Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 04:57:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vb7_31874/04_2023/7vb7_31874_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vb7_31874/04_2023/7vb7_31874.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vb7_31874/04_2023/7vb7_31874_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vb7_31874/04_2023/7vb7_31874_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vb7_31874/04_2023/7vb7_31874_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vb7_31874/04_2023/7vb7_31874.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vb7_31874/04_2023/7vb7_31874.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vb7_31874/04_2023/7vb7_31874_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vb7_31874/04_2023/7vb7_31874_neut_updated.pdb" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 8 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 11 5.49 5 Mg 1 5.21 5 S 189 5.16 5 C 18096 2.51 5 N 4957 2.21 5 O 5996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 38": "OE1" <-> "OE2" Residue "A GLU 67": "OE1" <-> "OE2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A GLU 301": "OE1" <-> "OE2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "G GLU 77": "OE1" <-> "OE2" Residue "H GLU 49": "OE1" <-> "OE2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H GLU 69": "OE1" <-> "OE2" Residue "H GLU 79": "OE1" <-> "OE2" Residue "J GLU 107": "OE1" <-> "OE2" Residue "J GLU 158": "OE1" <-> "OE2" Residue "J GLU 188": "OE1" <-> "OE2" Residue "J GLU 190": "OE1" <-> "OE2" Residue "J ARG 212": "NH1" <-> "NH2" Residue "J GLU 311": "OE1" <-> "OE2" Residue "J GLU 351": "OE1" <-> "OE2" Residue "K ARG 74": "NH1" <-> "NH2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "L GLU 148": "OE1" <-> "OE2" Residue "M GLU 44": "OE1" <-> "OE2" Residue "M GLU 107": "OE1" <-> "OE2" Residue "M GLU 118": "OE1" <-> "OE2" Residue "M GLU 244": "OE1" <-> "OE2" Residue "M GLU 283": "OE1" <-> "OE2" Residue "M GLU 395": "OE1" <-> "OE2" Residue "M GLU 468": "OE1" <-> "OE2" Residue "M GLU 535": "OE1" <-> "OE2" Residue "M GLU 628": "OE1" <-> "OE2" Residue "M GLU 647": "OE1" <-> "OE2" Residue "M GLU 648": "OE1" <-> "OE2" Residue "M GLU 660": "OE1" <-> "OE2" Residue "N GLU 136": "OE1" <-> "OE2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "O GLU 58": "OE1" <-> "OE2" Residue "O GLU 64": "OE1" <-> "OE2" Residue "O GLU 72": "OE1" <-> "OE2" Residue "O GLU 103": "OE1" <-> "OE2" Residue "O GLU 114": "OE1" <-> "OE2" Residue "O GLU 150": "OE1" <-> "OE2" Residue "O GLU 162": "OE1" <-> "OE2" Residue "O GLU 194": "OE1" <-> "OE2" Residue "O GLU 202": "OE1" <-> "OE2" Residue "O GLU 207": "OE1" <-> "OE2" Residue "P GLU 127": "OE1" <-> "OE2" Residue "Q GLU 259": "OE1" <-> "OE2" Residue "Q GLU 260": "OE1" <-> "OE2" Residue "Q GLU 281": "OE1" <-> "OE2" Residue "Q GLU 336": "OE1" <-> "OE2" Residue "T GLU 61": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 29279 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3330 Classifications: {'peptide': 433} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 410} Chain: "B" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1412 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 971 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 687 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 693 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 910 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "J" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2751 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 22, 'TRANS': 319} Chain: "K" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 366 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 3, 'TRANS': 39} Chain: "L" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "M" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5296 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 32, 'TRANS': 657} Chain: "N" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1204 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "O" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1671 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Chain: "P" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1738 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "Q" Number of atoms: 3096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3096 Classifications: {'peptide': 386} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 364} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "W" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 212 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 23} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" 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: "C" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'PEE': 1, 'PLX': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 50 Chain: "J" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 81 Unusual residues: {' UQ': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 30 Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' MG': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'DCQ': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "B" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "J" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "K" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "M" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 196 Classifications: {'water': 196} Link IDs: {None: 195} Chain: "N" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "O" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "P" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Classifications: {'water': 74} Link IDs: {None: 73} Chain: "Q" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 189 Classifications: {'water': 189} Link IDs: {None: 188} Chain: "T" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2718 SG CYS A 382 48.556 49.082 105.808 1.00 8.93 S ATOM 3060 SG CYS A 425 47.499 46.092 111.653 1.00 11.64 S ATOM 2738 SG CYS A 385 45.121 44.880 105.671 1.00 10.66 S ATOM 2699 SG CYS A 379 43.088 49.981 109.411 1.00 11.28 S ATOM 3961 SG CYS B 113 39.438 64.023 70.056 1.00 8.63 S ATOM 3980 SG CYS B 116 44.377 61.788 74.194 1.00 7.24 S ATOM 4003 SG CYS B 119 45.707 64.349 68.693 1.00 6.41 S ATOM 4332 SG CYS B 162 43.004 58.591 69.320 1.00 6.59 S ATOM 4030 SG CYS B 123 52.120 66.933 64.479 1.00 5.57 S ATOM 4256 SG CYS B 152 50.545 65.148 58.494 1.00 5.43 S ATOM 4303 SG CYS B 158 48.370 61.508 63.408 1.00 5.61 S ATOM 4282 SG CYS B 155 54.394 61.529 62.271 1.00 5.57 S ATOM 5724 SG CYS C 166 57.314 65.013 54.642 1.00 6.57 S ATOM 4996 SG CYS C 72 58.148 66.196 48.326 1.00 8.24 S ATOM 4990 SG CYS C 71 63.268 64.477 51.590 1.00 8.34 S ATOM 5494 SG CYS C 136 59.936 69.865 53.540 1.00 6.60 S ATOM 14949 SG CYS M 131 42.973 62.176 86.061 1.00 6.82 S ATOM 14928 SG CYS M 128 46.679 57.604 83.300 1.00 6.60 S ATOM 14989 SG CYS M 137 48.651 61.178 88.530 1.00 6.51 S ATOM 15321 SG CYS M 179 45.500 61.778 99.423 1.00 8.52 S ATOM 15675 SG CYS M 226 43.313 64.242 94.985 1.00 7.88 S ATOM 15345 SG CYS M 182 40.710 64.308 100.890 1.00 9.62 S ATOM 15298 SG CYS M 176 40.484 58.749 97.700 1.00 7.38 S ATOM 14546 SG CYS M 78 57.322 56.828 104.024 1.00 8.22 S ATOM 14647 SG CYS M 92 55.469 59.100 106.300 1.00 9.99 S ATOM 14435 SG CYS M 64 51.367 58.893 103.902 1.00 7.47 S ATOM 14521 SG CYS M 75 52.503 56.937 100.800 1.00 6.61 S ATOM 21484 SG CYS O 135 31.831 32.022 113.306 1.00 24.01 S ATOM 21518 SG CYS O 140 31.508 28.762 114.646 1.00 24.93 S ATOM 21798 SG CYS O 176 36.374 33.585 115.775 1.00 23.24 S ATOM 21821 SG CYS O 180 36.476 30.445 117.286 1.00 26.54 S ATOM 27631 SG CYS T 86 31.390 51.061 77.794 1.00 12.46 S ATOM 27809 SG CYS T 111 32.693 54.523 78.780 1.00 13.20 S Time building chain proxies: 15.62, per 1000 atoms: 0.53 Number of scatterers: 29279 At special positions: 0 Unit cell: (127.293, 139.109, 161.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 189 16.00 P 11 15.00 Mg 1 11.99 O 5996 8.00 N 4957 7.00 C 18096 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 58 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.31 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb=" FES O 301 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb=" SF4 A 501 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb=" SF4 B 301 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb=" SF4 C 301 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb=" SF4 M 802 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6576 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 153 helices and 25 sheets defined 39.3% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.90 Creating SS restraints... Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 95 through 102 removed outlier: 3.672A pdb=" N PHE A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N MET A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 296 through 303 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 329 through 332 No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 363 through 377 Processing helix chain 'A' and resid 383 through 401 removed outlier: 4.427A pdb=" N ASP A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 4.089A pdb=" N ASP A 410 " --> pdb=" O PRO A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 456 Proline residue: A 434 - end of helix removed outlier: 3.602A pdb=" N ARG A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Proline residue: A 444 - end of helix Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 64 through 78 removed outlier: 3.516A pdb=" N PHE B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 187 through 211 removed outlier: 5.664A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LEU B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N TYR B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 60 Processing helix chain 'C' and resid 71 through 80 removed outlier: 3.728A pdb=" N GLU C 75 " --> pdb=" O CYS C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 111 through 122 Proline residue: C 115 - end of helix Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 189 through 194 Processing helix chain 'E' and resid 25 through 49 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 56 through 70 removed outlier: 4.107A pdb=" N ASN E 70 " --> pdb=" O MET E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 94 Processing helix chain 'E' and resid 100 through 106 removed outlier: 4.230A pdb=" N PHE E 106 " --> pdb=" O HIS E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'F' and resid 28 through 39 removed outlier: 4.999A pdb=" N GLY F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 47 Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 84 through 95 Processing helix chain 'G' and resid 76 through 89 Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 132 through 137 removed outlier: 4.010A pdb=" N LYS G 137 " --> pdb=" O ILE G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 4.046A pdb=" N GLN H 37 " --> pdb=" O ASP H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 61 Processing helix chain 'H' and resid 65 through 72 Processing helix chain 'H' and resid 77 through 97 Processing helix chain 'I' and resid 6 through 16 Processing helix chain 'I' and resid 54 through 56 No H-bonds generated for 'chain 'I' and resid 54 through 56' Processing helix chain 'I' and resid 60 through 62 No H-bonds generated for 'chain 'I' and resid 60 through 62' Processing helix chain 'J' and resid 38 through 40 No H-bonds generated for 'chain 'J' and resid 38 through 40' Processing helix chain 'J' and resid 64 through 75 removed outlier: 4.122A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 3.521A pdb=" N MET J 92 " --> pdb=" O TYR J 89 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N HIS J 93 " --> pdb=" O ASP J 90 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 113 through 120 Processing helix chain 'J' and resid 141 through 145 Processing helix chain 'J' and resid 147 through 159 Processing helix chain 'J' and resid 179 through 194 Processing helix chain 'J' and resid 214 through 218 Processing helix chain 'J' and resid 221 through 223 No H-bonds generated for 'chain 'J' and resid 221 through 223' Processing helix chain 'J' and resid 229 through 232 Processing helix chain 'J' and resid 242 through 254 Processing helix chain 'J' and resid 256 through 258 No H-bonds generated for 'chain 'J' and resid 256 through 258' Processing helix chain 'J' and resid 273 through 283 Processing helix chain 'J' and resid 295 through 307 removed outlier: 3.757A pdb=" N VAL J 307 " --> pdb=" O ARG J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 316 through 322 Processing helix chain 'J' and resid 336 through 338 No H-bonds generated for 'chain 'J' and resid 336 through 338' Processing helix chain 'J' and resid 345 through 347 No H-bonds generated for 'chain 'J' and resid 345 through 347' Processing helix chain 'J' and resid 350 through 356 removed outlier: 5.876A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N HIS J 356 " --> pdb=" O VAL J 352 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 361 No H-bonds generated for 'chain 'J' and resid 359 through 361' Processing helix chain 'J' and resid 366 through 368 No H-bonds generated for 'chain 'J' and resid 366 through 368' Processing helix chain 'K' and resid 77 through 80 Processing helix chain 'K' and resid 85 through 96 removed outlier: 4.540A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N PHE K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'L' and resid 69 through 73 removed outlier: 3.909A pdb=" N LYS L 73 " --> pdb=" O GLU L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 140 Processing helix chain 'L' and resid 161 through 164 Processing helix chain 'M' and resid 49 through 56 removed outlier: 3.846A pdb=" N VAL M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 122 Processing helix chain 'M' and resid 138 through 146 Processing helix chain 'M' and resid 173 through 175 No H-bonds generated for 'chain 'M' and resid 173 through 175' Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 201 through 203 No H-bonds generated for 'chain 'M' and resid 201 through 203' Processing helix chain 'M' and resid 219 through 225 removed outlier: 3.813A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 244 No H-bonds generated for 'chain 'M' and resid 242 through 244' Processing helix chain 'M' and resid 288 through 298 removed outlier: 5.261A pdb=" N TYR M 294 " --> pdb=" O THR M 290 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASP M 295 " --> pdb=" O ARG M 291 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N GLY M 296 " --> pdb=" O PHE M 292 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU M 297 " --> pdb=" O ALA M 293 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LYS M 298 " --> pdb=" O TYR M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 319 through 332 Processing helix chain 'M' and resid 335 through 337 No H-bonds generated for 'chain 'M' and resid 335 through 337' Processing helix chain 'M' and resid 348 through 360 Processing helix chain 'M' and resid 382 through 385 Processing helix chain 'M' and resid 392 through 396 Processing helix chain 'M' and resid 407 through 410 No H-bonds generated for 'chain 'M' and resid 407 through 410' Processing helix chain 'M' and resid 412 through 424 Processing helix chain 'M' and resid 449 through 456 Processing helix chain 'M' and resid 461 through 467 Processing helix chain 'M' and resid 478 through 482 removed outlier: 3.535A pdb=" N GLN M 482 " --> pdb=" O SER M 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 478 through 482' Processing helix chain 'M' and resid 484 through 503 removed outlier: 4.319A pdb=" N THR M 487 " --> pdb=" O SER M 484 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER M 503 " --> pdb=" O ILE M 500 " (cutoff:3.500A) Processing helix chain 'M' and resid 522 through 528 Processing helix chain 'M' and resid 535 through 539 Processing helix chain 'M' and resid 557 through 559 No H-bonds generated for 'chain 'M' and resid 557 through 559' Processing helix chain 'M' and resid 575 through 578 No H-bonds generated for 'chain 'M' and resid 575 through 578' Processing helix chain 'M' and resid 589 through 591 No H-bonds generated for 'chain 'M' and resid 589 through 591' Processing helix chain 'M' and resid 619 through 630 Processing helix chain 'M' and resid 639 through 649 Processing helix chain 'M' and resid 651 through 654 Processing helix chain 'M' and resid 665 through 672 Processing helix chain 'M' and resid 691 through 693 No H-bonds generated for 'chain 'M' and resid 691 through 693' Processing helix chain 'M' and resid 699 through 702 No H-bonds generated for 'chain 'M' and resid 699 through 702' Processing helix chain 'M' and resid 705 through 715 Processing helix chain 'N' and resid 3 through 17 removed outlier: 3.525A pdb=" N HIS N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 30 Processing helix chain 'N' and resid 79 through 81 No H-bonds generated for 'chain 'N' and resid 79 through 81' Processing helix chain 'N' and resid 84 through 90 Processing helix chain 'O' and resid 57 through 69 removed outlier: 3.702A pdb=" N ASN O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 90 removed outlier: 4.322A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix Processing helix chain 'O' and resid 95 through 104 Processing helix chain 'O' and resid 109 through 118 Processing helix chain 'O' and resid 138 through 142 Processing helix chain 'O' and resid 145 through 156 Processing helix chain 'O' and resid 180 through 182 No H-bonds generated for 'chain 'O' and resid 180 through 182' Processing helix chain 'O' and resid 198 through 209 Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 4.558A pdb=" N ILE P 94 " --> pdb=" O ASP P 91 " (cutoff:3.500A) Proline residue: P 95 - end of helix removed outlier: 3.847A pdb=" N THR P 98 " --> pdb=" O PRO P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 161 through 174 removed outlier: 3.839A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE P 174 " --> pdb=" O TRP P 171 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 245 No H-bonds generated for 'chain 'P' and resid 243 through 245' Processing helix chain 'Q' and resid 120 through 126 removed outlier: 3.852A pdb=" N GLU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TYR Q 126 " --> pdb=" O LYS Q 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 129 through 137 Proline residue: Q 134 - end of helix removed outlier: 4.025A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 159 Processing helix chain 'Q' and resid 165 through 194 Processing helix chain 'Q' and resid 198 through 218 removed outlier: 3.752A pdb=" N GLU Q 205 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 262 removed outlier: 3.776A pdb=" N ASN Q 250 " --> pdb=" O GLU Q 246 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N SER Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N PHE Q 253 " --> pdb=" O LYS Q 249 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG Q 254 " --> pdb=" O ASN Q 250 " (cutoff:3.500A) Processing helix chain 'Q' and resid 266 through 272 Processing helix chain 'Q' and resid 280 through 285 Processing helix chain 'Q' and resid 290 through 296 removed outlier: 4.829A pdb=" N GLY Q 295 " --> pdb=" O MET Q 292 " (cutoff:3.500A) Processing helix chain 'Q' and resid 302 through 305 No H-bonds generated for 'chain 'Q' and resid 302 through 305' Processing helix chain 'Q' and resid 311 through 313 No H-bonds generated for 'chain 'Q' and resid 311 through 313' Processing helix chain 'Q' and resid 326 through 349 Processing helix chain 'Q' and resid 368 through 371 No H-bonds generated for 'chain 'Q' and resid 368 through 371' Processing helix chain 'Q' and resid 375 through 386 Processing helix chain 'Q' and resid 427 through 433 Processing helix chain 'Q' and resid 435 through 438 No H-bonds generated for 'chain 'Q' and resid 435 through 438' Processing helix chain 'Q' and resid 444 through 454 Processing helix chain 'Q' and resid 458 through 462 Processing helix chain 'T' and resid 50 through 55 Processing helix chain 'T' and resid 67 through 73 Processing helix chain 'T' and resid 91 through 93 No H-bonds generated for 'chain 'T' and resid 91 through 93' Processing sheet with id= A, first strand: chain 'A' and resid 240 through 244 removed outlier: 6.946A pdb=" N TYR A 112 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ALA A 243 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL A 114 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL A 198 " --> pdb=" O ILE A 158 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 286 through 291 Processing sheet with id= C, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= D, first strand: chain 'B' and resid 128 through 134 removed outlier: 6.046A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N THR B 142 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 102 through 106 removed outlier: 6.553A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE C 161 " --> pdb=" O SER C 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'F' and resid 52 through 58 removed outlier: 6.539A pdb=" N ARG F 68 " --> pdb=" O ARG F 17 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE F 19 " --> pdb=" O TRP F 66 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP F 66 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE F 21 " --> pdb=" O LYS F 64 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYS F 64 " --> pdb=" O ILE F 21 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 262 through 265 removed outlier: 6.463A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE J 81 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 226 through 228 Processing sheet with id= I, first strand: chain 'L' and resid 144 through 147 Processing sheet with id= J, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= K, first strand: chain 'M' and resid 32 through 36 Processing sheet with id= L, first strand: chain 'M' and resid 169 through 171 Processing sheet with id= M, first strand: chain 'M' and resid 196 through 198 Processing sheet with id= N, first strand: chain 'M' and resid 246 through 251 removed outlier: 6.160A pdb=" N ARG M 266 " --> pdb=" O VAL M 270 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N VAL M 270 " --> pdb=" O ARG M 266 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'M' and resid 306 through 308 Processing sheet with id= P, first strand: chain 'M' and resid 365 through 368 removed outlier: 4.680A pdb=" N SER M 365 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'M' and resid 513 through 516 removed outlier: 8.220A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASP M 443 " --> pdb=" O LEU M 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'M' and resid 595 through 597 Processing sheet with id= S, first strand: chain 'N' and resid 60 through 63 removed outlier: 3.610A pdb=" N GLY N 40 " --> pdb=" O TYR N 48 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU N 38 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.421A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 110 through 118 removed outlier: 6.842A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU P 84 " --> pdb=" O ARG P 140 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N TYR P 146 " --> pdb=" O ILE P 88 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 208 through 213 Processing sheet with id= W, first strand: chain 'Q' and resid 80 through 84 removed outlier: 6.380A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id= Y, first strand: chain 'T' and resid 83 through 86 907 hydrogen bonds defined for protein. 2445 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: 10.95 Time building geometry restraints manager: 13.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 11792 1.40 - 1.62: 17069 1.62 - 1.85: 278 1.85 - 2.07: 0 2.07 - 2.29: 80 Bond restraints: 29219 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.262 0.262 2.00e-02 2.50e+03 1.71e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.287 0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" C1B NAI A 503 " pdb=" O4B NAI A 503 " ideal model delta sigma weight residual 1.397 1.633 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.300 0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C18 UQ J 402 " pdb=" C19 UQ J 402 " ideal model delta sigma weight residual 1.336 1.555 -0.219 2.00e-02 2.50e+03 1.20e+02 ... (remaining 29214 not shown) Histogram of bond angle deviations from ideal: 73.64 - 86.02: 76 86.02 - 98.41: 5 98.41 - 110.79: 9598 110.79 - 123.17: 28397 123.17 - 135.55: 1522 Bond angle restraints: 39598 Sorted by residual: angle pdb=" N VAL Q 94 " pdb=" CA VAL Q 94 " pdb=" C VAL Q 94 " ideal model delta sigma weight residual 112.29 119.45 -7.16 9.40e-01 1.13e+00 5.81e+01 angle pdb=" C51 CDL I 201 " pdb=" CB5 CDL I 201 " pdb=" OB6 CDL I 201 " ideal model delta sigma weight residual 111.33 120.66 -9.33 1.32e+00 5.72e-01 4.98e+01 angle pdb=" N GLY M 576 " pdb=" CA GLY M 576 " pdb=" C GLY M 576 " ideal model delta sigma weight residual 112.77 121.08 -8.31 1.28e+00 6.10e-01 4.22e+01 angle pdb=" C11 CDL I 201 " pdb=" CA5 CDL I 201 " pdb=" OA6 CDL I 201 " ideal model delta sigma weight residual 111.33 119.85 -8.52 1.32e+00 5.72e-01 4.16e+01 angle pdb=" N ALA M 397 " pdb=" CA ALA M 397 " pdb=" C ALA M 397 " ideal model delta sigma weight residual 109.96 118.81 -8.85 1.50e+00 4.44e-01 3.48e+01 ... (remaining 39593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.01: 17018 35.01 - 70.02: 518 70.02 - 105.04: 54 105.04 - 140.05: 0 140.05 - 175.06: 3 Dihedral angle restraints: 17593 sinusoidal: 7364 harmonic: 10229 Sorted by residual: dihedral pdb=" C10 FMN A 502 " pdb=" C1' FMN A 502 " pdb=" N10 FMN A 502 " pdb=" C2' FMN A 502 " ideal model delta sinusoidal sigma weight residual 257.59 82.53 175.06 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' FMN A 502 " pdb=" O5' FMN A 502 " pdb=" P FMN A 502 " pdb=" O1P FMN A 502 " ideal model delta sinusoidal sigma weight residual 75.26 -74.81 150.07 1 2.00e+01 2.50e-03 4.48e+01 dihedral pdb=" CB CYS F 24 " pdb=" SG CYS F 24 " pdb=" SG CYS F 58 " pdb=" CB CYS F 58 " ideal model delta sinusoidal sigma weight residual -86.00 -128.79 42.79 1 1.00e+01 1.00e-02 2.56e+01 ... (remaining 17590 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3806 0.075 - 0.149: 446 0.149 - 0.224: 26 0.224 - 0.298: 3 0.298 - 0.373: 2 Chirality restraints: 4283 Sorted by residual: chirality pdb=" CA THR M 180 " pdb=" N THR M 180 " pdb=" C THR M 180 " pdb=" CB THR M 180 " both_signs ideal model delta sigma weight residual False 2.53 2.15 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA TYR Q 141 " pdb=" N TYR Q 141 " pdb=" C TYR Q 141 " pdb=" CB TYR Q 141 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" C3D NAI A 503 " pdb=" C2D NAI A 503 " pdb=" C4D NAI A 503 " pdb=" O3D NAI A 503 " both_signs ideal model delta sigma weight residual False -2.71 -2.44 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 4280 not shown) Planarity restraints: 5091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C22 UQ J 402 " -0.522 2.00e-02 2.50e+03 4.47e-01 2.50e+03 pdb=" C23 UQ J 402 " 0.610 2.00e-02 2.50e+03 pdb=" C24 UQ J 402 " 0.417 2.00e-02 2.50e+03 pdb=" C25 UQ J 402 " -0.087 2.00e-02 2.50e+03 pdb=" C26 UQ J 402 " -0.417 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ J 402 " -0.002 2.00e-02 2.50e+03 3.67e-01 1.68e+03 pdb=" C11 UQ J 402 " -0.406 2.00e-02 2.50e+03 pdb=" C7 UQ J 402 " -0.413 2.00e-02 2.50e+03 pdb=" C8 UQ J 402 " 0.422 2.00e-02 2.50e+03 pdb=" C9 UQ J 402 " 0.399 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ J 402 " -0.307 2.00e-02 2.50e+03 3.08e-01 1.19e+03 pdb=" C18 UQ J 402 " 0.569 2.00e-02 2.50e+03 pdb=" C19 UQ J 402 " -0.229 2.00e-02 2.50e+03 pdb=" C20 UQ J 402 " 0.029 2.00e-02 2.50e+03 pdb=" C21 UQ J 402 " -0.062 2.00e-02 2.50e+03 ... (remaining 5088 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 334 2.57 - 3.15: 23618 3.15 - 3.74: 49991 3.74 - 4.32: 74605 4.32 - 4.90: 113381 Nonbonded interactions: 261929 Sorted by model distance: nonbonded pdb=" NH2 ARG I 27 " pdb=" OE1 GLU Q 212 " model vdw 1.988 2.520 nonbonded pdb=" OE2 GLU Q 208 " pdb=" NH2 ARG Q 221 " model vdw 2.089 2.520 nonbonded pdb=" ND2 ASN L 109 " pdb=" O LEU L 111 " model vdw 2.106 2.520 nonbonded pdb=" OD1 ASN Q 147 " pdb=" O HOH Q 601 " model vdw 2.106 2.440 nonbonded pdb=" O PRO Q 89 " pdb=" O HOH Q 602 " model vdw 2.117 2.440 ... (remaining 261924 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.590 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: 0.020 Extract box with map and model: 24.510 Check model and map are aligned: 0.530 Set scattering table: 0.270 Process input model: 87.670 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:12.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 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 0.262 29219 Z= 0.438 Angle : 0.772 16.309 39598 Z= 0.428 Chirality : 0.048 0.373 4283 Planarity : 0.011 0.447 5091 Dihedral : 16.421 175.058 11014 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.00 % Favored : 96.89 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.48 (0.14), residues: 3502 helix: 0.93 (0.14), residues: 1361 sheet: 0.49 (0.26), residues: 378 loop : -0.11 (0.14), residues: 1763 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 415 time to evaluate : 3.347 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 32 residues processed: 442 average time/residue: 1.8281 time to fit residues: 921.5768 Evaluate side-chains 430 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 398 time to evaluate : 3.720 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 27 residues processed: 7 average time/residue: 0.9337 time to fit residues: 14.2696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 291 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 270 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 164 optimal weight: 0.3980 chunk 201 optimal weight: 8.9990 chunk 313 optimal weight: 5.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN B 59 GLN F 31 GLN H 41 ASN I 29 GLN J 323 HIS M 334 GLN M 498 GLN N 123 GLN O 106 GLN O 153 GLN O 182 ASN P 75 GLN P 77 GLN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 236 ASN P 247 GLN Q 88 HIS ** Q 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 117 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.0438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 29219 Z= 0.242 Angle : 0.600 12.225 39598 Z= 0.312 Chirality : 0.046 0.162 4283 Planarity : 0.005 0.061 5091 Dihedral : 8.695 172.639 4056 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.23 % Favored : 96.69 % Rotamer Outliers : 2.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.44 (0.14), residues: 3502 helix: 0.86 (0.14), residues: 1365 sheet: 0.43 (0.26), residues: 380 loop : -0.09 (0.14), residues: 1757 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 399 time to evaluate : 4.003 Fit side-chains outliers start: 79 outliers final: 46 residues processed: 445 average time/residue: 1.7663 time to fit residues: 898.5430 Evaluate side-chains 445 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 399 time to evaluate : 3.861 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 32 residues processed: 16 average time/residue: 0.9893 time to fit residues: 24.7312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 174 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 260 optimal weight: 0.8980 chunk 213 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 313 optimal weight: 8.9990 chunk 339 optimal weight: 10.0000 chunk 279 optimal weight: 7.9990 chunk 311 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 251 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN B 59 GLN F 31 GLN H 41 ASN J 323 HIS M 334 GLN M 498 GLN M 652 ASN O 153 GLN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 236 ASN P 247 GLN Q 92 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.0536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 29219 Z= 0.171 Angle : 0.530 11.611 39598 Z= 0.275 Chirality : 0.043 0.157 4283 Planarity : 0.004 0.080 5091 Dihedral : 8.307 171.853 4056 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.00 % Favored : 96.94 % Rotamer Outliers : 2.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.59 (0.14), residues: 3502 helix: 1.01 (0.14), residues: 1356 sheet: 0.49 (0.26), residues: 380 loop : -0.02 (0.15), residues: 1766 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 401 time to evaluate : 3.469 Fit side-chains outliers start: 78 outliers final: 44 residues processed: 450 average time/residue: 1.7929 time to fit residues: 925.2917 Evaluate side-chains 437 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 393 time to evaluate : 3.630 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 34 residues processed: 11 average time/residue: 0.9784 time to fit residues: 18.0262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 310 optimal weight: 2.9990 chunk 235 optimal weight: 6.9990 chunk 162 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 210 optimal weight: 0.7980 chunk 314 optimal weight: 6.9990 chunk 333 optimal weight: 9.9990 chunk 164 optimal weight: 9.9990 chunk 298 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN F 31 GLN H 41 ASN I 25 GLN J 323 HIS M 39 GLN M 334 GLN M 498 GLN O 153 GLN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 247 GLN Q 92 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.0687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.080 29219 Z= 0.310 Angle : 0.638 12.674 39598 Z= 0.334 Chirality : 0.048 0.166 4283 Planarity : 0.005 0.090 5091 Dihedral : 8.549 172.451 4056 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.26 % Favored : 96.69 % Rotamer Outliers : 3.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.39 (0.14), residues: 3502 helix: 0.78 (0.14), residues: 1369 sheet: 0.40 (0.26), residues: 381 loop : -0.08 (0.14), residues: 1752 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 396 time to evaluate : 3.415 Fit side-chains outliers start: 93 outliers final: 52 residues processed: 453 average time/residue: 1.8364 time to fit residues: 950.6135 Evaluate side-chains 452 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 400 time to evaluate : 3.805 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 39 residues processed: 14 average time/residue: 1.0805 time to fit residues: 23.6605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 277 optimal weight: 7.9990 chunk 189 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 chunk 137 optimal weight: 0.9980 chunk 284 optimal weight: 3.9990 chunk 230 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 170 optimal weight: 4.9990 chunk 299 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN F 31 GLN H 41 ASN I 25 GLN J 122 HIS J 323 HIS K 75 ASN M 498 GLN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 236 ASN P 247 GLN Q 92 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.0709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 29219 Z= 0.257 Angle : 0.598 12.350 39598 Z= 0.313 Chirality : 0.046 0.158 4283 Planarity : 0.005 0.060 5091 Dihedral : 8.433 172.260 4056 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.06 % Favored : 96.89 % Rotamer Outliers : 2.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.40 (0.14), residues: 3502 helix: 0.79 (0.14), residues: 1367 sheet: 0.38 (0.26), residues: 381 loop : -0.07 (0.14), residues: 1754 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 404 time to evaluate : 3.424 Fit side-chains outliers start: 78 outliers final: 49 residues processed: 455 average time/residue: 1.8638 time to fit residues: 970.4406 Evaluate side-chains 446 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 397 time to evaluate : 3.760 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 40 residues processed: 10 average time/residue: 1.0053 time to fit residues: 17.3674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 112 optimal weight: 0.1980 chunk 300 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 195 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 333 optimal weight: 6.9990 chunk 277 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 175 optimal weight: 4.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN F 31 GLN H 41 ASN I 25 GLN J 323 HIS M 334 GLN M 498 GLN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 236 ASN P 247 GLN Q 92 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.086 29219 Z= 0.333 Angle : 0.657 12.881 39598 Z= 0.345 Chirality : 0.049 0.176 4283 Planarity : 0.006 0.064 5091 Dihedral : 8.574 172.563 4056 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.40 % Favored : 96.54 % Rotamer Outliers : 2.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.28 (0.14), residues: 3502 helix: 0.71 (0.14), residues: 1357 sheet: 0.40 (0.26), residues: 364 loop : -0.17 (0.14), residues: 1781 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 397 time to evaluate : 3.789 Fit side-chains revert: symmetry clash outliers start: 79 outliers final: 55 residues processed: 449 average time/residue: 1.8578 time to fit residues: 965.2150 Evaluate side-chains 452 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 397 time to evaluate : 3.656 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 43 residues processed: 13 average time/residue: 1.1065 time to fit residues: 23.1756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 321 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 190 optimal weight: 0.5980 chunk 243 optimal weight: 0.0770 chunk 188 optimal weight: 2.9990 chunk 280 optimal weight: 4.9990 chunk 186 optimal weight: 0.9980 chunk 332 optimal weight: 5.9990 chunk 208 optimal weight: 0.7980 chunk 202 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 overall best weight: 1.0940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN F 31 GLN H 41 ASN I 25 GLN J 323 HIS K 75 ASN M 498 GLN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 236 ASN P 247 GLN Q 92 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.0786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 29219 Z= 0.151 Angle : 0.518 11.500 39598 Z= 0.269 Chirality : 0.042 0.154 4283 Planarity : 0.004 0.055 5091 Dihedral : 8.047 171.646 4056 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.83 % Favored : 97.12 % Rotamer Outliers : 2.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.52 (0.14), residues: 3502 helix: 0.92 (0.14), residues: 1368 sheet: 0.43 (0.25), residues: 391 loop : -0.04 (0.15), residues: 1743 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 406 time to evaluate : 3.762 Fit side-chains outliers start: 68 outliers final: 45 residues processed: 453 average time/residue: 1.8102 time to fit residues: 939.9389 Evaluate side-chains 439 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 394 time to evaluate : 3.546 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 39 residues processed: 8 average time/residue: 0.9375 time to fit residues: 14.0821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 205 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 198 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 211 optimal weight: 6.9990 chunk 226 optimal weight: 8.9990 chunk 164 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 HIS B 59 GLN F 31 GLN F 62 GLN H 41 ASN I 25 GLN J 323 HIS M 334 GLN M 498 GLN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 180 ASN P 247 GLN Q 92 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.107 29219 Z= 0.429 Angle : 0.724 13.505 39598 Z= 0.379 Chirality : 0.052 0.198 4283 Planarity : 0.006 0.065 5091 Dihedral : 8.632 172.878 4056 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.46 % Favored : 96.46 % Rotamer Outliers : 2.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.26 (0.14), residues: 3502 helix: 0.66 (0.14), residues: 1356 sheet: 0.49 (0.26), residues: 357 loop : -0.17 (0.14), residues: 1789 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 393 time to evaluate : 3.840 Fit side-chains outliers start: 67 outliers final: 45 residues processed: 440 average time/residue: 1.8155 time to fit residues: 915.1375 Evaluate side-chains 435 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 390 time to evaluate : 3.702 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 38 residues processed: 8 average time/residue: 1.2476 time to fit residues: 16.8819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 302 optimal weight: 0.8980 chunk 318 optimal weight: 2.9990 chunk 290 optimal weight: 2.9990 chunk 309 optimal weight: 0.6980 chunk 186 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 chunk 243 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 280 optimal weight: 1.9990 chunk 293 optimal weight: 1.9990 chunk 308 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN F 31 GLN F 62 GLN H 41 ASN I 25 GLN J 323 HIS K 75 ASN M 498 GLN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 236 ASN P 247 GLN Q 92 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 29219 Z= 0.148 Angle : 0.519 11.515 39598 Z= 0.269 Chirality : 0.042 0.153 4283 Planarity : 0.004 0.056 5091 Dihedral : 8.060 171.824 4056 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.74 % Favored : 97.20 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.51 (0.14), residues: 3502 helix: 0.92 (0.14), residues: 1368 sheet: 0.40 (0.25), residues: 391 loop : -0.04 (0.15), residues: 1743 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 402 time to evaluate : 3.819 Fit side-chains outliers start: 49 outliers final: 41 residues processed: 441 average time/residue: 1.7843 time to fit residues: 901.7747 Evaluate side-chains 434 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 393 time to evaluate : 3.466 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 38 residues processed: 5 average time/residue: 0.6496 time to fit residues: 9.2124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/iotbx/cli_parser.py", line 870, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.2315 > 50: distance: 27 - 141: 12.994 distance: 30 - 138: 16.260 distance: 44 - 126: 8.508 distance: 47 - 123: 5.432 distance: 73 - 79: 7.443 distance: 79 - 85: 4.515 distance: 80 - 81: 6.295 distance: 80 - 83: 4.406 distance: 81 - 82: 6.886 distance: 81 - 86: 4.841 distance: 83 - 84: 3.993 distance: 84 - 85: 6.043 distance: 87 - 88: 9.376 distance: 87 - 90: 8.091 distance: 88 - 89: 13.652 distance: 88 - 94: 3.982 distance: 90 - 91: 7.657 distance: 91 - 92: 8.686 distance: 91 - 93: 9.850 distance: 94 - 95: 5.992 distance: 95 - 96: 6.314 distance: 95 - 98: 8.044 distance: 96 - 97: 5.682 distance: 96 - 100: 5.680 distance: 98 - 99: 9.522 distance: 100 - 101: 11.480 distance: 101 - 102: 9.845 distance: 101 - 104: 15.254 distance: 102 - 103: 6.334 distance: 102 - 108: 4.568 distance: 104 - 105: 10.927 distance: 105 - 106: 3.146 distance: 105 - 107: 6.670 distance: 109 - 110: 4.999 distance: 109 - 112: 5.620 distance: 110 - 111: 5.043 distance: 110 - 116: 7.071 distance: 113 - 114: 5.561 distance: 113 - 115: 5.619 distance: 117 - 118: 4.258 distance: 117 - 120: 4.838 distance: 118 - 119: 8.476 distance: 118 - 123: 8.503 distance: 120 - 122: 4.236 distance: 123 - 124: 4.997 distance: 124 - 125: 4.878 distance: 124 - 127: 7.453 distance: 125 - 126: 6.632 distance: 125 - 131: 9.706 distance: 127 - 128: 7.445 distance: 128 - 129: 5.666 distance: 128 - 130: 5.054 distance: 131 - 132: 4.256 distance: 132 - 133: 3.714 distance: 132 - 135: 5.509 distance: 133 - 134: 5.079 distance: 133 - 138: 12.672 distance: 135 - 137: 11.648 distance: 138 - 139: 14.222 distance: 139 - 140: 14.098 distance: 139 - 142: 13.179 distance: 140 - 141: 19.703 distance: 140 - 149: 17.123 distance: 142 - 143: 4.496 distance: 143 - 144: 7.593 distance: 143 - 145: 10.351 distance: 144 - 146: 12.748 distance: 145 - 147: 7.773 distance: 146 - 148: 8.830 distance: 147 - 148: 8.705 distance: 149 - 150: 17.139 distance: 150 - 151: 25.700 distance: 150 - 153: 12.488 distance: 151 - 152: 16.260 distance: 151 - 155: 18.990 distance: 153 - 154: 26.504