Starting phenix.real_space_refine (version: dev) on Sun Feb 26 18:40:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkc_11244/02_2023/6zkc_11244_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkc_11244/02_2023/6zkc_11244.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkc_11244/02_2023/6zkc_11244_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkc_11244/02_2023/6zkc_11244_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkc_11244/02_2023/6zkc_11244_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkc_11244/02_2023/6zkc_11244.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkc_11244/02_2023/6zkc_11244.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkc_11244/02_2023/6zkc_11244_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkc_11244/02_2023/6zkc_11244_neut_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "1 ARG 68": "NH1" <-> "NH2" Residue "1 ARG 237": "NH1" <-> "NH2" Residue "1 ARG 249": "NH1" <-> "NH2" Residue "1 ARG 339": "NH1" <-> "NH2" Residue "1 ARG 423": "NH1" <-> "NH2" Residue "2 ARG 187": "NH1" <-> "NH2" Residue "3 ARG 53": "NH1" <-> "NH2" Residue "3 TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 418": "NH1" <-> "NH2" Residue "3 TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 460": "NH1" <-> "NH2" Residue "3 TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 2": "NH1" <-> "NH2" Residue "4 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 188": "NH1" <-> "NH2" Residue "4 TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 8": "NH1" <-> "NH2" Residue "5 ARG 12": "NH1" <-> "NH2" Residue "5 ARG 14": "NH1" <-> "NH2" Residue "5 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 25": "NH1" <-> "NH2" Residue "6 ARG 77": "NH1" <-> "NH2" Residue "6 ARG 138": "NH1" <-> "NH2" Residue "6 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 174": "NH1" <-> "NH2" Residue "6 ARG 178": "NH1" <-> "NH2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 195": "NH1" <-> "NH2" Residue "H TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 278": "NH1" <-> "NH2" Residue "M TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "V ARG 103": "NH1" <-> "NH2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ARG 77": "NH1" <-> "NH2" Residue "W ARG 115": "NH1" <-> "NH2" Residue "Y ARG 54": "NH1" <-> "NH2" Residue "Y ARG 165": "NH1" <-> "NH2" Residue "Y PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 14": "NH1" <-> "NH2" Residue "Z TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 64": "NH1" <-> "NH2" Residue "d ARG 82": "NH1" <-> "NH2" Residue "d ARG 97": "NH1" <-> "NH2" Residue "d TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 157": "NH1" <-> "NH2" Residue "d PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 186": "NH1" <-> "NH2" Residue "d ARG 251": "NH1" <-> "NH2" Residue "d PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 292": "NH1" <-> "NH2" Residue "d ARG 320": "NH1" <-> "NH2" Residue "d ARG 322": "NH1" <-> "NH2" Residue "d ARG 325": "NH1" <-> "NH2" Residue "e ARG 33": "NH1" <-> "NH2" Residue "g ARG 22": "NH1" <-> "NH2" Residue "g ARG 32": "NH1" <-> "NH2" Residue "h ARG 17": "NH1" <-> "NH2" Residue "i ARG 9": "NH1" <-> "NH2" Residue "i PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 106": "NH1" <-> "NH2" Residue "i PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 95": "NH1" <-> "NH2" Residue "k ARG 305": "NH1" <-> "NH2" Residue "l ARG 68": "NH1" <-> "NH2" Residue "l ARG 82": "NH1" <-> "NH2" Residue "l ARG 104": "NH1" <-> "NH2" Residue "n ARG 38": "NH1" <-> "NH2" Residue "o ARG 5": "NH1" <-> "NH2" Residue "o ARG 49": "NH1" <-> "NH2" Residue "o ARG 50": "NH1" <-> "NH2" Residue "o ARG 120": "NH1" <-> "NH2" Residue "p ARG 9": "NH1" <-> "NH2" Residue "p ARG 41": "NH1" <-> "NH2" Residue "p ARG 56": "NH1" <-> "NH2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 26": "NH1" <-> "NH2" Residue "q ARG 51": "NH1" <-> "NH2" Residue "q ARG 87": "NH1" <-> "NH2" Residue "r ARG 19": "NH1" <-> "NH2" Residue "r ARG 30": "NH1" <-> "NH2" Residue "r ARG 37": "NH1" <-> "NH2" Residue "r ARG 65": "NH1" <-> "NH2" Residue "s ARG 103": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "s ARG 114": "NH1" <-> "NH2" Residue "s ARG 117": "NH1" <-> "NH2" Residue "t ARG 29": "NH1" <-> "NH2" Residue "t ARG 37": "NH1" <-> "NH2" Residue "t ARG 44": "NH1" <-> "NH2" Residue "t ARG 64": "NH1" <-> "NH2" Residue "t ARG 92": "NH1" <-> "NH2" Residue "t ARG 121": "NH1" <-> "NH2" Residue "t ARG 128": "NH1" <-> "NH2" Residue "t ARG 134": "NH1" <-> "NH2" Residue "t ARG 149": "NH1" <-> "NH2" Residue "t ARG 176": "NH1" <-> "NH2" Residue "u ARG 19": "NH1" <-> "NH2" Residue "v ARG 70": "NH1" <-> "NH2" Residue "w ARG 25": "NH1" <-> "NH2" Residue "w ARG 84": "NH1" <-> "NH2" Residue "z PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 37": "NH1" <-> "NH2" Residue "z TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 67967 Number of models: 1 Model: "" Number of chains: 71 Chain: "1" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3312 Classifications: {'peptide': 430} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 408} Chain: "2" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1655 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 191} Chain: "3" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5275 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 32, 'TRANS': 655} Chain: "4" Number of atoms: 3457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3457 Classifications: {'peptide': 430} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 401} 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: "5" 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: "6" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "9" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "A" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 922 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "H" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2528 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 295} Chain: "J" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 3, 'TRANS': 171} Chain: "K" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 749 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4807 Classifications: {'peptide': 606} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 579} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3647 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 437} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2723 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 326} Chain: "V" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1028 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1155 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 10, 'TRANS': 128} Chain: "X" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 701 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "Y" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "Z" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1441 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "a" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 371 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "b" 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: "c" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1024 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "d" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2748 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 21, 'TRANS': 318} Chain: "e" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "f" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 917 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 104} Chain: "g" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 969 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "h" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 769 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 11, 'TRANS': 84} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1209 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} Chain: "j" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 660 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "k" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2596 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain: "l" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 874 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "m" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 626 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "n" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 634 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "o" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1004 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 10, 'TRANS': 109} Chain: "p" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1059 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 118} Chain: "q" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1142 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "r" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 846 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Chain: "s" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1047 Classifications: {'peptide': 122} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 114} Chain: "t" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1520 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 16, 'TRANS': 160} Chain: "u" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 563 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 7, 'TRANS': 57} Chain: "v" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1307 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 20, 'TRANS': 134} Chain: "w" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 846 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "x" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 412 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "z" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 576 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1" 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: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' K': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "4" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'DCQ': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "9" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'PC1': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'DCQ': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "L" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 321 Unusual residues: {'3PE': 2, 'CDL': 2, 'PC1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 35 Chain: "M" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 198 Unusual residues: {'3PE': 1, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "N" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "V" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 131 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "W" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "g" 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: "h" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 58 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Chain: "i" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Chain: "o" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 121 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "p" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 23 Chain: "s" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 75 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2715 SG CYS 1 365 102.258 54.012 238.143 1.00 60.33 S ATOM 2676 SG CYS 1 359 109.332 54.335 238.913 1.00 55.99 S ATOM 4116 SG CYS 2 103 100.288 48.147 256.901 1.00 90.83 S ATOM 4150 SG CYS 2 108 98.185 45.635 258.762 1.00 68.66 S ATOM 4430 SG CYS 2 144 101.961 44.928 253.070 1.00 94.27 S ATOM 4453 SG CYS 2 148 100.173 41.832 254.396 1.00 74.84 S ATOM 5793 SG CYS 3 114 104.195 72.953 224.324 1.00 45.11 S ATOM 5732 SG CYS 3 105 98.891 76.120 226.414 1.00 53.00 S ATOM 5753 SG CYS 3 108 104.985 77.952 228.110 1.00 46.76 S ATOM 6125 SG CYS 3 156 111.592 65.388 228.600 1.00 58.01 S ATOM 6102 SG CYS 3 153 109.493 68.180 234.232 1.00 41.38 S ATOM 6149 SG CYS 3 159 115.658 69.130 232.459 1.00 67.35 S ATOM 6479 SG CYS 3 203 111.357 71.753 228.995 1.00 93.72 S ATOM 5238 SG CYS 3 41 110.695 58.873 226.515 1.00 69.50 S ATOM 5324 SG CYS 3 52 107.051 59.944 225.814 1.00 32.57 S ATOM 5349 SG CYS 3 55 107.615 55.244 221.829 1.00 34.03 S ATOM 5450 SG CYS 3 69 111.191 55.185 223.428 1.00 74.97 S ATOM 16408 SG CYS 6 149 85.561 96.642 207.804 1.00 79.02 S ATOM 15674 SG CYS 6 54 82.078 96.772 202.013 1.00 66.36 S ATOM 17600 SG CYS 9 116 89.743 97.472 214.275 1.00 33.59 S ATOM 17647 SG CYS 9 122 90.345 92.908 218.772 1.00 22.63 S ATOM 17374 SG CYS 9 87 94.233 92.826 213.417 1.00 35.07 S ATOM 17676 SG CYS 9 126 92.740 89.280 225.935 1.00 66.78 S ATOM 17347 SG CYS 9 83 96.293 91.153 220.835 1.00 57.37 S ATOM 17305 SG CYS 9 77 98.417 92.702 226.540 1.00 53.82 S ATOM 17324 SG CYS 9 80 97.784 86.136 224.809 1.00 72.50 S ATOM 41371 SG CYS b 59 94.487 84.323 240.911 1.00 51.63 S ATOM 41549 SG CYS b 84 97.547 84.470 238.525 1.00 44.28 S ATOM 41571 SG CYS b 87 95.889 87.103 239.747 1.00 33.44 S Time building chain proxies: 28.41, per 1000 atoms: 0.42 Number of scatterers: 67967 At special positions: 0 Unit cell: (175.065, 197.346, 289.653, 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 K 1 19.00 S 468 16.00 P 44 15.00 O 12186 8.00 N 11233 7.00 C 44006 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS V 94 " - pdb=" SG CYS V 114 " distance=2.02 Simple disulfide: pdb=" SG CYS Z 112 " - pdb=" SG CYS Z 124 " distance=2.03 Simple disulfide: pdb=" SG CYS l 32 " - pdb=" SG CYS l 65 " distance=2.04 Simple disulfide: pdb=" SG CYS l 42 " - pdb=" SG CYS l 55 " distance=2.03 Simple disulfide: pdb=" SG CYS s 58 " - pdb=" SG CYS s 89 " distance=2.02 Simple disulfide: pdb=" SG CYS s 68 " - pdb=" SG CYS s 79 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.50 Conformation dependent library (CDL) restraints added in 7.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 300 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 103 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 148 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 108 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 144 " pdb=" FES 3 803 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 55 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 41 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 52 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 69 " pdb=" SF4 1 501 " pdb="FE1 SF4 1 501 " - pdb=" SG CYS 1 365 " pdb="FE3 SF4 1 501 " - pdb=" SG CYS 1 359 " pdb="FE4 SF4 1 501 " - pdb=" SG CYS 1 405 " pdb="FE2 SF4 1 501 " - pdb=" SG CYS 1 362 " pdb=" SF4 3 801 " pdb="FE3 SF4 3 801 " - pdb=" NE2 HIS 3 101 " pdb="FE4 SF4 3 801 " - pdb=" SG CYS 3 108 " pdb="FE1 SF4 3 801 " - pdb=" SG CYS 3 114 " pdb="FE2 SF4 3 801 " - pdb=" SG CYS 3 105 " pdb=" SF4 3 802 " pdb="FE3 SF4 3 802 " - pdb=" SG CYS 3 159 " pdb="FE4 SF4 3 802 " - pdb=" SG CYS 3 203 " pdb="FE1 SF4 3 802 " - pdb=" SG CYS 3 156 " pdb="FE2 SF4 3 802 " - pdb=" SG CYS 3 153 " pdb=" SF4 6 201 " pdb="FE4 SF4 6 201 " - pdb=" SG CYS 6 54 " pdb="FE3 SF4 6 201 " - pdb=" SG CYS 6 149 " pdb="FE2 SF4 6 201 " - pdb=" SG CYS 6 119 " pdb="FE1 SF4 6 201 " - pdb=" SG CYS 6 55 " pdb=" SF4 9 402 " pdb="FE3 SF4 9 402 " - pdb=" SG CYS 9 122 " pdb="FE2 SF4 9 402 " - pdb=" SG CYS 9 116 " pdb="FE4 SF4 9 402 " - pdb=" SG CYS 9 87 " pdb="FE1 SF4 9 402 " - pdb=" SG CYS 9 119 " pdb=" SF4 9 403 " pdb="FE2 SF4 9 403 " - pdb=" SG CYS 9 83 " pdb="FE4 SF4 9 403 " - pdb=" SG CYS 9 80 " pdb="FE3 SF4 9 403 " - pdb=" SG CYS 9 77 " pdb="FE1 SF4 9 403 " - pdb=" SG CYS 9 126 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN b 300 " pdb="ZN ZN b 300 " - pdb=" NE2 HIS b 68 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 87 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 84 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 59 " Number of angles added : 3 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15462 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 338 helices and 30 sheets defined 50.0% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.83 Creating SS restraints... Processing helix chain '1' and resid 33 through 36 No H-bonds generated for 'chain '1' and resid 33 through 36' Processing helix chain '1' and resid 45 through 62 removed outlier: 4.115A pdb=" N LYS 1 51 " --> pdb=" O GLU 1 47 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY 1 52 " --> pdb=" O ILE 1 48 " (cutoff:3.500A) Proline residue: 1 53 - end of helix removed outlier: 3.807A pdb=" N ILE 1 56 " --> pdb=" O GLY 1 52 " (cutoff:3.500A) Processing helix chain '1' and resid 75 through 81 removed outlier: 3.612A pdb=" N PHE 1 81 " --> pdb=" O LEU 1 77 " (cutoff:3.500A) Processing helix chain '1' and resid 106 through 113 Processing helix chain '1' and resid 115 through 128 Processing helix chain '1' and resid 143 through 158 Processing helix chain '1' and resid 166 through 168 No H-bonds generated for 'chain '1' and resid 166 through 168' Processing helix chain '1' and resid 185 through 187 No H-bonds generated for 'chain '1' and resid 185 through 187' Processing helix chain '1' and resid 189 through 196 Processing helix chain '1' and resid 215 through 217 No H-bonds generated for 'chain '1' and resid 215 through 217' Processing helix chain '1' and resid 225 through 229 Processing helix chain '1' and resid 231 through 237 Processing helix chain '1' and resid 239 through 243 Processing helix chain '1' and resid 276 through 283 Processing helix chain '1' and resid 291 through 293 No H-bonds generated for 'chain '1' and resid 291 through 293' Processing helix chain '1' and resid 319 through 323 Processing helix chain '1' and resid 343 through 356 Processing helix chain '1' and resid 363 through 381 removed outlier: 4.392A pdb=" N ASP 1 370 " --> pdb=" O ARG 1 366 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG 1 381 " --> pdb=" O ALA 1 377 " (cutoff:3.500A) Processing helix chain '1' and resid 386 through 398 removed outlier: 4.287A pdb=" N ASP 1 390 " --> pdb=" O ALA 1 387 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER 1 391 " --> pdb=" O GLU 1 388 " (cutoff:3.500A) Processing helix chain '1' and resid 407 through 437 Proline residue: 1 414 - end of helix Proline residue: 1 424 - end of helix Processing helix chain '2' and resid 25 through 37 removed outlier: 3.675A pdb=" N ASN 2 37 " --> pdb=" O ALA 2 33 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 58 removed outlier: 4.705A pdb=" N LEU 2 48 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) Proline residue: 2 49 - end of helix removed outlier: 3.960A pdb=" N GLN 2 57 " --> pdb=" O ALA 2 54 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN 2 58 " --> pdb=" O GLN 2 55 " (cutoff:3.500A) Processing helix chain '2' and resid 65 through 73 Processing helix chain '2' and resid 77 through 86 removed outlier: 3.771A pdb=" N VAL 2 83 " --> pdb=" O ARG 2 79 " (cutoff:3.500A) Processing helix chain '2' and resid 106 through 109 No H-bonds generated for 'chain '2' and resid 106 through 109' Processing helix chain '2' and resid 113 through 124 Processing helix chain '2' and resid 166 through 177 Processing helix chain '3' and resid 26 through 33 removed outlier: 3.921A pdb=" N VAL 3 33 " --> pdb=" O ALA 3 29 " (cutoff:3.500A) Processing helix chain '3' and resid 84 through 97 Processing helix chain '3' and resid 115 through 122 Processing helix chain '3' and resid 150 through 152 No H-bonds generated for 'chain '3' and resid 150 through 152' Processing helix chain '3' and resid 158 through 165 Processing helix chain '3' and resid 178 through 180 No H-bonds generated for 'chain '3' and resid 178 through 180' Processing helix chain '3' and resid 198 through 201 No H-bonds generated for 'chain '3' and resid 198 through 201' Processing helix chain '3' and resid 265 through 269 Processing helix chain '3' and resid 296 through 307 removed outlier: 3.808A pdb=" N MET 3 306 " --> pdb=" O ARG 3 302 " (cutoff:3.500A) Processing helix chain '3' and resid 312 through 314 No H-bonds generated for 'chain '3' and resid 312 through 314' Processing helix chain '3' and resid 325 through 337 Processing helix chain '3' and resid 369 through 372 Processing helix chain '3' and resid 384 through 387 No H-bonds generated for 'chain '3' and resid 384 through 387' Processing helix chain '3' and resid 389 through 401 Processing helix chain '3' and resid 426 through 432 removed outlier: 4.394A pdb=" N ILE 3 432 " --> pdb=" O LEU 3 429 " (cutoff:3.500A) Processing helix chain '3' and resid 438 through 445 removed outlier: 3.664A pdb=" N VAL 3 442 " --> pdb=" O PRO 3 438 " (cutoff:3.500A) Processing helix chain '3' and resid 457 through 459 No H-bonds generated for 'chain '3' and resid 457 through 459' Processing helix chain '3' and resid 463 through 480 Processing helix chain '3' and resid 497 through 505 removed outlier: 4.748A pdb=" N ALA 3 501 " --> pdb=" O ALA 3 497 " (cutoff:3.500A) Processing helix chain '3' and resid 512 through 516 Processing helix chain '3' and resid 596 through 606 Processing helix chain '3' and resid 616 through 626 Processing helix chain '3' and resid 642 through 649 Processing helix chain '3' and resid 669 through 671 No H-bonds generated for 'chain '3' and resid 669 through 671' Processing helix chain '3' and resid 676 through 679 No H-bonds generated for 'chain '3' and resid 676 through 679' Processing helix chain '3' and resid 683 through 692 Processing helix chain '4' and resid 8 through 11 No H-bonds generated for 'chain '4' and resid 8 through 11' Processing helix chain '4' and resid 24 through 26 No H-bonds generated for 'chain '4' and resid 24 through 26' Processing helix chain '4' and resid 87 through 90 No H-bonds generated for 'chain '4' and resid 87 through 90' Processing helix chain '4' and resid 96 through 104 Proline residue: 4 101 - end of helix removed outlier: 3.901A pdb=" N ASP 4 104 " --> pdb=" O LEU 4 100 " (cutoff:3.500A) Processing helix chain '4' and resid 111 through 126 Processing helix chain '4' and resid 132 through 161 Processing helix chain '4' and resid 165 through 184 removed outlier: 4.205A pdb=" N GLU 4 172 " --> pdb=" O PHE 4 168 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU 4 173 " --> pdb=" O TRP 4 169 " (cutoff:3.500A) Processing helix chain '4' and resid 207 through 215 Processing helix chain '4' and resid 218 through 229 Processing helix chain '4' and resid 233 through 237 Processing helix chain '4' and resid 247 through 252 Processing helix chain '4' and resid 257 through 261 Processing helix chain '4' and resid 293 through 316 Processing helix chain '4' and resid 335 through 338 No H-bonds generated for 'chain '4' and resid 335 through 338' Processing helix chain '4' and resid 342 through 353 Processing helix chain '4' and resid 394 through 405 removed outlier: 4.631A pdb=" N ASP 4 403 " --> pdb=" O LEU 4 399 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LYS 4 404 " --> pdb=" O ALA 4 400 " (cutoff:3.500A) Processing helix chain '4' and resid 411 through 420 removed outlier: 4.125A pdb=" N ALA 4 416 " --> pdb=" O ALA 4 412 " (cutoff:3.500A) Processing helix chain '4' and resid 425 through 429 Processing helix chain '5' and resid 16 through 32 Processing helix chain '5' and resid 57 through 66 Processing helix chain '5' and resid 120 through 122 No H-bonds generated for 'chain '5' and resid 120 through 122' Processing helix chain '5' and resid 125 through 137 removed outlier: 3.676A pdb=" N TRP 5 129 " --> pdb=" O ALA 5 126 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLU 5 131 " --> pdb=" O ASN 5 128 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET 5 137 " --> pdb=" O ILE 5 134 " (cutoff:3.500A) Processing helix chain '5' and resid 207 through 209 No H-bonds generated for 'chain '5' and resid 207 through 209' Processing helix chain '6' and resid 25 through 42 Processing helix chain '6' and resid 54 through 63 removed outlier: 3.539A pdb=" N GLU 6 58 " --> pdb=" O CYS 6 54 " (cutoff:3.500A) Processing helix chain '6' and resid 69 through 72 Processing helix chain '6' and resid 80 through 82 No H-bonds generated for 'chain '6' and resid 80 through 82' Processing helix chain '6' and resid 97 through 105 Processing helix chain '6' and resid 117 through 122 Processing helix chain '6' and resid 124 through 126 No H-bonds generated for 'chain '6' and resid 124 through 126' Processing helix chain '6' and resid 136 through 138 No H-bonds generated for 'chain '6' and resid 136 through 138' Processing helix chain '6' and resid 153 through 168 Processing helix chain '6' and resid 172 through 178 Processing helix chain '9' and resid 14 through 26 Processing helix chain '9' and resid 28 through 41 Processing helix chain '9' and resid 82 through 85 No H-bonds generated for 'chain '9' and resid 82 through 85' Processing helix chain '9' and resid 121 through 125 Processing helix chain '9' and resid 145 through 147 No H-bonds generated for 'chain '9' and resid 145 through 147' Processing helix chain '9' and resid 151 through 175 removed outlier: 5.784A pdb=" N ALA 9 163 " --> pdb=" O ASP 9 159 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLU 9 164 " --> pdb=" O LYS 9 160 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ALA 9 167 " --> pdb=" O ALA 9 163 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU 9 174 " --> pdb=" O GLN 9 170 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N TYR 9 175 " --> pdb=" O ALA 9 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 15 Processing helix chain 'A' and resid 19 through 22 No H-bonds generated for 'chain 'A' and resid 19 through 22' Processing helix chain 'A' and resid 56 through 65 removed outlier: 3.795A pdb=" N LEU A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 71 No H-bonds generated for 'chain 'A' and resid 68 through 71' Processing helix chain 'A' and resid 73 through 80 Proline residue: A 76 - end of helix removed outlier: 4.114A pdb=" N SER A 79 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 Processing helix chain 'H' and resid 2 through 10 Processing helix chain 'H' and resid 12 through 32 removed outlier: 4.055A pdb=" N VAL H 17 " --> pdb=" O ILE H 13 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 47 through 56 removed outlier: 4.008A pdb=" N PHE H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 83 Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 101 through 122 removed outlier: 3.718A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 154 removed outlier: 3.669A pdb=" N SER H 141 " --> pdb=" O ALA H 137 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA H 147 " --> pdb=" O GLU H 143 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ILE H 148 " --> pdb=" O VAL H 144 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU H 150 " --> pdb=" O LEU H 146 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU H 154 " --> pdb=" O LEU H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 168 Processing helix chain 'H' and resid 179 through 192 removed outlier: 3.780A pdb=" N ILE H 187 " --> pdb=" O MET H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 212 No H-bonds generated for 'chain 'H' and resid 210 through 212' Processing helix chain 'H' and resid 221 through 242 removed outlier: 3.910A pdb=" N ALA H 226 " --> pdb=" O LEU H 222 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 274 Processing helix chain 'H' and resid 282 through 289 removed outlier: 3.768A pdb=" N MET H 286 " --> pdb=" O TYR H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 310 Proline residue: H 308 - end of helix Processing helix chain 'J' and resid 5 through 21 Processing helix chain 'J' and resid 26 through 43 removed outlier: 4.126A pdb=" N GLY J 42 " --> pdb=" O GLY J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 73 removed outlier: 4.043A pdb=" N VAL J 56 " --> pdb=" O LEU J 52 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR J 60 " --> pdb=" O VAL J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 110 Processing helix chain 'J' and resid 138 through 148 removed outlier: 4.034A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TYR J 147 " --> pdb=" O ILE J 143 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER J 148 " --> pdb=" O ALA J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 Processing helix chain 'K' and resid 3 through 20 removed outlier: 3.954A pdb=" N ASN K 7 " --> pdb=" O LEU K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 51 removed outlier: 3.528A pdb=" N CYS K 32 " --> pdb=" O SER K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 84 removed outlier: 4.057A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 5.036A pdb=" N ALA K 72 " --> pdb=" O CYS K 69 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL K 79 " --> pdb=" O SER K 76 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N MET K 80 " --> pdb=" O LEU K 77 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASN K 83 " --> pdb=" O MET K 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 24 removed outlier: 3.775A pdb=" N LEU L 12 " --> pdb=" O THR L 8 " (cutoff:3.500A) Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 32 through 57 removed outlier: 3.932A pdb=" N ILE L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.830A pdb=" N THR L 57 " --> pdb=" O MET L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 107 Proline residue: L 91 - end of helix removed outlier: 3.864A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 132 Processing helix chain 'L' and resid 137 through 155 Processing helix chain 'L' and resid 162 through 193 removed outlier: 3.971A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 Processing helix chain 'L' and resid 210 through 224 Processing helix chain 'L' and resid 231 through 238 removed outlier: 4.171A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 250 removed outlier: 4.571A pdb=" N SER L 249 " --> pdb=" O ALA L 245 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER L 250 " --> pdb=" O LEU L 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 262 Processing helix chain 'L' and resid 264 through 267 No H-bonds generated for 'chain 'L' and resid 264 through 267' Processing helix chain 'L' and resid 271 through 293 removed outlier: 3.751A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 349 removed outlier: 4.624A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 358 No H-bonds generated for 'chain 'L' and resid 356 through 358' Processing helix chain 'L' and resid 362 through 365 No H-bonds generated for 'chain 'L' and resid 362 through 365' Processing helix chain 'L' and resid 367 through 381 Processing helix chain 'L' and resid 388 through 390 No H-bonds generated for 'chain 'L' and resid 388 through 390' Processing helix chain 'L' and resid 392 through 400 Processing helix chain 'L' and resid 406 through 431 removed outlier: 3.562A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 471 removed outlier: 3.789A pdb=" N LEU L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N PHE L 466 " --> pdb=" O LEU L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 487 No H-bonds generated for 'chain 'L' and resid 484 through 487' Processing helix chain 'L' and resid 489 through 506 Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 547 removed outlier: 4.015A pdb=" N TYR L 529 " --> pdb=" O LEU L 526 " (cutoff:3.500A) Proline residue: L 530 - end of helix removed outlier: 5.027A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU L 536 " --> pdb=" O MET L 533 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N THR L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 4.492A pdb=" N THR L 543 " --> pdb=" O MET L 540 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET L 544 " --> pdb=" O ASN L 541 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS L 547 " --> pdb=" O MET L 544 " (cutoff:3.500A) Processing helix chain 'L' and resid 557 through 561 Processing helix chain 'L' and resid 563 through 577 Processing helix chain 'L' and resid 584 through 599 Processing helix chain 'M' and resid 5 through 16 removed outlier: 4.114A pdb=" N MET M 12 " --> pdb=" O THR M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 23 through 42 removed outlier: 3.566A pdb=" N THR M 27 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 79 removed outlier: 3.781A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 107 Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.823A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 140 through 170 removed outlier: 3.720A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN M 144 " --> pdb=" O GLU M 141 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TYR M 148 " --> pdb=" O ALA M 145 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N PHE M 149 " --> pdb=" O GLY M 146 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE M 151 " --> pdb=" O TYR M 148 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LEU M 154 " --> pdb=" O PHE M 151 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LEU M 158 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix Processing helix chain 'M' and resid 176 through 179 No H-bonds generated for 'chain 'M' and resid 176 through 179' Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.757A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 221 Proline residue: M 217 - end of helix removed outlier: 4.382A pdb=" N HIS M 220 " --> pdb=" O PRO M 217 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL M 221 " --> pdb=" O LYS M 218 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 237 through 246 Processing helix chain 'M' and resid 253 through 257 removed outlier: 3.785A pdb=" N MET M 257 " --> pdb=" O THR M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 276 removed outlier: 4.242A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER M 273 " --> pdb=" O MET M 269 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 4.063A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 4.120A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 392 through 415 removed outlier: 3.561A pdb=" N ASN M 399 " --> pdb=" O LEU M 395 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA M 404 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR M 409 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU M 411 " --> pdb=" O SER M 407 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 448 Proline residue: M 443 - end of helix removed outlier: 4.139A pdb=" N SER M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 454 Processing helix chain 'M' and resid 456 through 458 No H-bonds generated for 'chain 'M' and resid 456 through 458' Processing helix chain 'N' and resid 3 through 22 Processing helix chain 'N' and resid 26 through 44 Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 81 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 115 through 121 Processing helix chain 'N' and resid 124 through 135 removed outlier: 3.788A pdb=" N GLN N 134 " --> pdb=" O LEU N 130 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 144 Processing helix chain 'N' and resid 151 through 171 removed outlier: 3.854A pdb=" N GLY N 169 " --> pdb=" O GLY N 165 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 193 removed outlier: 3.896A pdb=" N VAL N 193 " --> pdb=" O TRP N 189 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 222 Processing helix chain 'N' and resid 227 through 235 removed outlier: 4.284A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 removed outlier: 3.572A pdb=" N ILE N 242 " --> pdb=" O PRO N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 270 Proline residue: N 262 - end of helix Processing helix chain 'N' and resid 277 through 300 removed outlier: 3.775A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 310 through 316 removed outlier: 3.667A pdb=" N TRP N 315 " --> pdb=" O LYS N 312 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 334 Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix removed outlier: 3.749A pdb=" N SER N 344 " --> pdb=" O PRO N 341 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 9 Processing helix chain 'V' and resid 17 through 42 Processing helix chain 'V' and resid 48 through 80 Processing helix chain 'V' and resid 86 through 103 Processing helix chain 'V' and resid 107 through 130 Processing helix chain 'W' and resid 15 through 45 removed outlier: 4.739A pdb=" N THR W 32 " --> pdb=" O TYR W 28 " (cutoff:3.500A) Proline residue: W 35 - end of helix Processing helix chain 'W' and resid 70 through 78 Processing helix chain 'W' and resid 83 through 117 Processing helix chain 'X' and resid 8 through 20 Processing helix chain 'X' and resid 44 through 58 Processing helix chain 'X' and resid 64 through 67 No H-bonds generated for 'chain 'X' and resid 64 through 67' Processing helix chain 'X' and resid 73 through 84 Processing helix chain 'Y' and resid 21 through 26 Processing helix chain 'Y' and resid 28 through 34 Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 52 through 54 No H-bonds generated for 'chain 'Y' and resid 52 through 54' Processing helix chain 'Y' and resid 56 through 76 removed outlier: 3.767A pdb=" N LEU Y 67 " --> pdb=" O ASN Y 63 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N HIS Y 76 " --> pdb=" O GLN Y 72 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 90 Processing helix chain 'Y' and resid 100 through 113 Processing helix chain 'Z' and resid 28 through 39 Processing helix chain 'Z' and resid 41 through 56 Processing helix chain 'Z' and resid 73 through 75 No H-bonds generated for 'chain 'Z' and resid 73 through 75' Processing helix chain 'Z' and resid 81 through 115 removed outlier: 4.220A pdb=" N GLU Z 86 " --> pdb=" O LEU Z 82 " (cutoff:3.500A) Processing helix chain 'Z' and resid 119 through 123 removed outlier: 3.678A pdb=" N ASN Z 123 " --> pdb=" O HIS Z 120 " (cutoff:3.500A) Processing helix chain 'Z' and resid 125 through 142 Processing helix chain 'Z' and resid 151 through 170 Processing helix chain 'a' and resid 43 through 45 No H-bonds generated for 'chain 'a' and resid 43 through 45' Processing helix chain 'a' and resid 50 through 60 removed outlier: 4.527A pdb=" N LYS a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) Processing helix chain 'b' and resid 23 through 28 removed outlier: 3.786A pdb=" N ARG b 27 " --> pdb=" O ARG b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 43 No H-bonds generated for 'chain 'b' and resid 40 through 43' Processing helix chain 'c' and resid 27 through 29 No H-bonds generated for 'chain 'c' and resid 27 through 29' Processing helix chain 'c' and resid 50 through 52 No H-bonds generated for 'chain 'c' and resid 50 through 52' Processing helix chain 'c' and resid 89 through 98 Processing helix chain 'c' and resid 119 through 122 Processing helix chain 'd' and resid 29 through 39 removed outlier: 4.016A pdb=" N TYR d 33 " --> pdb=" O PHE d 29 " (cutoff:3.500A) Processing helix chain 'd' and resid 54 through 62 removed outlier: 5.221A pdb=" N HIS d 58 " --> pdb=" O ASP d 55 " (cutoff:3.500A) Proline residue: d 61 - end of helix Processing helix chain 'd' and resid 78 through 85 Processing helix chain 'd' and resid 106 through 110 Processing helix chain 'd' and resid 112 through 123 Processing helix chain 'd' and resid 144 through 159 Processing helix chain 'd' and resid 179 through 185 removed outlier: 3.734A pdb=" N ILE d 185 " --> pdb=" O TYR d 181 " (cutoff:3.500A) Processing helix chain 'd' and resid 194 through 197 Processing helix chain 'd' and resid 207 through 219 Processing helix chain 'd' and resid 221 through 223 No H-bonds generated for 'chain 'd' and resid 221 through 223' Processing helix chain 'd' and resid 238 through 248 Processing helix chain 'd' and resid 265 through 270 removed outlier: 3.541A pdb=" N PHE d 270 " --> pdb=" O ILE d 266 " (cutoff:3.500A) Processing helix chain 'd' and resid 281 through 287 Processing helix chain 'd' and resid 310 through 318 removed outlier: 5.817A pdb=" N ILE d 315 " --> pdb=" O GLU d 311 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLU d 316 " --> pdb=" O LEU d 312 " (cutoff:3.500A) Processing helix chain 'd' and resid 324 through 326 No H-bonds generated for 'chain 'd' and resid 324 through 326' Processing helix chain 'e' and resid 30 through 39 removed outlier: 3.640A pdb=" N LYS e 38 " --> pdb=" O ASP e 34 " (cutoff:3.500A) Processing helix chain 'e' and resid 41 through 44 No H-bonds generated for 'chain 'e' and resid 41 through 44' Processing helix chain 'e' and resid 69 through 71 No H-bonds generated for 'chain 'e' and resid 69 through 71' Processing helix chain 'e' and resid 83 through 96 Processing helix chain 'f' and resid 19 through 36 removed outlier: 4.454A pdb=" N HIS f 36 " --> pdb=" O ASP f 32 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 60 Processing helix chain 'f' and resid 65 through 71 Processing helix chain 'f' and resid 76 through 96 removed outlier: 3.912A pdb=" N GLN f 95 " --> pdb=" O ARG f 91 " (cutoff:3.500A) Processing helix chain 'g' and resid 24 through 48 Proline residue: g 43 - end of helix Processing helix chain 'g' and resid 55 through 69 removed outlier: 4.218A pdb=" N ASN g 69 " --> pdb=" O MET g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 75 through 93 Processing helix chain 'g' and resid 99 through 105 removed outlier: 4.503A pdb=" N PHE g 105 " --> pdb=" O HIS g 101 " (cutoff:3.500A) Processing helix chain 'g' and resid 117 through 123 Processing helix chain 'h' and resid 5 through 15 Processing helix chain 'h' and resid 53 through 56 Processing helix chain 'h' and resid 59 through 61 No H-bonds generated for 'chain 'h' and resid 59 through 61' Processing helix chain 'i' and resid 3 through 17 removed outlier: 3.706A pdb=" N HIS i 17 " --> pdb=" O GLN i 13 " (cutoff:3.500A) Processing helix chain 'i' and resid 20 through 30 Processing helix chain 'i' and resid 79 through 81 No H-bonds generated for 'chain 'i' and resid 79 through 81' Processing helix chain 'i' and resid 84 through 90 removed outlier: 3.984A pdb=" N ARG i 88 " --> pdb=" O PRO i 84 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TRP i 89 " --> pdb=" O GLU i 85 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 21 Processing helix chain 'j' and resid 44 through 58 Processing helix chain 'j' and resid 64 through 67 No H-bonds generated for 'chain 'j' and resid 64 through 67' Processing helix chain 'j' and resid 73 through 82 Processing helix chain 'k' and resid 5 through 10 Processing helix chain 'k' and resid 35 through 45 removed outlier: 4.373A pdb=" N ALA k 39 " --> pdb=" O SEP k 36 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS k 45 " --> pdb=" O VAL k 42 " (cutoff:3.500A) Processing helix chain 'k' and resid 56 through 62 removed outlier: 4.594A pdb=" N ALA k 59 " --> pdb=" O ILE k 56 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP k 60 " --> pdb=" O HIS k 57 " (cutoff:3.500A) Processing helix chain 'k' and resid 79 through 84 Processing helix chain 'k' and resid 92 through 118 Processing helix chain 'k' and resid 132 through 140 Processing helix chain 'k' and resid 146 through 162 removed outlier: 4.445A pdb=" N CYS k 161 " --> pdb=" O LYS k 157 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N GLU k 162 " --> pdb=" O VAL k 158 " (cutoff:3.500A) Processing helix chain 'k' and resid 176 through 186 Processing helix chain 'k' and resid 191 through 193 No H-bonds generated for 'chain 'k' and resid 191 through 193' Processing helix chain 'k' and resid 196 through 208 Processing helix chain 'k' and resid 210 through 214 Processing helix chain 'k' and resid 227 through 229 No H-bonds generated for 'chain 'k' and resid 227 through 229' Processing helix chain 'k' and resid 231 through 240 removed outlier: 4.245A pdb=" N TYR k 240 " --> pdb=" O GLU k 236 " (cutoff:3.500A) Processing helix chain 'k' and resid 253 through 263 Processing helix chain 'k' and resid 266 through 271 Processing helix chain 'k' and resid 286 through 297 Processing helix chain 'k' and resid 317 through 319 No H-bonds generated for 'chain 'k' and resid 317 through 319' Processing helix chain 'l' and resid 5 through 8 No H-bonds generated for 'chain 'l' and resid 5 through 8' Processing helix chain 'l' and resid 25 through 27 No H-bonds generated for 'chain 'l' and resid 25 through 27' Processing helix chain 'l' and resid 33 through 42 Processing helix chain 'l' and resid 47 through 54 removed outlier: 4.043A pdb=" N LYS l 53 " --> pdb=" O ILE l 49 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 67 Processing helix chain 'l' and resid 69 through 87 Processing helix chain 'l' and resid 95 through 97 No H-bonds generated for 'chain 'l' and resid 95 through 97' Processing helix chain 'm' and resid 5 through 14 Processing helix chain 'm' and resid 16 through 30 Processing helix chain 'm' and resid 32 through 34 No H-bonds generated for 'chain 'm' and resid 32 through 34' Processing helix chain 'm' and resid 38 through 46 removed outlier: 3.570A pdb=" N LEU m 42 " --> pdb=" O THR m 38 " (cutoff:3.500A) Processing helix chain 'm' and resid 78 through 82 Processing helix chain 'n' and resid 27 through 36 Processing helix chain 'n' and resid 45 through 48 No H-bonds generated for 'chain 'n' and resid 45 through 48' Processing helix chain 'n' and resid 54 through 56 No H-bonds generated for 'chain 'n' and resid 54 through 56' Processing helix chain 'n' and resid 62 through 66 Processing helix chain 'n' and resid 70 through 88 Processing helix chain 'o' and resid 5 through 7 No H-bonds generated for 'chain 'o' and resid 5 through 7' Processing helix chain 'o' and resid 16 through 20 Processing helix chain 'o' and resid 29 through 48 Processing helix chain 'o' and resid 58 through 95 removed outlier: 3.990A pdb=" N TYR o 74 " --> pdb=" O PHE o 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 27 through 50 removed outlier: 3.902A pdb=" N ALA p 31 " --> pdb=" O GLU p 27 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN p 32 " --> pdb=" O THR p 28 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN p 49 " --> pdb=" O GLU p 45 " (cutoff:3.500A) Processing helix chain 'p' and resid 62 through 71 Processing helix chain 'p' and resid 76 through 78 No H-bonds generated for 'chain 'p' and resid 76 through 78' Processing helix chain 'p' and resid 83 through 93 Processing helix chain 'p' and resid 95 through 116 Processing helix chain 'q' and resid 31 through 96 Proline residue: q 72 - end of helix removed outlier: 3.521A pdb=" N GLU q 92 " --> pdb=" O GLU q 88 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR q 95 " --> pdb=" O GLU q 91 " (cutoff:3.500A) Processing helix chain 'q' and resid 120 through 126 removed outlier: 6.170A pdb=" N LEU q 126 " --> pdb=" O GLU q 122 " (cutoff:3.500A) Processing helix chain 'q' and resid 129 through 136 Processing helix chain 'r' and resid 5 through 25 Processing helix chain 'r' and resid 69 through 72 No H-bonds generated for 'chain 'r' and resid 69 through 72' Processing helix chain 'r' and resid 75 through 87 Processing helix chain 's' and resid 2 through 8 Processing helix chain 's' and resid 42 through 47 Processing helix chain 's' and resid 59 through 71 Processing helix chain 's' and resid 80 through 121 Processing helix chain 't' and resid 11 through 29 Processing helix chain 't' and resid 33 through 49 Processing helix chain 't' and resid 56 through 72 Processing helix chain 't' and resid 93 through 96 Processing helix chain 't' and resid 100 through 105 Processing helix chain 't' and resid 108 through 111 No H-bonds generated for 'chain 't' and resid 108 through 111' Processing helix chain 't' and resid 115 through 142 removed outlier: 3.821A pdb=" N GLN t 123 " --> pdb=" O ALA t 119 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP t 124 " --> pdb=" O LYS t 120 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLU t 133 " --> pdb=" O ARG t 129 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ARG t 134 " --> pdb=" O GLU t 130 " (cutoff:3.500A) Processing helix chain 't' and resid 167 through 170 No H-bonds generated for 'chain 't' and resid 167 through 170' Processing helix chain 'u' and resid 19 through 42 Processing helix chain 'u' and resid 45 through 48 No H-bonds generated for 'chain 'u' and resid 45 through 48' Processing helix chain 'u' and resid 56 through 58 No H-bonds generated for 'chain 'u' and resid 56 through 58' Processing helix chain 'v' and resid 6 through 8 No H-bonds generated for 'chain 'v' and resid 6 through 8' Processing helix chain 'v' and resid 17 through 26 Processing helix chain 'v' and resid 55 through 57 No H-bonds generated for 'chain 'v' and resid 55 through 57' Processing helix chain 'v' and resid 98 through 121 Processing helix chain 'v' and resid 134 through 138 Processing helix chain 'w' and resid 51 through 65 Processing helix chain 'w' and resid 71 through 78 Processing helix chain 'w' and resid 83 through 102 removed outlier: 3.644A pdb=" N GLN w 86 " --> pdb=" O TYR w 83 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLU w 87 " --> pdb=" O ARG w 84 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP w 88 " --> pdb=" O MET w 85 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA w 89 " --> pdb=" O GLN w 86 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU w 92 " --> pdb=" O ALA w 89 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N VAL w 97 " --> pdb=" O GLU w 94 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU w 101 " --> pdb=" O LYS w 98 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA w 102 " --> pdb=" O TYR w 99 " (cutoff:3.500A) Processing helix chain 'w' and resid 115 through 117 No H-bonds generated for 'chain 'w' and resid 115 through 117' Processing helix chain 'x' and resid 14 through 45 Processing helix chain 'y' and resid 16 through 33 removed outlier: 3.669A pdb=" N GLU y 32 " --> pdb=" O ARG y 28 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS y 33 " --> pdb=" O LYS y 29 " (cutoff:3.500A) Processing helix chain 'z' and resid 2 through 29 Proline residue: z 7 - end of helix removed outlier: 4.704A pdb=" N ILE z 18 " --> pdb=" O CYS z 15 " (cutoff:3.500A) Proline residue: z 19 - end of helix Processing helix chain 'z' and resid 42 through 54 Processing sheet with id= A, first strand: chain '1' and resid 219 through 224 removed outlier: 5.858A pdb=" N ALA 1 133 " --> pdb=" O LEU 1 93 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL 1 95 " --> pdb=" O ALA 1 133 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TYR 1 135 " --> pdb=" O VAL 1 95 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ALA 1 97 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TYR 1 137 " --> pdb=" O ALA 1 97 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASP 1 174 " --> pdb=" O ALA 1 134 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE 1 136 " --> pdb=" O ASP 1 174 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE 1 176 " --> pdb=" O ILE 1 136 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE 1 138 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N VAL 1 178 " --> pdb=" O ILE 1 138 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '1' and resid 266 through 271 Processing sheet with id= C, first strand: chain '2' and resid 137 through 142 removed outlier: 6.801A pdb=" N TYR 2 98 " --> pdb=" O THR 2 138 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ILE 2 140 " --> pdb=" O TYR 2 98 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE 2 100 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL 2 142 " --> pdb=" O ILE 2 100 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N VAL 2 102 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '3' and resid 9 through 13 Processing sheet with id= E, first strand: chain '3' and resid 146 through 148 Processing sheet with id= F, first strand: chain '3' and resid 173 through 175 Processing sheet with id= G, first strand: chain '3' and resid 223 through 228 Processing sheet with id= H, first strand: chain '3' and resid 283 through 285 Processing sheet with id= I, first strand: chain '3' and resid 343 through 345 removed outlier: 8.528A pdb=" N CYS 3 344 " --> pdb=" O VAL 3 315 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ALA 3 317 " --> pdb=" O CYS 3 344 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N MET 3 521 " --> pdb=" O ALA 3 316 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE 3 318 " --> pdb=" O MET 3 521 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE 3 523 " --> pdb=" O ILE 3 318 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE 3 542 " --> pdb=" O LEU 3 522 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU 3 524 " --> pdb=" O PHE 3 542 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL 3 544 " --> pdb=" O LEU 3 524 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL 3 559 " --> pdb=" O TYR 3 545 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N GLY 3 547 " --> pdb=" O VAL 3 559 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU 3 561 " --> pdb=" O GLY 3 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain '3' and resid 490 through 493 removed outlier: 8.425A pdb=" N ASN 3 491 " --> pdb=" O PRO 3 449 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL 3 451 " --> pdb=" O ASN 3 491 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LEU 3 493 " --> pdb=" O VAL 3 451 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU 3 453 " --> pdb=" O LEU 3 493 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL 3 376 " --> pdb=" O MET 3 450 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N VAL 3 452 " --> pdb=" O VAL 3 376 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU 3 378 " --> pdb=" O VAL 3 452 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLY 3 454 " --> pdb=" O LEU 3 378 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL 3 380 " --> pdb=" O GLY 3 454 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LYS 3 405 " --> pdb=" O VAL 3 377 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU 3 379 " --> pdb=" O LYS 3 405 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ALA 3 407 " --> pdb=" O LEU 3 379 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASP 3 420 " --> pdb=" O LEU 3 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain '3' and resid 571 through 574 removed outlier: 3.737A pdb=" N ALA 3 571 " --> pdb=" O THR 3 583 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '4' and resid 47 through 51 removed outlier: 3.518A pdb=" N LYS 4 75 " --> pdb=" O GLU 4 67 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N SER 4 69 " --> pdb=" O VAL 4 73 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL 4 73 " --> pdb=" O SER 4 69 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '4' and resid 361 through 369 Processing sheet with id= N, first strand: chain '5' and resid 74 through 82 removed outlier: 6.724A pdb=" N ASN 5 95 " --> pdb=" O ALA 5 76 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU 5 78 " --> pdb=" O VAL 5 93 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL 5 93 " --> pdb=" O LEU 5 78 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA 5 80 " --> pdb=" O GLU 5 91 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLU 5 91 " --> pdb=" O ALA 5 80 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU 5 48 " --> pdb=" O ARG 5 104 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N TYR 5 110 " --> pdb=" O ILE 5 52 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '5' and resid 172 through 177 Processing sheet with id= P, first strand: chain '6' and resid 85 through 89 removed outlier: 6.600A pdb=" N TYR 6 112 " --> pdb=" O MET 6 86 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL 6 88 " --> pdb=" O TYR 6 112 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL 6 114 " --> pdb=" O VAL 6 88 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE 6 144 " --> pdb=" O SER 6 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain '9' and resid 65 through 67 Processing sheet with id= R, first strand: chain '9' and resid 92 through 98 removed outlier: 6.192A pdb=" N GLU 9 97 " --> pdb=" O THR 9 106 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N THR 9 106 " --> pdb=" O GLU 9 97 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 112 through 115 Processing sheet with id= T, first strand: chain 'L' and resid 69 through 71 Processing sheet with id= U, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.441A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'b' and resid 50 through 52 Processing sheet with id= W, first strand: chain 'b' and resid 56 through 59 Processing sheet with id= X, first strand: chain 'c' and resid 102 through 105 Processing sheet with id= Y, first strand: chain 'c' and resid 64 through 66 Processing sheet with id= Z, first strand: chain 'd' and resid 227 through 230 removed outlier: 6.502A pdb=" N ILE d 165 " --> pdb=" O PHE d 228 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N PHE d 230 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LYS d 167 " --> pdb=" O PHE d 230 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE d 132 " --> pdb=" O ASN d 93 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLN d 44 " --> pdb=" O ALA d 21 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N VAL d 23 " --> pdb=" O GLN d 44 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE d 46 " --> pdb=" O VAL d 23 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'd' and resid 192 through 194 removed outlier: 6.195A pdb=" N TYR d 256 " --> pdb=" O LEU d 193 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'e' and resid 51 through 57 removed outlier: 6.876A pdb=" N ARG e 67 " --> pdb=" O ARG e 16 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE e 18 " --> pdb=" O TRP e 65 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP e 65 " --> pdb=" O ILE e 18 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE e 20 " --> pdb=" O LYS e 63 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LYS e 63 " --> pdb=" O ILE e 20 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'i' and resid 60 through 63 removed outlier: 6.407A pdb=" N GLU i 50 " --> pdb=" O LEU i 38 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LEU i 38 " --> pdb=" O GLU i 50 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'k' and resid 123 through 125 removed outlier: 6.608A pdb=" N ILE k 25 " --> pdb=" O LEU k 124 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL k 168 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP k 28 " --> pdb=" O VAL k 168 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE k 170 " --> pdb=" O ASP k 28 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLU k 219 " --> pdb=" O VAL k 169 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N TYR k 171 " --> pdb=" O GLU k 219 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU k 221 " --> pdb=" O TYR k 171 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD 2739 hydrogen bonds defined for protein. 7725 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: 21.46 Time building geometry restraints manager: 23.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.43: 28558 1.43 - 1.66: 40255 1.66 - 1.89: 761 1.89 - 2.13: 0 2.13 - 2.36: 80 Bond restraints: 69654 Sorted by residual: bond pdb=" O2B NDP d 401 " pdb=" P2B NDP d 401 " ideal model delta sigma weight residual 1.833 1.591 0.242 3.80e-02 6.93e+02 4.07e+01 bond pdb=" C16 ZMP g 201 " pdb=" N2 ZMP g 201 " ideal model delta sigma weight residual 1.452 1.330 0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" OB3 CDL W 201 " pdb=" PB2 CDL W 201 " ideal model delta sigma weight residual 1.529 1.471 0.058 1.00e-02 1.00e+04 3.42e+01 bond pdb=" OB3 CDL h 201 " pdb=" PB2 CDL h 201 " ideal model delta sigma weight residual 1.529 1.471 0.058 1.00e-02 1.00e+04 3.41e+01 bond pdb=" OA3 CDL h 201 " pdb=" PA1 CDL h 201 " ideal model delta sigma weight residual 1.529 1.471 0.058 1.00e-02 1.00e+04 3.35e+01 ... (remaining 69649 not shown) Histogram of bond angle deviations from ideal: 62.38 - 78.08: 74 78.08 - 93.77: 9 93.77 - 109.47: 9102 109.47 - 125.16: 83435 125.16 - 140.86: 1546 Bond angle restraints: 94166 Sorted by residual: angle pdb=" O1A NAI 1 503 " pdb=" PA NAI 1 503 " pdb=" O2A NAI 1 503 " ideal model delta sigma weight residual 120.60 72.91 47.69 3.00e+00 1.11e-01 2.53e+02 angle pdb=" O1A NAI 1 503 " pdb=" PA NAI 1 503 " pdb=" O5B NAI 1 503 " ideal model delta sigma weight residual 109.30 71.15 38.15 3.00e+00 1.11e-01 1.62e+02 angle pdb=" PA NDP d 401 " pdb=" O3 NDP d 401 " pdb=" PN NDP d 401 " ideal model delta sigma weight residual 107.74 131.64 -23.90 1.95e+00 2.62e-01 1.50e+02 angle pdb=" S1 FES 3 803 " pdb="FE2 FES 3 803 " pdb=" S2 FES 3 803 " ideal model delta sigma weight residual 104.33 90.66 13.67 1.14e+00 7.69e-01 1.44e+02 angle pdb=" S1 FES 3 803 " pdb="FE1 FES 3 803 " pdb=" S2 FES 3 803 " ideal model delta sigma weight residual 104.33 90.73 13.60 1.20e+00 6.94e-01 1.28e+02 ... (remaining 94161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.24: 41301 34.24 - 68.48: 590 68.48 - 102.72: 37 102.72 - 136.96: 2 136.96 - 171.21: 2 Dihedral angle restraints: 41932 sinusoidal: 17957 harmonic: 23975 Sorted by residual: dihedral pdb=" CA ILE J 115 " pdb=" C ILE J 115 " pdb=" N VAL J 116 " pdb=" CA VAL J 116 " ideal model delta harmonic sigma weight residual -180.00 -114.48 -65.52 0 5.00e+00 4.00e-02 1.72e+02 dihedral pdb=" CA TYR 4 275 " pdb=" C TYR 4 275 " pdb=" N ASP 4 276 " pdb=" CA ASP 4 276 " ideal model delta harmonic sigma weight residual -180.00 -130.11 -49.89 0 5.00e+00 4.00e-02 9.96e+01 dihedral pdb=" CA ASN 3 259 " pdb=" C ASN 3 259 " pdb=" N GLU 3 260 " pdb=" CA GLU 3 260 " ideal model delta harmonic sigma weight residual -180.00 -133.90 -46.10 0 5.00e+00 4.00e-02 8.50e+01 ... (remaining 41929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.237: 10161 4.237 - 8.475: 5 8.475 - 12.712: 0 12.712 - 16.950: 0 16.950 - 21.187: 24 Chirality restraints: 10190 Sorted by residual: chirality pdb="FE4 SF4 3 802 " pdb=" S1 SF4 3 802 " pdb=" S2 SF4 3 802 " pdb=" S3 SF4 3 802 " both_signs ideal model delta sigma weight residual False 10.55 -10.63 21.19 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 6 201 " pdb=" S1 SF4 6 201 " pdb=" S2 SF4 6 201 " pdb=" S3 SF4 6 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.59 21.14 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE2 SF4 3 802 " pdb=" S1 SF4 3 802 " pdb=" S3 SF4 3 802 " pdb=" S4 SF4 3 802 " both_signs ideal model delta sigma weight residual False 10.55 -10.57 21.12 2.00e-01 2.50e+01 1.12e+04 ... (remaining 10187 not shown) Planarity restraints: 11749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 DCQ H 501 " 0.066 2.00e-02 2.50e+03 1.41e-01 5.96e+02 pdb=" C1M DCQ H 501 " 0.294 2.00e-02 2.50e+03 pdb=" C2 DCQ H 501 " -0.060 2.00e-02 2.50e+03 pdb=" C3 DCQ H 501 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DCQ H 501 " 0.024 2.00e-02 2.50e+03 pdb=" C5 DCQ H 501 " -0.046 2.00e-02 2.50e+03 pdb=" C6 DCQ H 501 " -0.047 2.00e-02 2.50e+03 pdb=" C7 DCQ H 501 " -0.057 2.00e-02 2.50e+03 pdb=" O2 DCQ H 501 " -0.300 2.00e-02 2.50e+03 pdb=" O3 DCQ H 501 " 0.087 2.00e-02 2.50e+03 pdb=" O4 DCQ H 501 " 0.155 2.00e-02 2.50e+03 pdb=" O5 DCQ H 501 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 DCQ 4 501 " -0.047 2.00e-02 2.50e+03 8.20e-02 2.02e+02 pdb=" C1M DCQ 4 501 " -0.171 2.00e-02 2.50e+03 pdb=" C2 DCQ 4 501 " 0.024 2.00e-02 2.50e+03 pdb=" C3 DCQ 4 501 " 0.035 2.00e-02 2.50e+03 pdb=" C4 DCQ 4 501 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DCQ 4 501 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DCQ 4 501 " 0.055 2.00e-02 2.50e+03 pdb=" C7 DCQ 4 501 " 0.166 2.00e-02 2.50e+03 pdb=" O2 DCQ 4 501 " 0.067 2.00e-02 2.50e+03 pdb=" O3 DCQ 4 501 " 0.006 2.00e-02 2.50e+03 pdb=" O4 DCQ 4 501 " -0.030 2.00e-02 2.50e+03 pdb=" O5 DCQ 4 501 " -0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 9 40 " 0.024 2.00e-02 2.50e+03 3.01e-02 1.82e+01 pdb=" CG TYR 9 40 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR 9 40 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR 9 40 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR 9 40 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR 9 40 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR 9 40 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR 9 40 " 0.002 2.00e-02 2.50e+03 ... (remaining 11746 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.80: 18039 2.80 - 3.39: 72917 3.39 - 3.97: 140335 3.97 - 4.56: 198407 4.56 - 5.14: 289806 Nonbonded interactions: 719504 Sorted by model distance: nonbonded pdb=" NH1 ARG 6 81 " pdb=" O LYS A 33 " model vdw 2.216 2.520 nonbonded pdb=" OE2 GLU 4 224 " pdb=" OH TYR 9 40 " model vdw 2.220 2.440 nonbonded pdb=" OH TYR k 108 " pdb=" O LEU k 164 " model vdw 2.230 2.440 nonbonded pdb=" O PHE M 105 " pdb=" OG1 THR M 109 " model vdw 2.234 2.440 nonbonded pdb=" OH TYR H 114 " pdb=" O LEU J 61 " model vdw 2.239 2.440 ... (remaining 719499 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 'X' and resid 5 through 86) selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 1 8.98 5 Fe 28 7.16 5 Zn 1 6.06 5 P 44 5.49 5 S 468 5.16 5 C 44006 2.51 5 N 11233 2.21 5 O 12186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 6.750 Check model and map are aligned: 0.720 Process input model: 152.720 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Set scattering table: 0.460 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 165.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 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 0.242 69654 Z= 0.490 Angle : 1.018 47.692 94166 Z= 0.535 Chirality : 1.023 21.187 10190 Planarity : 0.008 0.141 11749 Dihedral : 11.689 171.206 26452 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.19 % Favored : 95.80 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.11 (0.08), residues: 8122 helix: -2.08 (0.06), residues: 4211 sheet: -1.89 (0.23), residues: 369 loop : -1.89 (0.09), residues: 3542 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2012 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 2005 time to evaluate : 5.986 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 outliers start: 7 outliers final: 2 residues processed: 2011 average time/residue: 0.7748 time to fit residues: 2552.3227 Evaluate side-chains 1190 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1188 time to evaluate : 5.933 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5072 time to fit residues: 10.0384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 677 optimal weight: 20.0000 chunk 607 optimal weight: 5.9990 chunk 337 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 410 optimal weight: 4.9990 chunk 324 optimal weight: 8.9990 chunk 628 optimal weight: 20.0000 chunk 243 optimal weight: 8.9990 chunk 382 optimal weight: 10.0000 chunk 467 optimal weight: 0.0770 chunk 728 optimal weight: 8.9990 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 148 ASN 1 250 ASN 1 373 ASN 2 99 HIS 2 101 GLN ** 2 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 179 ASN ** 3 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 401 HIS 3 444 GLN ** 3 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 98 GLN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 252 ASN 5 87 GLN 5 95 ASN 5 160 HIS 5 211 GLN 9 65 HIS ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 GLN H 235 ASN H 287 HIS ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 HIS ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 210 ASN L 348 HIS L 446 ASN ** L 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 HIS M 169 ASN M 279 GLN N 144 GLN Y 103 GLN ** Z 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 55 ASN ** b 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 37 HIS d 87 HIS ** d 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 216 ASN d 288 HIS e 72 GLN e 85 GLN f 49 GLN f 70 GLN g 25 ASN g 125 HIS ** k 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 141 GLN k 180 GLN l 6 GLN m 45 ASN o 61 GLN p 49 GLN ** r 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 13 GLN t 50 HIS u 58 GLN v 87 ASN v 155 HIS z 31 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.264 69654 Z= 0.569 Angle : 1.577 51.304 94166 Z= 1.017 Chirality : 0.306 6.407 10190 Planarity : 0.005 0.059 11749 Dihedral : 11.051 170.263 10189 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.26 % Favored : 96.72 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.09), residues: 8122 helix: -0.42 (0.07), residues: 4253 sheet: -1.51 (0.23), residues: 392 loop : -1.31 (0.10), residues: 3477 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1393 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1277 time to evaluate : 6.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 116 outliers final: 72 residues processed: 1342 average time/residue: 0.6785 time to fit residues: 1547.7675 Evaluate side-chains 1216 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 1144 time to evaluate : 6.800 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 0 residues processed: 72 average time/residue: 0.5376 time to fit residues: 81.1373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 404 optimal weight: 0.9980 chunk 226 optimal weight: 10.0000 chunk 606 optimal weight: 10.0000 chunk 495 optimal weight: 9.9990 chunk 200 optimal weight: 3.9990 chunk 729 optimal weight: 8.9990 chunk 788 optimal weight: 20.0000 chunk 649 optimal weight: 7.9990 chunk 723 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 585 optimal weight: 10.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 546 GLN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 69 ASN H 235 ASN H 287 HIS ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 HIS K 50 ASN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 270 ASN L 570 GLN N 144 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 103 GLN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 139 GLN ** b 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 44 ASN d 184 ASN e 72 GLN f 70 GLN ** k 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 287 HIS ** p 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 13 GLN u 58 GLN v 66 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.244 69654 Z= 0.560 Angle : 1.565 50.742 94166 Z= 1.011 Chirality : 0.309 6.546 10190 Planarity : 0.005 0.055 11749 Dihedral : 10.517 170.094 10189 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.67 % Favored : 96.32 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.56 (0.09), residues: 8122 helix: 0.29 (0.08), residues: 4268 sheet: -1.25 (0.24), residues: 389 loop : -1.01 (0.10), residues: 3465 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1298 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1209 time to evaluate : 6.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 29 residues processed: 1260 average time/residue: 0.6977 time to fit residues: 1488.7164 Evaluate side-chains 1152 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1123 time to evaluate : 5.916 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.5649 time to fit residues: 38.4698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 720 optimal weight: 0.8980 chunk 548 optimal weight: 10.0000 chunk 378 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 348 optimal weight: 30.0000 chunk 489 optimal weight: 20.0000 chunk 732 optimal weight: 20.0000 chunk 775 optimal weight: 20.0000 chunk 382 optimal weight: 9.9990 chunk 693 optimal weight: 4.9990 chunk 208 optimal weight: 9.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 437 HIS ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 287 HIS H 292 ASN ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 ASN L 170 GLN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 333 ASN N 144 GLN N 235 ASN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 103 GLN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 139 GLN ** b 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 243 GLN e 85 GLN f 70 GLN ** k 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 184 GLN l 96 HIS ** p 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 23 ASN r 12 GLN r 13 GLN s 43 GLN ** t 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 24 GLN ** y 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 40 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.245 69654 Z= 0.563 Angle : 1.562 50.694 94166 Z= 1.010 Chirality : 0.309 6.456 10190 Planarity : 0.004 0.054 11749 Dihedral : 10.266 169.939 10189 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.64 % Favored : 96.34 % Rotamer Outliers : 1.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.17 (0.09), residues: 8122 helix: 0.61 (0.08), residues: 4276 sheet: -1.21 (0.24), residues: 392 loop : -0.82 (0.11), residues: 3454 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1288 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 1166 time to evaluate : 5.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 122 outliers final: 63 residues processed: 1233 average time/residue: 0.6947 time to fit residues: 1455.8593 Evaluate side-chains 1164 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1101 time to evaluate : 5.945 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.5477 time to fit residues: 72.4418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 645 optimal weight: 6.9990 chunk 440 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 chunk 577 optimal weight: 8.9990 chunk 319 optimal weight: 5.9990 chunk 661 optimal weight: 20.0000 chunk 535 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 395 optimal weight: 10.0000 chunk 695 optimal weight: 9.9990 chunk 195 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 27 ASN ** 2 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN H 287 HIS ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 ASN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 15 GLN Y 103 GLN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 72 GLN f 70 GLN o 46 ASN o 61 GLN p 49 GLN ** p 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 12 GLN ** t 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.242 69654 Z= 0.563 Angle : 1.561 50.864 94166 Z= 1.010 Chirality : 0.309 6.443 10190 Planarity : 0.004 0.054 11749 Dihedral : 10.080 169.426 10189 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.69 % Favored : 96.29 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.04 (0.09), residues: 8122 helix: 0.77 (0.08), residues: 4273 sheet: -1.04 (0.24), residues: 398 loop : -0.71 (0.11), residues: 3451 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1236 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 1159 time to evaluate : 6.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 30 residues processed: 1197 average time/residue: 0.7014 time to fit residues: 1423.4614 Evaluate side-chains 1132 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1102 time to evaluate : 5.981 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.5249 time to fit residues: 38.1990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 260 optimal weight: 9.9990 chunk 698 optimal weight: 8.9990 chunk 153 optimal weight: 9.9990 chunk 455 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 775 optimal weight: 40.0000 chunk 644 optimal weight: 5.9990 chunk 359 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 256 optimal weight: 6.9990 chunk 407 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 444 GLN 3 499 GLN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 26 GLN H 230 ASN H 287 HIS ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 ASN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 184 GLN N 235 ASN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 243 GLN f 70 GLN ** p 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 23 ASN r 82 HIS ** t 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.242 69654 Z= 0.564 Angle : 1.561 50.808 94166 Z= 1.010 Chirality : 0.309 6.404 10190 Planarity : 0.004 0.050 11749 Dihedral : 9.979 169.347 10189 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.60 % Favored : 96.39 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.15 (0.09), residues: 8122 helix: 0.85 (0.08), residues: 4284 sheet: -0.93 (0.25), residues: 392 loop : -0.64 (0.11), residues: 3446 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1208 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1128 time to evaluate : 6.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 45 residues processed: 1173 average time/residue: 0.6999 time to fit residues: 1388.5007 Evaluate side-chains 1146 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1101 time to evaluate : 6.002 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.5481 time to fit residues: 54.1053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 748 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 442 optimal weight: 5.9990 chunk 566 optimal weight: 7.9990 chunk 439 optimal weight: 10.0000 chunk 653 optimal weight: 6.9990 chunk 433 optimal weight: 9.9990 chunk 772 optimal weight: 20.0000 chunk 483 optimal weight: 9.9990 chunk 471 optimal weight: 30.0000 chunk 356 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 250 ASN ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 144 ASN H 287 HIS ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 HIS ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 446 ASN ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 63 GLN N 235 ASN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 103 GLN Z 58 ASN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 72 GLN f 70 GLN g 94 ASN ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 23 ASN t 74 GLN ** y 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.239 69654 Z= 0.601 Angle : 1.578 50.829 94166 Z= 1.016 Chirality : 0.310 6.446 10190 Planarity : 0.005 0.053 11749 Dihedral : 10.120 169.572 10189 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.10 % Favored : 95.89 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.09 (0.09), residues: 8122 helix: 0.76 (0.08), residues: 4303 sheet: -0.93 (0.25), residues: 385 loop : -0.62 (0.11), residues: 3434 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1164 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 1099 time to evaluate : 6.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 30 residues processed: 1134 average time/residue: 0.7366 time to fit residues: 1423.7800 Evaluate side-chains 1102 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1072 time to evaluate : 5.973 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.5819 time to fit residues: 40.0608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 478 optimal weight: 9.9990 chunk 308 optimal weight: 10.0000 chunk 461 optimal weight: 8.9990 chunk 232 optimal weight: 0.9990 chunk 151 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 chunk 491 optimal weight: 20.0000 chunk 526 optimal weight: 5.9990 chunk 382 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 607 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 499 GLN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 134 GLN N 235 ASN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 36 HIS f 70 GLN ** p 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 43 GLN t 74 GLN ** y 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 68 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.243 69654 Z= 0.554 Angle : 1.558 50.826 94166 Z= 1.009 Chirality : 0.309 6.423 10190 Planarity : 0.004 0.055 11749 Dihedral : 9.902 169.652 10189 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.77 % Favored : 96.22 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.25 (0.09), residues: 8122 helix: 0.89 (0.08), residues: 4295 sheet: -0.92 (0.25), residues: 396 loop : -0.53 (0.11), residues: 3431 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1160 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1117 time to evaluate : 6.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 18 residues processed: 1136 average time/residue: 0.7043 time to fit residues: 1354.9541 Evaluate side-chains 1107 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1089 time to evaluate : 6.137 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.5628 time to fit residues: 27.0582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 703 optimal weight: 8.9990 chunk 740 optimal weight: 9.9990 chunk 675 optimal weight: 20.0000 chunk 720 optimal weight: 7.9990 chunk 433 optimal weight: 0.9990 chunk 313 optimal weight: 6.9990 chunk 565 optimal weight: 0.9980 chunk 221 optimal weight: 7.9990 chunk 650 optimal weight: 6.9990 chunk 681 optimal weight: 8.9990 chunk 717 optimal weight: 9.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 26 GLN H 230 ASN ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 103 GLN Z 58 ASN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 70 GLN g 94 ASN ** p 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 23 ASN s 43 GLN t 74 GLN u 24 GLN ** y 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.243 69654 Z= 0.557 Angle : 1.562 50.800 94166 Z= 1.010 Chirality : 0.309 6.407 10190 Planarity : 0.004 0.054 11749 Dihedral : 9.823 170.043 10189 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.87 % Favored : 96.12 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.30 (0.09), residues: 8122 helix: 0.92 (0.08), residues: 4292 sheet: -0.87 (0.25), residues: 396 loop : -0.49 (0.11), residues: 3434 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1128 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1097 time to evaluate : 6.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 15 residues processed: 1108 average time/residue: 0.7179 time to fit residues: 1350.0081 Evaluate side-chains 1086 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1071 time to evaluate : 6.013 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.5372 time to fit residues: 23.4595 ------------------------------------------------------------------------------- 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-dev-4877/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.9145 > 50: distance: 22 - 27: 29.366 distance: 27 - 28: 43.057 distance: 28 - 29: 45.190 distance: 29 - 30: 43.785 distance: 29 - 34: 44.208 distance: 31 - 32: 40.379 distance: 34 - 35: 57.412 distance: 35 - 36: 48.652 distance: 36 - 37: 25.324 distance: 36 - 41: 47.187 distance: 38 - 39: 40.309 distance: 38 - 40: 39.662 distance: 41 - 42: 41.365 distance: 42 - 43: 57.314 distance: 42 - 45: 40.740 distance: 43 - 44: 55.377 distance: 43 - 49: 56.997 distance: 44 - 69: 41.019 distance: 45 - 46: 39.955 distance: 46 - 48: 40.283 distance: 49 - 50: 40.951 distance: 50 - 51: 57.551 distance: 50 - 53: 55.869 distance: 51 - 52: 40.434 distance: 51 - 58: 38.779 distance: 52 - 78: 25.837 distance: 53 - 54: 40.865 distance: 55 - 56: 36.418 distance: 55 - 57: 4.429 distance: 65 - 66: 40.094 distance: 65 - 69: 40.252 distance: 67 - 68: 39.515 distance: 69 - 70: 41.425 distance: 70 - 71: 39.627 distance: 70 - 73: 57.237 distance: 71 - 72: 56.932 distance: 71 - 78: 12.133 distance: 73 - 74: 56.376 distance: 78 - 79: 47.157 distance: 79 - 80: 55.741 distance: 79 - 82: 40.378 distance: 80 - 81: 55.798 distance: 80 - 87: 54.494 distance: 83 - 84: 40.889 distance: 84 - 85: 56.486 distance: 85 - 86: 55.908 distance: 87 - 88: 36.275 distance: 88 - 89: 41.330 distance: 88 - 91: 55.998 distance: 89 - 90: 11.503 distance: 91 - 92: 41.392 distance: 94 - 95: 39.741 distance: 95 - 96: 40.949 distance: 96 - 98: 34.238