 44.622 140.550 62.885 1.00 64.53 S ATOM 19038 SG CYSS6 84 47.970 141.695 60.381 1.00 55.02 S ATOM 19060 SG CYSS6 87 45.903 138.657 61.088 1.00 52.75 S Time building chain proxies: 27.46, per 1000 atoms: 0.42 Number of scatterers: 65403 At special positions: 0 Unit cell: (270.2, 228.2, 154, 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 13 15.00 O 11738 8.00 N 11035 7.00 C 42126 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYSAK 17 " - pdb=" SG CYSAK 74 " distance=2.03 Simple disulfide: pdb=" SG CYSAK 94 " - pdb=" SG CYSAK 114 " distance=2.03 Simple disulfide: pdb=" SG CYSA8 35 " - pdb=" SG CYSA8 65 " distance=2.04 Simple disulfide: pdb=" SG CYSA8 45 " - pdb=" SG CYSA8 55 " distance=2.03 Simple disulfide: pdb=" SG CYSA8 77 " - pdb=" SG CYSA8 109 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYSB7 58 " - pdb=" SG CYSB7 89 " distance=2.03 Simple disulfide: pdb=" SG CYSB7 68 " - pdb=" SG CYSB7 79 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.73 Conformation dependent library (CDL) restraints added in 8.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FESS1 803 " pdb="FE2 FESS1 803 " - pdb=" SG CYSS1 55 " pdb="FE1 FESS1 803 " - pdb=" SG CYSS1 52 " 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="FE1 FESV2 300 " - pdb=" SG CYSV2 103 " pdb="FE2 FESV2 300 " - pdb=" SG CYSV2 144 " pdb="FE1 FESV2 300 " - pdb=" SG CYSV2 108 " pdb=" SF4S1 801 " pdb="FE3 SF4S1 801 " - pdb=" NE2 HISS1 101 " pdb="FE4 SF4S1 801 " - pdb=" SG CYSS1 108 " pdb="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="FE1 SF4S1 802 " - pdb=" SG CYSS1 156 " pdb="FE3 SF4S1 802 " - pdb=" SG CYSS1 159 " pdb="FE4 SF4S1 802 " - pdb=" SG CYSS1 203 " pdb=" SF4S7 300 " pdb="FE1 SF4S7 300 " - pdb=" SG CYSS7 119 " pdb="FE4 SF4S7 300 " - pdb=" SG CYSS7 54 " pdb="FE2 SF4S7 300 " - pdb=" SG CYSS7 149 " pdb="FE3 SF4S7 300 " - pdb=" SG CYSS7 55 " pdb=" SF4S8 201 " pdb="FE3 SF4S8 201 " - pdb=" SG CYSS8 122 " pdb="FE4 SF4S8 201 " - pdb=" SG CYSS8 87 " pdb="FE2 SF4S8 201 " - pdb=" SG CYSS8 116 " pdb="FE1 SF4S8 201 " - pdb=" SG CYSS8 119 " pdb=" SF4S8 202 " pdb="FE1 SF4S8 202 " - pdb=" SG CYSS8 126 " pdb="FE2 SF4S8 202 " - pdb=" SG CYSS8 83 " pdb="FE4 SF4S8 202 " - pdb=" SG CYSS8 80 " pdb="FE3 SF4S8 202 " - pdb=" SG CYSS8 77 " pdb=" SF4V1 500 " pdb="FE3 SF4V1 500 " - pdb=" SG CYSV1 362 " pdb="FE1 SF4V1 500 " - pdb=" SG CYSV1 365 " pdb="FE4 SF4V1 500 " - pdb=" SG CYSV1 359 " pdb="FE2 SF4V1 500 " - pdb=" SG CYSV1 405 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZNS6 300 " pdb="ZN ZNS6 300 " - pdb=" NE2 HISS6 68 " pdb="ZN ZNS6 300 " - pdb=" SG CYSS6 84 " pdb="ZN ZNS6 300 " - pdb=" SG CYSS6 59 " pdb="ZN ZNS6 300 " - pdb=" SG CYSS6 87 " Number of angles added : 3 15966 Ramachandran restraints generated. 7983 Oldfield, 0 Emsley, 7983 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15208 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 299 helices and 26 sheets defined 48.5% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.49 Creating SS restraints... Processing helix chain 'V1' and resid 33 through 39 Processing helix chain 'V1' and resid 45 through 49 Processing helix chain 'V1' and resid 53 through 63 Processing helix chain 'V1' and resid 75 through 81 Processing helix chain 'V1' and resid 106 through 113 removed outlier: 4.085A pdb=" N ILEV1 110 " --> pdb=" O LYSV1 106 " (cutoff:3.500A) Processing helix chain 'V1' and resid 115 through 128 Processing helix chain 'V1' and resid 143 through 158 Processing helix chain 'V1' and resid 184 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 Processing helix chain 'V1' and resid 242 through 244 No H-bonds generated for 'chain 'V1' and resid 242 through 244' Processing helix chain 'V1' and resid 276 through 281 Processing helix chain 'V1' and resid 291 through 293 No H-bonds generated for 'chain 'V1' and resid 291 through 293' Processing helix chain 'V1' and resid 309 through 312 No H-bonds generated for 'chain 'V1' and resid 309 through 312' Processing helix chain 'V1' and resid 319 through 324 Processing helix chain 'V1' and resid 343 through 356 Processing helix chain 'V1' and resid 363 through 381 Processing helix chain 'V1' and resid 386 through 399 Processing helix chain 'V1' and resid 407 through 421 Proline residue: V1 414 - end of helix Processing helix chain 'V1' and resid 423 through 437 Processing helix chain 'V2' and resid 25 through 37 Processing helix chain 'V2' and resid 43 through 57 removed outlier: 3.776A pdb=" N ALAV2 46 " --> pdb=" O LYSV2 43 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VALV2 47 " --> pdb=" O ALAV2 44 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEUV2 48 " --> pdb=" O ALAV2 45 " (cutoff:3.500A) Proline residue: V2 49 - end of helix Processing helix chain 'V2' and resid 63 through 73 Processing helix chain 'V2' and resid 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 178 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 122 Processing helix chain 'S1' and resid 159 through 166 Processing helix chain 'S1' and resid 196 through 202 removed outlier: 3.642A 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 274 No H-bonds generated for 'chain 'S1' and resid 271 through 274' Processing helix chain 'S1' and resid 296 through 308 Processing helix chain 'S1' and resid 326 through 338 Processing helix chain 'S1' and resid 369 through 373 Processing helix chain 'S1' and resid 389 through 401 Processing helix chain 'S1' and resid 426 through 434 Processing helix chain 'S1' and resid 438 through 444 Processing helix chain 'S1' and resid 461 through 479 removed outlier: 4.392A pdb=" N ALAS1 464 " --> pdb=" O ASNS1 461 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILES1 466 " --> pdb=" O GLYS1 463 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEUS1 467 " --> pdb=" O ALAS1 464 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALAS1 474 " --> pdb=" O SERS1 471 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THRS1 479 " --> pdb=" O LYSS1 476 " (cutoff:3.500A) Processing helix chain 'S1' and resid 497 through 504 Processing helix chain 'S1' and resid 511 through 516 removed outlier: 4.196A pdb=" N LYSS1 516 " --> pdb=" O ALAS1 513 " (cutoff:3.500A) 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 648 Processing helix chain 'S1' and resid 668 through 672 Processing helix chain 'S1' and resid 676 through 680 Processing helix chain 'S1' and resid 682 through 692 Processing helix chain 'S2' and resid 8 through 13 Processing helix chain 'S2' and resid 25 through 27 No H-bonds generated for 'chain 'S2' and resid 25 through 27' Processing helix chain 'S2' and resid 87 through 92 Processing helix chain 'S2' and resid 98 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: 4.207A 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 removed outlier: 3.541A pdb=" N ARGS2 261 " --> pdb=" O VALS2 258 " (cutoff:3.500A) Processing helix chain 'S2' and resid 269 through 272 No H-bonds generated for 'chain 'S2' and resid 269 through 272' Processing helix chain 'S2' and resid 277 through 280 Processing helix chain 'S2' and resid 293 through 316 Processing helix chain 'S2' and resid 335 through 340 Processing helix chain 'S2' and resid 342 through 353 Processing helix chain 'S2' and resid 394 through 400 Processing helix chain 'S2' and resid 402 through 405 No H-bonds generated for 'chain 'S2' and resid 402 through 405' 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 65 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: 4.314A pdb=" N TRPS3 129 " --> pdb=" O ALAS3 126 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYRS3 130 " --> pdb=" O ALAS3 127 " (cutoff:3.500A) removed outlier: 3.540A 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 41 Processing helix chain 'S7' and resid 54 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 80 through 82 No H-bonds generated for 'chain 'S7' and resid 80 through 82' 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 151 through 158 Processing helix chain 'S8' and resid 163 through 171 Processing helix chain 'V3' and resid 48 through 57 removed outlier: 4.381A pdb=" N PHEV3 51 " --> pdb=" O THRV3 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASPV3 53 " --> pdb=" O THRV3 50 " (cutoff:3.500A) 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 49 through 51 No H-bonds generated for 'chain 'S4' and resid 49 through 51' Processing helix chain 'S4' and resid 89 through 98 Processing helix chain 'S4' and resid 118 through 121 No H-bonds generated for 'chain 'S4' and resid 118 through 121' Processing helix chain 'A9' and resid 29 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 249 Processing helix chain 'A9' and resid 281 through 288 Processing helix chain 'A9' and resid 311 through 317 Processing helix chain 'A2' and resid 27 through 38 Processing helix chain 'A2' and resid 41 through 46 Processing helix chain 'A2' and resid 83 through 93 Processing helix chain 'A5' and resid 19 through 35 Processing helix chain 'A5' and resid 42 through 59 Processing helix chain 'A5' and resid 65 through 70 Processing helix chain 'A5' and resid 77 through 94 Processing helix chain 'A6' and resid 24 through 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 119 through 122 No H-bonds generated for 'chain 'A6' and resid 119 through 122' Processing helix chain 'A7' and resid 5 through 14 Processing helix chain 'AL' and resid 4 through 15 removed outlier: 3.809A pdb=" N LEUAL 11 " --> pdb=" O LEUAL 7 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLNAL 12 " --> pdb=" O LYSAL 8 " (cutoff:3.500A) Processing helix chain 'AL' and resid 20 through 27 Processing helix chain 'AL' and resid 84 through 90 Processing helix chain 'AA' and resid 8 through 21 Processing helix chain 'AA' and resid 44 through 58 Processing helix chain 'AA' and resid 64 through 68 Processing helix chain 'AA' and resid 73 through 83 Processing helix chain 'D3' and resid 2 through 22 Processing helix chain 'D3' and resid 54 through 79 removed outlier: 4.114A pdb=" N VALD3 58 " --> pdb=" O LYSD3 54 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALAD3 59 " --> pdb=" O PHED3 55 " (cutoff:3.500A) Proline residue: D3 74 - end of helix removed outlier: 5.698A pdb=" N TRPD3 77 " --> pdb=" O LEUD3 73 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALAD3 78 " --> pdb=" O PROD3 74 " (cutoff:3.500A) Processing helix chain 'D3' and resid 84 through 107 Processing helix chain 'D1' and resid 2 through 10 Processing helix chain 'D1' and resid 12 through 31 Processing helix chain 'D1' and resid 46 through 57 Processing helix chain 'D1' and resid 68 through 84 Proline residue: D1 75 - end of helix Processing helix chain 'D1' and resid 102 through 122 Processing helix chain 'D1' and resid 127 through 157 removed outlier: 4.000A pdb=" N TYRD1 142 " --> pdb=" O GLND1 138 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLUD1 143 " --> pdb=" O THRD1 139 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VALD1 144 " --> pdb=" O ILED1 140 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N THRD1 145 " --> pdb=" O SERD1 141 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N METD1 156 " --> pdb=" O SERD1 152 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASND1 157 " --> pdb=" O VALD1 153 " (cutoff:3.500A) Processing helix chain 'D1' and resid 163 through 170 removed outlier: 4.487A pdb=" N GLUD1 170 " --> pdb=" O ILED1 166 " (cutoff:3.500A) Processing helix chain 'D1' and resid 174 through 177 No H-bonds generated for 'chain 'D1' and resid 174 through 177' Processing helix chain 'D1' and resid 180 through 192 Processing helix chain 'D1' and resid 220 through 242 Processing helix chain 'D1' and resid 252 through 274 Processing helix chain 'D1' and resid 282 through 311 Proline residue: D1 295 - end of helix Proline residue: D1 308 - end of helix Processing helix chain 'D6' and resid 5 through 21 Processing helix chain 'D6' and resid 26 through 47 Processing helix chain 'D6' and resid 52 through 60 removed outlier: 3.737A pdb=" N LEUD6 58 " --> pdb=" O LEUD6 54 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILED6 59 " --> pdb=" O METD6 55 " (cutoff:3.500A) Processing helix chain 'D6' and resid 65 through 75 Processing helix chain 'D6' and resid 87 through 108 Processing helix chain 'D6' and resid 139 through 143 Processing helix chain 'D6' and resid 152 through 171 Processing helix chain '4L' and resid 4 through 20 Processing helix chain '4L' and resid 27 through 50 Processing helix chain '4L' and resid 59 through 83 Processing helix chain 'D5' and resid 2 through 15 removed outlier: 4.381A pdb=" N LEUD5 15 " --> pdb=" O THRD5 11 " (cutoff:3.500A) Processing helix chain 'D5' and resid 17 through 23 Processing helix chain 'D5' and resid 32 through 57 removed outlier: 4.507A 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: 4.430A 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 211 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: 3.655A pdb=" N LEUD5 260 " --> pdb=" O GLYD5 256 " (cutoff:3.500A) Processing helix chain 'D5' and resid 266 through 268 No H-bonds generated for 'chain 'D5' and resid 266 through 268' Processing helix chain 'D5' and resid 271 through 292 Processing helix chain 'D5' and resid 298 through 318 Processing helix chain 'D5' and resid 322 through 350 Processing helix chain 'D5' and resid 367 through 379 Processing helix chain 'D5' and resid 387 through 400 removed outlier: 3.780A pdb=" N SERD5 391 " --> pdb=" O THRD5 387 " (cutoff:3.500A) removed outlier: 3.760A 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: 5.747A pdb=" N GLYD5 465 " --> pdb=" O SERD5 461 " (cutoff:3.500A) removed outlier: 5.378A 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: 3.685A pdb=" N TYRD5 529 " --> pdb=" O LEUD5 526 " (cutoff:3.500A) Proline residue: D5 530 - end of helix removed outlier: 3.661A pdb=" N METD5 533 " --> pdb=" O PROD5 530 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HISD5 534 " --> pdb=" O THRD5 531 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N THRD5 537 " --> pdb=" O HISD5 534 " (cutoff:3.500A) Proline residue: D5 538 - end of helix removed outlier: 4.067A pdb=" N ASND5 541 " --> pdb=" O PROD5 538 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEUD5 542 " --> pdb=" O TYRD5 539 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N METD5 544 " --> pdb=" O ASND5 541 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SERD5 545 " --> pdb=" O LEUD5 542 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYSD5 547 " --> pdb=" O METD5 544 " (cutoff:3.500A) Processing helix chain 'D5' and resid 555 through 561 Processing helix chain 'D5' and resid 563 through 577 Processing helix chain 'D5' and resid 585 through 599 Processing helix chain 'D4' and resid 2 through 16 Proline residue: D4 7 - end of helix Proline residue: D4 13 - end of helix removed outlier: 3.708A pdb=" N TRPD4 16 " --> pdb=" O METD4 12 " (cutoff:3.500A) Processing helix chain 'D4' and resid 23 through 41 removed outlier: 4.241A 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: 3.775A 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 171 Processing helix chain 'D4' and resid 176 through 181 Processing helix chain 'D4' and resid 191 through 206 Processing helix chain 'D4' and resid 210 through 221 removed outlier: 3.861A pdb=" N HISD4 213 " --> pdb=" O TYRD4 210 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEUD4 214 " --> pdb=" O GLYD4 211 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TRPD4 215 " --> pdb=" O LEUD4 212 " (cutoff:3.500A) Proline residue: D4 217 - end of helix Processing helix chain 'D4' and resid 225 through 248 removed outlier: 4.432A pdb=" N LEUD4 248 " --> pdb=" O METD4 244 " (cutoff:3.500A) Processing helix chain 'D4' and resid 254 through 257 No H-bonds generated for 'chain 'D4' and resid 254 through 257' Processing helix chain 'D4' and resid 259 through 277 removed outlier: 3.543A pdb=" N LEUD4 277 " --> pdb=" O SERD4 273 " (cutoff:3.500A) Processing helix chain 'D4' and resid 282 through 302 removed outlier: 3.680A pdb=" N ILED4 286 " --> pdb=" O LYSD4 283 " (cutoff:3.500A) Processing helix chain 'D4' and resid 306 through 336 Processing helix chain 'D4' and resid 355 through 366 Processing helix chain 'D4' and resid 373 through 388 Processing helix chain 'D4' and resid 393 through 414 removed outlier: 4.083A pdb=" N THRD4 414 " --> pdb=" O METD4 410 " (cutoff:3.500A) Processing helix chain 'D4' and resid 431 through 449 removed outlier: 3.580A 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 120 removed outlier: 3.731A pdb=" N HISD2 112 " --> pdb=" O ALAD2 109 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N PHED2 113 " --> pdb=" O PROD2 110 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TRPD2 114 " --> pdb=" O PHED2 111 " (cutoff:3.500A) Proline residue: D2 116 - end of helix removed outlier: 3.903A pdb=" N GLND2 120 " --> pdb=" O GLUD2 117 " (cutoff:3.500A) Processing helix chain 'D2' and resid 124 through 148 Proline residue: D2 138 - end of helix removed outlier: 3.931A 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 191 Processing helix chain 'D2' and resid 198 through 219 Processing helix chain 'D2' and resid 227 through 236 Processing helix chain 'D2' and resid 238 through 252 removed outlier: 3.622A pdb=" N ILED2 242 " --> pdb=" O PROD2 238 " (cutoff:3.500A) Processing helix chain 'D2' and resid 258 through 271 Proline residue: D2 262 - end of helix removed outlier: 4.092A pdb=" N METD2 265 " --> pdb=" O PROD2 262 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLUD2 269 " --> pdb=" O ILED2 266 " (cutoff:3.500A) Processing helix chain 'D2' and resid 277 through 300 removed outlier: 4.099A pdb=" N LEUD2 290 " --> pdb=" O ALAD2 286 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TYRD2 291 " --> pdb=" O LEUD2 287 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N PHED2 292 " --> pdb=" O LEUD2 288 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYRD2 293 " --> pdb=" O ASND2 289 " (cutoff:3.500A) Processing helix chain 'D2' and resid 311 through 316 removed outlier: 4.197A pdb=" N GLND2 316 " --> pdb=" O LYSD2 312 " (cutoff:3.500A) Processing helix chain 'D2' and resid 326 through 334 Processing helix chain 'D2' and resid 340 through 342 No H-bonds generated for 'chain 'D2' and resid 340 through 342' Processing helix chain 'D2' and resid 344 through 346 No H-bonds generated for 'chain 'D2' and resid 344 through 346' Processing helix chain 'AK' and resid 2 through 10 Processing helix chain 'AK' and resid 19 through 41 Processing helix chain 'AK' and resid 48 through 79 Processing helix chain 'AK' and resid 87 through 103 Processing helix chain 'AK' and resid 108 through 130 Processing helix chain 'B5' and resid 16 through 30 Processing helix chain 'B5' and resid 34 through 46 Processing helix chain 'B5' and resid 70 through 78 Processing helix chain 'B5' and resid 83 through 117 Processing helix chain 'AB' and resid 8 through 20 Processing helix chain 'AB' and resid 44 through 58 Processing helix chain 'AB' and resid 64 through 67 No H-bonds generated for 'chain 'AB' and resid 64 through 67' Processing helix chain 'AB' and resid 73 through 84 Processing helix chain 'A8' and resid 21 through 26 Processing helix chain 'A8' and resid 28 through 33 Processing helix chain 'A8' and resid 39 through 48 Processing helix chain 'A8' and resid 56 through 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 57 removed outlier: 4.860A pdb=" N ARGBJ 42 " --> pdb=" O LEUBJ 38 " (cutoff:3.500A) Proline residue: BJ 43 - end of helix Processing helix chain 'BJ' and resid 81 through 116 removed outlier: 3.695A pdb=" N PHEBJ 85 " --> pdb=" O VALBJ 81 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N GLUBJ 86 " --> pdb=" O LEUBJ 82 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 126 through 141 Processing helix chain 'BJ' and resid 152 through 172 Processing helix chain 'AJ' and resid 4 through 10 Processing helix chain 'AJ' and resid 36 through 46 Processing helix chain 'AJ' and resid 58 through 62 Processing helix chain 'AJ' and resid 79 through 84 Processing helix chain 'AJ' and resid 93 through 116 Processing helix chain 'AJ' and resid 128 through 140 Processing helix chain 'AJ' and resid 146 through 159 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 240 Processing helix chain 'AJ' and resid 247 through 249 No H-bonds generated for 'chain 'AJ' and resid 247 through 249' Processing helix chain 'AJ' and resid 254 through 263 Processing helix chain 'AJ' and resid 266 through 272 removed outlier: 5.252A pdb=" N TYRAJ 272 " --> pdb=" O GLUAJ 268 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 286 through 297 Processing helix chain 'S5' and resid 5 through 8 No H-bonds generated for 'chain 'S5' and resid 5 through 8' Processing helix chain 'S5' and resid 33 through 42 Processing helix chain 'S5' and resid 50 through 54 Processing helix chain 'S5' and resid 56 through 66 Processing helix chain 'S5' and resid 69 through 88 Processing helix chain 'A3' and resid 16 through 33 Proline residue: A3 32 - end of helix Processing helix chain 'A3' and resid 38 through 46 Processing helix chain 'B3' and resid 26 through 38 Processing helix chain 'B3' and resid 62 through 68 removed outlier: 3.891A pdb=" N LEUB3 66 " --> pdb=" O PHEB3 62 " (cutoff:3.500A) Processing helix chain 'B3' and resid 70 through 82 removed outlier: 5.385A pdb=" N ALAB3 75 " --> pdb=" O LYSB3 71 " (cutoff:3.500A) Processing helix chain 'C2' and resid 17 through 19 No H-bonds generated for 'chain 'C2' and resid 17 through 19' Processing helix chain 'C2' and resid 29 through 48 Processing helix chain 'C2' and resid 58 through 96 Processing helix chain 'B4' and resid 26 through 50 Processing helix chain 'B4' and resid 62 through 72 Processing helix chain 'B4' and resid 83 through 117 Proline residue: B4 96 - end of helix Processing helix chain 'AM' and resid 31 through 96 Proline residue: AM 72 - end of helix Processing helix chain 'AM' and resid 130 through 136 Processing helix chain 'B6' and resid 5 through 25 Processing helix chain 'B6' and resid 68 through 91 Proline residue: B6 77 - end of helix removed outlier: 3.701A pdb=" N TYRB6 87 " --> pdb=" O TYRB6 83 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N HISB6 88 " --> pdb=" O TYRB6 84 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VALB6 89 " --> pdb=" O LEUB6 85 " (cutoff:3.500A) Processing helix chain 'B7' and resid 3 through 9 Processing helix chain 'B7' and resid 42 through 47 Processing helix chain 'B7' and resid 59 through 71 Processing helix chain 'B7' and resid 81 through 117 Processing helix chain 'B9' and resid 11 through 29 Processing helix chain 'B9' and resid 34 through 49 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 removed outlier: 3.516A pdb=" N TRPB2 41 " --> pdb=" O LEUB2 37 " (cutoff:3.500A) Processing helix chain 'B8' and resid 5 through 7 No H-bonds generated for 'chain 'B8' and resid 5 through 7' Processing helix chain 'B8' and resid 18 through 26 Processing helix chain 'B8' and resid 60 through 62 No H-bonds generated for 'chain 'B8' and resid 60 through 62' Processing helix chain 'B8' and resid 81 through 83 No H-bonds generated for 'chain 'B8' and resid 81 through 83' Processing helix chain 'B8' and resid 99 through 121 Processing helix chain 'BK' and resid 51 through 63 removed outlier: 3.549A 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: 6.215A pdb=" N GLUBK 87 " --> pdb=" O ARGBK 84 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLUBK 101 " --> pdb=" O LYSBK 98 " (cutoff:3.500A) Processing helix chain 'C1' and resid 16 through 45 Processing helix chain 'B1' and resid 7 through 9 No H-bonds generated for 'chain 'B1' and resid 7 through 9' Processing helix chain 'B1' and resid 15 through 33 Processing helix chain 'A1' and resid 5 through 29 Proline residue: A1 19 - end of helix Processing helix chain 'A1' and resid 42 through 55 Processing sheet with id= A, first strand: chain 'V1' and resid 221 through 224 removed outlier: 6.379A pdb=" N ALAV1 133 " --> pdb=" O LEUV1 93 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VALV1 95 " --> pdb=" O ALAV1 133 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N TYRV1 135 " --> pdb=" O VALV1 95 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ALAV1 97 " --> pdb=" O TYRV1 135 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYRV1 137 " --> pdb=" O ALAV1 97 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASPV1 174 " --> pdb=" O ALAV1 134 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILEV1 136 " --> pdb=" O ASPV1 174 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHEV1 176 " --> pdb=" O ILEV1 136 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ILEV1 138 " --> pdb=" O PHEV1 176 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VALV1 178 " --> pdb=" O ILEV1 138 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'V1' and resid 253 through 258 Processing sheet with id= C, first strand: chain 'V1' and resid 294 through 298 removed outlier: 6.706A pdb=" N METV1 337 " --> pdb=" O LEUV1 295 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N VALV1 297 " --> pdb=" O ILEV1 335 " (cutoff:3.500A) removed outlier: 6.839A 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: 6.513A 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 342 through 344 removed outlier: 6.421A pdb=" N METS1 521 " --> pdb=" O ALAS1 316 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ILES1 318 " --> pdb=" O METS1 521 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N PHES1 523 " --> pdb=" O ILES1 318 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VALS1 559 " --> pdb=" O TYRS1 545 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLYS1 547 " --> pdb=" O VALS1 559 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEUS1 561 " --> pdb=" O GLYS1 547 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S1' and resid 490 through 492 removed outlier: 7.281A pdb=" N ASNS1 491 " --> pdb=" O PROS1 449 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N VALS1 451 " --> pdb=" O ASNS1 491 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VALS1 376 " --> pdb=" O METS1 450 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VALS1 452 " --> pdb=" O VALS1 376 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEUS1 378 " --> pdb=" O VALS1 452 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LYSS1 405 " --> pdb=" O VALS1 377 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEUS1 379 " --> pdb=" O LYSS1 405 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALAS1 407 " --> pdb=" O LEUS1 379 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASPS1 420 " --> pdb=" O LEUS1 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'S1' and resid 572 through 574 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: 6.901A pdb=" N LEUS3 48 " --> pdb=" O ARGS3 106 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LYSS3 108 " --> pdb=" O LEUS3 48 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILES3 50 " --> pdb=" O LYSS3 108 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N TYRS3 110 " --> pdb=" O ILES3 50 " (cutoff:3.500A) removed outlier: 7.484A 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 85 through 89 removed outlier: 6.376A pdb=" N TYRS7 112 " --> pdb=" O METS7 86 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VALS7 88 " --> pdb=" O TYRS7 112 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VALS7 114 " --> pdb=" O VALS7 88 " (cutoff:3.500A) removed outlier: 6.377A 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 96 Processing sheet with id= R, first strand: chain 'S6' and resid 56 through 59 Processing sheet with id= S, first strand: chain 'S4' and resid 103 through 105 removed outlier: 6.554A pdb=" N ALAS4 35 " --> pdb=" O ASPS4 104 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A9' and resid 90 through 92 removed outlier: 6.628A pdb=" N GLNA9 44 " --> pdb=" O ALAA9 21 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VALA9 23 " --> pdb=" O GLNA9 44 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILEA9 46 " --> pdb=" O VALA9 23 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A9' and resid 130 through 134 removed outlier: 6.272A pdb=" N THRA9 164 " --> pdb=" O HISA9 131 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N SERA9 133 " --> pdb=" O THRA9 164 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILEA9 166 " --> pdb=" O SERA9 133 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'A9' and resid 170 through 172 Processing sheet with id= W, first strand: chain 'A2' and resid 51 through 56 removed outlier: 3.635A pdb=" N ILEA2 18 " --> pdb=" O PROA2 51 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARGA2 16 " --> pdb=" O ARGA2 67 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ARGA2 67 " --> pdb=" O ARGA2 16 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILEA2 18 " --> pdb=" O TRPA2 65 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TRPA2 65 " --> pdb=" O ILEA2 18 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ILEA2 20 " --> pdb=" O LYSA2 63 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYSA2 63 " --> pdb=" O ILEA2 20 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'AL' and resid 40 through 42 Processing sheet with id= Y, first strand: chain 'D5' and resid 61 through 68 removed outlier: 4.759A pdb=" N HISD5 67 " --> pdb=" O LEUD5 76 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEUD5 76 " --> pdb=" O HISD5 67 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'AJ' and resid 122 through 125 removed outlier: 6.710A pdb=" N VALAJ 168 " --> pdb=" O THRAJ 26 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ASPAJ 28 " --> pdb=" O VALAJ 168 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ILEAJ 170 " --> pdb=" O ASPAJ 28 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLUAJ 219 " --> pdb=" O VALAJ 169 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TYRAJ 171 " --> pdb=" O GLUAJ 219 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LEUAJ 221 " --> pdb=" O TYRAJ 171 " (cutoff:3.500A) 2753 hydrogen bonds defined for protein. 7908 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.51 Time building geometry restraints manager: 22.70 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: 27770 1.42 - 1.64: 38460 1.64 - 1.86: 750 1.86 - 2.08: 0 2.08 - 2.30: 80 Bond restraints: 67060 Sorted by residual: bond pdb=" C16 ZMPB9 201 " pdb=" N2 ZMPB9 201 " ideal model delta sigma weight residual 1.452 1.334 0.118 2.00e-02 2.50e+03 3.46e+01 bond pdb=" C16 ZMPAA 101 " pdb=" N2 ZMPAA 101 " ideal model delta sigma weight residual 1.452 1.336 0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" O2B NDPA9 401 " pdb=" P2B NDPA9 401 " ideal model delta sigma weight residual 1.833 1.625 0.208 3.80e-02 6.93e+02 2.98e+01 bond pdb=" C13 ZMPB9 201 " pdb=" N1 ZMPB9 201 " ideal model delta sigma weight residual 1.451 1.342 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C13 ZMPAA 101 " pdb=" N1 ZMPAA 101 " ideal model delta sigma weight residual 1.451 1.344 0.107 2.00e-02 2.50e+03 2.88e+01 ... (remaining 67055 not shown) Histogram of bond angle deviations from ideal: 69.97 - 83.80: 72 83.80 - 97.63: 18 97.63 - 111.46: 28573 111.46 - 125.29: 60584 125.29 - 139.11: 1702 Bond angle restraints: 90949 Sorted by residual: angle pdb=" PA NDPA9 401 " pdb=" O3 NDPA9 401 " pdb=" PN NDPA9 401 " ideal model delta sigma weight residual 107.74 133.63 -25.89 1.95e+00 2.62e-01 1.76e+02 angle pdb=" S1 FESV2 300 " pdb="FE2 FESV2 300 " pdb=" S2 FESV2 300 " ideal model delta sigma weight residual 104.33 91.33 13.00 1.14e+00 7.69e-01 1.30e+02 angle pdb="FE1 FESV2 300 " pdb=" S2 FESV2 300 " pdb="FE2 FESV2 300 " ideal model delta sigma weight residual 75.66 88.60 -12.94 1.14e+00 7.69e-01 1.29e+02 angle pdb="FE1 FESV2 300 " pdb=" S1 FESV2 300 " pdb="FE2 FESV2 300 " ideal model delta sigma weight residual 75.66 88.84 -13.18 1.20e+00 6.94e-01 1.21e+02 angle pdb=" S1 FESV2 300 " pdb="FE1 FESV2 300 " pdb=" S2 FESV2 300 " ideal model delta sigma weight residual 104.33 91.23 13.10 1.20e+00 6.94e-01 1.19e+02 ... (remaining 90944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 37855 16.99 - 33.98: 1896 33.98 - 50.97: 503 50.97 - 67.96: 57 67.96 - 84.95: 47 Dihedral angle restraints: 40358 sinusoidal: 16787 harmonic: 23571 Sorted by residual: dihedral pdb=" CA PHED4 52 " pdb=" C PHED4 52 " pdb=" N SERD4 53 " pdb=" CA SERD4 53 " ideal model delta harmonic sigma weight residual 180.00 121.08 58.92 0 5.00e+00 4.00e-02 1.39e+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 180.00 123.04 56.96 0 5.00e+00 4.00e-02 1.30e+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 -123.37 -56.63 0 5.00e+00 4.00e-02 1.28e+02 ... (remaining 40355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.210: 9972 4.210 - 8.421: 0 8.421 - 12.631: 0 12.631 - 16.842: 0 16.842 - 21.052: 24 Chirality restraints: 9996 Sorted by residual: chirality pdb="FE1 SF4S1 801 " pdb=" S2 SF4S1 801 " pdb=" S3 SF4S1 801 " pdb=" S4 SF4S1 801 " both_signs ideal model delta sigma weight residual False -10.55 10.50 -21.05 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE3 SF4S1 801 " pdb=" S1 SF4S1 801 " pdb=" S2 SF4S1 801 " pdb=" S4 SF4S1 801 " both_signs ideal model delta sigma weight residual False -10.55 10.50 -21.05 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE2 SF4S7 300 " pdb=" S1 SF4S7 300 " pdb=" S3 SF4S7 300 " pdb=" S4 SF4S7 300 " both_signs ideal model delta sigma weight residual False 10.55 -10.49 21.05 2.00e-01 2.50e+01 1.11e+04 ... (remaining 9993 not shown) Planarity restraints: 11492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMNV1 501 " -0.100 2.00e-02 2.50e+03 2.92e-02 4.04e+01 pdb=" C10 FMNV1 501 " 0.032 2.00e-02 2.50e+03 pdb=" C2 FMNV1 501 " 0.010 2.00e-02 2.50e+03 pdb=" C4 FMNV1 501 " -0.003 2.00e-02 2.50e+03 pdb=" C4A FMNV1 501 " 0.016 2.00e-02 2.50e+03 pdb=" C5A FMNV1 501 " 0.006 2.00e-02 2.50e+03 pdb=" C6 FMNV1 501 " -0.017 2.00e-02 2.50e+03 pdb=" C7 FMNV1 501 " -0.012 2.00e-02 2.50e+03 pdb=" C7M FMNV1 501 " -0.013 2.00e-02 2.50e+03 pdb=" C8 FMNV1 501 " 0.008 2.00e-02 2.50e+03 pdb=" C8M FMNV1 501 " 0.005 2.00e-02 2.50e+03 pdb=" C9 FMNV1 501 " 0.030 2.00e-02 2.50e+03 pdb=" C9A FMNV1 501 " 0.026 2.00e-02 2.50e+03 pdb=" N1 FMNV1 501 " 0.031 2.00e-02 2.50e+03 pdb=" N10 FMNV1 501 " 0.025 2.00e-02 2.50e+03 pdb=" N3 FMNV1 501 " -0.004 2.00e-02 2.50e+03 pdb=" N5 FMNV1 501 " -0.000 2.00e-02 2.50e+03 pdb=" O2 FMNV1 501 " -0.011 2.00e-02 2.50e+03 pdb=" O4 FMNV1 501 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHED4 52 " -0.022 2.00e-02 2.50e+03 4.48e-02 2.01e+01 pdb=" C PHED4 52 " 0.077 2.00e-02 2.50e+03 pdb=" O PHED4 52 " -0.030 2.00e-02 2.50e+03 pdb=" N SERD4 53 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PROS5 94 " -0.065 5.00e-02 4.00e+02 9.65e-02 1.49e+01 pdb=" N PROS5 95 " 0.167 5.00e-02 4.00e+02 pdb=" CA PROS5 95 " -0.047 5.00e-02 4.00e+02 pdb=" CD PROS5 95 " -0.055 5.00e-02 4.00e+02 ... (remaining 11489 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 10664 2.76 - 3.30: 64612 3.30 - 3.83: 111101 3.83 - 4.37: 125475 4.37 - 4.90: 208323 Nonbonded interactions: 520175 Sorted by model distance: nonbonded pdb=" OG1 THRS6 12 " pdb=" O THRS6 14 " model vdw 2.226 2.440 nonbonded pdb=" OH TYRAJ 101 " pdb=" OG1 THRAJ 159 " model vdw 2.239 2.440 nonbonded pdb=" O GLUA9 285 " pdb=" OG1 THRA9 289 " model vdw 2.246 2.440 nonbonded pdb=" O GLUV1 101 " pdb=" OG1 THRV1 104 " model vdw 2.252 2.440 nonbonded pdb=" OG SERD5 77 " pdb=" OG SERD5 79 " model vdw 2.254 2.440 ... (remaining 520170 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) selection = (chain 'AB' and resid 5 through 84) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.060 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: 28.860 Check model and map are aligned: 0.720 Set scattering table: 0.450 Process input model: 155.710 Find NCS groups from input model: 2.010 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 196.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.208 67060 Z= 0.457 Angle : 1.214 25.893 90949 Z= 0.636 Chirality : 1.031 21.052 9996 Planarity : 0.008 0.097 11492 Dihedral : 11.600 84.954 25114 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.98 % Favored : 87.96 % Rotamer: Outliers : 0.44 % Allowed : 5.79 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.32 % Twisted Proline : 1.46 % 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: -3.97 (0.08), residues: 7983 helix: -1.82 (0.06), residues: 4140 sheet: -2.22 (0.25), residues: 366 loop : -3.73 (0.09), residues: 3477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRPV1 413 HIS 0.015 0.002 HISA9 288 PHE 0.060 0.004 PHED1 270 TYR 0.063 0.003 TYRS7 125 ARG 0.014 0.001 ARGS2 174 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15966 Ramachandran restraints generated. 7983 Oldfield, 0 Emsley, 7983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15966 Ramachandran restraints generated. 7983 Oldfield, 0 Emsley, 7983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2879 residues out of total 7078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 2848 time to evaluate : 5.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 3 residues processed: 2860 average time/residue: 0.7059 time to fit residues: 3363.2490 Evaluate side-chains 1612 residues out of total 7078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1609 time to evaluate : 5.713 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4671 time to fit residues: 10.3990 ------------------------------------------------------------------------------- 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: 8.9990 chunk 596 optimal weight: 3.9990 chunk 330 optimal weight: 10.0000 chunk 203 optimal weight: 0.9990 chunk 402 optimal weight: 0.8980 chunk 318 optimal weight: 8.9990 chunk 616 optimal weight: 6.9990 chunk 238 optimal weight: 0.9980 chunk 375 optimal weight: 0.8980 chunk 459 optimal weight: 1.9990 chunk 714 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 V2 42 HIS V2 150 ASN ** S1 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 517 ASN ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 621 ASN S2 46 ASN S2 50 ASN S2 84 HIS S2 135 GLN S2 201 GLN S2 347 HIS ** S3 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 88 ASN ** S7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 164 GLN ** S8 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S8 90 GLN S6 16 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S4 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S4 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN ** A9 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 87 HIS A9 148 ASN ** A9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 296 HIS A9 321 HIS A2 61 GLN ** A2 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 49 GLN ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A7 8 GLN AL 12 GLN AL 13 GLN AL 31 ASN ** AL 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 52 ASN AL 69 ASN AL 112 ASN ** AL 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 10 ASN D1 287 HIS ** D6 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D6 175 ASN 4L 25 HIS D5 136 ASN ** D5 139 GLN ** 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 ** D5 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 296 ASN D5 323 HIS D5 400 ASN ** D5 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 484 HIS D5 541 ASN D5 546 GLN ** D4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 82 HIS ** D4 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4 304 GLN D4 450 ASN D2 63 GLN ** D2 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN ** D2 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 316 GLN ** AK 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 69 HIS B5 143 ASN ** A8 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 76 HIS BJ 54 GLN BJ 55 HIS BJ 113 GLN BJ 148 HIS AJ 97 GLN ** AJ 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 204 ASN AJ 251 GLN A3 45 ASN A3 68 HIS ** B3 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 75 GLN ** B6 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B6 73 HIS B6 82 HIS B7 91 HIS B7 109 GLN B9 13 GLN ** B9 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B9 75 HIS B9 77 GLN B2 16 GLN B8 97 ASN ** BK 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 119 GLN ** C1 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 71 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.284 67060 Z= 0.554 Angle : 1.689 51.344 90949 Z= 1.068 Chirality : 0.314 6.556 9996 Planarity : 0.006 0.078 11492 Dihedral : 8.745 86.099 9102 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer: Outliers : 0.31 % Allowed : 4.04 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.34 % Twisted Proline : 0.84 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.09), residues: 7983 helix: -0.55 (0.07), residues: 4164 sheet: -2.27 (0.25), residues: 366 loop : -3.43 (0.09), residues: 3453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRPAM 141 HIS 0.017 0.001 HIS4L 52 PHE 0.040 0.002 PHED1 270 TYR 0.030 0.002 TYRB5 125 ARG 0.018 0.001 ARGB2 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15966 Ramachandran restraints generated. 7983 Oldfield, 0 Emsley, 7983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15966 Ramachandran restraints generated. 7983 Oldfield, 0 Emsley, 7983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2196 residues out of total 7078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 2174 time to evaluate : 5.882 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 outliers start: 22 outliers final: 5 residues processed: 2183 average time/residue: 0.6218 time to fit residues: 2302.7847 Evaluate side-chains 1585 residues out of total 7078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1580 time to evaluate : 5.728 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4638 time to fit residues: 12.0079 ------------------------------------------------------------------------------- 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: 9.9990 chunk 221 optimal weight: 0.9980 chunk 594 optimal weight: 8.9990 chunk 486 optimal weight: 0.2980 chunk 197 optimal weight: 6.9990 chunk 715 optimal weight: 0.0020 chunk 773 optimal weight: 1.9990 chunk 637 optimal weight: 6.9990 chunk 710 optimal weight: 0.8980 chunk 244 optimal weight: 7.9990 chunk 574 optimal weight: 9.9990 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V2 9 HIS V2 37 ASN V2 150 ASN V2 157 ASN ** S1 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 198 ASN S1 259 ASN ** S1 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S3 88 ASN ** S3 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 6 ASN ** S8 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S6 16 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN A9 2 HIS ** A2 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 13 GLN AL 112 ASN ** AL 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3 108 GLN D1 99 ASN D1 235 ASN D1 292 ASN ** D6 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D6 175 ASN D5 136 ASN D5 139 GLN ** D5 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 226 GLN ** D5 274 GLN ** 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** D5 546 GLN ** D4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 103 GLN ** D4 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 77 ASN ** D2 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 204 ASN ** D2 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN A8 29 HIS A8 63 ASN BJ 99 GLN BJ 103 ASN ** BJ 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 122 GLN AJ 120 GLN ** AJ 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 68 HIS ** C2 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 59 HIS AM 60 GLN ** B6 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 16 GLN BK 86 GLN ** C1 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.242 67060 Z= 0.537 Angle : 1.670 50.835 90949 Z= 1.059 Chirality : 0.313 6.529 9996 Planarity : 0.005 0.080 11492 Dihedral : 8.187 87.638 9102 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer: Outliers : 0.17 % Allowed : 4.18 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.34 % 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: -2.19 (0.09), residues: 7983 helix: -0.08 (0.08), residues: 4158 sheet: -1.84 (0.27), residues: 353 loop : -3.25 (0.10), residues: 3472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRPD2 234 HIS 0.016 0.001 HISD4 319 PHE 0.041 0.002 PHED3 56 TYR 0.026 0.002 TYRS8 118 ARG 0.009 0.001 ARGA7 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15966 Ramachandran restraints generated. 7983 Oldfield, 0 Emsley, 7983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15966 Ramachandran restraints generated. 7983 Oldfield, 0 Emsley, 7983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2016 residues out of total 7078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 2004 time to evaluate : 6.008 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 outliers start: 12 outliers final: 3 residues processed: 2011 average time/residue: 0.6082 time to fit residues: 2086.9177 Evaluate side-chains 1508 residues out of total 7078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1505 time to evaluate : 5.748 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4757 time to fit residues: 10.4851 ------------------------------------------------------------------------------- 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: 0.9980 chunk 538 optimal weight: 10.0000 chunk 371 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 341 optimal weight: 7.9990 chunk 480 optimal weight: 7.9990 chunk 718 optimal weight: 0.9990 chunk 760 optimal weight: 20.0000 chunk 375 optimal weight: 6.9990 chunk 680 optimal weight: 9.9990 chunk 205 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S1 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 198 ASN ** S1 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 88 ASN ** S3 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S4 43 ASN S4 50 ASN A9 296 HIS ** A2 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 52 ASN ** AL 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3 83 ASN D1 194 ASN D1 235 ASN D1 292 ASN ** D6 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 136 ASN ** D5 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 226 GLN D5 248 HIS ** D5 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 354 GLN D5 400 ASN ** D5 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 546 GLN D5 580 GLN ** D4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 81 GLN ** D4 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4 304 GLN ** D2 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN ** A8 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 103 ASN ** BJ 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 45 ASN ** A3 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AM 53 ASN ** B6 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2 16 GLN C1 35 HIS ** C1 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.240 67060 Z= 0.558 Angle : 1.678 50.948 90949 Z= 1.065 Chirality : 0.311 6.352 9996 Planarity : 0.005 0.083 11492 Dihedral : 7.964 86.668 9102 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 0.10 % Allowed : 3.45 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.34 % 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: -1.92 (0.09), residues: 7983 helix: 0.18 (0.08), residues: 4138 sheet: -1.76 (0.26), residues: 367 loop : -3.16 (0.10), residues: 3478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRPD2 234 HIS 0.012 0.001 HISA9 58 PHE 0.064 0.002 PHED1 270 TYR 0.039 0.002 TYRD1 43 ARG 0.012 0.001 ARGD1 274 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15966 Ramachandran restraints generated. 7983 Oldfield, 0 Emsley, 7983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15966 Ramachandran restraints generated. 7983 Oldfield, 0 Emsley, 7983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1852 residues out of total 7078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1845 time to evaluate : 5.801 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 outliers start: 7 outliers final: 1 residues processed: 1850 average time/residue: 0.6152 time to fit residues: 1945.8026 Evaluate side-chains 1442 residues out of total 7078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1441 time to evaluate : 5.757 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5398 time to fit residues: 8.5688 ------------------------------------------------------------------------------- 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: 10.0000 chunk 431 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 566 optimal weight: 2.9990 chunk 313 optimal weight: 8.9990 chunk 649 optimal weight: 0.8980 chunk 525 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 388 optimal weight: 1.9990 chunk 682 optimal weight: 10.0000 chunk 191 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V2 37 ASN ** S1 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 198 ASN S1 259 ASN ** S1 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2 135 GLN ** S3 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 88 ASN ** S3 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN A9 8 HIS A9 216 ASN ** A2 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A7 12 ASN ** AL 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3 108 GLN D1 235 ASN D1 292 ASN ** D6 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 136 ASN ** D5 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 248 HIS ** D5 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 400 ASN ** D5 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 81 GLN ** D4 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN AB 35 HIS ** A8 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 204 ASN ** AJ 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 258 ASN A3 45 ASN ** A3 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AM 60 GLN ** B6 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B9 13 GLN B9 17 GLN ** B9 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.239 67060 Z= 0.545 Angle : 1.675 50.738 90949 Z= 1.063 Chirality : 0.312 6.387 9996 Planarity : 0.005 0.084 11492 Dihedral : 7.819 86.104 9102 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.01 % Allowed : 11.07 % Favored : 88.91 % Rotamer: Outliers : 0.06 % Allowed : 3.46 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.36 % Twisted Proline : 0.63 % 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: -1.80 (0.09), residues: 7983 helix: 0.30 (0.08), residues: 4158 sheet: -1.80 (0.26), residues: 371 loop : -3.14 (0.10), residues: 3454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRPD2 234 HIS 0.009 0.001 HISD4 440 PHE 0.046 0.002 PHED1 270 TYR 0.028 0.002 TYRS2 193 ARG 0.011 0.001 ARGBK 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15966 Ramachandran restraints generated. 7983 Oldfield, 0 Emsley, 7983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15966 Ramachandran restraints generated. 7983 Oldfield, 0 Emsley, 7983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1818 residues out of total 7078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1814 time to evaluate : 5.735 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: 1817 average time/residue: 0.6398 time to fit residues: 1998.5200 Evaluate side-chains 1434 residues out of total 7078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1434 time to evaluate : 7.182 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.7096 ------------------------------------------------------------------------------- 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: 2.9990 chunk 685 optimal weight: 0.0770 chunk 150 optimal weight: 1.9990 chunk 446 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 761 optimal weight: 6.9990 chunk 632 optimal weight: 8.9990 chunk 352 optimal weight: 0.8980 chunk 63 optimal weight: 0.0000 chunk 251 optimal weight: 4.9990 chunk 399 optimal weight: 0.9980 overall best weight: 0.7944 ------------------------------------------------------------------------------- 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** ** S1 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 198 ASN ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2 135 GLN ** S3 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 88 ASN ** S3 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S7 162 GLN S8 168 ASN V3 44 HIS ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S4 43 ASN S4 50 ASN ** A2 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 20 HIS ** A5 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 98 GLN AL 113 HIS D3 108 GLN ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 226 GLN D5 309 GLN ** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 446 ASN ** D5 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 541 ASN ** D4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 168 GLN ** D4 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN AB 35 HIS ** A8 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S5 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 45 ASN ** A3 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AM 60 GLN ** B6 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B9 17 GLN ** B9 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1 68 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.249 67060 Z= 0.534 Angle : 1.666 50.647 90949 Z= 1.058 Chirality : 0.312 6.457 9996 Planarity : 0.005 0.086 11492 Dihedral : 7.584 84.814 9102 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.42 % Favored : 89.55 % Rotamer: Outliers : 0.01 % Allowed : 2.70 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.36 % Twisted Proline : 0.42 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.09), residues: 7983 helix: 0.43 (0.08), residues: 4135 sheet: -1.69 (0.25), residues: 387 loop : -3.04 (0.10), residues: 3461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRPD2 234 HIS 0.018 0.001 HISB2 50 PHE 0.048 0.002 PHEAJ 134 TYR 0.023 0.002 TYRB5 125 ARG 0.012 0.000 ARGBK 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15966 Ramachandran restraints generated. 7983 Oldfield, 0 Emsley, 7983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15966 Ramachandran restraints generated. 7983 Oldfield, 0 Emsley, 7983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1876 residues out of total 7078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1875 time to evaluate : 5.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 1876 average time/residue: 0.6456 time to fit residues: 2092.5637 Evaluate side-chains 1455 residues out of total 7078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1455 time to evaluate : 5.787 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.8438 ------------------------------------------------------------------------------- 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: 5.9990 chunk 85 optimal weight: 1.9990 chunk 433 optimal weight: 5.9990 chunk 556 optimal weight: 9.9990 chunk 430 optimal weight: 8.9990 chunk 640 optimal weight: 0.0870 chunk 425 optimal weight: 9.9990 chunk 758 optimal weight: 4.9990 chunk 474 optimal weight: 0.9990 chunk 462 optimal weight: 7.9990 chunk 350 optimal weight: 4.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1 373 ASN S1 198 ASN ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 135 GLN ** S3 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 88 ASN ** S3 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 144 ASN ** S3 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN ** A9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 2 ASN D1 292 ASN D5 136 ASN ** D5 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 81 GLN D4 168 GLN D4 279 GLN D4 304 GLN ** D4 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN ** D2 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 35 HIS ** A8 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S5 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 10 ASN A3 45 ASN ** A3 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 60 GLN ** B6 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B6 25 GLN ** B2 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.234 67060 Z= 0.561 Angle : 1.690 50.726 90949 Z= 1.069 Chirality : 0.311 6.384 9996 Planarity : 0.005 0.090 11492 Dihedral : 7.606 83.709 9102 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 0.01 % Allowed : 2.01 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.36 % Twisted Proline : 0.63 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.09), residues: 7983 helix: 0.42 (0.08), residues: 4152 sheet: -1.66 (0.26), residues: 376 loop : -3.04 (0.10), residues: 3455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRPD2 234 HIS 0.009 0.001 HISAK 18 PHE 0.054 0.002 PHED6 13 TYR 0.024 0.002 TYRC2 81 ARG 0.013 0.001 ARGBK 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15966 Ramachandran restraints generated. 7983 Oldfield, 0 Emsley, 7983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15966 Ramachandran restraints generated. 7983 Oldfield, 0 Emsley, 7983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1758 residues out of total 7078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1757 time to evaluate : 5.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1758 average time/residue: 0.6287 time to fit residues: 1906.6854 Evaluate side-chains 1387 residues out of total 7078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1386 time to evaluate : 5.843 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4790 time to fit residues: 8.6304 ------------------------------------------------------------------------------- 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: 1.9990 chunk 302 optimal weight: 7.9990 chunk 453 optimal weight: 6.9990 chunk 228 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 chunk 482 optimal weight: 1.9990 chunk 516 optimal weight: 0.9990 chunk 375 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 596 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 198 ASN ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 88 ASN ** S3 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 164 GLN S6 16 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S4 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN ** A9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 91 HIS ** D1 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 175 ASN ** D5 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 248 HIS D5 354 GLN ** D5 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 541 ASN ** D4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN ** D2 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 35 HIS ** A8 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 76 HIS ** BJ 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S5 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 45 ASN ** A3 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AM 53 ASN ** B6 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.239 67060 Z= 0.543 Angle : 1.685 50.680 90949 Z= 1.065 Chirality : 0.311 6.359 9996 Planarity : 0.005 0.092 11492 Dihedral : 7.551 83.665 9102 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 0.01 % Allowed : 1.31 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.36 % Twisted Proline : 0.42 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.09), residues: 7983 helix: 0.45 (0.08), residues: 4137 sheet: -1.64 (0.25), residues: 379 loop : -2.99 (0.10), residues: 3467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRPD2 234 HIS 0.010 0.001 HISS7 61 PHE 0.052 0.002 PHE4L 66 TYR 0.024 0.002 TYRC2 39 ARG 0.013 0.001 ARGBK 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15966 Ramachandran restraints generated. 7983 Oldfield, 0 Emsley, 7983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15966 Ramachandran restraints generated. 7983 Oldfield, 0 Emsley, 7983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1759 residues out of total 7078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1758 time to evaluate : 6.556 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 outliers start: 1 outliers final: 0 residues processed: 1759 average time/residue: 0.6229 time to fit residues: 1897.3158 Evaluate side-chains 1386 residues out of total 7078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1386 time to evaluate : 5.803 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.7951 ------------------------------------------------------------------------------- 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: 0.4980 chunk 726 optimal weight: 0.9990 chunk 663 optimal weight: 9.9990 chunk 706 optimal weight: 0.9990 chunk 425 optimal weight: 6.9990 chunk 307 optimal weight: 3.9990 chunk 555 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 chunk 638 optimal weight: 0.8980 chunk 668 optimal weight: 0.2980 chunk 704 optimal weight: 3.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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** ** S1 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 336 ASN ** S1 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2 135 GLN ** S3 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S3 88 ASN ** S3 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 164 GLN S8 90 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S4 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN ** A2 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 110 GLN ** AL 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 175 ASN ** D5 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 199 GLN D5 248 HIS ** D5 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 446 ASN ** D5 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 26 ASN D4 168 GLN D4 279 GLN D4 331 ASN ** D4 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN ** AK 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 35 HIS ** A8 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 114 GLN ** AJ 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S5 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 45 ASN ** A3 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AM 60 GLN ** B6 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 45 HIS ** C1 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 13 HIS ** A1 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.5595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 67060 Z= 0.537 Angle : 1.682 50.842 90949 Z= 1.063 Chirality : 0.311 6.368 9996 Planarity : 0.005 0.091 11492 Dihedral : 7.419 84.098 9102 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.32 % Favored : 89.68 % Rotamer: Outliers : 0.01 % Allowed : 0.71 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.36 % Twisted Proline : 0.42 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.10), residues: 7983 helix: 0.49 (0.08), residues: 4152 sheet: -1.46 (0.26), residues: 377 loop : -2.97 (0.10), residues: 3454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRPD2 234 HIS 0.009 0.001 HISB9 168 PHE 0.042 0.002 PHED6 13 TYR 0.025 0.002 TYRS8 118 ARG 0.014 0.000 ARGBK 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15966 Ramachandran restraints generated. 7983 Oldfield, 0 Emsley, 7983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15966 Ramachandran restraints generated. 7983 Oldfield, 0 Emsley, 7983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1787 residues out of total 7078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1786 time to evaluate : 5.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 1787 average time/residue: 0.6038 time to fit residues: 1863.4533 Evaluate side-chains 1394 residues out of total 7078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1394 time to evaluate : 5.819 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.6708 ------------------------------------------------------------------------------- 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: 6.9990 chunk 747 optimal weight: 3.9990 chunk 456 optimal weight: 9.9990 chunk 354 optimal weight: 0.8980 chunk 519 optimal weight: 0.9990 chunk 784 optimal weight: 0.9980 chunk 721 optimal weight: 0.6980 chunk 624 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 482 optimal weight: 2.9990 chunk 382 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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** ** S1 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 200 ASN ** S7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S7 164 GLN S8 65 HIS ** S8 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN ** A2 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 85 ASN A6 125 HIS ** AL 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 91 HIS ** AA 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 452 ASN D5 541 ASN D4 168 GLN D4 279 GLN D4 415 GLN ** D4 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN ** AK 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 103 ASN ** BJ 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S5 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 45 ASN ** A3 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AM 60 GLN ** B6 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B7 60 HIS ** B9 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 50 HIS ** C1 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 13 HIS ** A1 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.5770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.247 67060 Z= 0.539 Angle : 1.693 50.692 90949 Z= 1.067 Chirality : 0.312 6.409 9996 Planarity : 0.005 0.091 11492 Dihedral : 7.364 84.509 9102 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.22 % Favored : 89.77 % Rotamer: Outliers : 0.01 % Allowed : 0.49 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.36 % Twisted Proline : 0.42 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.09), residues: 7983 helix: 0.47 (0.08), residues: 4143 sheet: -1.38 (0.26), residues: 369 loop : -2.92 (0.10), residues: 3471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRPB4 100 HIS 0.009 0.001 HISS7 61 PHE 0.066 0.002 PHED1 270 TYR 0.029 0.002 TYRS2 102 ARG 0.014 0.000 ARGBK 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15966 Ramachandran restraints generated. 7983 Oldfield, 0 Emsley, 7983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15966 Ramachandran restraints generated. 7983 Oldfield, 0 Emsley, 7983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1748 residues out of total 7078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1747 time to evaluate : 5.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 1747 average time/residue: 0.6243 time to fit residues: 1893.2815 Evaluate side-chains 1414 residues out of total 7078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1414 time to evaluate : 5.783 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.6824 ------------------------------------------------------------------------------- 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: 2.9990 chunk 665 optimal weight: 0.0060 chunk 191 optimal weight: 4.9990 chunk 575 optimal weight: 5.9990 chunk 92 optimal weight: 0.4980 chunk 173 optimal weight: 2.9990 chunk 625 optimal weight: 6.9990 chunk 261 optimal weight: 0.6980 chunk 642 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- 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** ** S1 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S3 88 ASN ** S3 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 200 ASN ** S7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 164 GLN S8 90 GLN ** S8 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S4 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S4 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN ** A2 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 110 GLN ** AL 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 91 HIS D3 83 ASN ** D1 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 194 ASN D5 248 HIS ** D5 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 279 GLN ** D4 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN ** AK 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 106 GLN ** AJ 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 258 ASN ** S5 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 45 ASN A3 68 HIS ** B6 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 50 HIS ** C1 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.078627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.067274 restraints weight = 281492.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.069135 restraints weight = 164081.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.070403 restraints weight = 109190.621| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.5886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.245 67060 Z= 0.539 Angle : 1.690 50.655 90949 Z= 1.065 Chirality : 0.312 6.400 9996 Planarity : 0.005 0.089 11492 Dihedral : 7.280 85.068 9102 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.23 % Favored : 89.74 % Rotamer: Outliers : 0.01 % Allowed : 0.37 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.36 % Twisted Proline : 0.42 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.10), residues: 7983 helix: 0.53 (0.08), residues: 4125 sheet: -1.41 (0.26), residues: 371 loop : -2.88 (0.10), residues: 3487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRPV1 371 HIS 0.008 0.001 HISAK 18 PHE 0.062 0.002 PHED1 270 TYR 0.038 0.002 TYRA1 41 ARG 0.015 0.001 ARGBK 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26531.22 seconds wall clock time: 462 minutes 35.57 seconds (27755.57 seconds total)