Starting phenix.real_space_refine on Sat Dec 9 05:53:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfq_4872/12_2023/6rfq_4872_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfq_4872/12_2023/6rfq_4872.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfq_4872/12_2023/6rfq_4872_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfq_4872/12_2023/6rfq_4872_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfq_4872/12_2023/6rfq_4872_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfq_4872/12_2023/6rfq_4872.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfq_4872/12_2023/6rfq_4872.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfq_4872/12_2023/6rfq_4872_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfq_4872/12_2023/6rfq_4872_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 28 7.16 5 P 32 5.49 5 S 300 5.16 5 C 40281 2.51 5 N 10136 2.21 5 O 11275 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 150": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "A TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A ARG 315": "NH1" <-> "NH2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 705": "NH1" <-> "NH2" Residue "B ARG 113": "NH1" <-> "NH2" 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 54": "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 269": "NH1" <-> "NH2" Residue "C ARG 274": "NH1" <-> "NH2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 162": "NH1" <-> "NH2" Residue "E ARG 201": "NH1" <-> "NH2" Residue "E ARG 208": "NH1" <-> "NH2" Residue "G ARG 63": "NH1" <-> "NH2" Residue "G PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "H ARG 216": "NH1" <-> "NH2" Residue "I ARG 59": "NH1" <-> "NH2" Residue "I ARG 197": "NH1" <-> "NH2" Residue "J ARG 55": "NH1" <-> "NH2" Residue "J ARG 91": "NH1" <-> "NH2" Residue "J ARG 143": "NH1" <-> "NH2" Residue "J ARG 183": "NH1" <-> "NH2" Residue "K ARG 102": "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 "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 120": "NH1" <-> "NH2" Residue "S ARG 135": "NH1" <-> "NH2" Residue "S ARG 188": "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 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 "Y ARG 54": "NH1" <-> "NH2" Residue "Y ARG 79": "NH1" <-> "NH2" Residue "Y ARG 90": "NH1" <-> "NH2" Residue "Y ARG 140": "NH1" <-> "NH2" Residue "Y ARG 159": "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 16": "NH1" <-> "NH2" Residue "e ARG 41": "NH1" <-> "NH2" Residue "f ARG 6": "NH1" <-> "NH2" Residue "f ARG 9": "NH1" <-> "NH2" Residue "f PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "i TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 53": "NH1" <-> "NH2" Residue "i ARG 55": "NH1" <-> "NH2" Residue "i ARG 75": "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 "k ARG 62": "NH1" <-> "NH2" Residue "k ARG 88": "NH1" <-> "NH2" Residue "k ARG 91": "NH1" <-> "NH2" Residue "k ARG 106": "NH1" <-> "NH2" Residue "n TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 250": "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 "5 TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 115": "NH1" <-> "NH2" Residue "5 ARG 303": "NH1" <-> "NH2" Residue "5 ASP 478": "OD1" <-> "OD2" Residue "5 ARG 594": "NH1" <-> "NH2" Residue "5 ARG 611": "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" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 62052 Number of models: 1 Model: "" Number of chains: 59 Chain: "A" Number of atoms: 5274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5274 Classifications: {'peptide': 694} Link IDs: {'PTRANS': 34, 'TRANS': 659} Chain: "B" Number of atoms: 3421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3421 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} Chain: "C" Number of atoms: 3415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3415 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 23, 'TRANS': 406} Chain breaks: 1 Chain: "D" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 681 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "E" Number of atoms: 2075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2075 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 9, 'TRANS': 253} Chain breaks: 3 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: 1739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1739 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 15, 'TRANS': 194} Chain: "H" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1680 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 18, 'TRANS': 196} 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: 1329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1329 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain: "K" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1190 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 12, 'TRANS': 140} Chain breaks: 2 Chain: "L" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 691 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} 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: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1036 Classifications: {'peptide': 123} 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: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} 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: {'CIS': 1, 'PTRANS': 6, 'TRANS': 166} Chain breaks: 2 Chain: "U" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1345 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "W" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 961 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 9, 'TRANS': 109} Chain: "X" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1305 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 11, 'TRANS': 156} Chain: "Y" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1021 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "Z" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 922 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 10, 'TRANS': 109} 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: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 760 Classifications: {'peptide': 90} 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: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 620 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} 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: "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: "k" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 828 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 9, 'TRANS': 88} Chain breaks: 1 Chain: "n" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 914 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 9, 'TRANS': 104} Chain: "1" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2540 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 13, 'TRANS': 304} Chain breaks: 2 Chain: "2" Number of atoms: 3774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3774 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 7, 'TRANS': 461} Chain: "3" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 869 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain breaks: 1 Chain: "4" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3855 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 14, 'TRANS': 471} Chain: "5" Number of atoms: 5197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 654, 5197 Classifications: {'peptide': 654} Link IDs: {'PTRANS': 15, 'TRANS': 638} Chain: "6" Number of atoms: 1443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1443 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 3, 'TRANS': 179} Chain: "8" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 672 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "9" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} 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: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 232 Unusual residues: {'3PE': 2, 'CDL': 1, 'LMN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 39 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: "O" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Chain: "Q" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Chain: "W" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'PLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "X" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 82 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "g" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 126 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "j" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 65 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "n" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'CPL': 1, 'T7X': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "4" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 271 Unusual residues: {'3PE': 3, 'CDL': 1, 'T7X': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'T7X:plan-5': 1, 'T7X:plan-4': 1, 'T7X:plan-6': 1} Unresolved non-hydrogen planarities: 9 Chain: "5" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 124 Unusual residues: {'3PE': 2, 'PLC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "6" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 809 SG CYS A 142 63.954 151.249 161.700 1.00 26.99 S ATOM 749 SG CYS A 133 61.707 154.081 156.623 1.00 21.32 S ATOM 769 SG CYS A 136 65.614 156.869 160.504 1.00 26.08 S ATOM 1163 SG CYS A 186 62.955 151.911 172.965 1.00 29.18 S ATOM 1139 SG CYS A 183 60.602 157.331 171.449 1.00 29.56 S ATOM 1187 SG CYS A 189 65.388 156.913 176.007 1.00 32.14 S ATOM 1511 SG CYS A 233 65.828 155.107 169.543 1.00 26.81 S ATOM 255 SG CYS A 69 59.973 146.388 175.886 1.00 29.27 S ATOM 338 SG CYS A 80 58.433 145.274 173.001 1.00 29.77 S ATOM 363 SG CYS A 83 58.130 139.707 174.560 1.00 34.27 S ATOM 465 SG CYS A 97 59.348 141.529 177.896 1.00 34.91 S ATOM 8015 SG CYS B 384 49.610 148.954 177.047 1.00 36.24 S ATOM 8035 SG CYS B 387 45.185 151.526 176.761 1.00 39.31 S ATOM 7996 SG CYS B 381 49.623 153.514 181.615 1.00 46.43 S ATOM 8366 SG CYS B 427 46.182 149.160 182.225 1.00 39.57 S ATOM 18412 SG CYS H 127 32.006 165.005 184.671 1.00 77.48 S ATOM 18446 SG CYS H 132 28.532 165.328 184.969 1.00 75.33 S ATOM 18715 SG CYS H 168 32.528 160.287 186.952 1.00 74.52 S ATOM 18738 SG CYS H 172 29.585 159.452 187.690 1.00 79.31 S ATOM 20332 SG CYS I 172 68.131 149.666 134.950 1.00 25.78 S ATOM 20306 SG CYS I 169 72.053 154.218 132.376 1.00 27.62 S ATOM 20354 SG CYS I 175 67.613 155.753 136.591 1.00 20.80 S ATOM 20079 SG CYS I 140 72.993 151.585 137.716 1.00 16.98 S ATOM 20384 SG CYS I 179 63.938 160.133 143.351 1.00 24.00 S ATOM 20051 SG CYS I 136 69.976 157.550 142.645 1.00 18.78 S ATOM 20009 SG CYS I 130 69.281 163.287 144.504 1.00 34.39 S ATOM 20028 SG CYS I 133 66.255 158.649 147.881 1.00 22.64 S ATOM 22897 SG CYS K 150 77.201 145.756 126.615 1.00 24.33 S ATOM 22417 SG CYS K 86 74.593 147.724 120.876 1.00 35.26 S ATOM 22411 SG CYS K 85 72.519 142.381 123.323 1.00 33.00 S ATOM 23125 SG CYS K 180 72.882 147.692 126.989 1.00 29.64 S Time building chain proxies: 23.85, per 1000 atoms: 0.38 Number of scatterers: 62052 At special positions: 0 Unit cell: (214.323, 198.168, 232.632, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 28 26.01 S 300 16.00 P 32 15.00 O 11275 8.00 N 10136 7.00 C 40281 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=2.05 Simple disulfide: pdb=" SG CYS U 56 " - pdb=" SG CYS U 68 " distance=2.00 Simple disulfide: pdb=" SG CYS U 90 " - pdb=" SG CYS U 121 " distance=1.98 Simple disulfide: pdb=" SG CYS U 100 " - pdb=" SG CYS U 111 " distance=2.05 Simple disulfide: pdb=" SG CYS d 51 " - pdb=" SG CYS d 63 " distance=2.10 Simple disulfide: pdb=" SG CYS 8 26 " - pdb=" SG CYS 8 57 " distance=2.14 Simple disulfide: pdb=" SG CYS 8 36 " - pdb=" SG CYS 8 47 " distance=2.11 Simple disulfide: pdb=" SG CYS 9 15 " - pdb=" SG CYS 9 47 " distance=2.07 Simple disulfide: pdb=" SG CYS 9 25 " - pdb=" SG CYS 9 37 " distance=2.10 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.07 Conformation dependent library (CDL) restraints added in 7.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 803 " pdb="FE1 FES A 803 " - pdb=" SG CYS A 69 " pdb="FE2 FES A 803 " - pdb=" SG CYS A 83 " pdb="FE2 FES A 803 " - pdb=" SG CYS A 97 " pdb="FE1 FES A 803 " - pdb=" SG CYS A 80 " 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="FE1 FES H 301 " - pdb=" SG CYS H 132 " pdb="FE2 FES H 301 " - pdb=" SG CYS H 168 " pdb=" SF4 A 801 " pdb="FE3 SF4 A 801 " - pdb=" NE2 HIS A 129 " pdb="FE1 SF4 A 801 " - pdb=" SG CYS A 142 " pdb="FE4 SF4 A 801 " - pdb=" SG CYS A 136 " pdb="FE2 SF4 A 801 " - pdb=" SG CYS A 133 " pdb=" SF4 A 802 " pdb="FE1 SF4 A 802 " - pdb=" SG CYS A 186 " pdb="FE4 SF4 A 802 " - pdb=" SG CYS A 233 " pdb="FE3 SF4 A 802 " - pdb=" SG CYS A 189 " pdb="FE2 SF4 A 802 " - pdb=" SG CYS A 183 " pdb=" SF4 B 501 " pdb="FE4 SF4 B 501 " - pdb=" SG CYS B 427 " pdb="FE1 SF4 B 501 " - pdb=" SG CYS B 384 " pdb="FE2 SF4 B 501 " - pdb=" SG CYS B 387 " pdb="FE3 SF4 B 501 " - pdb=" SG CYS B 381 " pdb=" SF4 I 301 " pdb="FE2 SF4 I 301 " - pdb=" SG CYS I 169 " pdb="FE4 SF4 I 301 " - pdb=" SG CYS I 140 " pdb="FE3 SF4 I 301 " - pdb=" SG CYS I 175 " pdb="FE1 SF4 I 301 " - pdb=" SG CYS I 172 " pdb=" SF4 I 302 " pdb="FE1 SF4 I 302 " - pdb=" SG CYS I 179 " pdb="FE3 SF4 I 302 " - pdb=" SG CYS I 130 " pdb="FE2 SF4 I 302 " - pdb=" SG CYS I 136 " pdb="FE4 SF4 I 302 " - pdb=" SG CYS I 133 " pdb=" SF4 K 301 " pdb="FE2 SF4 K 301 " - pdb=" SG CYS K 86 " pdb="FE4 SF4 K 301 " - pdb=" SG CYS K 180 " pdb="FE3 SF4 K 301 " - pdb=" SG CYS K 85 " pdb="FE1 SF4 K 301 " - pdb=" SG CYS K 150 " Number of angles added : 81 15062 Ramachandran restraints generated. 7531 Oldfield, 0 Emsley, 7531 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14282 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 302 helices and 30 sheets defined 49.7% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.07 Creating SS restraints... Processing helix chain 'A' and resid 54 through 61 Processing helix chain 'A' and resid 112 through 125 Processing helix chain 'A' and resid 143 through 150 removed outlier: 3.859A pdb=" N MET A 149 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 3.707A 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 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 295 through 298 No H-bonds generated for 'chain 'A' and resid 295 through 298' Processing helix chain 'A' and resid 325 through 339 removed outlier: 3.671A pdb=" N ALA A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 369 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 406 Processing helix chain 'A' and resid 422 through 434 removed outlier: 3.633A pdb=" N ALA A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 468 Processing helix chain 'A' and resid 470 through 476 removed outlier: 4.333A pdb=" N LYS A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 507 removed outlier: 3.724A pdb=" N THR A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE A 501 " --> pdb=" O PHE A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 534 removed outlier: 3.992A pdb=" N TYR A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A 534 " --> pdb=" O GLY A 530 " (cutoff:3.500A) No H-bonds generated for '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: 3.684A pdb=" N LEU A 626 " --> pdb=" O ASP A 622 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU A 631 " --> pdb=" O ARG A 627 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 652 Processing helix chain 'A' and resid 668 through 678 removed outlier: 3.602A pdb=" N GLN A 673 " --> pdb=" O ASP A 669 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY A 678 " --> pdb=" O HIS A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 716 removed outlier: 4.245A pdb=" N ILE A 715 " --> pdb=" O ALA A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 38 No H-bonds generated for 'chain 'B' and resid 36 through 38' Processing helix chain 'B' and resid 52 through 58 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 72 through 82 removed outlier: 3.635A pdb=" N LYS B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 106 through 109 removed outlier: 3.866A pdb=" N ASN B 109 " --> pdb=" O TRP B 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 106 through 109' Processing helix chain 'B' and resid 128 through 133 removed outlier: 3.584A pdb=" N MET B 133 " --> pdb=" O ASP B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 150 removed outlier: 4.022A pdb=" N ALA B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 180 removed outlier: 3.526A pdb=" N GLN B 172 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR B 173 " --> pdb=" O ALA B 169 " (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 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 266 removed outlier: 3.612A pdb=" N SER B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 342 through 345 No H-bonds generated for 'chain 'B' and resid 342 through 345' Processing helix chain 'B' and resid 365 through 379 removed outlier: 3.878A pdb=" N PHE B 372 " --> pdb=" O ALA B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 403 removed outlier: 3.923A pdb=" N THR B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR B 403 " --> pdb=" O ASP B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 422 Processing helix chain 'B' and resid 429 through 443 removed outlier: 3.566A pdb=" N TRP B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) Proline residue: B 436 - end of helix Processing helix chain 'B' and resid 445 through 458 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 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 123 through 129 removed outlier: 3.969A pdb=" N ILE C 127 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU C 128 " --> pdb=" O GLU C 124 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TYR C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 123 through 129' Processing helix chain 'C' and resid 132 through 135 No H-bonds generated for 'chain 'C' and resid 132 through 135' Processing helix chain 'C' and resid 138 through 141 No H-bonds generated for 'chain 'C' and resid 138 through 141' Processing helix chain 'C' and resid 147 through 162 removed outlier: 3.862A pdb=" N PHE C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU C 159 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 197 removed outlier: 3.888A pdb=" N CYS C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET C 195 " --> pdb=" O CYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 218 removed outlier: 3.612A pdb=" N GLU C 208 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU C 209 " --> pdb=" O TRP C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 266 removed outlier: 3.972A pdb=" N GLN C 253 " --> pdb=" O MET C 249 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASP C 256 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE C 261 " --> pdb=" O ARG C 257 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU C 265 " --> pdb=" O ILE C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 274 Processing helix chain 'C' and resid 285 through 288 No H-bonds generated for 'chain 'C' and resid 285 through 288' Processing helix chain 'C' and resid 329 through 352 removed outlier: 4.052A pdb=" N ARG C 341 " --> pdb=" O MET C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 376 No H-bonds generated for 'chain 'C' and resid 373 through 376' Processing helix chain 'C' and resid 378 through 389 Processing helix chain 'C' and resid 430 through 436 removed outlier: 3.571A 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 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' 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 Processing helix chain 'D' and resid 44 through 57 Processing helix chain 'E' and resid 64 through 76 removed outlier: 4.290A pdb=" N TYR E 68 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N HIS E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 112 through 119 removed outlier: 3.556A pdb=" N VAL E 119 " --> pdb=" O ILE E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 144 Processing helix chain 'E' and resid 146 through 158 Processing helix chain 'E' and resid 178 through 193 Processing helix chain 'E' and resid 238 through 250 removed outlier: 3.788A pdb=" N PHE E 250 " --> pdb=" O GLU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 276 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 345 removed outlier: 4.648A pdb=" N PHE E 345 " --> pdb=" O PRO E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 369 No H-bonds generated for 'chain 'E' and resid 366 through 369' Processing helix chain 'F' and resid 42 through 60 Processing helix chain 'F' and resid 66 through 84 removed outlier: 3.688A pdb=" N ILE F 81 " --> pdb=" O HIS F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 95 Processing helix chain 'F' and resid 100 through 120 removed outlier: 3.715A pdb=" N SER F 118 " --> pdb=" O ALA F 114 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 81 removed outlier: 3.594A pdb=" N GLN G 73 " --> pdb=" O SER G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 114 removed outlier: 3.575A pdb=" N VAL G 105 " --> pdb=" O PRO G 102 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ILE G 106 " --> pdb=" O SER G 103 " (cutoff:3.500A) Proline residue: G 107 - end of helix removed outlier: 3.588A pdb=" N ASP G 114 " --> pdb=" O PHE G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 186 removed outlier: 4.138A pdb=" N ASN G 176 " --> pdb=" O GLU G 173 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TRP G 177 " --> pdb=" O GLY G 174 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG G 180 " --> pdb=" O TRP G 177 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET G 185 " --> pdb=" O ALA G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 266 No H-bonds generated for 'chain 'G' and resid 264 through 266' Processing helix chain 'H' and resid 49 through 61 removed outlier: 3.740A pdb=" N LYS H 61 " --> pdb=" O GLU H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 81 removed outlier: 4.340A pdb=" N MET H 72 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Proline residue: H 73 - end of helix removed outlier: 4.081A pdb=" N ASP H 76 " --> pdb=" O PRO H 73 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN H 81 " --> pdb=" O GLY H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 96 Processing helix chain 'H' and resid 101 through 110 removed outlier: 3.917A pdb=" N VAL H 107 " --> pdb=" O ARG H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 133 No H-bonds generated for 'chain 'H' and resid 130 through 133' Processing helix chain 'H' and resid 137 through 147 Processing helix chain 'H' and resid 190 through 202 removed outlier: 3.929A pdb=" N VAL H 194 " --> pdb=" O PRO H 190 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS H 195 " --> pdb=" O GLU H 191 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU H 196 " --> pdb=" O GLY H 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 79 removed outlier: 3.566A pdb=" N LYS I 76 " --> pdb=" O SER I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 95 removed outlier: 3.793A pdb=" N ARG I 85 " --> pdb=" O ALA I 81 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE I 95 " --> pdb=" O LEU I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 139 No H-bonds generated for 'chain 'I' and resid 136 through 139' Processing helix chain 'I' and resid 174 through 178 Processing helix chain 'I' and resid 204 through 213 Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'J' and resid 25 through 49 removed outlier: 3.647A pdb=" N SER J 49 " --> pdb=" O ALA J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 60 No H-bonds generated for 'chain 'J' and resid 58 through 60' Processing helix chain 'J' and resid 67 through 89 removed outlier: 3.679A pdb=" N SER J 75 " --> pdb=" O PHE J 71 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL J 79 " --> pdb=" O SER J 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 109 Processing helix chain 'J' and resid 115 through 135 removed outlier: 3.762A pdb=" N THR J 135 " --> pdb=" O LEU J 131 " (cutoff:3.500A) 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 178 removed outlier: 3.584A pdb=" N GLU J 177 " --> pdb=" O SER J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 190 through 193 No H-bonds generated for 'chain 'J' and resid 190 through 193' Processing helix chain 'K' and resid 66 through 73 Processing helix chain 'K' and resid 85 through 93 removed outlier: 3.594A pdb=" N MET K 90 " --> pdb=" O ALA K 87 " (cutoff:3.500A) 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 201 Processing helix chain 'L' and resid 2 through 16 Processing helix chain 'L' and resid 23 through 47 removed outlier: 3.538A pdb=" N LEU L 33 " --> pdb=" O LEU L 29 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE L 39 " --> pdb=" O GLY L 35 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG L 42 " --> pdb=" O LEU L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 80 removed outlier: 3.823A pdb=" N ILE L 61 " --> pdb=" O ILE L 57 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU L 80 " --> pdb=" O SER L 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 42 removed outlier: 3.747A 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: 3.929A pdb=" N VAL O 74 " --> pdb=" O VAL O 70 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU O 79 " --> pdb=" O ALA O 75 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE O 80 " --> pdb=" O ILE O 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 104 removed outlier: 5.141A pdb=" N LEU O 103 " --> pdb=" O VAL O 99 " (cutoff:3.500A) removed outlier: 6.011A 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: 3.880A pdb=" N ALA P 40 " --> pdb=" O ALA P 36 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP P 41 " --> pdb=" O PRO P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 61 Processing helix chain 'P' and resid 69 through 87 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: 4.324A pdb=" N LYS P 121 " --> pdb=" O ASP P 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 65 removed outlier: 3.558A pdb=" N SER Q 65 " --> pdb=" O ALA Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 102 Processing helix chain 'Q' and resid 118 through 127 removed outlier: 3.785A pdb=" N ALA Q 127 " --> pdb=" O ASP Q 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 27 removed outlier: 3.747A pdb=" N LEU R 14 " --> pdb=" O ALA R 10 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA R 26 " --> pdb=" O SER R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 49 Processing helix chain 'R' and resid 56 through 72 Processing helix chain 'S' and resid 53 through 65 removed outlier: 3.863A pdb=" N LYS S 60 " --> pdb=" O GLU S 56 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLN S 65 " --> pdb=" O GLN S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 88 through 99 removed outlier: 3.633A pdb=" N ALA S 92 " --> pdb=" O LEU S 88 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU S 93 " --> pdb=" O ALA S 89 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA S 96 " --> pdb=" O ALA S 92 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR S 98 " --> pdb=" O ILE S 94 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS S 99 " --> pdb=" O ALA S 95 " (cutoff:3.500A) Processing helix chain 'S' and resid 113 through 136 removed outlier: 3.710A pdb=" N LEU S 118 " --> pdb=" O LYS S 114 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP S 128 " --> pdb=" O ALA S 124 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY S 133 " --> pdb=" O TYR S 129 " (cutoff:3.500A) Processing helix chain 'S' and resid 165 through 169 removed outlier: 3.604A pdb=" N TYR S 169 " --> pdb=" O VAL S 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 165 through 169' Processing helix chain 'S' and resid 172 through 186 removed outlier: 3.714A pdb=" N LEU S 180 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing helix chain 'S' and resid 191 through 206 removed outlier: 3.982A pdb=" N LYS S 197 " --> pdb=" O PHE S 193 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS S 206 " --> pdb=" O ARG S 202 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 211 Processing helix chain 'S' and resid 218 through 228 removed outlier: 4.057A pdb=" N VAL S 223 " --> pdb=" O ASP S 219 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU S 224 " --> pdb=" O ALA S 220 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG S 225 " --> pdb=" O LEU S 221 " (cutoff:3.500A) 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 72 through 101 removed outlier: 3.887A pdb=" N THR U 76 " --> pdb=" O GLY U 72 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ASP U 92 " --> pdb=" O LYS U 88 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N GLU U 93 " --> pdb=" O SER U 89 " (cutoff:3.500A) 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 125 removed outlier: 3.769A pdb=" N LEU U 117 " --> pdb=" O LYS U 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 142 through 144 No H-bonds generated for 'chain 'U' and resid 142 through 144' Processing helix chain 'U' and resid 157 through 169 Processing helix chain 'W' and resid 30 through 95 Proline residue: W 71 - end of helix Processing helix chain 'X' and resid 28 through 34 Processing helix chain 'X' and resid 37 through 60 removed outlier: 3.526A pdb=" N VAL X 42 " --> pdb=" O SER X 38 " (cutoff:3.500A) removed outlier: 3.631A 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 99 removed outlier: 3.609A pdb=" N VAL X 77 " --> pdb=" O LYS X 73 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE X 98 " --> pdb=" O SER X 94 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE X 99 " --> pdb=" O SER X 95 " (cutoff:3.500A) Processing helix chain 'X' and resid 108 through 119 removed outlier: 3.635A pdb=" N MET X 115 " --> pdb=" O ASP X 111 " (cutoff:3.500A) Processing helix chain 'X' and resid 133 through 142 Processing helix chain 'Y' and resid 51 through 54 No H-bonds generated for 'chain 'Y' and resid 51 through 54' Processing helix chain 'Y' and resid 115 through 124 Processing helix chain 'Y' and resid 144 through 147 Processing helix chain 'Z' and resid 91 through 99 removed outlier: 3.726A pdb=" N THR Z 95 " --> pdb=" O GLN Z 91 " (cutoff:3.500A) Processing helix chain 'Z' and resid 111 through 123 removed outlier: 4.046A pdb=" N THR Z 115 " --> pdb=" O GLY Z 111 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS Z 116 " --> pdb=" O GLU Z 112 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN Z 120 " --> pdb=" O LYS Z 116 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE Z 121 " --> pdb=" O ALA Z 117 " (cutoff:3.500A) Processing helix chain 'Z' and resid 128 through 133 Processing helix chain 'Z' and resid 137 through 143 Processing helix chain 'a' and resid 28 through 33 removed outlier: 3.595A pdb=" N ALA a 32 " --> pdb=" O SER a 28 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU a 33 " --> pdb=" O PHE a 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 28 through 33' 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 112 removed outlier: 3.568A pdb=" N ALA a 107 " --> pdb=" O ILE a 103 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR a 109 " --> pdb=" O PHE a 105 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR a 112 " --> pdb=" O SER a 108 " (cutoff:3.500A) Processing helix chain 'a' and resid 127 through 130 No H-bonds generated for 'chain 'a' and resid 127 through 130' Processing helix chain 'b' and resid 3 through 24 removed outlier: 3.820A pdb=" N ALA b 10 " --> pdb=" O SER b 6 " (cutoff:3.500A) Processing helix chain 'b' and resid 35 through 64 removed outlier: 3.788A pdb=" N LYS b 64 " --> pdb=" O VAL b 60 " (cutoff:3.500A) Processing helix chain 'c' and resid 11 through 14 removed outlier: 3.813A pdb=" N ALA c 14 " --> pdb=" O ARG c 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 11 through 14' Processing helix chain 'c' and resid 34 through 47 removed outlier: 4.160A pdb=" N VAL c 39 " --> pdb=" O GLY c 35 " (cutoff:3.500A) Processing helix chain 'd' and resid 20 through 55 removed outlier: 3.624A pdb=" N ALA d 40 " --> pdb=" O ILE d 36 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU d 41 " --> pdb=" O ARG d 37 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS d 46 " --> pdb=" O LYS d 42 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS d 50 " --> pdb=" O LYS d 46 " (cutoff:3.500A) Processing helix chain 'd' and resid 58 through 62 removed outlier: 3.852A pdb=" N ASP d 62 " --> pdb=" O HIS d 59 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 73 Processing helix chain 'd' and resid 83 through 86 No H-bonds generated for 'chain 'd' and resid 83 through 86' Processing helix chain 'e' and resid 21 through 50 removed outlier: 3.591A pdb=" N GLU e 45 " --> pdb=" O ARG e 41 " (cutoff:3.500A) Proline residue: e 47 - end of helix Processing helix chain 'f' and resid 20 through 28 removed outlier: 3.543A pdb=" N ASN f 28 " --> pdb=" O GLN f 24 " (cutoff:3.500A) Processing helix chain 'f' and resid 30 through 36 removed outlier: 3.997A pdb=" N LYS f 35 " --> pdb=" O GLY f 31 " (cutoff:3.500A) Processing helix chain 'f' and resid 73 through 83 Processing helix chain 'g' and resid 12 through 22 removed outlier: 3.583A pdb=" N HIS g 21 " --> pdb=" O ARG g 17 " (cutoff:3.500A) Processing helix chain 'g' and resid 24 through 37 removed outlier: 4.404A pdb=" N ALA g 29 " --> pdb=" O HIS g 25 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE g 30 " --> pdb=" O LEU g 26 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE g 32 " --> pdb=" O PHE g 28 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY g 33 " --> pdb=" O ALA g 29 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA g 35 " --> pdb=" O ALA g 31 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY g 36 " --> pdb=" O ILE g 32 " (cutoff:3.500A) Proline residue: g 37 - end of helix Processing helix chain 'g' and resid 44 through 50 Processing helix chain 'i' and resid 26 through 47 removed outlier: 3.651A pdb=" N LEU i 31 " --> pdb=" O LYS i 27 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE i 32 " --> pdb=" O LEU i 28 " (cutoff:3.500A) Processing helix chain 'i' and resid 61 through 77 Processing helix chain 'j' and resid 30 through 40 Processing helix chain 'j' and resid 42 through 44 No H-bonds generated for 'chain 'j' and resid 42 through 44' Processing helix chain 'j' and resid 50 through 60 Processing helix chain 'j' and resid 62 through 73 Processing helix chain 'k' and resid 81 through 87 removed outlier: 4.154A pdb=" N GLN k 85 " --> pdb=" O PRO k 81 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TRP k 86 " --> pdb=" O GLN k 82 " (cutoff:3.500A) Processing helix chain 'k' and resid 97 through 120 removed outlier: 3.681A pdb=" N ALA k 112 " --> pdb=" O GLU k 108 " (cutoff:3.500A) Processing helix chain 'n' and resid 19 through 39 Processing helix chain 'n' and resid 50 through 53 Processing helix chain 'n' and resid 59 through 61 No H-bonds generated for 'chain 'n' and resid 59 through 61' Processing helix chain 'n' and resid 63 through 88 removed outlier: 3.778A pdb=" N ILE n 69 " --> pdb=" O GLU n 65 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN n 76 " --> pdb=" O ALA n 72 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS n 87 " --> pdb=" O MET n 83 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ARG n 88 " --> pdb=" O HIS n 84 " (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 2 through 33 removed outlier: 4.149A pdb=" N GLU 1 7 " --> pdb=" O ILE 1 3 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA 1 20 " --> pdb=" O LEU 1 16 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR 1 23 " --> pdb=" O VAL 1 19 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG 1 27 " --> pdb=" O THR 1 23 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 59 removed outlier: 3.734A pdb=" N GLN 1 49 " --> pdb=" O GLY 1 46 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE 1 51 " --> pdb=" O LEU 1 48 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP 1 53 " --> pdb=" O ALA 1 50 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU 1 57 " --> pdb=" O ALA 1 54 " (cutoff:3.500A) Processing helix chain '1' and resid 72 through 88 Proline residue: 1 77 - end of helix removed outlier: 4.095A pdb=" N GLY 1 87 " --> pdb=" O THR 1 83 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N TRP 1 88 " --> pdb=" O ALA 1 84 " (cutoff:3.500A) Processing helix chain '1' and resid 105 through 125 removed outlier: 4.725A pdb=" N VAL 1 117 " --> pdb=" O GLY 1 113 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N PHE 1 118 " --> pdb=" O SER 1 114 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N GLY 1 119 " --> pdb=" O LEU 1 115 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N SER 1 120 " --> pdb=" O GLY 1 116 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU 1 121 " --> pdb=" O VAL 1 117 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY 1 124 " --> pdb=" O SER 1 120 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TRP 1 125 " --> pdb=" O LEU 1 121 " (cutoff:3.500A) Processing helix chain '1' and resid 130 through 161 removed outlier: 4.131A pdb=" N ILE 1 149 " --> pdb=" O SER 1 145 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE 1 160 " --> pdb=" O ILE 1 156 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL 1 161 " --> pdb=" O ILE 1 157 " (cutoff:3.500A) Processing helix chain '1' and resid 166 through 175 removed outlier: 5.109A pdb=" N VAL 1 175 " --> pdb=" O GLU 1 171 " (cutoff:3.500A) Processing helix chain '1' and resid 178 through 181 No H-bonds generated for 'chain '1' and resid 178 through 181' Processing helix chain '1' and resid 183 through 196 Processing helix chain '1' and resid 224 through 245 removed outlier: 3.600A pdb=" N TYR 1 232 " --> pdb=" O PHE 1 228 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU 1 245 " --> pdb=" O PHE 1 241 " (cutoff:3.500A) Processing helix chain '1' and resid 256 through 262 removed outlier: 3.799A pdb=" N ASN 1 260 " --> pdb=" O SER 1 256 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE 1 261 " --> pdb=" O TYR 1 257 " (cutoff:3.500A) Processing helix chain '1' and resid 268 through 298 removed outlier: 3.709A pdb=" N LYS 1 285 " --> pdb=" O ALA 1 281 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE 1 294 " --> pdb=" O MET 1 290 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA 1 298 " --> pdb=" O ILE 1 294 " (cutoff:3.500A) Processing helix chain '1' and resid 305 through 313 Processing helix chain '1' and resid 316 through 333 Proline residue: 1 328 - end of helix Processing helix chain '2' and resid 3 through 15 removed outlier: 3.781A pdb=" N SER 2 8 " --> pdb=" O LEU 2 4 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR 2 11 " --> pdb=" O ILE 2 7 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET 2 15 " --> pdb=" O THR 2 11 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 38 removed outlier: 3.851A pdb=" N ASN 2 21 " --> pdb=" O LEU 2 18 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ARG 2 22 " --> pdb=" O SER 2 19 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU 2 38 " --> pdb=" O VAL 2 35 " (cutoff:3.500A) Processing helix chain '2' and resid 42 through 45 removed outlier: 3.530A pdb=" N LEU 2 45 " --> pdb=" O LEU 2 42 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 42 through 45' Processing helix chain '2' and resid 63 through 83 removed outlier: 4.009A pdb=" N TYR 2 73 " --> pdb=" O ASP 2 69 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU 2 82 " --> pdb=" O VAL 2 78 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR 2 83 " --> pdb=" O ILE 2 79 " (cutoff:3.500A) Processing helix chain '2' and resid 91 through 95 Processing helix chain '2' and resid 103 through 118 removed outlier: 3.775A pdb=" N LEU 2 108 " --> pdb=" O ILE 2 104 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE 2 117 " --> pdb=" O GLY 2 113 " (cutoff:3.500A) removed outlier: 3.721A 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: 3.754A pdb=" N PHE 2 159 " --> pdb=" O MET 2 155 " (cutoff:3.500A) Processing helix chain '2' and resid 184 through 186 No H-bonds generated for 'chain '2' and resid 184 through 186' 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 212 removed outlier: 3.679A pdb=" N LEU 2 208 " --> pdb=" O LEU 2 204 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS 2 211 " --> pdb=" O GLY 2 207 " (cutoff:3.500A) Processing helix chain '2' and resid 215 through 217 No H-bonds generated for 'chain '2' and resid 215 through 217' Processing helix chain '2' and resid 219 through 227 removed outlier: 3.530A pdb=" N SER 2 223 " --> pdb=" O LYS 2 219 " (cutoff:3.500A) Processing helix chain '2' and resid 232 through 250 Proline residue: 2 240 - end of helix Processing helix chain '2' and resid 258 through 274 removed outlier: 3.839A pdb=" N SER 2 272 " --> pdb=" O LEU 2 268 " (cutoff:3.500A) Processing helix chain '2' and resid 281 through 294 removed outlier: 3.543A pdb=" N ASN 2 292 " --> pdb=" O SER 2 288 " (cutoff:3.500A) Processing helix chain '2' and resid 297 through 301 Processing helix chain '2' and resid 308 through 332 removed outlier: 5.155A pdb=" N TYR 2 332 " --> pdb=" O ILE 2 328 " (cutoff:3.500A) Processing helix chain '2' and resid 347 through 350 removed outlier: 3.617A pdb=" N LEU 2 350 " --> pdb=" O VAL 2 347 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 347 through 350' Processing helix chain '2' and resid 353 through 356 No H-bonds generated for 'chain '2' and resid 353 through 356' Processing helix chain '2' and resid 359 through 371 Processing helix chain '2' and resid 378 through 390 removed outlier: 3.971A pdb=" N GLY 2 382 " --> pdb=" O LEU 2 378 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS 2 383 " --> pdb=" O GLY 2 379 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER 2 389 " --> pdb=" O ASN 2 385 " (cutoff:3.500A) Processing helix chain '2' and resid 396 through 420 removed outlier: 3.775A pdb=" N LEU 2 411 " --> pdb=" O LEU 2 407 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYR 2 412 " --> pdb=" O ILE 2 408 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR 2 415 " --> pdb=" O LEU 2 411 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU 2 416 " --> pdb=" O TYR 2 412 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU 2 417 " --> pdb=" O TYR 2 413 " (cutoff:3.500A) Processing helix chain '2' and resid 437 through 452 removed outlier: 4.122A pdb=" N LEU 2 443 " --> pdb=" O LEU 2 439 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE 2 450 " --> pdb=" O LEU 2 446 " (cutoff:3.500A) Processing helix chain '2' and resid 457 through 468 Processing helix chain '3' and resid 5 through 24 Proline residue: 3 12 - end of helix removed outlier: 3.668A pdb=" N ASN 3 22 " --> pdb=" O LEU 3 18 " (cutoff:3.500A) Processing helix chain '3' and resid 54 through 78 removed outlier: 4.004A pdb=" N ALA 3 60 " --> pdb=" O PHE 3 56 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU 3 64 " --> pdb=" O ALA 3 60 " (cutoff:3.500A) Proline residue: 3 65 - end of helix removed outlier: 3.742A pdb=" N GLU 3 69 " --> pdb=" O PRO 3 65 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE 3 70 " --> pdb=" O PHE 3 66 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER 3 71 " --> pdb=" O ASP 3 67 " (cutoff:3.500A) Proline residue: 3 75 - end of helix removed outlier: 3.710A pdb=" N MET 3 78 " --> pdb=" O LEU 3 74 " (cutoff:3.500A) Processing helix chain '3' and resid 87 through 107 removed outlier: 3.807A pdb=" N ILE 3 100 " --> pdb=" O LEU 3 96 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY 3 101 " --> pdb=" O ILE 3 97 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 20 removed outlier: 3.651A pdb=" N TYR 4 12 " --> pdb=" O LEU 4 8 " (cutoff:3.500A) Processing helix chain '4' and resid 25 through 44 removed outlier: 3.973A pdb=" N LEU 4 36 " --> pdb=" O SER 4 32 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU 4 37 " --> pdb=" O ASN 4 33 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL 4 41 " --> pdb=" O LEU 4 37 " (cutoff:3.500A) Processing helix chain '4' and resid 83 through 102 removed outlier: 3.570A pdb=" N THR 4 87 " --> pdb=" O LEU 4 84 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE 4 88 " --> pdb=" O SER 4 85 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL 4 93 " --> pdb=" O LEU 4 90 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU 4 94 " --> pdb=" O LEU 4 91 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE 4 96 " --> pdb=" O VAL 4 93 " (cutoff:3.500A) Proline residue: 4 97 - end of helix removed outlier: 3.665A pdb=" N LEU 4 100 " --> pdb=" O PRO 4 97 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU 4 101 " --> pdb=" O LEU 4 98 " (cutoff:3.500A) Processing helix chain '4' and resid 111 through 130 removed outlier: 3.559A pdb=" N THR 4 116 " --> pdb=" O ASN 4 112 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE 4 125 " --> pdb=" O ILE 4 121 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE 4 129 " --> pdb=" O ILE 4 125 " (cutoff:3.500A) Processing helix chain '4' and resid 134 through 141 removed outlier: 4.141A pdb=" N LEU 4 140 " --> pdb=" O SER 4 136 " (cutoff:3.500A) Processing helix chain '4' and resid 143 through 153 removed outlier: 4.543A pdb=" N LEU 4 147 " --> pdb=" O ALA 4 143 " (cutoff:3.500A) Processing helix chain '4' and resid 160 through 188 removed outlier: 4.245A pdb=" N THR 4 171 " --> pdb=" O VAL 4 167 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE 4 177 " --> pdb=" O SER 4 173 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET 4 178 " --> pdb=" O GLY 4 174 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE 4 185 " --> pdb=" O SER 4 181 " (cutoff:3.500A) Processing helix chain '4' and resid 204 through 221 removed outlier: 4.007A pdb=" N ILE 4 209 " --> pdb=" O ASP 4 205 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU 4 212 " --> pdb=" O THR 4 208 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLY 4 213 " --> pdb=" O ILE 4 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU 4 214 " --> pdb=" O ILE 4 210 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA 4 217 " --> pdb=" O GLY 4 213 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL 4 220 " --> pdb=" O ILE 4 216 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS 4 221 " --> pdb=" O ALA 4 217 " (cutoff:3.500A) Processing helix chain '4' and resid 231 through 235 Processing helix chain '4' and resid 241 through 260 removed outlier: 3.829A pdb=" N LEU 4 246 " --> pdb=" O GLY 4 242 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LEU 4 251 " --> pdb=" O ALA 4 247 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LYS 4 252 " --> pdb=" O GLY 4 248 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA 4 254 " --> pdb=" O ILE 4 250 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU 4 255 " --> pdb=" O LEU 4 251 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU 4 259 " --> pdb=" O LEU 4 255 " (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 271 removed outlier: 4.116A pdb=" N ILE 4 271 " --> pdb=" O CYS 4 267 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 267 through 271' Processing helix chain '4' and resid 274 through 288 removed outlier: 4.049A pdb=" N ILE 4 279 " --> pdb=" O PRO 4 275 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU 4 287 " --> pdb=" O LEU 4 283 " (cutoff:3.500A) Processing helix chain '4' and resid 299 through 319 removed outlier: 3.624A pdb=" N ILE 4 314 " --> pdb=" O MET 4 310 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU 4 315 " --> pdb=" O GLY 4 311 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY 4 316 " --> pdb=" O ILE 4 312 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS 4 318 " --> pdb=" O ILE 4 314 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER 4 319 " --> pdb=" O LEU 4 315 " (cutoff:3.500A) Processing helix chain '4' and resid 322 through 346 removed outlier: 4.135A pdb=" N TYR 4 326 " --> pdb=" O SER 4 322 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY 4 336 " --> pdb=" O GLY 4 332 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE 4 337 " --> pdb=" O VAL 4 333 " (cutoff:3.500A) Proline residue: 4 340 - end of helix Processing helix chain '4' and resid 349 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 370 through 384 removed outlier: 4.926A pdb=" N TYR 4 375 " --> pdb=" O GLN 4 371 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU 4 379 " --> pdb=" O TYR 4 375 " (cutoff:3.500A) Processing helix chain '4' and resid 391 through 405 removed outlier: 3.561A pdb=" N ARG 4 405 " --> pdb=" O GLY 4 401 " (cutoff:3.500A) Processing helix chain '4' and resid 407 through 432 removed outlier: 4.526A pdb=" N ILE 4 415 " --> pdb=" O GLY 4 411 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N SER 4 416 " --> pdb=" O ILE 4 412 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N VAL 4 417 " --> pdb=" O SER 4 413 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LEU 4 418 " --> pdb=" O CYS 4 414 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR 4 423 " --> pdb=" O LEU 4 419 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN 4 424 " --> pdb=" O ALA 4 420 " (cutoff:3.500A) Processing helix chain '4' and resid 448 through 466 removed outlier: 4.426A pdb=" N MET 4 454 " --> pdb=" O GLU 4 450 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE 4 456 " --> pdb=" O PHE 4 452 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR 4 461 " --> pdb=" O LEU 4 457 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE 4 464 " --> pdb=" O SER 4 460 " (cutoff:3.500A) Processing helix chain '4' and resid 468 through 475 removed outlier: 3.949A pdb=" N MET 4 471 " --> pdb=" O PRO 4 468 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASN 4 473 " --> pdb=" O ILE 4 470 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU 4 474 " --> pdb=" O MET 4 471 " (cutoff:3.500A) Processing helix chain '5' and resid 6 through 21 removed outlier: 4.043A pdb=" N LEU 5 11 " --> pdb=" O LEU 5 7 " (cutoff:3.500A) Proline residue: 5 12 - end of helix Proline residue: 5 19 - end of helix Processing helix chain '5' and resid 28 through 55 removed outlier: 3.918A pdb=" N ARG 5 33 " --> pdb=" O VAL 5 29 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER 5 36 " --> pdb=" O THR 5 32 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR 5 37 " --> pdb=" O ARG 5 33 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE 5 39 " --> pdb=" O THR 5 35 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR 5 48 " --> pdb=" O LEU 5 44 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY 5 55 " --> pdb=" O TYR 5 51 " (cutoff:3.500A) Processing helix chain '5' and resid 83 through 105 removed outlier: 3.888A pdb=" N MET 5 88 " --> pdb=" O LEU 5 84 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR 5 94 " --> pdb=" O LEU 5 90 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE 5 104 " --> pdb=" O HIS 5 100 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY 5 105 " --> pdb=" O ILE 5 101 " (cutoff:3.500A) Processing helix chain '5' and resid 113 through 132 removed outlier: 3.575A pdb=" N PHE 5 117 " --> pdb=" O GLN 5 113 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR 5 132 " --> pdb=" O ILE 5 128 " (cutoff:3.500A) Processing helix chain '5' and resid 138 through 154 removed outlier: 3.575A pdb=" N TRP 5 143 " --> pdb=" O LEU 5 139 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY 5 147 " --> pdb=" O TRP 5 143 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE 5 154 " --> pdb=" O SER 5 150 " (cutoff:3.500A) Processing helix chain '5' and resid 161 through 191 removed outlier: 3.714A pdb=" N GLY 5 177 " --> pdb=" O MET 5 173 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE 5 180 " --> pdb=" O PHE 5 176 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR 5 190 " --> pdb=" O CYS 5 186 " (cutoff:3.500A) Processing helix chain '5' and resid 197 through 203 removed outlier: 3.711A pdb=" N ALA 5 202 " --> pdb=" O SER 5 198 " (cutoff:3.500A) Processing helix chain '5' and resid 209 through 226 removed outlier: 4.121A pdb=" N LEU 5 214 " --> pdb=" O ASP 5 210 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA 5 218 " --> pdb=" O LEU 5 214 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA 5 223 " --> pdb=" O LEU 5 219 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS 5 226 " --> pdb=" O ALA 5 222 " (cutoff:3.500A) Processing helix chain '5' and resid 237 through 239 No H-bonds generated for 'chain '5' and resid 237 through 239' Processing helix chain '5' and resid 244 through 250 removed outlier: 3.618A pdb=" N LEU 5 249 " --> pdb=" O PRO 5 245 " (cutoff:3.500A) Processing helix chain '5' and resid 254 through 270 removed outlier: 4.385A pdb=" N GLY 5 259 " --> pdb=" O LEU 5 255 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE 5 260 " --> pdb=" O VAL 5 256 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU 5 263 " --> pdb=" O GLY 5 259 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA 5 267 " --> pdb=" O LEU 5 263 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ASN 5 268 " --> pdb=" O LEU 5 264 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ILE 5 269 " --> pdb=" O ARG 5 265 " (cutoff:3.500A) Processing helix chain '5' and resid 274 through 297 removed outlier: 3.626A pdb=" N PHE 5 278 " --> pdb=" O PRO 5 274 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE 5 279 " --> pdb=" O THR 5 275 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU 5 286 " --> pdb=" O TRP 5 282 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR 5 288 " --> pdb=" O GLY 5 284 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU 5 289 " --> pdb=" O ALA 5 285 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N CYS 5 297 " --> pdb=" O LEU 5 293 " (cutoff:3.500A) Processing helix chain '5' and resid 301 through 321 removed outlier: 3.762A pdb=" N ILE 5 305 " --> pdb=" O LEU 5 301 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY 5 314 " --> pdb=" O MET 5 310 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET 5 315 " --> pdb=" O SER 5 311 " (cutoff:3.500A) Processing helix chain '5' and resid 325 through 351 removed outlier: 3.761A pdb=" N ALA 5 336 " --> pdb=" O LEU 5 332 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE 5 337 " --> pdb=" O LEU 5 333 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU 5 341 " --> pdb=" O PHE 5 337 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER 5 348 " --> pdb=" O MET 5 344 " (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 Processing helix chain '5' and resid 391 through 405 removed outlier: 3.851A pdb=" N ASP 5 397 " --> pdb=" O TYR 5 393 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ILE 5 398 " --> pdb=" O TYR 5 394 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE 5 399 " --> pdb=" O THR 5 395 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE 5 400 " --> pdb=" O LYS 5 396 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR 5 403 " --> pdb=" O ILE 5 399 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR 5 404 " --> pdb=" O ILE 5 400 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY 5 405 " --> pdb=" O GLU 5 401 " (cutoff:3.500A) Processing helix chain '5' and resid 409 through 437 removed outlier: 3.710A pdb=" N VAL 5 414 " --> pdb=" O ASN 5 411 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE 5 417 " --> pdb=" O VAL 5 414 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU 5 420 " --> pdb=" O ILE 5 417 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER 5 421 " --> pdb=" O ALA 5 418 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU 5 424 " --> pdb=" O SER 5 421 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR 5 428 " --> pdb=" O THR 5 425 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N MET 5 430 " --> pdb=" O VAL 5 427 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR 5 434 " --> pdb=" O LYS 5 431 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU 5 435 " --> pdb=" O ILE 5 432 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR 5 436 " --> pdb=" O LEU 5 433 " (cutoff:3.500A) Processing helix chain '5' and resid 446 through 449 No H-bonds generated for 'chain '5' and resid 446 through 449' Processing helix chain '5' and resid 459 through 477 removed outlier: 6.405A pdb=" N GLY 5 473 " --> pdb=" O ALA 5 469 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N TRP 5 474 " --> pdb=" O MET 5 470 " (cutoff:3.500A) Processing helix chain '5' and resid 499 through 504 removed outlier: 4.153A pdb=" N PHE 5 504 " --> pdb=" O PHE 5 500 " (cutoff:3.500A) Processing helix chain '5' and resid 508 through 530 Proline residue: 5 514 - end of helix removed outlier: 3.935A pdb=" N VAL 5 526 " --> pdb=" O SER 5 522 " (cutoff:3.500A) Processing helix chain '5' and resid 541 through 551 removed outlier: 3.580A pdb=" N THR 5 545 " --> pdb=" O LYS 5 541 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL 5 546 " --> pdb=" O TYR 5 542 " (cutoff:3.500A) Processing helix chain '5' and resid 557 through 563 Processing helix chain '5' and resid 565 through 573 Processing helix chain '5' and resid 591 through 607 removed outlier: 5.367A pdb=" N SER 5 607 " --> pdb=" O VAL 5 603 " (cutoff:3.500A) Processing helix chain '5' and resid 613 through 618 Processing helix chain '5' and resid 620 through 635 removed outlier: 3.559A pdb=" N ILE 5 625 " --> pdb=" O ILE 5 621 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LEU 5 628 " --> pdb=" O THR 5 624 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU 5 629 " --> pdb=" O ILE 5 625 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU 5 633 " --> pdb=" O LEU 5 629 " (cutoff:3.500A) Processing helix chain '5' and resid 640 through 654 Proline residue: 5 644 - end of helix Processing helix chain '6' and resid 3 through 6 removed outlier: 3.715A pdb=" N TYR 6 6 " --> pdb=" O TYR 6 3 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 3 through 6' Processing helix chain '6' and resid 8 through 23 removed outlier: 3.564A pdb=" N THR 6 12 " --> pdb=" O PHE 6 8 " (cutoff:3.500A) Processing helix chain '6' and resid 29 through 50 removed outlier: 3.850A pdb=" N ILE 6 33 " --> pdb=" O PRO 6 29 " (cutoff:3.500A) Processing helix chain '6' and resid 53 through 62 removed outlier: 3.909A pdb=" N LEU 6 57 " --> pdb=" O GLY 6 53 " (cutoff:3.500A) Processing helix chain '6' and resid 66 through 76 Processing helix chain '6' and resid 87 through 90 No H-bonds generated for 'chain '6' and resid 87 through 90' Processing helix chain '6' and resid 94 through 110 removed outlier: 3.698A pdb=" N ILE 6 99 " --> pdb=" O PRO 6 95 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE 6 102 " --> pdb=" O LEU 6 98 " (cutoff:3.500A) Processing helix chain '6' and resid 123 through 126 No H-bonds generated for 'chain '6' and resid 123 through 126' Processing helix chain '6' and resid 146 through 153 Processing helix chain '6' and resid 159 through 179 removed outlier: 4.001A 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 16 removed outlier: 4.124A pdb=" N LYS 8 14 " --> pdb=" O GLN 8 10 " (cutoff:3.500A) 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 30 through 39 removed outlier: 4.170A pdb=" N GLU 8 35 " --> pdb=" O VAL 8 31 " (cutoff:3.500A) Processing helix chain '8' and resid 49 through 82 removed outlier: 3.855A pdb=" N ARG 8 64 " --> pdb=" O ALA 8 60 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG 8 65 " --> pdb=" O ASP 8 61 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA 8 74 " --> pdb=" O ASP 8 70 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU 8 75 " --> pdb=" O LYS 8 71 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS 8 76 " --> pdb=" O LEU 8 72 " (cutoff:3.500A) Processing helix chain '9' and resid 16 through 27 Processing helix chain '9' and resid 38 through 49 Processing helix chain '9' and resid 51 through 65 Processing helix chain '9' and resid 81 through 83 No H-bonds generated for 'chain '9' and resid 81 through 83' 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 255 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 349 removed outlier: 6.307A pdb=" N MET A 549 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL A 349 " --> pdb=" O MET A 549 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N TRP A 551 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N PHE A 568 " --> pdb=" O VAL A 550 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU A 552 " --> pdb=" O PHE A 568 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL A 570 " --> pdb=" O LEU A 552 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 438 through 442 removed outlier: 3.621A pdb=" N ALA A 440 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU A 481 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N VAL A 413 " --> pdb=" O LEU A 481 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE A 483 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 598 through 600 Processing sheet with id= H, first strand: chain 'B' and resid 242 through 246 removed outlier: 7.357A pdb=" N TYR B 114 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N THR B 245 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL B 116 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA B 155 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N VAL B 117 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TYR B 157 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ALA B 119 " --> pdb=" O TYR B 157 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR B 159 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASP B 196 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE B 158 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TYR B 198 " --> pdb=" O ILE B 158 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ILE B 160 " --> pdb=" O TYR B 198 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N HIS B 200 " --> pdb=" O ILE B 160 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 288 through 293 removed outlier: 5.811A pdb=" N VAL B 356 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY B 318 " --> pdb=" O ILE B 359 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 83 through 86 removed outlier: 3.993A pdb=" N ARG C 111 " --> pdb=" O GLU C 103 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N SER C 105 " --> pdb=" O ILE C 109 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ILE C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 397 through 405 Processing sheet with id= L, first strand: chain 'E' and resid 31 through 33 Processing sheet with id= M, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.440A pdb=" N VAL E 125 " --> pdb=" O ILE E 164 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL E 166 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ASN E 127 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 9.068A pdb=" N ALA E 168 " --> pdb=" O ASN E 127 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N THR E 79 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL E 58 " --> pdb=" O THR E 79 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL E 81 " --> pdb=" O VAL E 58 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 204 through 206 Processing sheet with id= O, first strand: chain 'G' and resid 123 through 130 removed outlier: 7.145A pdb=" N ASN G 143 " --> pdb=" O ILE G 124 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE G 126 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL G 141 " --> pdb=" O ILE G 126 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA G 128 " --> pdb=" O GLU G 139 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLU G 139 " --> pdb=" O ALA G 128 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LEU G 96 " --> pdb=" O ARG G 152 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR G 158 " --> pdb=" O VAL G 100 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 164 through 166 removed outlier: 5.612A pdb=" N PHE G 189 " --> pdb=" O VAL G 165 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'G' and resid 220 through 225 removed outlier: 3.737A pdb=" N ARG G 230 " --> pdb=" O ASP G 225 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 122 through 127 Processing sheet with id= S, first strand: chain 'H' and resid 177 through 179 Processing sheet with id= T, first strand: chain 'I' and resid 118 through 120 Processing sheet with id= U, first strand: chain 'I' and resid 148 through 151 removed outlier: 6.235A pdb=" N GLU I 150 " --> pdb=" O THR I 159 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N THR I 159 " --> pdb=" O GLU I 150 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 79 through 82 removed outlier: 3.688A pdb=" N ILE K 118 " --> pdb=" O VAL K 79 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA K 120 " --> pdb=" O PHE K 81 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TRP K 143 " --> pdb=" O MET K 117 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL K 119 " --> pdb=" O TRP K 143 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE K 145 " --> pdb=" O VAL K 119 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL K 175 " --> pdb=" O SER K 146 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'Y' and resid 58 through 62 Processing sheet with id= X, first strand: chain 'Y' and resid 90 through 92 Processing sheet with id= Y, first strand: chain 'f' and resid 41 through 46 Processing sheet with id= Z, first strand: chain 'k' and resid 48 through 51 Processing sheet with id= AA, first strand: chain '2' and resid 52 through 54 Processing sheet with id= AB, first strand: chain '4' and resid 57 through 59 Processing sheet with id= AC, first strand: chain '5' and resid 61 through 63 Processing sheet with id= AD, first strand: chain '5' and resid 66 through 70 removed outlier: 6.713A pdb=" N ILE 5 75 " --> pdb=" O TYR 5 67 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASN 5 69 " --> pdb=" O LEU 5 73 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LEU 5 73 " --> pdb=" O ASN 5 69 " (cutoff:3.500A) 2348 hydrogen bonds defined for protein. 6744 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: 19.14 Time building geometry restraints manager: 20.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.39: 25308 1.39 - 1.62: 37595 1.62 - 1.85: 504 1.85 - 2.08: 5 2.08 - 2.32: 80 Bond restraints: 63492 Sorted by residual: bond pdb=" NE ARG B 113 " pdb=" CZ ARG B 113 " ideal model delta sigma weight residual 1.326 1.503 -0.177 1.10e-02 8.26e+03 2.60e+02 bond pdb=" CB7 CDL J 204 " pdb=" OB8 CDL J 204 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.18e+02 bond pdb=" CA7 CDL J 204 " pdb=" OA8 CDL J 204 " ideal model delta sigma weight residual 1.334 1.451 -0.117 1.10e-02 8.26e+03 1.14e+02 bond pdb=" C5N NDP E 401 " pdb=" C6N NDP E 401 " ideal model delta sigma weight residual 1.337 1.547 -0.210 2.40e-02 1.74e+03 7.66e+01 bond pdb=" CD ARG B 113 " pdb=" NE ARG B 113 " ideal model delta sigma weight residual 1.458 1.341 0.117 1.40e-02 5.10e+03 6.97e+01 ... (remaining 63487 not shown) Histogram of bond angle deviations from ideal: 67.85 - 84.30: 72 84.30 - 100.74: 125 100.74 - 117.19: 44517 117.19 - 133.64: 41152 133.64 - 150.08: 119 Bond angle restraints: 85985 Sorted by residual: angle pdb=" NE ARG B 113 " pdb=" CZ ARG B 113 " pdb=" NH2 ARG B 113 " ideal model delta sigma weight residual 119.20 131.43 -12.23 9.00e-01 1.23e+00 1.85e+02 angle pdb=" S1 FES A 803 " pdb="FE2 FES A 803 " pdb=" S2 FES A 803 " ideal model delta sigma weight residual 104.33 89.45 14.88 1.14e+00 7.69e-01 1.70e+02 angle pdb=" S1 FES A 803 " pdb="FE1 FES A 803 " pdb=" S2 FES A 803 " ideal model delta sigma weight residual 104.33 88.85 15.48 1.20e+00 6.94e-01 1.66e+02 angle pdb=" S1 FES H 301 " pdb="FE2 FES H 301 " pdb=" S2 FES H 301 " ideal model delta sigma weight residual 104.33 91.38 12.95 1.14e+00 7.69e-01 1.29e+02 angle pdb=" CA3 CDL 4 502 " pdb=" OA5 CDL 4 502 " pdb=" PA1 CDL 4 502 " ideal model delta sigma weight residual 121.27 109.93 11.34 1.00e+00 1.00e+00 1.29e+02 ... (remaining 85980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 37482 35.00 - 70.01: 677 70.01 - 105.01: 106 105.01 - 140.02: 46 140.02 - 175.02: 10 Dihedral angle restraints: 38321 sinusoidal: 16097 harmonic: 22224 Sorted by residual: 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 180.00 121.39 58.61 0 5.00e+00 4.00e-02 1.37e+02 dihedral pdb=" CA GLY j 82 " pdb=" C GLY j 82 " pdb=" N LYS j 83 " pdb=" CA LYS j 83 " ideal model delta harmonic sigma weight residual 180.00 128.45 51.55 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" CA LEU 5 554 " pdb=" C LEU 5 554 " pdb=" N VAL 5 555 " pdb=" CA VAL 5 555 " ideal model delta harmonic sigma weight residual -180.00 -130.59 -49.41 0 5.00e+00 4.00e-02 9.77e+01 ... (remaining 38318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.190: 9572 4.190 - 8.379: 3 8.379 - 12.569: 0 12.569 - 16.759: 0 16.759 - 20.948: 20 Chirality restraints: 9595 Sorted by residual: chirality pdb="FE3 SF4 K 301 " pdb=" S1 SF4 K 301 " pdb=" S2 SF4 K 301 " pdb=" S4 SF4 K 301 " both_signs ideal model delta sigma weight residual False -10.55 10.39 -20.95 2.00e-01 2.50e+01 1.10e+04 chirality pdb="FE1 SF4 I 302 " pdb=" S2 SF4 I 302 " pdb=" S3 SF4 I 302 " pdb=" S4 SF4 I 302 " both_signs ideal model delta sigma weight residual False -10.55 10.32 -20.87 2.00e-01 2.50e+01 1.09e+04 chirality pdb="FE4 SF4 A 801 " pdb=" S1 SF4 A 801 " pdb=" S2 SF4 A 801 " pdb=" S3 SF4 A 801 " both_signs ideal model delta sigma weight residual False 10.55 -10.32 20.87 2.00e-01 2.50e+01 1.09e+04 ... (remaining 9592 not shown) Planarity restraints: 10740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP E 401 " -0.139 2.00e-02 2.50e+03 1.02e-01 1.30e+02 pdb=" C3N NDP E 401 " -0.078 2.00e-02 2.50e+03 pdb=" C4N NDP E 401 " -0.012 2.00e-02 2.50e+03 pdb=" C7N NDP E 401 " 0.104 2.00e-02 2.50e+03 pdb=" N1N NDP E 401 " 0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 269 " 0.584 9.50e-02 1.11e+02 2.62e-01 4.19e+01 pdb=" NE ARG C 269 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG C 269 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG C 269 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 269 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4N NDP E 401 " -0.037 2.00e-02 2.50e+03 6.06e-02 3.68e+01 pdb=" C5N NDP E 401 " 0.075 2.00e-02 2.50e+03 pdb=" C6N NDP E 401 " -0.078 2.00e-02 2.50e+03 pdb=" N1N NDP E 401 " 0.040 2.00e-02 2.50e+03 ... (remaining 10737 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 220 2.49 - 3.09: 42848 3.09 - 3.70: 96104 3.70 - 4.30: 140189 4.30 - 4.90: 229336 Nonbonded interactions: 508697 Sorted by model distance: nonbonded pdb=" O GLY 5 484 " pdb=" OD1 ASN 8 34 " model vdw 1.889 3.040 nonbonded pdb=" O ASP A 447 " pdb=" OD1 ASP A 447 " model vdw 1.983 3.040 nonbonded pdb=" OD2 ASP 5 478 " pdb=" NH1 ARG 8 51 " model vdw 2.011 2.520 nonbonded pdb=" O ASN B 43 " pdb=" OD1 ASN B 43 " model vdw 2.102 3.040 nonbonded pdb=" O ASP 3 122 " pdb=" OD1 ASP 3 122 " model vdw 2.123 3.040 ... (remaining 508692 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.70 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.100 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: 21.150 Check model and map are aligned: 0.680 Set scattering table: 0.420 Process input model: 131.010 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 161.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 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 : 0.013 0.262 63492 Z= 0.867 Angle : 1.570 29.274 85985 Z= 0.773 Chirality : 0.950 20.948 9595 Planarity : 0.011 0.262 10740 Dihedral : 14.614 175.023 24012 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.04 % Favored : 92.82 % Rotamer: Outliers : 0.17 % Allowed : 3.23 % Favored : 96.60 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 0.84 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.08), residues: 7531 helix: -2.63 (0.06), residues: 3876 sheet: -1.86 (0.27), residues: 331 loop : -2.79 (0.09), residues: 3324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.005 TRP G 177 HIS 0.032 0.003 HIS 2 185 PHE 0.051 0.005 PHE 3 7 TYR 0.061 0.005 TYR 1 45 ARG 0.050 0.002 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15062 Ramachandran restraints generated. 7531 Oldfield, 0 Emsley, 7531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15062 Ramachandran restraints generated. 7531 Oldfield, 0 Emsley, 7531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2234 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 2223 time to evaluate : 5.175 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 outliers start: 11 outliers final: 2 residues processed: 2230 average time/residue: 0.6841 time to fit residues: 2505.0776 Evaluate side-chains 1202 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1200 time to evaluate : 5.131 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4484 time to fit residues: 8.7404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 629 optimal weight: 0.8980 chunk 565 optimal weight: 5.9990 chunk 313 optimal weight: 3.9990 chunk 193 optimal weight: 0.7980 chunk 381 optimal weight: 0.8980 chunk 302 optimal weight: 0.7980 chunk 584 optimal weight: 0.6980 chunk 226 optimal weight: 2.9990 chunk 355 optimal weight: 0.8980 chunk 435 optimal weight: 0.8980 chunk 677 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN A 228 ASN A 398 ASN A 674 HIS A 680 ASN A 724 ASN B 43 ASN B 424 HIS B 438 GLN ** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 GLN D 29 HIS D 33 ASN D 76 HIS E 26 ASN E 62 ASN E 76 HIS E 121 HIS E 137 ASN E 365 ASN F 69 GLN F 77 HIS F 93 ASN F 106 GLN ** F 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 HIS H 123 HIS H 125 GLN H 174 ASN H 224 GLN I 118 HIS I 210 ASN K 158 HIS P 63 HIS P 84 GLN Q 70 ASN R 32 ASN R 49 GLN S 132 ASN U 97 HIS U 99 GLN U 119 ASN X 13 ASN X 27 HIS ** X 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 142 ASN X 145 HIS Y 99 GLN Y 146 ASN a 87 HIS a 90 ASN b 51 HIS c 18 GLN ** d 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 59 HIS ** d 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 7 ASN e 23 HIS e 54 ASN f 11 HIS g 10 ASN ** g 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 78 HIS k 93 HIS n 64 ASN 1 49 GLN 1 307 ASN 2 29 ASN 2 86 ASN 2 90 ASN ** 2 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 173 ASN ** 2 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 278 GLN 2 292 ASN 4 23 ASN 4 26 HIS 4 103 ASN 4 106 ASN 4 153 HIS ** 4 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 335 HIS ** 4 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 76 ASN 5 100 HIS 5 135 ASN 5 251 HIS 5 299 ASN ** 5 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 491 HIS 5 537 ASN ** 5 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 638 ASN 6 128 ASN 6 183 HIS ** 8 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 13 ASN 9 36 GLN Total number of N/Q/H flips: 87 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.272 63492 Z= 0.541 Angle : 1.561 50.922 85985 Z= 0.988 Chirality : 0.294 6.534 9595 Planarity : 0.006 0.093 10740 Dihedral : 14.999 176.530 9740 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.62 % Favored : 95.34 % Rotamer: Outliers : 3.19 % Allowed : 11.81 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.28 % Cis-general : 0.01 % Twisted Proline : 0.28 % Twisted General : 0.08 % 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: -2.46 (0.09), residues: 7531 helix: -1.03 (0.08), residues: 3897 sheet: -1.47 (0.28), residues: 338 loop : -2.35 (0.09), residues: 3296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP 5 126 HIS 0.009 0.001 HIS 2 185 PHE 0.025 0.002 PHE 2 107 TYR 0.028 0.002 TYR Y 130 ARG 0.008 0.001 ARG R 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15062 Ramachandran restraints generated. 7531 Oldfield, 0 Emsley, 7531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15062 Ramachandran restraints generated. 7531 Oldfield, 0 Emsley, 7531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1527 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1319 time to evaluate : 5.202 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 outliers start: 208 outliers final: 113 residues processed: 1445 average time/residue: 0.6161 time to fit residues: 1489.8510 Evaluate side-chains 1189 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1076 time to evaluate : 5.186 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 113 outliers final: 1 residues processed: 113 average time/residue: 0.4652 time to fit residues: 105.5729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 376 optimal weight: 8.9990 chunk 210 optimal weight: 5.9990 chunk 563 optimal weight: 2.9990 chunk 461 optimal weight: 7.9990 chunk 186 optimal weight: 5.9990 chunk 678 optimal weight: 0.8980 chunk 733 optimal weight: 4.9990 chunk 604 optimal weight: 3.9990 chunk 673 optimal weight: 2.9990 chunk 231 optimal weight: 0.0980 chunk 544 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 517 ASN A 674 HIS A 680 ASN C 120 HIS ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN ** E 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN E 188 GLN E 365 ASN F 58 GLN ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 HIS H 40 ASN H 145 GLN H 224 GLN P 73 ASN R 32 ASN U 8 HIS W 74 GLN ** X 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 60 GLN b 54 HIS d 4 HIS d 69 GLN f 60 HIS ** g 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 76 GLN 1 173 GLN ** 2 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 278 GLN 2 292 ASN 4 21 GLN 4 128 ASN ** 4 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 52 GLN 5 299 ASN ** 5 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 326 ASN 5 617 ASN 5 638 ASN 8 49 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.255 63492 Z= 0.553 Angle : 1.550 50.670 85985 Z= 0.985 Chirality : 0.292 6.406 9595 Planarity : 0.005 0.099 10740 Dihedral : 13.462 178.306 9740 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.26 % Favored : 94.70 % Rotamer: Outliers : 2.80 % Allowed : 13.62 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.28 % Cis-general : 0.01 % Twisted Proline : 0.28 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.09), residues: 7531 helix: -0.34 (0.08), residues: 3939 sheet: -1.32 (0.28), residues: 335 loop : -2.12 (0.10), residues: 3257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP 5 143 HIS 0.009 0.001 HIS 2 185 PHE 0.025 0.002 PHE G 189 TYR 0.025 0.002 TYR 1 244 ARG 0.009 0.001 ARG K 199 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15062 Ramachandran restraints generated. 7531 Oldfield, 0 Emsley, 7531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15062 Ramachandran restraints generated. 7531 Oldfield, 0 Emsley, 7531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1343 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1160 time to evaluate : 5.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 183 outliers final: 79 residues processed: 1278 average time/residue: 0.6067 time to fit residues: 1313.6540 Evaluate side-chains 1116 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1037 time to evaluate : 5.196 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 0 residues processed: 79 average time/residue: 0.4656 time to fit residues: 75.6624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 670 optimal weight: 2.9990 chunk 510 optimal weight: 0.8980 chunk 352 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 323 optimal weight: 10.0000 chunk 455 optimal weight: 0.3980 chunk 681 optimal weight: 2.9990 chunk 721 optimal weight: 0.8980 chunk 355 optimal weight: 3.9990 chunk 645 optimal weight: 0.7980 chunk 194 optimal weight: 10.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 ASN B 305 HIS ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 GLN D 26 GLN ** E 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN K 193 GLN P 95 GLN R 32 ASN U 169 ASN ** X 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 142 ASN a 65 ASN d 88 ASN f 24 GLN ** g 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 64 ASN ** 2 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 173 ASN ** 2 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 106 ASN ** 4 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 128 ASN 5 233 HIS ** 5 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 152 ASN ** 8 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 49 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.248 63492 Z= 0.523 Angle : 1.523 50.848 85985 Z= 0.975 Chirality : 0.291 6.369 9595 Planarity : 0.005 0.094 10740 Dihedral : 12.683 177.976 9740 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.34 % Favored : 95.62 % Rotamer: Outliers : 2.28 % Allowed : 15.18 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.28 % Cis-general : 0.01 % Twisted Proline : 0.28 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.09), residues: 7531 helix: 0.14 (0.08), residues: 3921 sheet: -1.14 (0.28), residues: 340 loop : -1.90 (0.10), residues: 3270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP c 15 HIS 0.009 0.001 HIS 8 49 PHE 0.021 0.002 PHE Y 129 TYR 0.026 0.002 TYR B 159 ARG 0.017 0.001 ARG P 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15062 Ramachandran restraints generated. 7531 Oldfield, 0 Emsley, 7531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15062 Ramachandran restraints generated. 7531 Oldfield, 0 Emsley, 7531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1268 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1119 time to evaluate : 5.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 149 outliers final: 63 residues processed: 1215 average time/residue: 0.6073 time to fit residues: 1240.7887 Evaluate side-chains 1081 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1018 time to evaluate : 5.188 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.4675 time to fit residues: 62.1760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 600 optimal weight: 0.7980 chunk 409 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 536 optimal weight: 6.9990 chunk 297 optimal weight: 0.8980 chunk 615 optimal weight: 3.9990 chunk 498 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 368 optimal weight: 2.9990 chunk 647 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 HIS ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN F 58 GLN K 195 GLN Q 128 GLN R 32 ASN S 115 HIS U 99 GLN ** X 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 20 ASN ** g 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 11 GLN k 54 ASN ** 2 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 173 ASN ** 5 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 49 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.249 63492 Z= 0.559 Angle : 1.544 51.034 85985 Z= 0.983 Chirality : 0.291 6.412 9595 Planarity : 0.005 0.096 10740 Dihedral : 12.504 177.491 9740 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.23 % Favored : 94.73 % Rotamer: Outliers : 2.31 % Allowed : 16.19 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.28 % Cis-general : 0.01 % Twisted Proline : 0.28 % 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: -1.02 (0.09), residues: 7531 helix: 0.29 (0.08), residues: 3925 sheet: -1.17 (0.28), residues: 344 loop : -1.82 (0.10), residues: 3262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 393 HIS 0.009 0.001 HIS 5 578 PHE 0.027 0.002 PHE G 189 TYR 0.026 0.002 TYR I 103 ARG 0.009 0.001 ARG P 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15062 Ramachandran restraints generated. 7531 Oldfield, 0 Emsley, 7531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15062 Ramachandran restraints generated. 7531 Oldfield, 0 Emsley, 7531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1211 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1060 time to evaluate : 5.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 151 outliers final: 68 residues processed: 1158 average time/residue: 0.6053 time to fit residues: 1185.9005 Evaluate side-chains 1044 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 976 time to evaluate : 5.246 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 0 residues processed: 68 average time/residue: 0.4668 time to fit residues: 66.6858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 242 optimal weight: 20.0000 chunk 649 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 423 optimal weight: 1.9990 chunk 178 optimal weight: 9.9990 chunk 721 optimal weight: 0.9990 chunk 599 optimal weight: 2.9990 chunk 334 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 238 optimal weight: 0.6980 chunk 378 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 HIS ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 ASN H 125 GLN K 193 GLN R 32 ASN ** W 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 157 ASN Z 130 GLN ** g 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 11 GLN ** 2 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 112 ASN 4 391 ASN ** 4 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.248 63492 Z= 0.525 Angle : 1.521 50.691 85985 Z= 0.974 Chirality : 0.291 6.375 9595 Planarity : 0.004 0.092 10740 Dihedral : 12.172 176.267 9740 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.54 % Favored : 95.43 % Rotamer: Outliers : 1.55 % Allowed : 17.51 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.28 % Cis-general : 0.01 % Twisted Proline : 0.28 % 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: -0.77 (0.10), residues: 7531 helix: 0.51 (0.08), residues: 3919 sheet: -1.03 (0.28), residues: 339 loop : -1.73 (0.10), residues: 3273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP c 15 HIS 0.010 0.001 HIS R 45 PHE 0.021 0.001 PHE H 47 TYR 0.024 0.001 TYR a 96 ARG 0.007 0.000 ARG Y 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15062 Ramachandran restraints generated. 7531 Oldfield, 0 Emsley, 7531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15062 Ramachandran restraints generated. 7531 Oldfield, 0 Emsley, 7531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1122 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1021 time to evaluate : 5.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 52 residues processed: 1081 average time/residue: 0.6530 time to fit residues: 1195.2843 Evaluate side-chains 1003 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 951 time to evaluate : 5.292 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.5302 time to fit residues: 57.0363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 695 optimal weight: 0.0670 chunk 81 optimal weight: 9.9990 chunk 411 optimal weight: 1.9990 chunk 527 optimal weight: 4.9990 chunk 408 optimal weight: 0.9990 chunk 607 optimal weight: 3.9990 chunk 403 optimal weight: 0.8980 chunk 719 optimal weight: 2.9990 chunk 449 optimal weight: 1.9990 chunk 438 optimal weight: 3.9990 chunk 331 optimal weight: 4.9990 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 HIS ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 ASN H 145 GLN K 193 GLN S 238 GLN ** X 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 130 GLN c 20 ASN ** g 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 49 GLN ** 2 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 312 GLN 5 537 ASN ** 5 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.5335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.247 63492 Z= 0.520 Angle : 1.518 50.910 85985 Z= 0.973 Chirality : 0.291 6.410 9595 Planarity : 0.004 0.095 10740 Dihedral : 11.874 175.770 9740 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.91 % Favored : 95.06 % Rotamer: Outliers : 1.21 % Allowed : 18.29 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.28 % Cis-general : 0.01 % Twisted Proline : 0.28 % 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: -0.61 (0.10), residues: 7531 helix: 0.65 (0.08), residues: 3922 sheet: -1.06 (0.28), residues: 348 loop : -1.64 (0.10), residues: 3261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 106 HIS 0.007 0.001 HIS 2 185 PHE 0.020 0.001 PHE R 73 TYR 0.027 0.001 TYR H 84 ARG 0.011 0.000 ARG H 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15062 Ramachandran restraints generated. 7531 Oldfield, 0 Emsley, 7531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15062 Ramachandran restraints generated. 7531 Oldfield, 0 Emsley, 7531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1086 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1007 time to evaluate : 5.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 31 residues processed: 1058 average time/residue: 0.6253 time to fit residues: 1117.3011 Evaluate side-chains 960 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 929 time to evaluate : 5.239 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.4843 time to fit residues: 35.7837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 444 optimal weight: 5.9990 chunk 287 optimal weight: 0.7980 chunk 429 optimal weight: 0.9980 chunk 216 optimal weight: 0.2980 chunk 141 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 457 optimal weight: 2.9990 chunk 489 optimal weight: 0.7980 chunk 355 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 565 optimal weight: 0.0370 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 HIS C 163 ASN D 26 GLN ** E 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN F 38 GLN ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 HIS H 145 GLN K 193 GLN P 73 ASN P 95 GLN ** X 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 62 GLN Y 109 GLN Z 85 GLN f 48 ASN f 60 HIS ** g 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 13 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.248 63492 Z= 0.507 Angle : 1.509 50.765 85985 Z= 0.970 Chirality : 0.291 6.404 9595 Planarity : 0.004 0.091 10740 Dihedral : 11.561 175.535 9740 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.54 % Favored : 95.43 % Rotamer: Outliers : 0.67 % Allowed : 19.21 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.28 % Cis-general : 0.01 % Twisted Proline : 0.28 % 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: -0.39 (0.10), residues: 7531 helix: 0.84 (0.09), residues: 3914 sheet: -1.00 (0.27), residues: 358 loop : -1.56 (0.10), residues: 3259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP c 15 HIS 0.008 0.001 HIS 4 228 PHE 0.018 0.001 PHE R 73 TYR 0.034 0.001 TYR A 395 ARG 0.009 0.000 ARG Y 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15062 Ramachandran restraints generated. 7531 Oldfield, 0 Emsley, 7531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15062 Ramachandran restraints generated. 7531 Oldfield, 0 Emsley, 7531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1054 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1010 time to evaluate : 5.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 18 residues processed: 1028 average time/residue: 0.6359 time to fit residues: 1109.9649 Evaluate side-chains 960 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 942 time to evaluate : 5.266 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4925 time to fit residues: 24.5508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 654 optimal weight: 4.9990 chunk 688 optimal weight: 2.9990 chunk 628 optimal weight: 2.9990 chunk 670 optimal weight: 2.9990 chunk 403 optimal weight: 1.9990 chunk 291 optimal weight: 6.9990 chunk 526 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 605 optimal weight: 3.9990 chunk 633 optimal weight: 0.7980 chunk 667 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 HIS D 64 GLN ** E 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 GLN ** R 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 20 ASN ** g 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 13 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.5635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.246 63492 Z= 0.555 Angle : 1.539 50.743 85985 Z= 0.981 Chirality : 0.292 6.410 9595 Planarity : 0.005 0.099 10740 Dihedral : 11.698 176.343 9740 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.27 % Favored : 94.70 % Rotamer: Outliers : 0.84 % Allowed : 19.35 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.28 % Cis-general : 0.01 % Twisted Proline : 0.28 % 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: -0.52 (0.10), residues: 7531 helix: 0.69 (0.08), residues: 3924 sheet: -1.13 (0.27), residues: 360 loop : -1.55 (0.10), residues: 3247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP c 15 HIS 0.008 0.001 HIS 2 185 PHE 0.023 0.002 PHE 6 73 TYR 0.026 0.002 TYR Y 130 ARG 0.014 0.001 ARG H 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15062 Ramachandran restraints generated. 7531 Oldfield, 0 Emsley, 7531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15062 Ramachandran restraints generated. 7531 Oldfield, 0 Emsley, 7531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1025 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 970 time to evaluate : 5.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 30 residues processed: 996 average time/residue: 0.6314 time to fit residues: 1065.5332 Evaluate side-chains 943 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 913 time to evaluate : 5.297 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.4628 time to fit residues: 33.9614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 439 optimal weight: 1.9990 chunk 708 optimal weight: 8.9990 chunk 432 optimal weight: 2.9990 chunk 336 optimal weight: 7.9990 chunk 492 optimal weight: 0.8980 chunk 743 optimal weight: 0.9990 chunk 684 optimal weight: 0.8980 chunk 591 optimal weight: 0.2980 chunk 61 optimal weight: 0.9980 chunk 457 optimal weight: 2.9990 chunk 362 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 GLN ** E 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 GLN P 95 GLN R 45 HIS R 49 GLN ** X 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 109 GLN ** g 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.5730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.247 63492 Z= 0.511 Angle : 1.516 50.740 85985 Z= 0.972 Chirality : 0.291 6.397 9595 Planarity : 0.004 0.090 10740 Dihedral : 11.446 176.005 9740 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.50 % Favored : 95.47 % Rotamer: Outliers : 0.38 % Allowed : 19.89 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.28 % Cis-general : 0.01 % Twisted Proline : 0.28 % 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: -0.35 (0.10), residues: 7531 helix: 0.83 (0.08), residues: 3940 sheet: -1.01 (0.27), residues: 353 loop : -1.48 (0.11), residues: 3238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP c 15 HIS 0.008 0.001 HIS 4 228 PHE 0.023 0.001 PHE P 14 TYR 0.021 0.001 TYR A 395 ARG 0.010 0.000 ARG P 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15062 Ramachandran restraints generated. 7531 Oldfield, 0 Emsley, 7531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15062 Ramachandran restraints generated. 7531 Oldfield, 0 Emsley, 7531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 996 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 971 time to evaluate : 5.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 15 residues processed: 981 average time/residue: 0.6288 time to fit residues: 1041.8391 Evaluate side-chains 943 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 928 time to evaluate : 6.874 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.4997 time to fit residues: 20.8834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 470 optimal weight: 2.9990 chunk 630 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 545 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 592 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 608 optimal weight: 0.5980 chunk 75 optimal weight: 9.9990 chunk 109 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 GLN J 48 ASN K 193 GLN P 73 ASN ** X 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 109 GLN c 20 ASN ** g 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.134522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.105504 restraints weight = 88978.083| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.57 r_work: 0.3105 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.5841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.246 63492 Z= 0.543 Angle : 1.532 50.730 85985 Z= 0.979 Chirality : 0.291 6.402 9595 Planarity : 0.004 0.098 10740 Dihedral : 11.528 176.388 9740 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.17 % Favored : 94.81 % Rotamer: Outliers : 0.32 % Allowed : 20.18 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.28 % Cis-general : 0.01 % Twisted Proline : 0.28 % 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: -0.40 (0.10), residues: 7531 helix: 0.78 (0.08), residues: 3939 sheet: -1.06 (0.27), residues: 358 loop : -1.48 (0.11), residues: 3234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP c 15 HIS 0.007 0.001 HIS 4 228 PHE 0.022 0.002 PHE 6 73 TYR 0.022 0.002 TYR H 84 ARG 0.008 0.001 ARG Y 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19709.57 seconds wall clock time: 343 minutes 58.83 seconds (20638.83 seconds total)