Starting phenix.real_space_refine (version: dev) on Thu Feb 23 12:31:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfs_4874/02_2023/6rfs_4874_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfs_4874/02_2023/6rfs_4874.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfs_4874/02_2023/6rfs_4874_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfs_4874/02_2023/6rfs_4874_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfs_4874/02_2023/6rfs_4874_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfs_4874/02_2023/6rfs_4874.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfs_4874/02_2023/6rfs_4874.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfs_4874/02_2023/6rfs_4874_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfs_4874/02_2023/6rfs_4874_updated.pdb" } resolution = 4.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 "A ARG 67": "NH1" <-> "NH2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ARG 108": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A ARG 427": "NH1" <-> "NH2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 646": "NH1" <-> "NH2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B ARG 201": "NH1" <-> "NH2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B ARG 240": "NH1" <-> "NH2" Residue "B ARG 258": "NH1" <-> "NH2" Residue "B ARG 259": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B ARG 299": "NH1" <-> "NH2" Residue "B ARG 367": "NH1" <-> "NH2" Residue "B ARG 388": "NH1" <-> "NH2" Residue "B ARG 402": "NH1" <-> "NH2" Residue "B ARG 409": "NH1" <-> "NH2" Residue "C ARG 121": "NH1" <-> "NH2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C ARG 219": "NH1" <-> "NH2" Residue "C ARG 224": "NH1" <-> "NH2" Residue "C ARG 231": "NH1" <-> "NH2" Residue "C ARG 257": "NH1" <-> "NH2" Residue "C ARG 274": "NH1" <-> "NH2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "D ARG 32": "NH1" <-> "NH2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ARG 62": "NH1" <-> "NH2" Residue "E ARG 48": "NH1" <-> "NH2" Residue "E ARG 51": "NH1" <-> "NH2" Residue "E ARG 85": "NH1" <-> "NH2" Residue "E ARG 91": "NH1" <-> "NH2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E ARG 120": "NH1" <-> "NH2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E ARG 149": "NH1" <-> "NH2" Residue "E ARG 150": "NH1" <-> "NH2" Residue "E ARG 201": "NH1" <-> "NH2" Residue "E ARG 208": "NH1" <-> "NH2" Residue "E ARG 216": "NH1" <-> "NH2" Residue "E ARG 349": "NH1" <-> "NH2" Residue "G ARG 43": "NH1" <-> "NH2" Residue "G ARG 113": "NH1" <-> "NH2" Residue "G ARG 223": "NH1" <-> "NH2" Residue "G ARG 230": "NH1" <-> "NH2" Residue "G ARG 259": "NH1" <-> "NH2" Residue "G ARG 262": "NH1" <-> "NH2" Residue "H ARG 116": "NH1" <-> "NH2" Residue "H ARG 215": "NH1" <-> "NH2" Residue "I ARG 59": "NH1" <-> "NH2" Residue "I ARG 197": "NH1" <-> "NH2" Residue "J ARG 143": "NH1" <-> "NH2" Residue "J ARG 183": "NH1" <-> "NH2" Residue "K ARG 108": "NH1" <-> "NH2" Residue "K ARG 196": "NH1" <-> "NH2" Residue "K ARG 199": "NH1" <-> "NH2" Residue "L ARG 19": "NH1" <-> "NH2" Residue "L ARG 79": "NH1" <-> "NH2" Residue "M ARG 42": "NH1" <-> "NH2" Residue "M ARG 88": "NH1" <-> "NH2" Residue "M ARG 131": "NH1" <-> "NH2" Residue "O ARG 35": "NH1" <-> "NH2" Residue "P ARG 30": "NH1" <-> "NH2" Residue "P ARG 57": "NH1" <-> "NH2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "R ARG 27": "NH1" <-> "NH2" Residue "R ARG 57": "NH1" <-> "NH2" Residue "R ARG 67": "NH1" <-> "NH2" Residue "S ARG 62": "NH1" <-> "NH2" Residue "S ARG 120": "NH1" <-> "NH2" Residue "S ARG 135": "NH1" <-> "NH2" Residue "S ARG 188": "NH1" <-> "NH2" Residue "U ARG 3": "NH1" <-> "NH2" Residue "U ARG 74": "NH1" <-> "NH2" Residue "U ARG 95": "NH1" <-> "NH2" Residue "U ARG 112": "NH1" <-> "NH2" Residue "W ARG 20": "NH1" <-> "NH2" Residue "W ARG 21": "NH1" <-> "NH2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ARG 29": "NH1" <-> "NH2" Residue "W ARG 47": "NH1" <-> "NH2" Residue "W ARG 60": "NH1" <-> "NH2" Residue "W ARG 66": "NH1" <-> "NH2" Residue "W ARG 83": "NH1" <-> "NH2" Residue "W ARG 84": "NH1" <-> "NH2" Residue "W ARG 91": "NH1" <-> "NH2" Residue "X ARG 76": "NH1" <-> "NH2" Residue "X ARG 166": "NH1" <-> "NH2" Residue "Z ARG 77": "NH1" <-> "NH2" Residue "Z ARG 80": "NH1" <-> "NH2" Residue "Z ARG 179": "NH1" <-> "NH2" Residue "a ARG 84": "NH1" <-> "NH2" Residue "a ARG 123": "NH1" <-> "NH2" Residue "b ARG 25": "NH1" <-> "NH2" Residue "c ARG 11": "NH1" <-> "NH2" Residue "c ARG 16": "NH1" <-> "NH2" Residue "c ARG 23": "NH1" <-> "NH2" Residue "c ARG 26": "NH1" <-> "NH2" Residue "d ARG 6": "NH1" <-> "NH2" Residue "d ARG 24": "NH1" <-> "NH2" Residue "d ARG 32": "NH1" <-> "NH2" Residue "d ARG 37": "NH1" <-> "NH2" Residue "d ARG 45": "NH1" <-> "NH2" Residue "e ARG 41": "NH1" <-> "NH2" Residue "f ARG 6": "NH1" <-> "NH2" Residue "f ARG 9": "NH1" <-> "NH2" Residue "f ARG 23": "NH1" <-> "NH2" Residue "f ARG 45": "NH1" <-> "NH2" Residue "f ARG 57": "NH1" <-> "NH2" Residue "f ARG 79": "NH1" <-> "NH2" Residue "g ARG 17": "NH1" <-> "NH2" Residue "g ARG 47": "NH1" <-> "NH2" Residue "g ARG 69": "NH1" <-> "NH2" Residue "h ARG 18": "NH1" <-> "NH2" Residue "h ARG 34": "NH1" <-> "NH2" Residue "h ARG 137": "NH1" <-> "NH2" Residue "i TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 53": "NH1" <-> "NH2" Residue "i ARG 55": "NH1" <-> "NH2" Residue "i ARG 75": "NH1" <-> "NH2" Residue "i ARG 77": "NH1" <-> "NH2" Residue "j ARG 34": "NH1" <-> "NH2" Residue "j ARG 39": "NH1" <-> "NH2" Residue "j ARG 50": "NH1" <-> "NH2" Residue "j ARG 92": "NH1" <-> "NH2" Residue "n TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 162": "NH1" <-> "NH2" Residue "4 ARG 353": "NH1" <-> "NH2" Residue "4 ARG 405": "NH1" <-> "NH2" Residue "4 ARG 449": "NH1" <-> "NH2" Residue "4 TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 115": "NH1" <-> "NH2" Residue "5 ARG 303": "NH1" <-> "NH2" Residue "8 ARG 37": "NH1" <-> "NH2" Residue "8 ARG 51": "NH1" <-> "NH2" Residue "8 ARG 65": "NH1" <-> "NH2" Residue "9 ARG 14": "NH1" <-> "NH2" Residue "9 ARG 58": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 60966 Number of models: 1 Model: "" Number of chains: 49 Chain: "A" Number of atoms: 5258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5258 Classifications: {'peptide': 692} Link IDs: {'PTRANS': 34, 'TRANS': 657} Chain: "B" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3528 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 22, 'TRANS': 433} Chain: "C" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3052 Classifications: {'peptide': 387} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 365} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 682 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "E" Number of atoms: 2650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2650 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 15, 'TRANS': 315} Chain: "F" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 990 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "G" Number of atoms: 1978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1978 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 18, 'TRANS': 220} Chain: "H" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1664 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 194} Chain: "I" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1519 Classifications: {'peptide': 190} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 177} Chain: "J" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 790 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain breaks: 2 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 58 Chain: "K" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 155} Chain: "L" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 645 Classifications: {'peptide': 83} Link IDs: {'TRANS': 82} Chain: "M" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 912 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 9, 'TRANS': 107} Chain: "O" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 591 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "P" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1037 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 648 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "R" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 885 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 95} Chain: "S" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1430 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain breaks: 2 Chain: "U" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1346 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "W" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 974 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 9, 'TRANS': 111} Chain: "X" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1300 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 155} Chain: "Z" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 160} Chain: "a" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1030 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 10, 'TRANS': 113} Chain: "b" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 490 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "c" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 353 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain: "d" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 761 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain: "e" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 436 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 6, 'TRANS': 45} Chain: "f" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 629 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "g" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 617 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 10, 'TRANS': 65} Chain: "h" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1130 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 10, 'TRANS': 125} Chain: "i" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 646 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "j" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 724 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain: "n" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 904 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 9, 'TRANS': 103} Chain: "1" Number of atoms: 2682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2682 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 14, 'TRANS': 325} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "2" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3775 Classifications: {'peptide': 469} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 461} Chain: "3" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 911 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "4" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3856 Classifications: {'peptide': 486} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 471} Chain: "5" Number of atoms: 4954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 632, 4954 Classifications: {'peptide': 632} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 14, 'TRANS': 617} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "6" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1096 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain breaks: 1 Chain: "8" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 662 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "9" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 528 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 809 SG CYS A 142 63.314 149.558 160.158 1.00109.75 S ATOM 749 SG CYS A 133 60.133 152.200 154.960 1.00106.29 S ATOM 769 SG CYS A 136 64.874 155.068 159.060 1.00102.62 S ATOM 1163 SG CYS A 186 62.703 151.192 170.969 1.00106.43 S ATOM 1139 SG CYS A 183 60.094 156.524 169.532 1.00108.67 S ATOM 1187 SG CYS A 189 64.484 156.005 174.071 1.00112.32 S ATOM 1511 SG CYS A 233 65.117 154.352 167.569 1.00108.79 S ATOM 255 SG CYS A 69 59.678 145.809 174.514 1.00119.79 S ATOM 338 SG CYS A 80 58.543 143.402 172.111 1.00115.39 S ATOM 363 SG CYS A 83 58.419 138.877 174.212 1.00131.04 S ATOM 465 SG CYS A 97 59.011 140.789 177.092 1.00140.11 S ATOM 7999 SG CYS B 384 49.786 146.772 176.305 1.00125.98 S ATOM 8019 SG CYS B 387 45.450 150.681 175.088 1.00121.90 S ATOM 7980 SG CYS B 381 50.108 152.417 179.655 1.00115.18 S ATOM 8350 SG CYS B 427 46.124 148.141 180.853 1.00120.65 S ATOM 18930 SG CYS H 127 31.485 163.936 181.210 1.00165.64 S ATOM 18964 SG CYS H 132 28.331 163.584 182.338 1.00160.42 S ATOM 19233 SG CYS H 168 31.692 159.376 184.456 1.00183.67 S ATOM 19256 SG CYS H 172 29.742 158.669 185.515 1.00201.21 S ATOM 20859 SG CYS I 172 67.610 148.097 134.305 1.00 96.41 S ATOM 20833 SG CYS I 169 70.912 152.675 131.127 1.00105.74 S ATOM 20881 SG CYS I 175 67.037 153.094 135.239 1.00 89.45 S ATOM 20606 SG CYS I 140 72.411 149.637 136.402 1.00 88.82 S ATOM 20911 SG CYS I 179 63.036 157.980 142.341 1.00 91.70 S ATOM 20578 SG CYS I 136 69.474 155.364 141.816 1.00 91.83 S ATOM 20536 SG CYS I 130 68.087 160.928 142.944 1.00100.72 S ATOM 20555 SG CYS I 133 66.203 155.490 146.133 1.00 93.20 S ATOM 22969 SG CYS K 150 76.947 143.650 126.054 1.00109.76 S ATOM 22465 SG CYS K 86 74.228 145.211 120.452 1.00113.31 S ATOM 22459 SG CYS K 85 72.734 140.693 122.854 1.00113.04 S ATOM 23197 SG CYS K 180 72.093 145.933 126.273 1.00109.85 S ATOM 24732 SG CYS M 97 54.845 167.665 150.313 1.00127.11 S ATOM 24927 SG CYS M 125 56.931 166.676 152.582 1.00131.97 S ATOM 24954 SG CYS M 128 57.085 169.011 149.631 1.00123.17 S Time building chain proxies: 24.89, per 1000 atoms: 0.41 Number of scatterers: 60966 At special positions: 0 Unit cell: (213.64, 197.29, 231.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 298 16.00 P 5 15.00 O 11073 8.00 N 10169 7.00 C 39392 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS U 46 " - pdb=" SG CYS U 78 " distance=2.03 Simple disulfide: pdb=" SG CYS U 56 " - pdb=" SG CYS U 68 " distance=2.07 Simple disulfide: pdb=" SG CYS U 90 " - pdb=" SG CYS U 121 " distance=2.05 Simple disulfide: pdb=" SG CYS U 100 " - pdb=" SG CYS U 111 " distance=2.04 Simple disulfide: pdb=" SG CYS d 51 " - pdb=" SG CYS d 63 " distance=2.03 Simple disulfide: pdb=" SG CYS 8 26 " - pdb=" SG CYS 8 57 " distance=2.03 Simple disulfide: pdb=" SG CYS 8 36 " - pdb=" SG CYS 8 47 " distance=2.03 Simple disulfide: pdb=" SG CYS 9 15 " - pdb=" SG CYS 9 47 " distance=2.00 Simple disulfide: pdb=" SG CYS 9 25 " - pdb=" SG CYS 9 37 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.00 Conformation dependent library (CDL) restraints added in 7.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 803 " pdb="FE2 FES A 803 " - pdb=" SG CYS A 83 " pdb="FE1 FES A 803 " - pdb=" SG CYS A 69 " pdb="FE1 FES A 803 " - pdb=" SG CYS A 80 " pdb="FE2 FES A 803 " - pdb=" SG CYS A 97 " pdb=" FES H 301 " pdb="FE1 FES H 301 " - pdb=" SG CYS H 127 " pdb="FE2 FES H 301 " - pdb=" SG CYS H 172 " pdb="FE2 FES H 301 " - pdb=" SG CYS H 168 " pdb="FE1 FES H 301 " - pdb=" SG CYS H 132 " pdb=" SF4 A 801 " pdb="FE3 SF4 A 801 " - pdb=" NE2 HIS A 129 " pdb="FE4 SF4 A 801 " - pdb=" SG CYS A 136 " pdb="FE2 SF4 A 801 " - pdb=" SG CYS A 133 " pdb="FE1 SF4 A 801 " - pdb=" SG CYS A 142 " pdb=" SF4 A 802 " pdb="FE3 SF4 A 802 " - pdb=" SG CYS A 189 " pdb="FE1 SF4 A 802 " - pdb=" SG CYS A 186 " pdb="FE2 SF4 A 802 " - pdb=" SG CYS A 183 " pdb="FE4 SF4 A 802 " - pdb=" SG CYS A 233 " pdb=" SF4 B 501 " pdb="FE2 SF4 B 501 " - pdb=" SG CYS B 387 " pdb="FE4 SF4 B 501 " - pdb=" SG CYS B 427 " pdb="FE3 SF4 B 501 " - pdb=" SG CYS B 381 " pdb="FE1 SF4 B 501 " - pdb=" SG CYS B 384 " pdb=" SF4 I 301 " pdb="FE3 SF4 I 301 " - pdb=" SG CYS I 175 " pdb="FE2 SF4 I 301 " - pdb=" SG CYS I 169 " pdb="FE4 SF4 I 301 " - pdb=" SG CYS I 140 " pdb="FE1 SF4 I 301 " - pdb=" SG CYS I 172 " pdb="FE2 SF4 I 301 " - pdb=" NE2 HIS I 118 " pdb=" SF4 I 302 " pdb="FE3 SF4 I 302 " - pdb=" SG CYS I 130 " pdb="FE4 SF4 I 302 " - pdb=" SG CYS I 133 " pdb="FE2 SF4 I 302 " - pdb=" SG CYS I 136 " pdb="FE1 SF4 I 302 " - pdb=" SG CYS I 179 " pdb=" SF4 K 301 " pdb="FE2 SF4 K 301 " - pdb=" SG CYS K 86 " pdb="FE1 SF4 K 301 " - pdb=" SG CYS K 150 " pdb="FE4 SF4 K 301 " - pdb=" SG CYS K 180 " pdb="FE3 SF4 K 301 " - pdb=" SG CYS K 85 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" NE2 HIS M 110 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 97 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 125 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 128 " Number of angles added : 3 15174 Ramachandran restraints generated. 7587 Oldfield, 0 Emsley, 7587 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14366 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 308 helices and 27 sheets defined 49.6% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.75 Creating SS restraints... Processing helix chain 'A' and resid 54 through 61 Processing helix chain 'A' and resid 112 through 127 removed outlier: 3.753A pdb=" N GLU A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 150 removed outlier: 3.645A pdb=" N ARG A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 188 through 195 removed outlier: 3.720A pdb=" N PHE A 192 " --> pdb=" O ARG A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 295 through 301 removed outlier: 5.685A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 325 through 339 removed outlier: 3.899A pdb=" N LEU A 329 " --> pdb=" O TRP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 369 removed outlier: 3.676A pdb=" N ALA A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 422 through 434 Processing helix chain 'A' and resid 459 through 466 Processing helix chain 'A' and resid 470 through 476 removed outlier: 3.635A pdb=" N LYS A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 489 Processing helix chain 'A' and resid 492 through 507 removed outlier: 4.558A pdb=" N GLY A 495 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA A 496 " --> pdb=" O ASP A 493 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR A 500 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY A 502 " --> pdb=" O ASN A 499 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL A 505 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 578 through 581 No H-bonds generated for 'chain 'A' and resid 578 through 581' Processing helix chain 'A' and resid 622 through 632 removed outlier: 3.542A pdb=" N ALA A 628 " --> pdb=" O LYS A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 652 Processing helix chain 'A' and resid 669 through 678 removed outlier: 3.705A pdb=" N GLY A 678 " --> pdb=" O HIS A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 717 removed outlier: 3.609A pdb=" N ALA A 716 " --> pdb=" O LYS A 712 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A 717 " --> pdb=" O SER A 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 58 Processing helix chain 'B' and resid 64 through 69 Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 107 through 109 No H-bonds generated for 'chain 'B' and resid 107 through 109' Processing helix chain 'B' and resid 128 through 133 removed outlier: 3.595A pdb=" N MET B 133 " --> pdb=" O ASP B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 148 removed outlier: 4.018A pdb=" N LEU B 145 " --> pdb=" O VAL B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 180 removed outlier: 3.804A pdb=" N VAL B 170 " --> pdb=" O ASN B 166 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN B 172 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'B' and resid 206 through 209 Processing helix chain 'B' and resid 211 through 219 removed outlier: 3.629A pdb=" N ILE B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 239 No H-bonds generated for 'chain 'B' and resid 237 through 239' Processing helix chain 'B' and resid 247 through 251 Processing helix chain 'B' and resid 253 through 258 Processing helix chain 'B' and resid 261 through 264 No H-bonds generated for 'chain 'B' and resid 261 through 264' Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.530A pdb=" N LYS B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 334 No H-bonds generated for 'chain 'B' and resid 331 through 334' Processing helix chain 'B' and resid 342 through 346 Processing helix chain 'B' and resid 365 through 379 removed outlier: 3.753A pdb=" N PHE B 372 " --> pdb=" O ALA B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 403 removed outlier: 4.054A pdb=" N THR B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS B 396 " --> pdb=" O THR B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 422 removed outlier: 3.887A pdb=" N ILE B 411 " --> pdb=" O GLU B 408 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU B 422 " --> pdb=" O LYS B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 443 removed outlier: 3.628A pdb=" N TRP B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) Proline residue: B 436 - end of helix removed outlier: 3.673A pdb=" N LEU B 440 " --> pdb=" O PRO B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 458 removed outlier: 3.548A pdb=" N GLU B 449 " --> pdb=" O ARG B 445 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG B 451 " --> pdb=" O GLU B 447 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP B 457 " --> pdb=" O LYS B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'C' and resid 123 through 127 Processing helix chain 'C' and resid 134 through 138 Proline residue: C 137 - end of helix No H-bonds generated for 'chain 'C' and resid 134 through 138' Processing helix chain 'C' and resid 147 through 162 Processing helix chain 'C' and resid 168 through 197 removed outlier: 3.580A pdb=" N ARG C 182 " --> pdb=" O GLY C 178 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 220 removed outlier: 3.584A pdb=" N LEU C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE C 207 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU C 209 " --> pdb=" O TRP C 205 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL C 220 " --> pdb=" O PHE C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 264 removed outlier: 4.127A pdb=" N TYR C 248 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET C 249 " --> pdb=" O ASP C 245 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN C 253 " --> pdb=" O MET C 249 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASP C 256 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE C 261 " --> pdb=" O ARG C 257 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 274 Processing helix chain 'C' and resid 283 through 288 Processing helix chain 'C' and resid 293 through 299 Processing helix chain 'C' and resid 329 through 351 removed outlier: 4.045A pdb=" N ARG C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE C 340 " --> pdb=" O ARG C 336 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG C 341 " --> pdb=" O MET C 337 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG C 345 " --> pdb=" O ARG C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 389 removed outlier: 3.858A pdb=" N ILE C 382 " --> pdb=" O MET C 378 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR C 388 " --> pdb=" O HIS C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 436 removed outlier: 3.752A pdb=" N HIS C 434 " --> pdb=" O PRO C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 441 No H-bonds generated for 'chain 'C' and resid 438 through 441' Processing helix chain 'C' and resid 449 through 452 No H-bonds generated for 'chain 'C' and resid 449 through 452' Processing helix chain 'C' and resid 454 through 457 No H-bonds generated for 'chain 'C' and resid 454 through 457' Processing helix chain 'D' and resid 5 through 33 Proline residue: D 10 - end of helix removed outlier: 3.550A pdb=" N THR D 19 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N HIS D 29 " --> pdb=" O MET D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 57 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'E' and resid 64 through 75 removed outlier: 4.053A pdb=" N TYR E 68 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS E 72 " --> pdb=" O TYR E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 96 removed outlier: 4.901A pdb=" N VAL E 95 " --> pdb=" O HIS E 92 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR E 96 " --> pdb=" O LEU E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 119 removed outlier: 3.630A pdb=" N VAL E 119 " --> pdb=" O ILE E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 143 No H-bonds generated for 'chain 'E' and resid 140 through 143' Processing helix chain 'E' and resid 146 through 158 removed outlier: 4.018A pdb=" N ALA E 154 " --> pdb=" O ARG E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 192 removed outlier: 3.861A pdb=" N GLY E 184 " --> pdb=" O ASN E 180 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU E 185 " --> pdb=" O HIS E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 218 No H-bonds generated for 'chain 'E' and resid 215 through 218' Processing helix chain 'E' and resid 238 through 250 removed outlier: 3.915A pdb=" N PHE E 250 " --> pdb=" O GLU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 280 removed outlier: 3.842A pdb=" N THR E 279 " --> pdb=" O MET E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 303 removed outlier: 3.891A pdb=" N ALA E 296 " --> pdb=" O ALA E 292 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR E 297 " --> pdb=" O LEU E 293 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR E 298 " --> pdb=" O TYR E 294 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA E 300 " --> pdb=" O ALA E 296 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR E 301 " --> pdb=" O TYR E 297 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLN E 302 " --> pdb=" O THR E 298 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ALA E 303 " --> pdb=" O LYS E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 317 removed outlier: 3.755A pdb=" N GLN E 317 " --> pdb=" O GLN E 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 313 through 317' Processing helix chain 'E' and resid 330 through 332 No H-bonds generated for 'chain 'E' and resid 330 through 332' Processing helix chain 'E' and resid 340 through 342 No H-bonds generated for 'chain 'E' and resid 340 through 342' Processing helix chain 'E' and resid 344 through 347 No H-bonds generated for 'chain 'E' and resid 344 through 347' Processing helix chain 'F' and resid 42 through 60 removed outlier: 3.651A pdb=" N THR F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN F 58 " --> pdb=" O LEU F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 84 removed outlier: 3.643A pdb=" N ASN F 73 " --> pdb=" O GLN F 69 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE F 81 " --> pdb=" O HIS F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 95 removed outlier: 3.941A pdb=" N GLU F 92 " --> pdb=" O SER F 88 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASN F 93 " --> pdb=" O GLU F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 120 removed outlier: 3.580A pdb=" N LYS F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 38 No H-bonds generated for 'chain 'G' and resid 36 through 38' Processing helix chain 'G' and resid 62 through 81 removed outlier: 4.305A pdb=" N GLN G 66 " --> pdb=" O ASP G 62 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N HIS G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN G 73 " --> pdb=" O SER G 69 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR G 74 " --> pdb=" O ASP G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 114 removed outlier: 3.999A pdb=" N VAL G 105 " --> pdb=" O PRO G 102 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE G 106 " --> pdb=" O SER G 103 " (cutoff:3.500A) Proline residue: G 107 - end of helix removed outlier: 4.099A pdb=" N THR G 110 " --> pdb=" O PRO G 107 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU G 112 " --> pdb=" O THR G 109 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP G 114 " --> pdb=" O PHE G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 170 No H-bonds generated for 'chain 'G' and resid 168 through 170' Processing helix chain 'G' and resid 174 through 186 removed outlier: 3.856A pdb=" N GLU G 179 " --> pdb=" O ASN G 176 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA G 182 " --> pdb=" O GLU G 179 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR G 183 " --> pdb=" O ARG G 180 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N MET G 185 " --> pdb=" O ALA G 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 61 removed outlier: 3.636A pdb=" N ALA H 60 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS H 61 " --> pdb=" O GLU H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 81 removed outlier: 3.985A pdb=" N ALA H 70 " --> pdb=" O LYS H 67 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N MET H 72 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Proline residue: H 73 - end of helix Processing helix chain 'H' and resid 87 through 96 Processing helix chain 'H' and resid 101 through 110 Processing helix chain 'H' and resid 130 through 134 Processing helix chain 'H' and resid 137 through 147 Processing helix chain 'H' and resid 190 through 202 removed outlier: 3.572A pdb=" N VAL H 194 " --> pdb=" O PRO H 190 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS H 195 " --> pdb=" O GLU H 191 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU H 196 " --> pdb=" O GLY H 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 78 removed outlier: 3.520A pdb=" N LYS I 76 " --> pdb=" O SER I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 95 removed outlier: 3.895A pdb=" N GLY I 86 " --> pdb=" O GLU I 82 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE I 95 " --> pdb=" O LEU I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 138 No H-bonds generated for 'chain 'I' and resid 135 through 138' Processing helix chain 'I' and resid 174 through 177 No H-bonds generated for 'chain 'I' and resid 174 through 177' Processing helix chain 'I' and resid 198 through 200 No H-bonds generated for 'chain 'I' and resid 198 through 200' Processing helix chain 'I' and resid 204 through 225 removed outlier: 3.610A pdb=" N GLU I 215 " --> pdb=" O GLY I 211 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEU I 216 " --> pdb=" O ASP I 212 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N GLU I 217 " --> pdb=" O LYS I 213 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA I 224 " --> pdb=" O TYR I 220 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 81 removed outlier: 3.658A pdb=" N ARG J 73 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU J 74 " --> pdb=" O ASN J 71 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ARG J 75 " --> pdb=" O LEU J 72 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS J 76 " --> pdb=" O ARG J 73 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY J 78 " --> pdb=" O ARG J 75 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N HIS J 81 " --> pdb=" O GLY J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 109 removed outlier: 3.674A pdb=" N THR J 99 " --> pdb=" O ALA J 95 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY J 100 " --> pdb=" O GLY J 96 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR J 107 " --> pdb=" O LEU J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 119 through 122 No H-bonds generated for 'chain 'J' and resid 119 through 122' Processing helix chain 'J' and resid 124 through 134 Processing helix chain 'J' and resid 147 through 149 No H-bonds generated for 'chain 'J' and resid 147 through 149' Processing helix chain 'J' and resid 172 through 179 removed outlier: 3.575A pdb=" N GLU J 177 " --> pdb=" O SER J 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 74 Processing helix chain 'K' and resid 88 through 94 Processing helix chain 'K' and resid 128 through 136 Processing helix chain 'K' and resid 155 through 157 No H-bonds generated for 'chain 'K' and resid 155 through 157' Processing helix chain 'K' and resid 167 through 169 No H-bonds generated for 'chain 'K' and resid 167 through 169' Processing helix chain 'K' and resid 184 through 199 Processing helix chain 'L' and resid 2 through 16 Processing helix chain 'L' and resid 22 through 46 removed outlier: 3.563A pdb=" N PHE L 26 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN L 37 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG L 42 " --> pdb=" O LEU L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 79 removed outlier: 3.603A pdb=" N VAL L 58 " --> pdb=" O LEU L 54 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU L 71 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER L 72 " --> pdb=" O ALA L 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 60 removed outlier: 3.892A pdb=" N LYS M 58 " --> pdb=" O THR M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 83 removed outlier: 3.714A pdb=" N ALA M 83 " --> pdb=" O ILE M 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 42 removed outlier: 3.833A pdb=" N SER O 42 " --> pdb=" O ALA O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 51 No H-bonds generated for 'chain 'O' and resid 49 through 51' Processing helix chain 'O' and resid 66 through 80 removed outlier: 3.908A pdb=" N VAL O 70 " --> pdb=" O SER O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 86 through 90 Processing helix chain 'O' and resid 95 through 104 removed outlier: 4.788A pdb=" N LEU O 103 " --> pdb=" O VAL O 99 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ALA O 104 " --> pdb=" O GLU O 100 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 42 Proline residue: P 37 - end of helix removed outlier: 3.621A pdb=" N ALA P 40 " --> pdb=" O ALA P 36 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP P 41 " --> pdb=" O PRO P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 62 removed outlier: 3.546A pdb=" N GLN P 58 " --> pdb=" O THR P 54 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE P 60 " --> pdb=" O ILE P 56 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 87 Processing helix chain 'P' and resid 93 through 99 removed outlier: 3.829A pdb=" N LYS P 98 " --> pdb=" O ALA P 94 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TYR P 99 " --> pdb=" O GLN P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 101 through 104 No H-bonds generated for 'chain 'P' and resid 101 through 104' Processing helix chain 'P' and resid 115 through 121 removed outlier: 4.066A pdb=" N LYS P 121 " --> pdb=" O ASP P 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 64 Processing helix chain 'Q' and resid 91 through 103 Processing helix chain 'Q' and resid 118 through 127 Processing helix chain 'R' and resid 9 through 27 Processing helix chain 'R' and resid 33 through 49 removed outlier: 3.552A pdb=" N GLU R 42 " --> pdb=" O GLN R 38 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE R 47 " --> pdb=" O ILE R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 72 removed outlier: 3.550A pdb=" N GLU R 65 " --> pdb=" O ARG R 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 54 through 65 removed outlier: 4.037A pdb=" N LYS S 60 " --> pdb=" O GLU S 56 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN S 61 " --> pdb=" O LEU S 57 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN S 65 " --> pdb=" O GLN S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 88 through 99 removed outlier: 3.936A pdb=" N GLU S 93 " --> pdb=" O ALA S 89 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ALA S 96 " --> pdb=" O ALA S 92 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU S 97 " --> pdb=" O GLU S 93 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TYR S 98 " --> pdb=" O ILE S 94 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS S 99 " --> pdb=" O ALA S 95 " (cutoff:3.500A) Processing helix chain 'S' and resid 107 through 110 Processing helix chain 'S' and resid 113 through 136 removed outlier: 4.333A pdb=" N GLY S 133 " --> pdb=" O TYR S 129 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG S 134 " --> pdb=" O TYR S 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 166 through 169 No H-bonds generated for 'chain 'S' and resid 166 through 169' Processing helix chain 'S' and resid 172 through 188 removed outlier: 3.700A pdb=" N SER S 187 " --> pdb=" O MET S 183 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG S 188 " --> pdb=" O VAL S 184 " (cutoff:3.500A) Processing helix chain 'S' and resid 191 through 206 removed outlier: 3.516A pdb=" N LEU S 204 " --> pdb=" O ASP S 200 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 Processing helix chain 'S' and resid 215 through 228 removed outlier: 4.282A pdb=" N ASP S 219 " --> pdb=" O GLU S 215 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA S 220 " --> pdb=" O ASN S 216 " (cutoff:3.500A) Processing helix chain 'S' and resid 234 through 238 Processing helix chain 'U' and resid 32 through 37 Processing helix chain 'U' and resid 39 through 45 Processing helix chain 'U' and resid 47 through 59 Processing helix chain 'U' and resid 64 through 66 No H-bonds generated for 'chain 'U' and resid 64 through 66' Processing helix chain 'U' and resid 69 through 89 removed outlier: 3.724A pdb=" N THR U 76 " --> pdb=" O GLY U 72 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG U 77 " --> pdb=" O ARG U 73 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N CYS U 78 " --> pdb=" O ARG U 74 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA U 79 " --> pdb=" O VAL U 75 " (cutoff:3.500A) Processing helix chain 'U' and resid 91 through 101 Processing helix chain 'U' and resid 104 through 106 No H-bonds generated for 'chain 'U' and resid 104 through 106' Processing helix chain 'U' and resid 108 through 110 No H-bonds generated for 'chain 'U' and resid 108 through 110' Processing helix chain 'U' and resid 112 through 124 removed outlier: 3.870A pdb=" N LEU U 117 " --> pdb=" O LYS U 113 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU U 118 " --> pdb=" O ALA U 114 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS U 120 " --> pdb=" O ALA U 116 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS U 121 " --> pdb=" O LEU U 117 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE U 123 " --> pdb=" O ASN U 119 " (cutoff:3.500A) Processing helix chain 'U' and resid 157 through 168 removed outlier: 3.764A pdb=" N ARG U 161 " --> pdb=" O PHE U 157 " (cutoff:3.500A) Processing helix chain 'W' and resid 30 through 95 removed outlier: 3.923A pdb=" N GLY W 50 " --> pdb=" O TYR W 46 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY W 51 " --> pdb=" O ARG W 47 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA W 65 " --> pdb=" O GLU W 61 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU W 69 " --> pdb=" O ALA W 65 " (cutoff:3.500A) Proline residue: W 71 - end of helix removed outlier: 3.781A pdb=" N GLU W 76 " --> pdb=" O LEU W 72 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE W 86 " --> pdb=" O VAL W 82 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 34 Processing helix chain 'X' and resid 37 through 60 removed outlier: 3.913A pdb=" N GLY X 41 " --> pdb=" O PRO X 37 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL X 42 " --> pdb=" O SER X 38 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU X 50 " --> pdb=" O ALA X 46 " (cutoff:3.500A) Proline residue: X 51 - end of helix Processing helix chain 'X' and resid 72 through 95 Processing helix chain 'X' and resid 97 through 99 No H-bonds generated for 'chain 'X' and resid 97 through 99' Processing helix chain 'X' and resid 106 through 111 Processing helix chain 'X' and resid 114 through 120 Processing helix chain 'X' and resid 133 through 143 Processing helix chain 'Z' and resid 21 through 27 removed outlier: 3.903A pdb=" N LEU Z 27 " --> pdb=" O LYS Z 23 " (cutoff:3.500A) Processing helix chain 'Z' and resid 53 through 55 No H-bonds generated for 'chain 'Z' and resid 53 through 55' Processing helix chain 'Z' and resid 64 through 67 No H-bonds generated for 'chain 'Z' and resid 64 through 67' Processing helix chain 'Z' and resid 91 through 99 removed outlier: 3.537A pdb=" N THR Z 95 " --> pdb=" O GLN Z 91 " (cutoff:3.500A) Processing helix chain 'Z' and resid 111 through 123 removed outlier: 3.643A pdb=" N THR Z 115 " --> pdb=" O GLY Z 111 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS Z 116 " --> pdb=" O GLU Z 112 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN Z 120 " --> pdb=" O LYS Z 116 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE Z 121 " --> pdb=" O ALA Z 117 " (cutoff:3.500A) Processing helix chain 'Z' and resid 128 through 134 Processing helix chain 'Z' and resid 137 through 143 Processing helix chain 'a' and resid 28 through 31 No H-bonds generated for 'chain 'a' and resid 28 through 31' Processing helix chain 'a' and resid 34 through 36 No H-bonds generated for 'chain 'a' and resid 34 through 36' Processing helix chain 'a' and resid 74 through 76 No H-bonds generated for 'chain 'a' and resid 74 through 76' Processing helix chain 'a' and resid 90 through 113 removed outlier: 3.891A pdb=" N LYS a 95 " --> pdb=" O GLN a 91 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR a 96 " --> pdb=" O ASP a 92 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA a 107 " --> pdb=" O ILE a 103 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR a 113 " --> pdb=" O TYR a 109 " (cutoff:3.500A) Processing helix chain 'a' and resid 126 through 130 Processing helix chain 'a' and resid 141 through 143 No H-bonds generated for 'chain 'a' and resid 141 through 143' Processing helix chain 'b' and resid 3 through 24 removed outlier: 3.595A pdb=" N LYS b 23 " --> pdb=" O PHE b 19 " (cutoff:3.500A) Processing helix chain 'b' and resid 33 through 64 removed outlier: 3.847A pdb=" N VAL b 37 " --> pdb=" O PRO b 33 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TRP b 43 " --> pdb=" O SER b 39 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA b 44 " --> pdb=" O GLY b 40 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU b 59 " --> pdb=" O GLN b 55 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL b 60 " --> pdb=" O HIS b 56 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU b 61 " --> pdb=" O SER b 57 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS b 64 " --> pdb=" O VAL b 60 " (cutoff:3.500A) Processing helix chain 'c' and resid 15 through 17 No H-bonds generated for 'chain 'c' and resid 15 through 17' Processing helix chain 'c' and resid 34 through 46 removed outlier: 3.817A pdb=" N VAL c 39 " --> pdb=" O GLY c 35 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA c 46 " --> pdb=" O GLY c 42 " (cutoff:3.500A) Processing helix chain 'd' and resid 20 through 55 removed outlier: 3.710A pdb=" N ALA d 40 " --> pdb=" O ILE d 36 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU d 41 " --> pdb=" O ARG d 37 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS d 50 " --> pdb=" O LYS d 46 " (cutoff:3.500A) Processing helix chain 'd' and resid 58 through 62 removed outlier: 3.589A pdb=" N ASP d 62 " --> pdb=" O HIS d 59 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 76 Proline residue: d 75 - end of helix Processing helix chain 'd' and resid 82 through 87 Processing helix chain 'e' and resid 21 through 50 removed outlier: 3.637A pdb=" N ALA e 26 " --> pdb=" O GLY e 22 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE e 35 " --> pdb=" O GLY e 31 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS e 43 " --> pdb=" O PHE e 39 " (cutoff:3.500A) Proline residue: e 47 - end of helix removed outlier: 3.695A pdb=" N LEU e 50 " --> pdb=" O TYR e 46 " (cutoff:3.500A) Processing helix chain 'f' and resid 20 through 28 Processing helix chain 'f' and resid 30 through 36 removed outlier: 4.147A pdb=" N LYS f 35 " --> pdb=" O GLY f 31 " (cutoff:3.500A) Processing helix chain 'f' and resid 73 through 84 removed outlier: 3.641A pdb=" N ARG f 79 " --> pdb=" O GLU f 75 " (cutoff:3.500A) Processing helix chain 'g' and resid 12 through 22 Processing helix chain 'g' and resid 24 through 49 removed outlier: 3.823A pdb=" N ALA g 29 " --> pdb=" O HIS g 25 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE g 32 " --> pdb=" O PHE g 28 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY g 36 " --> pdb=" O ILE g 32 " (cutoff:3.500A) Proline residue: g 37 - end of helix removed outlier: 4.213A pdb=" N THR g 44 " --> pdb=" O ALA g 40 " (cutoff:3.500A) Proline residue: g 45 - end of helix removed outlier: 3.638A pdb=" N ARG g 48 " --> pdb=" O THR g 44 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 15 Processing helix chain 'h' and resid 17 through 26 removed outlier: 3.623A pdb=" N ASN h 25 " --> pdb=" O TRP h 21 " (cutoff:3.500A) Processing helix chain 'h' and resid 75 through 81 removed outlier: 4.473A pdb=" N TRP h 80 " --> pdb=" O GLY h 76 " (cutoff:3.500A) Processing helix chain 'i' and resid 26 through 47 removed outlier: 4.044A pdb=" N LEU i 31 " --> pdb=" O LYS i 27 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE i 32 " --> pdb=" O LEU i 28 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY i 35 " --> pdb=" O LEU i 31 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TRP i 43 " --> pdb=" O GLY i 39 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA i 47 " --> pdb=" O TRP i 43 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 51 No H-bonds generated for 'chain 'i' and resid 49 through 51' Processing helix chain 'i' and resid 61 through 78 Processing helix chain 'j' and resid 30 through 40 Processing helix chain 'j' and resid 50 through 58 Processing helix chain 'j' and resid 62 through 71 Processing helix chain 'n' and resid 19 through 42 removed outlier: 4.074A pdb=" N TYR n 41 " --> pdb=" O PHE n 37 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU n 42 " --> pdb=" O ASN n 38 " (cutoff:3.500A) Processing helix chain 'n' and resid 49 through 53 removed outlier: 4.062A pdb=" N PHE n 53 " --> pdb=" O TRP n 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 49 through 53' Processing helix chain 'n' and resid 59 through 88 removed outlier: 3.917A pdb=" N LYS n 82 " --> pdb=" O GLU n 78 " (cutoff:3.500A) Processing helix chain 'n' and resid 93 through 96 No H-bonds generated for 'chain 'n' and resid 93 through 96' Processing helix chain '1' and resid 5 through 33 removed outlier: 3.508A pdb=" N LEU 1 9 " --> pdb=" O ILE 1 5 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE 1 11 " --> pdb=" O GLU 1 7 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE 1 17 " --> pdb=" O VAL 1 13 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N SER 1 18 " --> pdb=" O CYS 1 14 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA 1 20 " --> pdb=" O LEU 1 16 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR 1 21 " --> pdb=" O PHE 1 17 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG 1 27 " --> pdb=" O THR 1 23 " (cutoff:3.500A) Processing helix chain '1' and resid 49 through 57 Processing helix chain '1' and resid 70 through 86 Proline residue: 1 77 - end of helix Processing helix chain '1' and resid 106 through 125 removed outlier: 3.888A pdb=" N GLY 1 113 " --> pdb=" O SER 1 109 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL 1 117 " --> pdb=" O GLY 1 113 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N PHE 1 118 " --> pdb=" O SER 1 114 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY 1 119 " --> pdb=" O LEU 1 115 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER 1 120 " --> pdb=" O GLY 1 116 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY 1 124 " --> pdb=" O SER 1 120 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TRP 1 125 " --> pdb=" O LEU 1 121 " (cutoff:3.500A) Processing helix chain '1' and resid 130 through 152 removed outlier: 3.684A pdb=" N SER 1 136 " --> pdb=" O SER 1 132 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN 1 142 " --> pdb=" O ARG 1 138 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU 1 147 " --> pdb=" O LEU 1 143 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE 1 149 " --> pdb=" O SER 1 145 " (cutoff:3.500A) Processing helix chain '1' and resid 154 through 158 Processing helix chain '1' and resid 166 through 174 removed outlier: 3.908A pdb=" N ILE 1 170 " --> pdb=" O ILE 1 166 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU 1 171 " --> pdb=" O THR 1 167 " (cutoff:3.500A) Processing helix chain '1' and resid 183 through 196 removed outlier: 3.522A pdb=" N LEU 1 187 " --> pdb=" O LEU 1 183 " (cutoff:3.500A) Processing helix chain '1' and resid 224 through 245 removed outlier: 3.681A pdb=" N ILE 1 236 " --> pdb=" O TYR 1 232 " (cutoff:3.500A) Processing helix chain '1' and resid 256 through 262 removed outlier: 3.566A pdb=" N ILE 1 261 " --> pdb=" O TYR 1 257 " (cutoff:3.500A) Processing helix chain '1' and resid 268 through 298 removed outlier: 3.544A pdb=" N PHE 1 291 " --> pdb=" O VAL 1 287 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE 1 294 " --> pdb=" O MET 1 290 " (cutoff:3.500A) Processing helix chain '1' and resid 305 through 313 Processing helix chain '1' and resid 317 through 333 Proline residue: 1 328 - end of helix Processing helix chain '2' and resid 2 through 14 removed outlier: 4.161A pdb=" N SER 2 8 " --> pdb=" O LEU 2 4 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR 2 11 " --> pdb=" O ILE 2 7 " (cutoff:3.500A) Processing helix chain '2' and resid 21 through 38 removed outlier: 3.673A pdb=" N ILE 2 25 " --> pdb=" O ASN 2 21 " (cutoff:3.500A) Processing helix chain '2' and resid 40 through 45 removed outlier: 3.683A pdb=" N TYR 2 43 " --> pdb=" O SER 2 40 " (cutoff:3.500A) Processing helix chain '2' and resid 65 through 84 removed outlier: 4.098A pdb=" N TYR 2 73 " --> pdb=" O ASP 2 69 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL 2 78 " --> pdb=" O PHE 2 74 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR 2 83 " --> pdb=" O ILE 2 79 " (cutoff:3.500A) Processing helix chain '2' and resid 92 through 95 No H-bonds generated for 'chain '2' and resid 92 through 95' Processing helix chain '2' and resid 103 through 118 removed outlier: 3.639A pdb=" N LEU 2 108 " --> pdb=" O ILE 2 104 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE 2 117 " --> pdb=" O GLY 2 113 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL 2 118 " --> pdb=" O ALA 2 114 " (cutoff:3.500A) Processing helix chain '2' and resid 123 through 142 Processing helix chain '2' and resid 148 through 178 removed outlier: 3.727A pdb=" N MET 2 160 " --> pdb=" O LEU 2 156 " (cutoff:3.500A) Processing helix chain '2' and resid 191 through 194 No H-bonds generated for 'chain '2' and resid 191 through 194' Processing helix chain '2' and resid 198 through 211 removed outlier: 4.422A pdb=" N LYS 2 211 " --> pdb=" O GLY 2 207 " (cutoff:3.500A) Processing helix chain '2' and resid 219 through 227 Processing helix chain '2' and resid 232 through 236 removed outlier: 3.525A pdb=" N ILE 2 236 " --> pdb=" O THR 2 233 " (cutoff:3.500A) Processing helix chain '2' and resid 239 through 250 removed outlier: 3.880A pdb=" N ILE 2 244 " --> pdb=" O PRO 2 240 " (cutoff:3.500A) Processing helix chain '2' and resid 258 through 274 Processing helix chain '2' and resid 281 through 301 removed outlier: 3.631A pdb=" N ALA 2 293 " --> pdb=" O GLY 2 289 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU 2 301 " --> pdb=" O MET 2 297 " (cutoff:3.500A) Processing helix chain '2' and resid 307 through 332 removed outlier: 3.804A pdb=" N ILE 2 318 " --> pdb=" O THR 2 314 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU 2 321 " --> pdb=" O SER 2 317 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE 2 324 " --> pdb=" O HIS 2 320 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET 2 325 " --> pdb=" O LEU 2 321 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE 2 331 " --> pdb=" O ILE 2 327 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N TYR 2 332 " --> pdb=" O ILE 2 328 " (cutoff:3.500A) Processing helix chain '2' and resid 347 through 349 No H-bonds generated for 'chain '2' and resid 347 through 349' Processing helix chain '2' and resid 353 through 355 No H-bonds generated for 'chain '2' and resid 353 through 355' Processing helix chain '2' and resid 359 through 370 Processing helix chain '2' and resid 378 through 390 removed outlier: 3.922A pdb=" N GLY 2 382 " --> pdb=" O LEU 2 378 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS 2 383 " --> pdb=" O GLY 2 379 " (cutoff:3.500A) Processing helix chain '2' and resid 396 through 420 removed outlier: 3.821A pdb=" N TYR 2 412 " --> pdb=" O ILE 2 408 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU 2 414 " --> pdb=" O ALA 2 410 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR 2 415 " --> pdb=" O LEU 2 411 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU 2 416 " --> pdb=" O TYR 2 412 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU 2 417 " --> pdb=" O TYR 2 413 " (cutoff:3.500A) Processing helix chain '2' and resid 437 through 467 removed outlier: 3.688A pdb=" N LEU 2 443 " --> pdb=" O LEU 2 439 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE 2 450 " --> pdb=" O LEU 2 446 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N PHE 2 454 " --> pdb=" O ILE 2 450 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE 2 455 " --> pdb=" O THR 2 451 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N TYR 2 456 " --> pdb=" O PHE 2 452 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN 2 457 " --> pdb=" O GLY 2 453 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N SER 2 458 " --> pdb=" O PHE 2 454 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU 2 459 " --> pdb=" O ILE 2 455 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 25 removed outlier: 3.671A pdb=" N ILE 3 8 " --> pdb=" O PHE 3 4 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE 3 9 " --> pdb=" O ILE 3 5 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE 3 11 " --> pdb=" O PHE 3 7 " (cutoff:3.500A) Proline residue: 3 12 - end of helix removed outlier: 3.955A pdb=" N VAL 3 21 " --> pdb=" O ALA 3 17 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ASN 3 22 " --> pdb=" O LEU 3 18 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE 3 23 " --> pdb=" O LEU 3 19 " (cutoff:3.500A) Processing helix chain '3' and resid 54 through 78 removed outlier: 4.252A pdb=" N VAL 3 59 " --> pdb=" O ALA 3 55 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA 3 60 " --> pdb=" O PHE 3 56 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE 3 61 " --> pdb=" O ILE 3 57 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU 3 64 " --> pdb=" O ALA 3 60 " (cutoff:3.500A) Proline residue: 3 65 - end of helix removed outlier: 4.061A pdb=" N ILE 3 70 " --> pdb=" O PHE 3 66 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER 3 71 " --> pdb=" O ASP 3 67 " (cutoff:3.500A) Proline residue: 3 75 - end of helix removed outlier: 3.828A pdb=" N MET 3 78 " --> pdb=" O LEU 3 74 " (cutoff:3.500A) Processing helix chain '3' and resid 87 through 108 removed outlier: 4.152A pdb=" N ILE 3 100 " --> pdb=" O LEU 3 96 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU 3 105 " --> pdb=" O GLY 3 101 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE 3 106 " --> pdb=" O PHE 3 102 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN 3 107 " --> pdb=" O VAL 3 103 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 20 removed outlier: 3.879A pdb=" N LEU 4 7 " --> pdb=" O LEU 4 3 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR 4 12 " --> pdb=" O LEU 4 8 " (cutoff:3.500A) Processing helix chain '4' and resid 25 through 44 removed outlier: 3.589A pdb=" N LEU 4 29 " --> pdb=" O LYS 4 25 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU 4 36 " --> pdb=" O SER 4 32 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU 4 37 " --> pdb=" O ASN 4 33 " (cutoff:3.500A) Processing helix chain '4' and resid 84 through 102 removed outlier: 4.213A pdb=" N PHE 4 88 " --> pdb=" O LEU 4 84 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE 4 89 " --> pdb=" O SER 4 85 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU 4 94 " --> pdb=" O LEU 4 90 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU 4 95 " --> pdb=" O LEU 4 91 " (cutoff:3.500A) Proline residue: 4 97 - end of helix Processing helix chain '4' and resid 111 through 130 removed outlier: 3.913A pdb=" N THR 4 116 " --> pdb=" O ASN 4 112 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY 4 122 " --> pdb=" O VAL 4 118 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU 4 127 " --> pdb=" O LEU 4 123 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE 4 129 " --> pdb=" O ILE 4 125 " (cutoff:3.500A) Processing helix chain '4' and resid 134 through 139 Processing helix chain '4' and resid 143 through 153 removed outlier: 4.550A pdb=" N LEU 4 147 " --> pdb=" O ALA 4 143 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU 4 151 " --> pdb=" O LEU 4 147 " (cutoff:3.500A) Processing helix chain '4' and resid 160 through 188 removed outlier: 4.271A pdb=" N THR 4 171 " --> pdb=" O VAL 4 167 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER 4 181 " --> pdb=" O PHE 4 177 " (cutoff:3.500A) Processing helix chain '4' and resid 196 through 199 Processing helix chain '4' and resid 204 through 221 removed outlier: 3.652A pdb=" N ILE 4 209 " --> pdb=" O ASP 4 205 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE 4 216 " --> pdb=" O LEU 4 212 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL 4 220 " --> pdb=" O ILE 4 216 " (cutoff:3.500A) Processing helix chain '4' and resid 230 through 235 removed outlier: 3.584A pdb=" N HIS 4 235 " --> pdb=" O LEU 4 231 " (cutoff:3.500A) Processing helix chain '4' and resid 240 through 260 removed outlier: 5.222A pdb=" N LEU 4 251 " --> pdb=" O ALA 4 247 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LYS 4 252 " --> pdb=" O GLY 4 248 " (cutoff:3.500A) Processing helix chain '4' and resid 262 through 265 No H-bonds generated for 'chain '4' and resid 262 through 265' Processing helix chain '4' and resid 267 through 291 removed outlier: 3.841A pdb=" N ILE 4 271 " --> pdb=" O CYS 4 267 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU 4 272 " --> pdb=" O GLU 4 268 " (cutoff:3.500A) Proline residue: 4 275 - end of helix removed outlier: 3.794A pdb=" N ILE 4 280 " --> pdb=" O MET 4 276 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR 4 288 " --> pdb=" O THR 4 284 " (cutoff:3.500A) Processing helix chain '4' and resid 299 through 319 removed outlier: 3.887A pdb=" N MET 4 310 " --> pdb=" O SER 4 306 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE 4 312 " --> pdb=" O SER 4 308 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU 4 315 " --> pdb=" O GLY 4 311 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY 4 316 " --> pdb=" O ILE 4 312 " (cutoff:3.500A) Processing helix chain '4' and resid 322 through 346 Proline residue: 4 340 - end of helix Processing helix chain '4' and resid 350 through 354 Processing helix chain '4' and resid 359 through 361 No H-bonds generated for 'chain '4' and resid 359 through 361' Processing helix chain '4' and resid 365 through 367 No H-bonds generated for 'chain '4' and resid 365 through 367' Processing helix chain '4' and resid 370 through 384 removed outlier: 4.645A pdb=" N TYR 4 375 " --> pdb=" O GLN 4 371 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU 4 379 " --> pdb=" O TYR 4 375 " (cutoff:3.500A) Processing helix chain '4' and resid 391 through 405 removed outlier: 3.627A pdb=" N LEU 4 397 " --> pdb=" O THR 4 393 " (cutoff:3.500A) Processing helix chain '4' and resid 407 through 432 removed outlier: 4.528A pdb=" N ILE 4 415 " --> pdb=" O GLY 4 411 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N SER 4 416 " --> pdb=" O ILE 4 412 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N VAL 4 417 " --> pdb=" O SER 4 413 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU 4 418 " --> pdb=" O CYS 4 414 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA 4 421 " --> pdb=" O VAL 4 417 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N TYR 4 423 " --> pdb=" O LEU 4 419 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN 4 424 " --> pdb=" O ALA 4 420 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS 4 430 " --> pdb=" O LYS 4 426 " (cutoff:3.500A) Processing helix chain '4' and resid 448 through 466 removed outlier: 3.913A pdb=" N MET 4 454 " --> pdb=" O GLU 4 450 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE 4 459 " --> pdb=" O ASN 4 455 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE 4 464 " --> pdb=" O SER 4 460 " (cutoff:3.500A) Processing helix chain '4' and resid 468 through 480 removed outlier: 3.772A pdb=" N MET 4 471 " --> pdb=" O PRO 4 468 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ASN 4 473 " --> pdb=" O ILE 4 470 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU 4 474 " --> pdb=" O MET 4 471 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N TYR 4 476 " --> pdb=" O ASN 4 473 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TRP 4 477 " --> pdb=" O LEU 4 474 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL 4 479 " --> pdb=" O TYR 4 476 " (cutoff:3.500A) Processing helix chain '5' and resid 6 through 55 removed outlier: 4.104A pdb=" N LEU 5 11 " --> pdb=" O LEU 5 7 " (cutoff:3.500A) Proline residue: 5 12 - end of helix removed outlier: 3.553A pdb=" N PHE 5 18 " --> pdb=" O ILE 5 14 " (cutoff:3.500A) Proline residue: 5 19 - end of helix removed outlier: 5.600A pdb=" N ARG 5 24 " --> pdb=" O LEU 5 20 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLN 5 25 " --> pdb=" O PHE 5 21 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N TYR 5 28 " --> pdb=" O ARG 5 24 " (cutoff:3.500A) removed outlier: 9.097A pdb=" N VAL 5 29 " --> pdb=" O GLN 5 25 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE 5 30 " --> pdb=" O LEU 5 26 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ARG 5 33 " --> pdb=" O VAL 5 29 " (cutoff:3.500A) Processing helix chain '5' and resid 83 through 106 removed outlier: 3.786A pdb=" N MET 5 88 " --> pdb=" O LEU 5 84 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA 5 91 " --> pdb=" O THR 5 87 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE 5 104 " --> pdb=" O HIS 5 100 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY 5 105 " --> pdb=" O ILE 5 101 " (cutoff:3.500A) Processing helix chain '5' and resid 113 through 132 removed outlier: 3.665A pdb=" N MET 5 127 " --> pdb=" O PHE 5 123 " (cutoff:3.500A) Processing helix chain '5' and resid 136 through 154 removed outlier: 3.573A pdb=" N ILE 5 146 " --> pdb=" O GLY 5 142 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY 5 147 " --> pdb=" O TRP 5 143 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE 5 154 " --> pdb=" O SER 5 150 " (cutoff:3.500A) Processing helix chain '5' and resid 161 through 191 removed outlier: 3.702A pdb=" N VAL 5 171 " --> pdb=" O ALA 5 167 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY 5 177 " --> pdb=" O MET 5 173 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE 5 180 " --> pdb=" O PHE 5 176 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL 5 187 " --> pdb=" O LEU 5 183 " (cutoff:3.500A) Processing helix chain '5' and resid 197 through 201 Processing helix chain '5' and resid 209 through 226 removed outlier: 4.097A pdb=" N LEU 5 214 " --> pdb=" O ASP 5 210 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA 5 218 " --> pdb=" O LEU 5 214 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA 5 222 " --> pdb=" O ALA 5 218 " (cutoff:3.500A) Processing helix chain '5' and resid 234 through 237 No H-bonds generated for 'chain '5' and resid 234 through 237' Processing helix chain '5' and resid 244 through 250 Processing helix chain '5' and resid 254 through 272 removed outlier: 4.470A pdb=" N GLY 5 259 " --> pdb=" O LEU 5 255 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE 5 260 " --> pdb=" O VAL 5 256 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU 5 263 " --> pdb=" O GLY 5 259 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ASN 5 268 " --> pdb=" O LEU 5 264 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE 5 269 " --> pdb=" O ARG 5 265 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU 5 271 " --> pdb=" O ALA 5 267 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N TYR 5 272 " --> pdb=" O ASN 5 268 " (cutoff:3.500A) Processing helix chain '5' and resid 274 through 297 removed outlier: 3.619A pdb=" N ILE 5 279 " --> pdb=" O THR 5 275 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU 5 281 " --> pdb=" O LEU 5 277 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TRP 5 282 " --> pdb=" O PHE 5 278 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N CYS 5 297 " --> pdb=" O LEU 5 293 " (cutoff:3.500A) Processing helix chain '5' and resid 301 through 321 removed outlier: 3.732A pdb=" N GLN 5 312 " --> pdb=" O SER 5 308 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY 5 314 " --> pdb=" O MET 5 310 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET 5 315 " --> pdb=" O SER 5 311 " (cutoff:3.500A) Processing helix chain '5' and resid 325 through 351 removed outlier: 3.864A pdb=" N PHE 5 337 " --> pdb=" O LEU 5 333 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA 5 340 " --> pdb=" O ALA 5 336 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU 5 341 " --> pdb=" O PHE 5 337 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU 5 342 " --> pdb=" O PHE 5 338 " (cutoff:3.500A) Processing helix chain '5' and resid 360 through 362 No H-bonds generated for 'chain '5' and resid 360 through 362' Processing helix chain '5' and resid 371 through 384 removed outlier: 3.657A pdb=" N ILE 5 379 " --> pdb=" O ILE 5 375 " (cutoff:3.500A) Processing helix chain '5' and resid 391 through 395 Processing helix chain '5' and resid 397 through 404 removed outlier: 3.779A pdb=" N TYR 5 404 " --> pdb=" O ILE 5 400 " (cutoff:3.500A) Processing helix chain '5' and resid 410 through 436 removed outlier: 3.697A pdb=" N VAL 5 414 " --> pdb=" O ASN 5 411 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ALA 5 418 " --> pdb=" O TYR 5 415 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL 5 427 " --> pdb=" O LEU 5 424 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR 5 428 " --> pdb=" O THR 5 425 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N MET 5 430 " --> pdb=" O VAL 5 427 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE 5 432 " --> pdb=" O SER 5 429 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR 5 434 " --> pdb=" O LYS 5 431 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR 5 436 " --> pdb=" O LEU 5 433 " (cutoff:3.500A) Processing helix chain '5' and resid 445 through 449 Processing helix chain '5' and resid 459 through 480 removed outlier: 3.883A pdb=" N ILE 5 467 " --> pdb=" O PHE 5 463 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE 5 468 " --> pdb=" O ILE 5 464 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLY 5 473 " --> pdb=" O ALA 5 469 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N TRP 5 474 " --> pdb=" O MET 5 470 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS 5 477 " --> pdb=" O GLY 5 473 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP 5 478 " --> pdb=" O TRP 5 474 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ILE 5 479 " --> pdb=" O ILE 5 475 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR 5 480 " --> pdb=" O LEU 5 476 " (cutoff:3.500A) Processing helix chain '5' and resid 494 through 496 No H-bonds generated for 'chain '5' and resid 494 through 496' Processing helix chain '5' and resid 499 through 502 No H-bonds generated for 'chain '5' and resid 499 through 502' Processing helix chain '5' and resid 509 through 530 Proline residue: 5 514 - end of helix removed outlier: 3.879A pdb=" N SER 5 517 " --> pdb=" O LEU 5 513 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA 5 518 " --> pdb=" O PRO 5 514 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER 5 522 " --> pdb=" O ALA 5 518 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL 5 526 " --> pdb=" O SER 5 522 " (cutoff:3.500A) Processing helix chain '5' and resid 535 through 537 No H-bonds generated for 'chain '5' and resid 535 through 537' Processing helix chain '5' and resid 541 through 551 removed outlier: 4.169A pdb=" N VAL 5 546 " --> pdb=" O TYR 5 542 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER 5 548 " --> pdb=" O ASN 5 544 " (cutoff:3.500A) Processing helix chain '5' and resid 557 through 562 Processing helix chain '5' and resid 565 through 576 Processing helix chain '5' and resid 591 through 604 Processing helix chain '5' and resid 614 through 622 Processing helix chain '5' and resid 639 through 651 removed outlier: 3.613A pdb=" N LEU 5 648 " --> pdb=" O ILE 5 644 " (cutoff:3.500A) Processing helix chain '6' and resid 4 through 23 removed outlier: 3.814A pdb=" N TYR 6 7 " --> pdb=" O LEU 6 4 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE 6 8 " --> pdb=" O THR 6 5 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ILE 6 9 " --> pdb=" O TYR 6 6 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE 6 13 " --> pdb=" O GLU 6 10 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU 6 15 " --> pdb=" O THR 6 12 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU 6 18 " --> pdb=" O LEU 6 15 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR 6 20 " --> pdb=" O ILE 6 17 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE 6 21 " --> pdb=" O LEU 6 18 " (cutoff:3.500A) Processing helix chain '6' and resid 29 through 50 removed outlier: 3.643A pdb=" N ILE 6 33 " --> pdb=" O PRO 6 29 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA 6 38 " --> pdb=" O LEU 6 34 " (cutoff:3.500A) Processing helix chain '6' and resid 53 through 62 removed outlier: 3.938A pdb=" N LEU 6 57 " --> pdb=" O GLY 6 53 " (cutoff:3.500A) Processing helix chain '6' and resid 67 through 76 Processing helix chain '6' and resid 146 through 153 Processing helix chain '6' and resid 159 through 179 removed outlier: 3.904A pdb=" N ILE 6 167 " --> pdb=" O LEU 6 163 " (cutoff:3.500A) Proline residue: 6 176 - end of helix Processing helix chain '8' and resid 10 through 15 Processing helix chain '8' and resid 20 through 22 No H-bonds generated for 'chain '8' and resid 20 through 22' Processing helix chain '8' and resid 25 through 39 removed outlier: 4.056A pdb=" N ALA 8 28 " --> pdb=" O ARG 8 25 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU 8 29 " --> pdb=" O CYS 8 26 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL 8 31 " --> pdb=" O ALA 8 28 " (cutoff:3.500A) Proline residue: 8 32 - end of helix Processing helix chain '8' and resid 49 through 82 removed outlier: 3.580A pdb=" N ARG 8 64 " --> pdb=" O ALA 8 60 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS 8 73 " --> pdb=" O MET 8 69 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA 8 74 " --> pdb=" O ASP 8 70 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLU 8 75 " --> pdb=" O LYS 8 71 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LYS 8 76 " --> pdb=" O LEU 8 72 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA 8 80 " --> pdb=" O LYS 8 76 " (cutoff:3.500A) Processing helix chain '9' and resid 17 through 27 Processing helix chain '9' and resid 35 through 48 Proline residue: 9 39 - end of helix removed outlier: 3.612A pdb=" N GLU 9 42 " --> pdb=" O PRO 9 39 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP 9 43 " --> pdb=" O ASN 9 40 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU 9 46 " --> pdb=" O ASP 9 43 " (cutoff:3.500A) Processing helix chain '9' and resid 51 through 66 removed outlier: 3.753A pdb=" N GLU 9 59 " --> pdb=" O ALA 9 55 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE 9 60 " --> pdb=" O ARG 9 56 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 36 through 41 Processing sheet with id= B, first strand: chain 'A' and resid 176 through 178 Processing sheet with id= C, first strand: chain 'A' and resid 253 through 258 Processing sheet with id= D, first strand: chain 'A' and resid 313 through 315 Processing sheet with id= E, first strand: chain 'A' and resid 346 through 350 removed outlier: 6.164A pdb=" N MET A 549 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL A 349 " --> pdb=" O MET A 549 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N TRP A 551 " --> pdb=" O VAL A 349 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 409 through 413 removed outlier: 6.114A pdb=" N GLU A 438 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU A 412 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA A 440 " --> pdb=" O LEU A 412 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 482 through 484 Processing sheet with id= H, first strand: chain 'A' and resid 571 through 573 Processing sheet with id= I, first strand: chain 'A' and resid 597 through 600 Processing sheet with id= J, first strand: chain 'B' and resid 242 through 246 removed outlier: 7.783A pdb=" N TYR B 114 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N THR B 245 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 116 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA B 155 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N VAL B 117 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N TYR B 157 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ASP B 196 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ILE B 158 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TYR B 198 " --> pdb=" O ILE B 158 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE B 160 " --> pdb=" O TYR B 198 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N HIS B 200 " --> pdb=" O ILE B 160 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 288 through 293 removed outlier: 5.616A pdb=" N VAL B 356 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY B 318 " --> pdb=" O ILE B 359 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 397 through 404 removed outlier: 3.730A pdb=" N GLY C 397 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 100 through 104 removed outlier: 4.004A pdb=" N ARG C 111 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 31 through 33 Processing sheet with id= O, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.384A pdb=" N VAL E 125 " --> pdb=" O ILE E 164 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N VAL E 166 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASN E 127 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N ALA E 168 " --> pdb=" O ASN E 127 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N THR E 79 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N VAL E 58 " --> pdb=" O THR E 79 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL E 81 " --> pdb=" O VAL E 58 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 123 through 130 removed outlier: 6.989A pdb=" N ASN G 143 " --> pdb=" O ILE G 124 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ILE G 126 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL G 141 " --> pdb=" O ILE G 126 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA G 128 " --> pdb=" O GLU G 139 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU G 139 " --> pdb=" O ALA G 128 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE G 153 " --> pdb=" O PHE G 144 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LEU G 96 " --> pdb=" O ARG G 152 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TYR G 158 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY G 88 " --> pdb=" O HIS G 99 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 220 through 225 Processing sheet with id= R, first strand: chain 'I' and resid 118 through 120 removed outlier: 3.672A pdb=" N ALA I 119 " --> pdb=" O VAL I 185 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 145 through 151 removed outlier: 5.936A pdb=" N GLU I 150 " --> pdb=" O THR I 159 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N THR I 159 " --> pdb=" O GLU I 150 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'K' and resid 116 through 119 removed outlier: 6.726A pdb=" N TRP K 143 " --> pdb=" O MET K 117 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL K 119 " --> pdb=" O TRP K 143 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE K 145 " --> pdb=" O VAL K 119 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL K 175 " --> pdb=" O SER K 146 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'M' and resid 20 through 22 Processing sheet with id= V, first strand: chain 'M' and resid 88 through 90 Processing sheet with id= W, first strand: chain 'M' and resid 94 through 97 removed outlier: 3.578A pdb=" N ILE M 113 " --> pdb=" O CYS M 97 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'f' and resid 44 through 46 removed outlier: 8.730A pdb=" N ARG f 45 " --> pdb=" O ILE f 8 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N PHE f 10 " --> pdb=" O ARG f 45 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'h' and resid 44 through 47 removed outlier: 3.666A pdb=" N TYR h 60 " --> pdb=" O TYR h 46 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain '2' and resid 52 through 54 Processing sheet with id= AA, first strand: chain '4' and resid 57 through 59 2241 hydrogen bonds defined for protein. 6402 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: 19.35 Time building geometry restraints manager: 23.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.41: 25794 1.41 - 1.63: 36118 1.63 - 1.86: 448 1.86 - 2.08: 1 2.08 - 2.30: 80 Bond restraints: 62441 Sorted by residual: bond pdb=" CA PRO C 395 " pdb=" C PRO C 395 " ideal model delta sigma weight residual 1.514 1.564 -0.050 5.50e-03 3.31e+04 8.14e+01 bond pdb=" C5N NDP E 401 " pdb=" C6N NDP E 401 " ideal model delta sigma weight residual 1.337 1.550 -0.213 2.40e-02 1.74e+03 7.88e+01 bond pdb=" C1D NDP E 401 " pdb=" C2D NDP E 401 " ideal model delta sigma weight residual 1.560 1.297 0.263 3.70e-02 7.30e+02 5.06e+01 bond pdb=" C1B NDP E 401 " pdb=" C2B NDP E 401 " ideal model delta sigma weight residual 1.575 1.323 0.252 3.70e-02 7.30e+02 4.63e+01 bond pdb=" C4 FMN B 502 " pdb=" C4A FMN B 502 " ideal model delta sigma weight residual 1.390 1.512 -0.122 2.00e-02 2.50e+03 3.70e+01 ... (remaining 62436 not shown) Histogram of bond angle deviations from ideal: 67.26 - 81.87: 72 81.87 - 96.47: 16 96.47 - 111.08: 23836 111.08 - 125.68: 59813 125.68 - 140.28: 1088 Bond angle restraints: 84825 Sorted by residual: angle pdb=" S1 FES H 301 " pdb="FE2 FES H 301 " pdb=" S2 FES H 301 " ideal model delta sigma weight residual 104.33 90.97 13.36 1.14e+00 7.69e-01 1.37e+02 angle pdb="FE1 FES H 301 " pdb=" S2 FES H 301 " pdb="FE2 FES H 301 " ideal model delta sigma weight residual 75.66 88.93 -13.27 1.14e+00 7.69e-01 1.36e+02 angle pdb="FE1 FES H 301 " pdb=" S1 FES H 301 " pdb="FE2 FES H 301 " ideal model delta sigma weight residual 75.66 88.86 -13.20 1.20e+00 6.94e-01 1.21e+02 angle pdb=" S1 FES H 301 " pdb="FE1 FES H 301 " pdb=" S2 FES H 301 " ideal model delta sigma weight residual 104.33 91.18 13.15 1.20e+00 6.94e-01 1.20e+02 angle pdb="FE1 FES A 803 " pdb=" S2 FES A 803 " pdb="FE2 FES A 803 " ideal model delta sigma weight residual 75.66 85.75 -10.09 1.14e+00 7.69e-01 7.84e+01 ... (remaining 84820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 36890 35.98 - 71.95: 204 71.95 - 107.93: 27 107.93 - 143.90: 1 143.90 - 179.88: 3 Dihedral angle restraints: 37125 sinusoidal: 14754 harmonic: 22371 Sorted by residual: dihedral pdb=" CA GLU S 160 " pdb=" C GLU S 160 " pdb=" N LYS S 161 " pdb=" CA LYS S 161 " ideal model delta harmonic sigma weight residual -180.00 -121.75 -58.25 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" CA TYR C 229 " pdb=" C TYR C 229 " pdb=" N VAL C 230 " pdb=" CA VAL C 230 " ideal model delta harmonic sigma weight residual -180.00 -124.68 -55.32 0 5.00e+00 4.00e-02 1.22e+02 dihedral pdb=" CA PRO 1 200 " pdb=" C PRO 1 200 " pdb=" N PRO 1 201 " pdb=" CA PRO 1 201 " ideal model delta harmonic sigma weight residual 180.00 128.95 51.05 0 5.00e+00 4.00e-02 1.04e+02 ... (remaining 37122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.151: 9489 4.151 - 8.301: 0 8.301 - 12.452: 0 12.452 - 16.603: 0 16.603 - 20.753: 20 Chirality restraints: 9509 Sorted by residual: chirality pdb="FE2 SF4 A 802 " pdb=" S1 SF4 A 802 " pdb=" S3 SF4 A 802 " pdb=" S4 SF4 A 802 " both_signs ideal model delta sigma weight residual False 10.55 -10.20 20.75 2.00e-01 2.50e+01 1.08e+04 chirality pdb="FE1 SF4 A 801 " pdb=" S2 SF4 A 801 " pdb=" S3 SF4 A 801 " pdb=" S4 SF4 A 801 " both_signs ideal model delta sigma weight residual False -10.55 10.18 -20.73 2.00e-01 2.50e+01 1.07e+04 chirality pdb="FE2 SF4 A 801 " pdb=" S1 SF4 A 801 " pdb=" S3 SF4 A 801 " pdb=" S4 SF4 A 801 " both_signs ideal model delta sigma weight residual False 10.55 -10.10 20.66 2.00e-01 2.50e+01 1.07e+04 ... (remaining 9506 not shown) Planarity restraints: 10767 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP E 401 " 0.021 2.00e-02 2.50e+03 9.70e-02 1.18e+02 pdb=" C3N NDP E 401 " 0.178 2.00e-02 2.50e+03 pdb=" C4N NDP E 401 " -0.041 2.00e-02 2.50e+03 pdb=" C7N NDP E 401 " -0.098 2.00e-02 2.50e+03 pdb=" N1N NDP E 401 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 103 " 0.060 2.00e-02 2.50e+03 3.16e-02 2.00e+01 pdb=" CG TYR I 103 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR I 103 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR I 103 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR I 103 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR I 103 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR I 103 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR I 103 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO 1 200 " -0.064 5.00e-02 4.00e+02 9.59e-02 1.47e+01 pdb=" N PRO 1 201 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO 1 201 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO 1 201 " -0.053 5.00e-02 4.00e+02 ... (remaining 10764 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 963 2.64 - 3.21: 58449 3.21 - 3.77: 100700 3.77 - 4.34: 135235 4.34 - 4.90: 212039 Nonbonded interactions: 507386 Sorted by model distance: nonbonded pdb=" N GLU H 211 " pdb=" OE1 GLU H 211 " model vdw 2.078 2.520 nonbonded pdb=" O PHE 4 109 " pdb=" OH TYR 4 155 " model vdw 2.198 2.440 nonbonded pdb=" OH TYR I 171 " pdb=" OH TYR I 192 " model vdw 2.211 2.440 nonbonded pdb=" O ASN 4 103 " pdb=" OH TYR 4 115 " model vdw 2.223 2.440 nonbonded pdb=" OD1 ASN 5 299 " pdb=" OH TYR 5 547 " model vdw 2.233 2.440 ... (remaining 507381 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 5 5.49 5 S 298 5.16 5 C 39392 2.51 5 N 10169 2.21 5 O 11073 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 22.320 Check model and map are aligned: 0.660 Process input model: 140.510 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.430 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 174.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 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 : 0.010 0.263 62441 Z= 0.653 Angle : 1.255 18.281 84825 Z= 0.663 Chirality : 0.944 20.753 9509 Planarity : 0.008 0.097 10767 Dihedral : 10.326 179.876 22732 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.30 % Favored : 91.51 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.08), residues: 7587 helix: -2.58 (0.06), residues: 3758 sheet: -2.62 (0.26), residues: 328 loop : -2.79 (0.09), residues: 3501 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15174 Ramachandran restraints generated. 7587 Oldfield, 0 Emsley, 7587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15174 Ramachandran restraints generated. 7587 Oldfield, 0 Emsley, 7587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1653 residues out of total 6575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1643 time to evaluate : 5.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 0 residues processed: 1653 average time/residue: 0.6684 time to fit residues: 1826.1198 Evaluate side-chains 741 residues out of total 6575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 741 time to evaluate : 5.549 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.4681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 753 random chunks: chunk 635 optimal weight: 0.8980 chunk 570 optimal weight: 1.9990 chunk 316 optimal weight: 9.9990 chunk 194 optimal weight: 7.9990 chunk 384 optimal weight: 0.0170 chunk 304 optimal weight: 0.6980 chunk 590 optimal weight: 0.8980 chunk 228 optimal weight: 3.9990 chunk 358 optimal weight: 2.9990 chunk 439 optimal weight: 7.9990 chunk 683 optimal weight: 0.9980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 ASN ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 HIS ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS E 32 ASN E 76 HIS E 103 ASN ** E 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 HIS E 170 ASN E 181 HIS E 295 GLN E 317 GLN E 321 GLN F 77 HIS F 108 HIS G 67 HIS ** G 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 ASN H 40 ASN H 79 GLN ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 174 ASN M 50 GLN ** M 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 105 GLN S 201 GLN U 97 HIS ** U 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 74 GLN Z 38 ASN ** Z 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 87 HIS a 146 GLN c 18 GLN d 20 HIS d 34 GLN d 59 HIS d 88 ASN e 23 HIS g 25 HIS h 23 GLN h 43 ASN h 50 HIS h 55 HIS 1 173 GLN 2 21 ASN ** 2 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 173 ASN ** 2 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 218 HIS 2 340 GLN 3 85 ASN 3 117 ASN 4 23 ASN 4 26 HIS 4 112 ASN ** 4 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 76 ASN ** 5 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 251 HIS 5 326 ASN ** 5 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 491 HIS 5 529 ASN 5 552 GLN 6 136 GLN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.305 62441 Z= 0.523 Angle : 1.567 51.417 84825 Z= 0.998 Chirality : 0.291 6.490 9509 Planarity : 0.006 0.135 10767 Dihedral : 8.124 178.873 8446 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.18 % Favored : 93.78 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -2.77 (0.09), residues: 7587 helix: -1.29 (0.07), residues: 3817 sheet: -2.21 (0.27), residues: 330 loop : -2.40 (0.10), residues: 3440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15174 Ramachandran restraints generated. 7587 Oldfield, 0 Emsley, 7587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15174 Ramachandran restraints generated. 7587 Oldfield, 0 Emsley, 7587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1163 residues out of total 6575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1154 time to evaluate : 5.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 1161 average time/residue: 0.5772 time to fit residues: 1137.3009 Evaluate side-chains 725 residues out of total 6575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 724 time to evaluate : 5.647 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4371 time to fit residues: 8.3834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 753 random chunks: chunk 380 optimal weight: 10.0000 chunk 212 optimal weight: 7.9990 chunk 569 optimal weight: 1.9990 chunk 465 optimal weight: 3.9990 chunk 188 optimal weight: 8.9990 chunk 685 optimal weight: 9.9990 chunk 740 optimal weight: 7.9990 chunk 610 optimal weight: 3.9990 chunk 679 optimal weight: 7.9990 chunk 233 optimal weight: 0.9980 chunk 549 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN ** E 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 HIS ** G 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN ** M 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 58 GLN ** P 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 211 ASN U 8 HIS U 106 HIS ** W 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 74 GLN X 13 ASN ** X 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 38 ASN ** a 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 4 HIS j 27 HIS 2 21 ASN ** 2 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 173 ASN ** 2 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 393 ASN 2 469 ASN ** 3 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 117 ASN ** 4 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 174 ASN ** 5 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.268 62441 Z= 0.565 Angle : 1.579 51.128 84825 Z= 1.006 Chirality : 0.292 6.521 9509 Planarity : 0.005 0.117 10767 Dihedral : 7.571 178.734 8446 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.28 % Favored : 92.67 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.06 % 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: -1.93 (0.09), residues: 7587 helix: -0.49 (0.08), residues: 3845 sheet: -2.16 (0.28), residues: 300 loop : -2.11 (0.10), residues: 3442 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15174 Ramachandran restraints generated. 7587 Oldfield, 0 Emsley, 7587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15174 Ramachandran restraints generated. 7587 Oldfield, 0 Emsley, 7587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 6575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 927 time to evaluate : 5.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 929 average time/residue: 0.5864 time to fit residues: 936.2498 Evaluate side-chains 641 residues out of total 6575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 639 time to evaluate : 5.580 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4779 time to fit residues: 9.2119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 753 random chunks: chunk 676 optimal weight: 0.7980 chunk 515 optimal weight: 8.9990 chunk 355 optimal weight: 9.9990 chunk 75 optimal weight: 0.0470 chunk 326 optimal weight: 9.9990 chunk 459 optimal weight: 8.9990 chunk 687 optimal weight: 2.9990 chunk 727 optimal weight: 1.9990 chunk 359 optimal weight: 10.0000 chunk 651 optimal weight: 9.9990 chunk 196 optimal weight: 6.9990 overall best weight: 2.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN A 145 GLN A 222 ASN ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 ASN ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 58 GLN ** P 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 73 ASN ** S 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 13 ASN ** X 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 27 HIS 1 173 GLN 2 133 GLN 2 173 ASN ** 2 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 22 ASN 4 103 ASN 4 106 ASN ** 4 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 424 GLN ** 4 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 233 HIS ** 5 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 537 ASN 5 574 ASN ** 5 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 79 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.250 62441 Z= 0.514 Angle : 1.547 50.827 84825 Z= 0.991 Chirality : 0.292 6.540 9509 Planarity : 0.005 0.111 10767 Dihedral : 7.265 177.735 8446 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.48 % Favored : 93.48 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.06 % 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: -1.43 (0.09), residues: 7587 helix: -0.03 (0.08), residues: 3864 sheet: -2.05 (0.27), residues: 312 loop : -1.92 (0.11), residues: 3411 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15174 Ramachandran restraints generated. 7587 Oldfield, 0 Emsley, 7587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15174 Ramachandran restraints generated. 7587 Oldfield, 0 Emsley, 7587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 908 residues out of total 6575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 907 time to evaluate : 5.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 908 average time/residue: 0.5779 time to fit residues: 903.8372 Evaluate side-chains 639 residues out of total 6575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 639 time to evaluate : 5.730 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.3879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 753 random chunks: chunk 606 optimal weight: 20.0000 chunk 413 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 541 optimal weight: 0.9990 chunk 300 optimal weight: 3.9990 chunk 621 optimal weight: 0.2980 chunk 503 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 371 optimal weight: 8.9990 chunk 653 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN C 134 GLN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN ** M 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 GLN ** M 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 58 GLN ** P 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 73 ASN R 21 GLN ** S 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 13 ASN ** X 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 123 ASN ** a 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 27 HIS 2 173 ASN 2 180 ASN 2 469 ASN 3 53 ASN 4 106 ASN ** 4 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 270 GLN ** 4 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 79 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.255 62441 Z= 0.505 Angle : 1.537 50.803 84825 Z= 0.986 Chirality : 0.292 6.487 9509 Planarity : 0.004 0.109 10767 Dihedral : 7.050 177.908 8446 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.48 % Favored : 93.48 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 0.26 % Twisted General : 0.06 % 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: -1.18 (0.10), residues: 7587 helix: 0.21 (0.08), residues: 3856 sheet: -1.87 (0.26), residues: 332 loop : -1.83 (0.11), residues: 3399 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15174 Ramachandran restraints generated. 7587 Oldfield, 0 Emsley, 7587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15174 Ramachandran restraints generated. 7587 Oldfield, 0 Emsley, 7587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 903 residues out of total 6575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 901 time to evaluate : 5.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 903 average time/residue: 0.6027 time to fit residues: 931.4701 Evaluate side-chains 632 residues out of total 6575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 632 time to evaluate : 5.632 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.4476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 753 random chunks: chunk 244 optimal weight: 4.9990 chunk 655 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 427 optimal weight: 0.0050 chunk 179 optimal weight: 10.0000 chunk 728 optimal weight: 10.0000 chunk 604 optimal weight: 0.9990 chunk 337 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 241 optimal weight: 9.9990 chunk 382 optimal weight: 0.0050 overall best weight: 1.0014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN ** M 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 58 GLN ** P 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 73 ASN ** S 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 13 ASN ** X 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 27 HIS 2 173 ASN 2 180 ASN 3 53 ASN 3 85 ASN 4 106 ASN 4 153 HIS ** 4 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 16 HIS 8 79 GLN 9 24 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.257 62441 Z= 0.492 Angle : 1.532 50.812 84825 Z= 0.982 Chirality : 0.291 6.503 9509 Planarity : 0.004 0.109 10767 Dihedral : 6.926 179.301 8446 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.08 % Favored : 93.88 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 0.26 % Twisted General : 0.06 % 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: -1.02 (0.10), residues: 7587 helix: 0.32 (0.08), residues: 3856 sheet: -1.58 (0.27), residues: 317 loop : -1.76 (0.11), residues: 3414 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15174 Ramachandran restraints generated. 7587 Oldfield, 0 Emsley, 7587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15174 Ramachandran restraints generated. 7587 Oldfield, 0 Emsley, 7587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 6575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 907 time to evaluate : 5.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 909 average time/residue: 0.5897 time to fit residues: 928.2490 Evaluate side-chains 640 residues out of total 6575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 639 time to evaluate : 5.599 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5602 time to fit residues: 8.3962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 753 random chunks: chunk 702 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 415 optimal weight: 5.9990 chunk 532 optimal weight: 4.9990 chunk 412 optimal weight: 10.0000 chunk 613 optimal weight: 0.9990 chunk 406 optimal weight: 5.9990 chunk 725 optimal weight: 50.0000 chunk 454 optimal weight: 9.9990 chunk 442 optimal weight: 2.9990 chunk 335 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 58 GLN ** P 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 73 ASN ** S 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 18 GLN j 27 HIS n 64 ASN 2 133 GLN ** 2 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 106 ASN ** 4 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 112 HIS ** 5 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 79 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.246 62441 Z= 0.537 Angle : 1.558 50.865 84825 Z= 0.995 Chirality : 0.291 6.477 9509 Planarity : 0.005 0.102 10767 Dihedral : 6.895 178.733 8446 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.87 % Favored : 93.09 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 0.26 % Twisted General : 0.06 % 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: -0.93 (0.10), residues: 7587 helix: 0.39 (0.08), residues: 3882 sheet: -1.71 (0.26), residues: 336 loop : -1.69 (0.11), residues: 3369 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15174 Ramachandran restraints generated. 7587 Oldfield, 0 Emsley, 7587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15174 Ramachandran restraints generated. 7587 Oldfield, 0 Emsley, 7587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 6575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 831 time to evaluate : 5.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 832 average time/residue: 0.5785 time to fit residues: 835.5065 Evaluate side-chains 587 residues out of total 6575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 586 time to evaluate : 5.593 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5329 time to fit residues: 8.3915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 753 random chunks: chunk 449 optimal weight: 6.9990 chunk 289 optimal weight: 0.9980 chunk 433 optimal weight: 1.9990 chunk 218 optimal weight: 0.9990 chunk 142 optimal weight: 8.9990 chunk 140 optimal weight: 0.8980 chunk 461 optimal weight: 8.9990 chunk 494 optimal weight: 3.9990 chunk 358 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 570 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 210 ASN L 43 ASN ** M 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 58 GLN ** P 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 73 ASN ** S 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 109 ASN ** X 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 27 HIS 2 173 ASN ** 2 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 106 ASN ** 4 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 79 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.249 62441 Z= 0.498 Angle : 1.544 50.716 84825 Z= 0.987 Chirality : 0.292 6.493 9509 Planarity : 0.004 0.107 10767 Dihedral : 6.830 179.313 8446 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.16 % Favored : 93.81 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 0.26 % Twisted General : 0.06 % 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: -0.83 (0.10), residues: 7587 helix: 0.46 (0.08), residues: 3851 sheet: -1.59 (0.27), residues: 327 loop : -1.63 (0.11), residues: 3409 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15174 Ramachandran restraints generated. 7587 Oldfield, 0 Emsley, 7587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15174 Ramachandran restraints generated. 7587 Oldfield, 0 Emsley, 7587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 6575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 838 time to evaluate : 6.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 840 average time/residue: 0.5874 time to fit residues: 859.9857 Evaluate side-chains 611 residues out of total 6575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 609 time to evaluate : 5.588 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4942 time to fit residues: 9.3213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 753 random chunks: chunk 660 optimal weight: 0.9990 chunk 695 optimal weight: 5.9990 chunk 634 optimal weight: 0.8980 chunk 676 optimal weight: 0.7980 chunk 407 optimal weight: 0.6980 chunk 294 optimal weight: 3.9990 chunk 531 optimal weight: 0.0770 chunk 207 optimal weight: 5.9990 chunk 611 optimal weight: 5.9990 chunk 639 optimal weight: 2.9990 chunk 673 optimal weight: 0.4980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 GLN A 222 ASN ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 GLN L 43 ASN ** M 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 58 GLN ** P 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 73 ASN ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 53 GLN ** X 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 145 HIS j 27 HIS ** 2 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 22 ASN 4 106 ASN 4 207 GLN ** 4 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 529 ASN ** 5 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 136 GLN 8 79 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.250 62441 Z= 0.492 Angle : 1.541 50.675 84825 Z= 0.985 Chirality : 0.292 6.500 9509 Planarity : 0.004 0.107 10767 Dihedral : 6.701 177.888 8446 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.97 % Favored : 93.99 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 0.26 % Twisted General : 0.03 % 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: -0.76 (0.10), residues: 7587 helix: 0.51 (0.08), residues: 3857 sheet: -1.49 (0.27), residues: 325 loop : -1.59 (0.11), residues: 3405 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15174 Ramachandran restraints generated. 7587 Oldfield, 0 Emsley, 7587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15174 Ramachandran restraints generated. 7587 Oldfield, 0 Emsley, 7587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 6575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 879 time to evaluate : 5.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 879 average time/residue: 0.5900 time to fit residues: 900.3178 Evaluate side-chains 629 residues out of total 6575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 629 time to evaluate : 5.632 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.4273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 753 random chunks: chunk 444 optimal weight: 9.9990 chunk 715 optimal weight: 2.9990 chunk 436 optimal weight: 1.9990 chunk 339 optimal weight: 0.9990 chunk 497 optimal weight: 8.9990 chunk 750 optimal weight: 8.9990 chunk 690 optimal weight: 0.0980 chunk 597 optimal weight: 0.0040 chunk 62 optimal weight: 0.7980 chunk 461 optimal weight: 1.9990 chunk 366 optimal weight: 7.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 GLN A 222 ASN ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 HIS ** E 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 286 HIS F 134 GLN ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN ** M 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 58 GLN ** P 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 73 ASN ** S 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 18 GLN W 109 ASN ** a 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 27 HIS 2 173 ASN 3 22 ASN 4 106 ASN 4 320 ASN ** 4 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 100 HIS ** 5 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 158 ASN 8 79 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.249 62441 Z= 0.494 Angle : 1.544 50.695 84825 Z= 0.986 Chirality : 0.291 6.498 9509 Planarity : 0.005 0.136 10767 Dihedral : 6.633 177.341 8446 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.81 % Favored : 94.15 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 0.26 % Twisted General : 0.03 % 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: -0.74 (0.10), residues: 7587 helix: 0.50 (0.09), residues: 3838 sheet: -1.43 (0.27), residues: 323 loop : -1.55 (0.11), residues: 3426 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15174 Ramachandran restraints generated. 7587 Oldfield, 0 Emsley, 7587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15174 Ramachandran restraints generated. 7587 Oldfield, 0 Emsley, 7587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 6575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 855 time to evaluate : 5.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 856 average time/residue: 0.6159 time to fit residues: 921.6736 Evaluate side-chains 630 residues out of total 6575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 629 time to evaluate : 5.636 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4636 time to fit residues: 8.4069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 753 random chunks: chunk 474 optimal weight: 5.9990 chunk 636 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 550 optimal weight: 6.9990 chunk 88 optimal weight: 0.0770 chunk 166 optimal weight: 6.9990 chunk 598 optimal weight: 0.9980 chunk 250 optimal weight: 2.9990 chunk 614 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 110 optimal weight: 0.9980 overall best weight: 1.1940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN ** M 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 58 GLN ** P 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 73 ASN ** S 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 62 HIS j 27 HIS ** 2 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 22 ASN 4 106 ASN 4 320 ASN ** 4 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 174 ASN ** 5 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 79 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.042858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.034495 restraints weight = 413524.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.035702 restraints weight = 216269.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.036526 restraints weight = 138076.936| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.249 62441 Z= 0.495 Angle : 1.539 50.681 84825 Z= 0.985 Chirality : 0.291 6.486 9509 Planarity : 0.004 0.102 10767 Dihedral : 6.566 176.840 8446 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.85 % Favored : 94.11 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 0.26 % Twisted General : 0.03 % 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: -0.68 (0.10), residues: 7587 helix: 0.54 (0.09), residues: 3843 sheet: -1.40 (0.27), residues: 335 loop : -1.50 (0.11), residues: 3409 =============================================================================== Job complete usr+sys time: 14738.50 seconds wall clock time: 259 minutes 59.41 seconds (15599.41 seconds total)