Starting phenix.real_space_refine on Wed Feb 14 19:08:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfq_4872/02_2024/6rfq_4872_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfq_4872/02_2024/6rfq_4872.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfq_4872/02_2024/6rfq_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_4872/02_2024/6rfq_4872_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfq_4872/02_2024/6rfq_4872_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfq_4872/02_2024/6rfq_4872.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfq_4872/02_2024/6rfq_4872.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfq_4872/02_2024/6rfq_4872_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rfq_4872/02_2024/6rfq_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: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 25.58, per 1000 atoms: 0.41 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: 19.73 Conformation dependent library (CDL) restraints added in 8.3 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: 8.85 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: 17.96 Time building geometry restraints manager: 21.55 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: 4.030 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: 21.140 Check model and map are aligned: 0.740 Set scattering table: 0.430 Process input model: 134.910 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 165.640 ------------------------------------------------------------------------------- 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 : 5.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 TYR cc_start: 0.7707 (t80) cc_final: 0.7430 (t80) REVERT: A 582 PHE cc_start: 0.7114 (m-80) cc_final: 0.6793 (m-10) REVERT: A 621 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6515 (mp0) REVERT: B 48 TYR cc_start: 0.5806 (m-10) cc_final: 0.5491 (m-10) REVERT: C 149 THR cc_start: 0.8743 (m) cc_final: 0.8406 (p) REVERT: C 275 THR cc_start: 0.7852 (m) cc_final: 0.7050 (p) REVERT: C 329 CYS cc_start: 0.8106 (t) cc_final: 0.7668 (t) REVERT: D 47 SER cc_start: 0.9164 (t) cc_final: 0.8946 (t) REVERT: D 57 ASN cc_start: 0.6857 (p0) cc_final: 0.6366 (p0) REVERT: E 136 LYS cc_start: 0.7734 (mtpp) cc_final: 0.7529 (tttm) REVERT: E 162 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.7172 (mmm160) REVERT: E 166 VAL cc_start: 0.8994 (p) cc_final: 0.8568 (p) REVERT: E 333 LEU cc_start: 0.7429 (pp) cc_final: 0.7184 (mt) REVERT: F 93 ASN cc_start: 0.8248 (m-40) cc_final: 0.7031 (m110) REVERT: G 84 LYS cc_start: 0.8375 (tttt) cc_final: 0.7809 (tttt) REVERT: G 114 ASP cc_start: 0.7943 (m-30) cc_final: 0.7654 (m-30) REVERT: H 102 MET cc_start: 0.8802 (tpt) cc_final: 0.8052 (tpp) REVERT: H 169 LEU cc_start: 0.7745 (mt) cc_final: 0.7219 (mt) REVERT: I 83 MET cc_start: 0.7986 (mmm) cc_final: 0.7580 (mmm) REVERT: J 70 ILE cc_start: 0.8076 (mt) cc_final: 0.7807 (mm) REVERT: J 173 SER cc_start: 0.7971 (p) cc_final: 0.7005 (p) REVERT: O 68 ASP cc_start: 0.7781 (m-30) cc_final: 0.7351 (m-30) REVERT: P 99 TYR cc_start: 0.7938 (m-80) cc_final: 0.7604 (m-80) REVERT: Q 102 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7397 (tm-30) REVERT: U 31 THR cc_start: 0.8499 (m) cc_final: 0.8184 (p) REVERT: U 159 SER cc_start: 0.9036 (p) cc_final: 0.8806 (p) REVERT: U 169 ASN cc_start: 0.7338 (m-40) cc_final: 0.7053 (m110) REVERT: a 118 LYS cc_start: 0.7522 (ttmp) cc_final: 0.7141 (ttmm) REVERT: b 11 SER cc_start: 0.8835 (t) cc_final: 0.8620 (t) REVERT: f 19 SER cc_start: 0.7724 (m) cc_final: 0.7356 (t) REVERT: i 81 ILE cc_start: 0.8303 (pt) cc_final: 0.8054 (pt) REVERT: 1 28 LYS cc_start: 0.7621 (mmmm) cc_final: 0.7370 (mmmt) REVERT: 1 114 SER cc_start: 0.7653 (t) cc_final: 0.7370 (m) REVERT: 2 67 TYR cc_start: 0.8489 (t80) cc_final: 0.8224 (t80) REVERT: 2 448 ILE cc_start: 0.8917 (mt) cc_final: 0.8690 (mm) REVERT: 3 1 MET cc_start: 0.4564 (tpt) cc_final: 0.3740 (mtp) REVERT: 4 105 TYR cc_start: 0.8413 (m-80) cc_final: 0.8186 (m-80) REVERT: 4 352 ASP cc_start: 0.6379 (m-30) cc_final: 0.6075 (m-30) REVERT: 4 485 ILE cc_start: 0.6674 (pt) cc_final: 0.6440 (pt) REVERT: 5 26 LEU cc_start: 0.9262 (mt) cc_final: 0.8991 (mt) REVERT: 5 393 TYR cc_start: 0.6953 (t80) cc_final: 0.6621 (t80) REVERT: 5 498 SER cc_start: 0.8165 (p) cc_final: 0.7803 (t) REVERT: 5 502 THR cc_start: 0.8430 (t) cc_final: 0.7935 (p) REVERT: 5 606 LEU cc_start: 0.8055 (tm) cc_final: 0.7730 (tp) REVERT: 5 631 LEU cc_start: 0.8510 (tm) cc_final: 0.8216 (mt) REVERT: 6 7 TYR cc_start: 0.8314 (m-80) cc_final: 0.8111 (m-80) REVERT: 6 120 ASN cc_start: 0.7089 (m-40) cc_final: 0.6272 (p0) REVERT: 9 18 GLU cc_start: 0.8170 (mp0) cc_final: 0.7874 (mp0) REVERT: 9 58 ARG cc_start: 0.7659 (ttt90) cc_final: 0.7284 (ttm110) outliers start: 11 outliers final: 2 residues processed: 2230 average time/residue: 0.6838 time to fit residues: 2509.1005 Evaluate side-chains 1226 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1223 time to evaluate : 5.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain F residue 111 LEU 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: 0.9980 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: 0.7980 ------------------------------------------------------------------------------- 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 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 365 ASN F 69 GLN F 77 HIS 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 73 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 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 6 120 ASN 6 128 ASN 6 183 HIS 8 34 ASN 9 13 ASN 9 36 GLN Total number of N/Q/H flips: 86 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.274 63492 Z= 0.554 Angle : 1.563 50.964 85985 Z= 0.989 Chirality : 0.291 6.482 9595 Planarity : 0.005 0.093 10740 Dihedral : 14.910 176.585 9748 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.57 % Favored : 95.38 % Rotamer: Outliers : 3.23 % Allowed : 11.71 % Favored : 85.06 % 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: -1.04 (0.08), residues: 3899 sheet: -1.48 (0.28), residues: 339 loop : -2.34 (0.09), residues: 3293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP 5 126 HIS 0.009 0.001 HIS D 29 PHE 0.026 0.002 PHE 2 107 TYR 0.029 0.002 TYR I 171 ARG 0.008 0.001 ARG B 388 *********************** 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 1545 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 1334 time to evaluate : 5.502 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: A 391 PHE cc_start: 0.7747 (m-80) cc_final: 0.7507 (m-80) REVERT: A 394 ASN cc_start: 0.7711 (m-40) cc_final: 0.7291 (m110) REVERT: A 621 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6430 (mp0) REVERT: B 44 LEU cc_start: 0.7879 (mt) cc_final: 0.7651 (tt) REVERT: C 149 THR cc_start: 0.8430 (m) cc_final: 0.8167 (p) REVERT: C 275 THR cc_start: 0.7843 (m) cc_final: 0.7378 (p) REVERT: C 312 ASP cc_start: 0.8494 (t70) cc_final: 0.8266 (t70) REVERT: D 6 GLU cc_start: 0.7187 (tp30) cc_final: 0.6243 (tt0) REVERT: D 47 SER cc_start: 0.9211 (t) cc_final: 0.8928 (t) REVERT: H 119 MET cc_start: 0.6966 (pmm) cc_final: 0.6331 (pmm) REVERT: H 133 GLN cc_start: 0.8552 (tp40) cc_final: 0.7636 (tp40) REVERT: H 141 MET cc_start: 0.7749 (tpp) cc_final: 0.7114 (tpp) REVERT: H 231 GLU cc_start: 0.6939 (mp0) cc_final: 0.6612 (mp0) REVERT: I 217 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7386 (pm20) REVERT: K 193 GLN cc_start: 0.7519 (mt0) cc_final: 0.7316 (mt0) REVERT: K 197 LYS cc_start: 0.8645 (ttmm) cc_final: 0.8253 (tttp) REVERT: P 57 ARG cc_start: 0.7204 (ttt-90) cc_final: 0.6884 (ttt-90) REVERT: P 81 MET cc_start: 0.8168 (mtt) cc_final: 0.7939 (mtp) REVERT: Q 107 ILE cc_start: 0.8079 (pt) cc_final: 0.7816 (pt) REVERT: R 67 ARG cc_start: 0.7622 (ttp-110) cc_final: 0.7386 (ttp-110) REVERT: S 199 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8190 (tp) REVERT: U 31 THR cc_start: 0.7962 (m) cc_final: 0.7684 (p) REVERT: U 159 SER cc_start: 0.8961 (p) cc_final: 0.8754 (p) REVERT: U 169 ASN cc_start: 0.7330 (m-40) cc_final: 0.7107 (m110) REVERT: X 23 ASP cc_start: 0.8233 (t0) cc_final: 0.7965 (t0) REVERT: Y 128 ASP cc_start: 0.7420 (p0) cc_final: 0.6951 (p0) REVERT: Z 72 ASN cc_start: 0.8038 (m110) cc_final: 0.7569 (m110) REVERT: Z 115 THR cc_start: 0.7713 (p) cc_final: 0.7489 (p) REVERT: Z 127 SER cc_start: 0.9090 (p) cc_final: 0.8600 (p) REVERT: a 75 ASP cc_start: 0.8403 (p0) cc_final: 0.8158 (p0) REVERT: c 15 TRP cc_start: 0.5533 (p90) cc_final: 0.4979 (p90) REVERT: d 72 ASP cc_start: 0.7910 (m-30) cc_final: 0.7627 (m-30) REVERT: e 28 LYS cc_start: 0.8953 (mmtm) cc_final: 0.8520 (mmtm) REVERT: 2 235 TYR cc_start: 0.8100 (t80) cc_final: 0.7686 (t80) REVERT: 2 244 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8117 (mt) REVERT: 2 448 ILE cc_start: 0.8982 (mt) cc_final: 0.8685 (mm) REVERT: 3 1 MET cc_start: 0.4491 (tpt) cc_final: 0.3507 (mtm) REVERT: 4 168 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8626 (tm) REVERT: 4 273 TYR cc_start: 0.5083 (m-10) cc_final: 0.4622 (m-10) REVERT: 4 369 MET cc_start: 0.8577 (mtm) cc_final: 0.8099 (mtt) REVERT: 4 412 ILE cc_start: 0.8369 (mt) cc_final: 0.8160 (mt) REVERT: 4 441 HIS cc_start: 0.7237 (OUTLIER) cc_final: 0.7005 (t-90) REVERT: 4 454 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7342 (mpp) REVERT: 5 393 TYR cc_start: 0.6817 (t80) cc_final: 0.6526 (t80) REVERT: 5 498 SER cc_start: 0.8107 (p) cc_final: 0.7765 (t) REVERT: 5 512 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8316 (mp) REVERT: 9 18 GLU cc_start: 0.8049 (mp0) cc_final: 0.7790 (mp0) REVERT: 9 48 LEU cc_start: 0.8288 (mt) cc_final: 0.7949 (tp) REVERT: 9 53 GLU cc_start: 0.7375 (tt0) cc_final: 0.7041 (mt-10) REVERT: 9 58 ARG cc_start: 0.7656 (ttt90) cc_final: 0.7345 (ttp-110) outliers start: 211 outliers final: 106 residues processed: 1466 average time/residue: 0.5913 time to fit residues: 1464.8970 Evaluate side-chains 1202 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1089 time to evaluate : 5.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 372 ASN Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain E residue 21 MET Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 262 ARG Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 217 GLU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 186 ASN Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain Q residue 82 THR Chi-restraints excluded: chain S residue 163 ASP Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 59 GLU Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 50 LEU Chi-restraints excluded: chain X residue 128 THR Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain Y residue 44 ILE Chi-restraints excluded: chain Y residue 70 SER Chi-restraints excluded: chain Y residue 101 SER Chi-restraints excluded: chain Y residue 131 ILE Chi-restraints excluded: chain Z residue 147 VAL Chi-restraints excluded: chain Z residue 156 THR Chi-restraints excluded: chain a residue 37 LEU Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain e residue 7 ASN Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain g residue 56 SER Chi-restraints excluded: chain g residue 61 SER Chi-restraints excluded: chain i residue 13 ILE Chi-restraints excluded: chain j residue 27 HIS Chi-restraints excluded: chain k residue 82 GLN Chi-restraints excluded: chain 1 residue 4 ASN Chi-restraints excluded: chain 1 residue 13 VAL Chi-restraints excluded: chain 1 residue 74 VAL Chi-restraints excluded: chain 1 residue 79 ILE Chi-restraints excluded: chain 1 residue 115 LEU Chi-restraints excluded: chain 1 residue 156 ILE Chi-restraints excluded: chain 1 residue 339 THR Chi-restraints excluded: chain 2 residue 192 ILE Chi-restraints excluded: chain 2 residue 194 THR Chi-restraints excluded: chain 2 residue 244 ILE Chi-restraints excluded: chain 2 residue 252 ASN Chi-restraints excluded: chain 2 residue 288 SER Chi-restraints excluded: chain 2 residue 340 GLN Chi-restraints excluded: chain 2 residue 386 ILE Chi-restraints excluded: chain 2 residue 428 LEU Chi-restraints excluded: chain 2 residue 429 ILE Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 3 residue 92 LEU Chi-restraints excluded: chain 4 residue 75 ASN Chi-restraints excluded: chain 4 residue 168 LEU Chi-restraints excluded: chain 4 residue 441 HIS Chi-restraints excluded: chain 4 residue 443 THR Chi-restraints excluded: chain 4 residue 450 GLU Chi-restraints excluded: chain 4 residue 454 MET Chi-restraints excluded: chain 4 residue 467 CYS Chi-restraints excluded: chain 5 residue 92 ILE Chi-restraints excluded: chain 5 residue 281 LEU Chi-restraints excluded: chain 5 residue 352 SER Chi-restraints excluded: chain 5 residue 368 SER Chi-restraints excluded: chain 5 residue 400 ILE Chi-restraints excluded: chain 5 residue 425 THR Chi-restraints excluded: chain 5 residue 475 ILE Chi-restraints excluded: chain 5 residue 495 ASN Chi-restraints excluded: chain 5 residue 512 LEU Chi-restraints excluded: chain 5 residue 516 ILE Chi-restraints excluded: chain 5 residue 548 SER Chi-restraints excluded: chain 5 residue 554 LEU Chi-restraints excluded: chain 6 residue 54 ILE Chi-restraints excluded: chain 6 residue 75 ILE Chi-restraints excluded: chain 6 residue 81 ASN Chi-restraints excluded: chain 6 residue 111 ILE Chi-restraints excluded: chain 6 residue 132 THR Chi-restraints excluded: chain 8 residue 34 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 376 optimal weight: 0.8980 chunk 210 optimal weight: 3.9990 chunk 563 optimal weight: 2.9990 chunk 461 optimal weight: 7.9990 chunk 186 optimal weight: 0.9980 chunk 678 optimal weight: 0.9990 chunk 733 optimal weight: 1.9990 chunk 604 optimal weight: 3.9990 chunk 673 optimal weight: 4.9990 chunk 231 optimal weight: 0.6980 chunk 544 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 680 ASN A 718 ASN B 43 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 62 ASN E 137 ASN E 188 GLN E 365 ASN 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** Y 99 GLN a 60 GLN b 54 HIS c 18 GLN d 69 GLN f 60 HIS ** g 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 76 GLN 1 173 GLN 2 50 GLN ** 2 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 173 ASN ** 2 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 278 GLN 4 128 ASN ** 4 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 299 ASN ** 5 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 617 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.252 63492 Z= 0.521 Angle : 1.533 50.636 85985 Z= 0.978 Chirality : 0.291 6.365 9595 Planarity : 0.005 0.099 10740 Dihedral : 13.267 177.880 9742 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.94 % Favored : 95.02 % Rotamer: Outliers : 3.72 % Allowed : 13.11 % Favored : 83.16 % 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: -1.63 (0.09), residues: 7531 helix: -0.24 (0.08), residues: 3918 sheet: -1.28 (0.28), residues: 334 loop : -2.09 (0.10), residues: 3279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 5 143 HIS 0.012 0.001 HIS W 114 PHE 0.023 0.002 PHE Y 129 TYR 0.023 0.002 TYR I 171 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 1437 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 1194 time to evaluate : 5.456 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: A 394 ASN cc_start: 0.7754 (m-40) cc_final: 0.7327 (m110) REVERT: A 608 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7776 (tt) REVERT: A 621 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6537 (mp0) REVERT: B 379 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7017 (mm-30) REVERT: C 149 THR cc_start: 0.8458 (m) cc_final: 0.8131 (p) REVERT: C 275 THR cc_start: 0.7962 (m) cc_final: 0.7634 (p) REVERT: D 6 GLU cc_start: 0.7277 (tp30) cc_final: 0.6256 (tt0) REVERT: D 47 SER cc_start: 0.9233 (t) cc_final: 0.9021 (t) REVERT: D 57 ASN cc_start: 0.6481 (p0) cc_final: 0.6172 (p0) REVERT: F 57 LEU cc_start: 0.7538 (pp) cc_final: 0.7238 (mp) REVERT: F 93 ASN cc_start: 0.8456 (m-40) cc_final: 0.8062 (t0) REVERT: G 91 VAL cc_start: 0.8584 (OUTLIER) cc_final: 0.8347 (t) REVERT: H 99 MET cc_start: 0.6530 (mtt) cc_final: 0.6225 (mtt) REVERT: H 133 GLN cc_start: 0.8347 (tp40) cc_final: 0.7912 (tp40) REVERT: H 141 MET cc_start: 0.7903 (tpp) cc_final: 0.7671 (tpp) REVERT: J 96 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8240 (m-40) REVERT: L 80 LEU cc_start: 0.8433 (mm) cc_final: 0.8174 (mm) REVERT: P 57 ARG cc_start: 0.7183 (ttt-90) cc_final: 0.6825 (ttm170) REVERT: S 199 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8323 (tp) REVERT: U 112 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7179 (mmp-170) REVERT: U 159 SER cc_start: 0.8949 (p) cc_final: 0.8706 (p) REVERT: U 169 ASN cc_start: 0.7144 (m-40) cc_final: 0.6886 (m110) REVERT: X 23 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.7990 (m-30) REVERT: Y 128 ASP cc_start: 0.7405 (p0) cc_final: 0.6930 (p0) REVERT: Z 72 ASN cc_start: 0.7931 (m110) cc_final: 0.7719 (m110) REVERT: Z 127 SER cc_start: 0.8806 (p) cc_final: 0.8515 (p) REVERT: a 94 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8820 (tp) REVERT: 2 448 ILE cc_start: 0.8957 (mt) cc_final: 0.8716 (mm) REVERT: 3 1 MET cc_start: 0.4040 (tpt) cc_final: 0.3056 (mtm) REVERT: 4 128 ASN cc_start: 0.8756 (t0) cc_final: 0.8387 (t0) REVERT: 4 142 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7479 (mt-10) REVERT: 4 168 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8590 (tm) REVERT: 4 273 TYR cc_start: 0.5366 (m-10) cc_final: 0.4904 (m-80) REVERT: 4 412 ILE cc_start: 0.8366 (mt) cc_final: 0.8154 (mt) REVERT: 4 454 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7395 (mpp) REVERT: 5 393 TYR cc_start: 0.7125 (t80) cc_final: 0.6797 (t80) REVERT: 6 178 SER cc_start: 0.8387 (t) cc_final: 0.8112 (p) REVERT: 9 53 GLU cc_start: 0.7397 (tt0) cc_final: 0.7034 (mt-10) REVERT: 9 58 ARG cc_start: 0.7646 (ttt90) cc_final: 0.7285 (ttm110) outliers start: 243 outliers final: 131 residues processed: 1352 average time/residue: 0.5795 time to fit residues: 1333.2475 Evaluate side-chains 1193 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1053 time to evaluate : 5.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 680 ASN Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 372 ASN Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain J residue 186 ASN Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 85 CYS Chi-restraints excluded: chain K residue 117 MET Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 147 MET Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 42 LEU Chi-restraints excluded: chain P residue 58 GLN Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 118 LEU Chi-restraints excluded: chain S residue 163 ASP Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain U residue 21 ASN Chi-restraints excluded: chain U residue 25 VAL Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 56 CYS Chi-restraints excluded: chain U residue 59 GLU Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 112 ARG Chi-restraints excluded: chain W residue 67 ILE Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 23 ASP Chi-restraints excluded: chain X residue 50 LEU Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain Y residue 44 ILE Chi-restraints excluded: chain Y residue 70 SER Chi-restraints excluded: chain Y residue 101 SER Chi-restraints excluded: chain Y residue 131 ILE Chi-restraints excluded: chain a residue 37 LEU Chi-restraints excluded: chain a residue 94 LEU Chi-restraints excluded: chain b residue 5 THR Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain d residue 76 THR Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain g residue 56 SER Chi-restraints excluded: chain i residue 13 ILE Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 83 LYS Chi-restraints excluded: chain k residue 82 GLN Chi-restraints excluded: chain 1 residue 4 ASN Chi-restraints excluded: chain 1 residue 74 VAL Chi-restraints excluded: chain 1 residue 79 ILE Chi-restraints excluded: chain 1 residue 114 SER Chi-restraints excluded: chain 1 residue 115 LEU Chi-restraints excluded: chain 1 residue 156 ILE Chi-restraints excluded: chain 2 residue 192 ILE Chi-restraints excluded: chain 2 residue 194 THR Chi-restraints excluded: chain 2 residue 212 ILE Chi-restraints excluded: chain 2 residue 288 SER Chi-restraints excluded: chain 2 residue 340 GLN Chi-restraints excluded: chain 2 residue 386 ILE Chi-restraints excluded: chain 2 residue 390 ILE Chi-restraints excluded: chain 2 residue 428 LEU Chi-restraints excluded: chain 2 residue 459 LEU Chi-restraints excluded: chain 3 residue 6 ILE Chi-restraints excluded: chain 3 residue 92 LEU Chi-restraints excluded: chain 4 residue 75 ASN Chi-restraints excluded: chain 4 residue 100 LEU Chi-restraints excluded: chain 4 residue 168 LEU Chi-restraints excluded: chain 4 residue 443 THR Chi-restraints excluded: chain 4 residue 450 GLU Chi-restraints excluded: chain 4 residue 454 MET Chi-restraints excluded: chain 5 residue 10 ILE Chi-restraints excluded: chain 5 residue 92 ILE Chi-restraints excluded: chain 5 residue 129 ILE Chi-restraints excluded: chain 5 residue 232 LEU Chi-restraints excluded: chain 5 residue 368 SER Chi-restraints excluded: chain 5 residue 432 ILE Chi-restraints excluded: chain 5 residue 495 ASN Chi-restraints excluded: chain 5 residue 502 THR Chi-restraints excluded: chain 5 residue 516 ILE Chi-restraints excluded: chain 5 residue 519 ILE Chi-restraints excluded: chain 5 residue 548 SER Chi-restraints excluded: chain 5 residue 634 VAL Chi-restraints excluded: chain 6 residue 49 LEU Chi-restraints excluded: chain 6 residue 54 ILE Chi-restraints excluded: chain 6 residue 75 ILE Chi-restraints excluded: chain 6 residue 81 ASN Chi-restraints excluded: chain 6 residue 100 SER Chi-restraints excluded: chain 6 residue 111 ILE Chi-restraints excluded: chain 6 residue 132 THR Chi-restraints excluded: chain 8 residue 12 ASP Chi-restraints excluded: chain 9 residue 2 THR Chi-restraints excluded: chain 9 residue 13 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 670 optimal weight: 4.9990 chunk 510 optimal weight: 0.1980 chunk 352 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 323 optimal weight: 10.0000 chunk 455 optimal weight: 3.9990 chunk 681 optimal weight: 4.9990 chunk 721 optimal weight: 1.9990 chunk 355 optimal weight: 5.9990 chunk 645 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 overall best weight: 2.6388 ------------------------------------------------------------------------------- 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 43 ASN C 115 HIS ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 HIS C 284 GLN ** E 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 HIS H 91 ASN P 95 GLN R 32 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 c 18 GLN c 20 ASN d 4 HIS d 88 ASN e 7 ASN f 24 GLN ** g 25 HIS ** 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** 2 292 ASN 4 371 GLN 4 441 HIS 5 233 HIS ** 5 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 326 ASN 6 152 ASN 8 49 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.245 63492 Z= 0.612 Angle : 1.585 50.731 85985 Z= 0.999 Chirality : 0.293 6.393 9595 Planarity : 0.006 0.095 10740 Dihedral : 13.093 178.925 9742 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.51 % Favored : 94.44 % Rotamer: Outliers : 4.92 % Allowed : 14.06 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.28 % Cis-general : 0.01 % Twisted Proline : 0.28 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.09), residues: 7531 helix: -0.09 (0.08), residues: 3938 sheet: -1.19 (0.28), residues: 344 loop : -1.93 (0.10), residues: 3249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP c 15 HIS 0.014 0.002 HIS 5 578 PHE 0.036 0.002 PHE G 189 TYR 0.032 0.003 TYR 2 415 ARG 0.010 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 1421 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 1100 time to evaluate : 5.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 ASN cc_start: 0.7795 (m-40) cc_final: 0.7401 (m110) REVERT: A 408 ASP cc_start: 0.7178 (OUTLIER) cc_final: 0.6976 (m-30) REVERT: A 608 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8137 (tt) REVERT: A 621 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6409 (mp0) REVERT: B 413 MET cc_start: 0.8075 (ttp) cc_final: 0.7865 (tmm) REVERT: C 68 ASP cc_start: 0.7744 (t0) cc_final: 0.7263 (t0) REVERT: C 149 THR cc_start: 0.8686 (m) cc_final: 0.8368 (p) REVERT: C 275 THR cc_start: 0.8060 (m) cc_final: 0.7702 (p) REVERT: D 6 GLU cc_start: 0.7253 (tp30) cc_final: 0.6376 (tt0) REVERT: D 47 SER cc_start: 0.9178 (t) cc_final: 0.8769 (m) REVERT: D 69 THR cc_start: 0.8517 (p) cc_final: 0.8304 (m) REVERT: D 83 GLU cc_start: 0.6875 (tt0) cc_final: 0.6454 (tt0) REVERT: E 133 TYR cc_start: 0.8014 (p90) cc_final: 0.7680 (p90) REVERT: F 93 ASN cc_start: 0.8476 (m-40) cc_final: 0.8175 (t0) REVERT: H 99 MET cc_start: 0.7111 (mtt) cc_final: 0.6891 (mtt) REVERT: H 133 GLN cc_start: 0.8460 (tp40) cc_final: 0.7949 (tp40) REVERT: K 41 MET cc_start: 0.3766 (ptp) cc_final: 0.1879 (ttm) REVERT: L 6 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8577 (tp) REVERT: L 38 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8660 (mt) REVERT: Q 57 GLU cc_start: 0.7961 (pt0) cc_final: 0.7623 (mt-10) REVERT: U 112 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7307 (mmp-170) REVERT: X 23 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.7968 (m-30) REVERT: Y 110 MET cc_start: 0.8101 (mtp) cc_final: 0.7773 (mtp) REVERT: Y 128 ASP cc_start: 0.7690 (p0) cc_final: 0.7049 (p0) REVERT: Y 148 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.7881 (p90) REVERT: Z 71 GLU cc_start: 0.7430 (tm-30) cc_final: 0.7114 (tm-30) REVERT: a 55 LYS cc_start: 0.8508 (mttt) cc_final: 0.8085 (mtpt) REVERT: c 15 TRP cc_start: 0.5954 (p90) cc_final: 0.5742 (p90) REVERT: d 72 ASP cc_start: 0.8021 (m-30) cc_final: 0.7752 (m-30) REVERT: e 28 LYS cc_start: 0.9095 (tppt) cc_final: 0.8892 (tppt) REVERT: k 106 ARG cc_start: 0.6860 (ttp80) cc_final: 0.6580 (ttp80) REVERT: 1 310 ASN cc_start: 0.8268 (t0) cc_final: 0.7917 (m-40) REVERT: 2 71 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8878 (tp) REVERT: 3 1 MET cc_start: 0.4656 (tpt) cc_final: 0.3585 (mtm) REVERT: 4 82 ASP cc_start: 0.8273 (p0) cc_final: 0.7963 (p0) REVERT: 4 142 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7596 (mt-10) REVERT: 4 168 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8617 (tm) REVERT: 4 273 TYR cc_start: 0.5935 (m-10) cc_final: 0.5445 (m-80) REVERT: 5 33 ARG cc_start: 0.8286 (mpt90) cc_final: 0.7868 (mmt180) REVERT: 5 606 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7968 (tp) REVERT: 9 58 ARG cc_start: 0.7683 (ttt90) cc_final: 0.7227 (ttm110) outliers start: 321 outliers final: 187 residues processed: 1325 average time/residue: 0.5962 time to fit residues: 1341.6411 Evaluate side-chains 1179 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 982 time to evaluate : 5.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 674 HIS Chi-restraints excluded: chain A residue 680 ASN Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 372 ASN Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 201 ARG Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 161 GLU Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 136 CYS Chi-restraints excluded: chain I residue 175 CYS Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain J residue 186 ASN Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 85 CYS Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 147 MET Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 58 GLN Chi-restraints excluded: chain Q residue 82 THR Chi-restraints excluded: chain Q residue 99 ILE Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 163 ASP Chi-restraints excluded: chain U residue 25 VAL Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 56 CYS Chi-restraints excluded: chain U residue 112 ARG Chi-restraints excluded: chain W residue 40 ILE Chi-restraints excluded: chain W residue 67 ILE Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 23 ASP Chi-restraints excluded: chain X residue 50 LEU Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain X residue 135 LEU Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain Y residue 44 ILE Chi-restraints excluded: chain Y residue 70 SER Chi-restraints excluded: chain Y residue 131 ILE Chi-restraints excluded: chain Y residue 148 PHE Chi-restraints excluded: chain Z residue 93 THR Chi-restraints excluded: chain Z residue 95 THR Chi-restraints excluded: chain Z residue 147 VAL Chi-restraints excluded: chain a residue 31 LYS Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 94 LEU Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 48 LEU Chi-restraints excluded: chain d residue 76 THR Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain f residue 40 THR Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain g residue 56 SER Chi-restraints excluded: chain g residue 61 SER Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 13 ILE Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 83 LYS Chi-restraints excluded: chain k residue 82 GLN Chi-restraints excluded: chain n residue 50 VAL Chi-restraints excluded: chain n residue 100 LEU Chi-restraints excluded: chain 1 residue 4 ASN Chi-restraints excluded: chain 1 residue 13 VAL Chi-restraints excluded: chain 1 residue 74 VAL Chi-restraints excluded: chain 1 residue 79 ILE Chi-restraints excluded: chain 1 residue 83 THR Chi-restraints excluded: chain 1 residue 147 GLU Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 156 ILE Chi-restraints excluded: chain 1 residue 264 ASN Chi-restraints excluded: chain 1 residue 276 LEU Chi-restraints excluded: chain 1 residue 296 VAL Chi-restraints excluded: chain 1 residue 339 THR Chi-restraints excluded: chain 2 residue 46 PHE Chi-restraints excluded: chain 2 residue 71 LEU Chi-restraints excluded: chain 2 residue 183 THR Chi-restraints excluded: chain 2 residue 192 ILE Chi-restraints excluded: chain 2 residue 194 THR Chi-restraints excluded: chain 2 residue 196 ASP Chi-restraints excluded: chain 2 residue 257 SER Chi-restraints excluded: chain 2 residue 288 SER Chi-restraints excluded: chain 2 residue 386 ILE Chi-restraints excluded: chain 2 residue 390 ILE Chi-restraints excluded: chain 2 residue 419 VAL Chi-restraints excluded: chain 2 residue 459 LEU Chi-restraints excluded: chain 3 residue 21 VAL Chi-restraints excluded: chain 3 residue 77 VAL Chi-restraints excluded: chain 3 residue 91 VAL Chi-restraints excluded: chain 3 residue 92 LEU Chi-restraints excluded: chain 4 residue 62 SER Chi-restraints excluded: chain 4 residue 75 ASN Chi-restraints excluded: chain 4 residue 91 LEU Chi-restraints excluded: chain 4 residue 93 VAL Chi-restraints excluded: chain 4 residue 94 LEU Chi-restraints excluded: chain 4 residue 100 LEU Chi-restraints excluded: chain 4 residue 168 LEU Chi-restraints excluded: chain 4 residue 209 ILE Chi-restraints excluded: chain 4 residue 265 LEU Chi-restraints excluded: chain 4 residue 317 VAL Chi-restraints excluded: chain 4 residue 450 GLU Chi-restraints excluded: chain 4 residue 454 MET Chi-restraints excluded: chain 5 residue 10 ILE Chi-restraints excluded: chain 5 residue 89 LEU Chi-restraints excluded: chain 5 residue 92 ILE Chi-restraints excluded: chain 5 residue 129 ILE Chi-restraints excluded: chain 5 residue 352 SER Chi-restraints excluded: chain 5 residue 368 SER Chi-restraints excluded: chain 5 residue 395 THR Chi-restraints excluded: chain 5 residue 414 VAL Chi-restraints excluded: chain 5 residue 421 SER Chi-restraints excluded: chain 5 residue 432 ILE Chi-restraints excluded: chain 5 residue 436 THR Chi-restraints excluded: chain 5 residue 439 SER Chi-restraints excluded: chain 5 residue 475 ILE Chi-restraints excluded: chain 5 residue 483 VAL Chi-restraints excluded: chain 5 residue 495 ASN Chi-restraints excluded: chain 5 residue 498 SER Chi-restraints excluded: chain 5 residue 519 ILE Chi-restraints excluded: chain 5 residue 548 SER Chi-restraints excluded: chain 5 residue 606 LEU Chi-restraints excluded: chain 5 residue 634 VAL Chi-restraints excluded: chain 6 residue 18 LEU Chi-restraints excluded: chain 6 residue 30 MET Chi-restraints excluded: chain 6 residue 54 ILE Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 6 residue 75 ILE Chi-restraints excluded: chain 6 residue 81 ASN Chi-restraints excluded: chain 6 residue 86 SER Chi-restraints excluded: chain 6 residue 100 SER Chi-restraints excluded: chain 6 residue 132 THR Chi-restraints excluded: chain 8 residue 12 ASP Chi-restraints excluded: chain 9 residue 2 THR Chi-restraints excluded: chain 9 residue 13 ASN Chi-restraints excluded: chain 9 residue 28 LYS Chi-restraints excluded: chain 9 residue 64 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 600 optimal weight: 3.9990 chunk 409 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 536 optimal weight: 0.9980 chunk 297 optimal weight: 0.9990 chunk 615 optimal weight: 1.9990 chunk 498 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 368 optimal weight: 0.9990 chunk 647 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 680 ASN ** 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 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN F 58 GLN G 99 HIS H 91 ASN K 195 GLN R 32 ASN ** X 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 150 HIS Z 130 GLN d 88 ASN e 7 ASN f 24 GLN ** g 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 11 GLN k 107 GLN ** 1 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 106 ASN 4 112 ASN 4 128 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** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.249 63492 Z= 0.515 Angle : 1.522 50.712 85985 Z= 0.974 Chirality : 0.291 6.368 9595 Planarity : 0.004 0.093 10740 Dihedral : 12.487 178.122 9742 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.63 % Favored : 95.31 % Rotamer: Outliers : 3.51 % Allowed : 16.62 % Favored : 79.87 % 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: -0.97 (0.09), residues: 7531 helix: 0.33 (0.08), residues: 3931 sheet: -1.10 (0.28), residues: 340 loop : -1.80 (0.10), residues: 3260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP c 15 HIS 0.007 0.001 HIS 2 185 PHE 0.022 0.001 PHE H 47 TYR 0.023 0.001 TYR a 96 ARG 0.009 0.000 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 1283 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 1054 time to evaluate : 5.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 THR cc_start: 0.7861 (m) cc_final: 0.7581 (m) REVERT: A 394 ASN cc_start: 0.7775 (m-40) cc_final: 0.7335 (m110) REVERT: C 68 ASP cc_start: 0.7683 (t0) cc_final: 0.7369 (t0) REVERT: C 149 THR cc_start: 0.8475 (m) cc_final: 0.8167 (p) REVERT: C 275 THR cc_start: 0.7927 (m) cc_final: 0.6706 (p) REVERT: D 6 GLU cc_start: 0.7092 (tp30) cc_final: 0.6333 (tt0) REVERT: D 47 SER cc_start: 0.9108 (t) cc_final: 0.8722 (m) REVERT: D 69 THR cc_start: 0.8579 (p) cc_final: 0.8299 (m) REVERT: D 83 GLU cc_start: 0.6935 (tt0) cc_final: 0.6657 (tt0) REVERT: E 133 TYR cc_start: 0.7993 (p90) cc_final: 0.7712 (p90) REVERT: E 205 MET cc_start: 0.7932 (mtm) cc_final: 0.7694 (mtm) REVERT: F 25 MET cc_start: 0.7496 (ptp) cc_final: 0.7282 (ptp) REVERT: F 93 ASN cc_start: 0.8488 (m-40) cc_final: 0.8163 (t0) REVERT: J 96 ASN cc_start: 0.8953 (OUTLIER) cc_final: 0.8674 (m-40) REVERT: K 41 MET cc_start: 0.3514 (ptp) cc_final: 0.1716 (ttm) REVERT: K 143 TRP cc_start: 0.8662 (m-90) cc_final: 0.8028 (m100) REVERT: L 38 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8773 (mt) REVERT: P 59 GLU cc_start: 0.7511 (mp0) cc_final: 0.6982 (mp0) REVERT: Q 57 GLU cc_start: 0.8036 (pt0) cc_final: 0.7719 (mt-10) REVERT: Q 106 GLU cc_start: 0.8120 (pp20) cc_final: 0.7876 (pp20) REVERT: R 18 MET cc_start: 0.7824 (ttm) cc_final: 0.7424 (mtp) REVERT: X 23 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.7931 (m-30) REVERT: Y 110 MET cc_start: 0.8058 (mtp) cc_final: 0.7834 (mtp) REVERT: Y 128 ASP cc_start: 0.7658 (p0) cc_final: 0.7110 (p0) REVERT: Y 148 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.7711 (p90) REVERT: a 94 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9012 (tp) REVERT: c 15 TRP cc_start: 0.5977 (p90) cc_final: 0.5188 (p90) REVERT: d 34 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7934 (mt0) REVERT: d 68 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7079 (mm-30) REVERT: k 106 ARG cc_start: 0.6831 (ttp80) cc_final: 0.6511 (ttp80) REVERT: 3 1 MET cc_start: 0.4717 (tpt) cc_final: 0.3689 (mtm) REVERT: 4 142 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7637 (mt-10) REVERT: 4 209 ILE cc_start: 0.8999 (pt) cc_final: 0.8672 (mt) REVERT: 4 273 TYR cc_start: 0.5736 (m-10) cc_final: 0.5286 (m-80) REVERT: 4 454 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7603 (mpp) REVERT: 5 33 ARG cc_start: 0.8197 (mpt90) cc_final: 0.7939 (mmt180) REVERT: 6 142 GLU cc_start: 0.8013 (pm20) cc_final: 0.7799 (pm20) REVERT: 8 24 ASP cc_start: 0.7961 (p0) cc_final: 0.7116 (t0) REVERT: 8 61 ASP cc_start: 0.8279 (t70) cc_final: 0.8045 (t0) REVERT: 9 38 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8619 (tp) REVERT: 9 58 ARG cc_start: 0.7678 (ttt90) cc_final: 0.7251 (ttm110) outliers start: 229 outliers final: 147 residues processed: 1211 average time/residue: 0.5762 time to fit residues: 1186.2927 Evaluate side-chains 1131 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 976 time to evaluate : 5.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 674 HIS Chi-restraints excluded: chain A residue 680 ASN Chi-restraints excluded: chain A residue 699 MET Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 372 ASN Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 201 ARG Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 274 ASP Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 161 GLU Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 136 CYS Chi-restraints excluded: chain I residue 175 CYS Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 186 ASN Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 85 CYS Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 58 GLN Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 163 ASP Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 56 CYS Chi-restraints excluded: chain W residue 67 ILE Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 23 ASP Chi-restraints excluded: chain X residue 50 LEU Chi-restraints excluded: chain X residue 128 THR Chi-restraints excluded: chain Y residue 44 ILE Chi-restraints excluded: chain Y residue 70 SER Chi-restraints excluded: chain Y residue 148 PHE Chi-restraints excluded: chain Z residue 147 VAL Chi-restraints excluded: chain Z residue 180 THR Chi-restraints excluded: chain a residue 37 LEU Chi-restraints excluded: chain a residue 74 ASP Chi-restraints excluded: chain a residue 94 LEU Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain d residue 34 GLN Chi-restraints excluded: chain d residue 88 ASN Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain f residue 8 ILE Chi-restraints excluded: chain g residue 56 SER Chi-restraints excluded: chain g residue 61 SER Chi-restraints excluded: chain i residue 13 ILE Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 83 LYS Chi-restraints excluded: chain 1 residue 4 ASN Chi-restraints excluded: chain 1 residue 74 VAL Chi-restraints excluded: chain 1 residue 79 ILE Chi-restraints excluded: chain 1 residue 156 ILE Chi-restraints excluded: chain 1 residue 157 ILE Chi-restraints excluded: chain 1 residue 276 LEU Chi-restraints excluded: chain 1 residue 339 THR Chi-restraints excluded: chain 2 residue 46 PHE Chi-restraints excluded: chain 2 residue 183 THR Chi-restraints excluded: chain 2 residue 192 ILE Chi-restraints excluded: chain 2 residue 194 THR Chi-restraints excluded: chain 2 residue 288 SER Chi-restraints excluded: chain 2 residue 386 ILE Chi-restraints excluded: chain 2 residue 390 ILE Chi-restraints excluded: chain 2 residue 419 VAL Chi-restraints excluded: chain 2 residue 459 LEU Chi-restraints excluded: chain 3 residue 92 LEU Chi-restraints excluded: chain 4 residue 62 SER Chi-restraints excluded: chain 4 residue 75 ASN Chi-restraints excluded: chain 4 residue 443 THR Chi-restraints excluded: chain 4 residue 450 GLU Chi-restraints excluded: chain 4 residue 454 MET Chi-restraints excluded: chain 5 residue 10 ILE Chi-restraints excluded: chain 5 residue 89 LEU Chi-restraints excluded: chain 5 residue 92 ILE Chi-restraints excluded: chain 5 residue 129 ILE Chi-restraints excluded: chain 5 residue 161 LEU Chi-restraints excluded: chain 5 residue 232 LEU Chi-restraints excluded: chain 5 residue 234 ASN Chi-restraints excluded: chain 5 residue 289 LEU Chi-restraints excluded: chain 5 residue 352 SER Chi-restraints excluded: chain 5 residue 368 SER Chi-restraints excluded: chain 5 residue 395 THR Chi-restraints excluded: chain 5 residue 421 SER Chi-restraints excluded: chain 5 residue 432 ILE Chi-restraints excluded: chain 5 residue 439 SER Chi-restraints excluded: chain 5 residue 483 VAL Chi-restraints excluded: chain 5 residue 488 VAL Chi-restraints excluded: chain 5 residue 495 ASN Chi-restraints excluded: chain 5 residue 498 SER Chi-restraints excluded: chain 5 residue 519 ILE Chi-restraints excluded: chain 5 residue 548 SER Chi-restraints excluded: chain 5 residue 554 LEU Chi-restraints excluded: chain 5 residue 634 VAL Chi-restraints excluded: chain 6 residue 75 ILE Chi-restraints excluded: chain 6 residue 100 SER Chi-restraints excluded: chain 8 residue 4 PHE Chi-restraints excluded: chain 8 residue 12 ASP Chi-restraints excluded: chain 9 residue 2 THR Chi-restraints excluded: chain 9 residue 13 ASN Chi-restraints excluded: chain 9 residue 38 LEU Chi-restraints excluded: chain 9 residue 48 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 242 optimal weight: 9.9990 chunk 649 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 chunk 423 optimal weight: 5.9990 chunk 178 optimal weight: 10.0000 chunk 721 optimal weight: 0.0370 chunk 599 optimal weight: 4.9990 chunk 334 optimal weight: 0.2980 chunk 60 optimal weight: 2.9990 chunk 238 optimal weight: 9.9990 chunk 378 optimal weight: 6.9990 overall best weight: 1.6062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 680 ASN ** 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** D 64 GLN ** E 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN H 145 GLN K 193 GLN U 99 GLN ** X 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 130 GLN ** g 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 11 GLN ** 1 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 49 GLN 4 371 GLN 5 312 GLN 5 537 ASN ** 5 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.5183 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= 0.540 Angle : 1.527 50.692 85985 Z= 0.976 Chirality : 0.291 6.372 9595 Planarity : 0.004 0.095 10740 Dihedral : 12.243 177.738 9742 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.13 % Favored : 94.83 % Rotamer: Outliers : 4.09 % Allowed : 16.67 % Favored : 79.24 % 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: -0.82 (0.10), residues: 7531 helix: 0.46 (0.08), residues: 3927 sheet: -1.11 (0.28), residues: 343 loop : -1.75 (0.10), residues: 3261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP c 15 HIS 0.009 0.001 HIS R 45 PHE 0.021 0.002 PHE A 450 TYR 0.022 0.002 TYR I 103 ARG 0.008 0.001 ARG P 30 *********************** 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 1272 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1005 time to evaluate : 5.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 ASN cc_start: 0.7797 (m-40) cc_final: 0.7391 (m110) REVERT: A 408 ASP cc_start: 0.7095 (OUTLIER) cc_final: 0.6894 (m-30) REVERT: A 549 MET cc_start: 0.7626 (ttm) cc_final: 0.7405 (ttm) REVERT: B 413 MET cc_start: 0.8005 (tmm) cc_final: 0.7621 (tmm) REVERT: C 68 ASP cc_start: 0.7826 (t0) cc_final: 0.7466 (t0) REVERT: C 149 THR cc_start: 0.8505 (m) cc_final: 0.8193 (p) REVERT: C 275 THR cc_start: 0.7883 (m) cc_final: 0.7490 (p) REVERT: D 6 GLU cc_start: 0.7083 (tp30) cc_final: 0.6444 (tt0) REVERT: D 47 SER cc_start: 0.9108 (t) cc_final: 0.8698 (m) REVERT: E 133 TYR cc_start: 0.8075 (p90) cc_final: 0.7712 (p90) REVERT: E 275 MET cc_start: 0.6493 (ttm) cc_final: 0.5940 (ttp) REVERT: F 93 ASN cc_start: 0.8551 (m-40) cc_final: 0.8187 (t0) REVERT: H 99 MET cc_start: 0.7020 (mtt) cc_final: 0.6680 (mtt) REVERT: H 133 GLN cc_start: 0.8230 (tp40) cc_final: 0.7741 (tp40) REVERT: I 107 LYS cc_start: 0.8136 (mmtt) cc_final: 0.7810 (mmtp) REVERT: J 96 ASN cc_start: 0.8967 (OUTLIER) cc_final: 0.8663 (m-40) REVERT: K 41 MET cc_start: 0.3554 (ptp) cc_final: 0.1770 (ttm) REVERT: L 38 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8568 (mt) REVERT: P 59 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: Q 57 GLU cc_start: 0.7998 (pt0) cc_final: 0.7692 (mt-10) REVERT: Q 106 GLU cc_start: 0.8142 (pp20) cc_final: 0.7926 (pp20) REVERT: Q 120 GLN cc_start: 0.7771 (mt0) cc_final: 0.7459 (mt0) REVERT: R 18 MET cc_start: 0.7925 (ttm) cc_final: 0.7530 (mtp) REVERT: X 23 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.7899 (m-30) REVERT: Y 55 ASN cc_start: 0.7512 (t0) cc_final: 0.6991 (t0) REVERT: Y 110 MET cc_start: 0.8054 (mtp) cc_final: 0.7790 (mtp) REVERT: Y 128 ASP cc_start: 0.7751 (p0) cc_final: 0.7182 (p0) REVERT: Y 148 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.7614 (p90) REVERT: a 94 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9063 (tp) REVERT: c 15 TRP cc_start: 0.6082 (p90) cc_final: 0.4926 (p90) REVERT: d 34 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8121 (mt0) REVERT: d 72 ASP cc_start: 0.8015 (m-30) cc_final: 0.7715 (m-30) REVERT: k 106 ARG cc_start: 0.6839 (ttp80) cc_final: 0.6503 (ttp80) REVERT: 1 310 ASN cc_start: 0.8054 (t0) cc_final: 0.7720 (m-40) REVERT: 2 285 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8858 (mt) REVERT: 3 1 MET cc_start: 0.5031 (tpt) cc_final: 0.3871 (mtm) REVERT: 4 82 ASP cc_start: 0.8168 (p0) cc_final: 0.7882 (p0) REVERT: 4 169 MET cc_start: 0.8566 (mmt) cc_final: 0.8315 (mmm) REVERT: 4 209 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8689 (mt) REVERT: 4 273 TYR cc_start: 0.5921 (m-10) cc_final: 0.5681 (m-10) REVERT: 4 296 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8571 (pp) REVERT: 4 352 ASP cc_start: 0.7546 (t0) cc_final: 0.7343 (t0) REVERT: 4 454 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.7673 (mpp) REVERT: 5 40 ILE cc_start: 0.9081 (mm) cc_final: 0.8827 (mt) REVERT: 5 606 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8037 (tp) REVERT: 5 616 MET cc_start: 0.7622 (tpp) cc_final: 0.7051 (ttm) REVERT: 8 24 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7312 (t0) REVERT: 8 61 ASP cc_start: 0.8333 (t70) cc_final: 0.8073 (t0) REVERT: 9 38 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8613 (tp) REVERT: 9 58 ARG cc_start: 0.7686 (ttt90) cc_final: 0.7224 (ttm110) outliers start: 267 outliers final: 178 residues processed: 1188 average time/residue: 0.5874 time to fit residues: 1188.7778 Evaluate side-chains 1157 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 964 time to evaluate : 5.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 674 HIS Chi-restraints excluded: chain A residue 680 ASN Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 372 ASN Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 201 ARG Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 161 GLU Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 136 CYS Chi-restraints excluded: chain I residue 175 CYS Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 186 ASN Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 85 CYS Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 147 MET Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 58 GLN Chi-restraints excluded: chain P residue 59 GLU Chi-restraints excluded: chain P residue 61 GLU Chi-restraints excluded: chain Q residue 99 ILE Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 163 ASP Chi-restraints excluded: chain U residue 25 VAL Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 56 CYS Chi-restraints excluded: chain U residue 59 GLU Chi-restraints excluded: chain U residue 112 ARG Chi-restraints excluded: chain W residue 67 ILE Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 23 ASP Chi-restraints excluded: chain X residue 50 LEU Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain X residue 135 LEU Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain Y residue 44 ILE Chi-restraints excluded: chain Y residue 70 SER Chi-restraints excluded: chain Y residue 148 PHE Chi-restraints excluded: chain Z residue 66 THR Chi-restraints excluded: chain Z residue 95 THR Chi-restraints excluded: chain Z residue 147 VAL Chi-restraints excluded: chain Z residue 180 THR Chi-restraints excluded: chain a residue 74 ASP Chi-restraints excluded: chain a residue 94 LEU Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain c residue 17 TYR Chi-restraints excluded: chain d residue 34 GLN Chi-restraints excluded: chain d residue 76 THR Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain e residue 46 TYR Chi-restraints excluded: chain f residue 8 ILE Chi-restraints excluded: chain g residue 56 SER Chi-restraints excluded: chain g residue 61 SER Chi-restraints excluded: chain i residue 13 ILE Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 80 PHE Chi-restraints excluded: chain j residue 83 LYS Chi-restraints excluded: chain n residue 50 VAL Chi-restraints excluded: chain n residue 100 LEU Chi-restraints excluded: chain 1 residue 4 ASN Chi-restraints excluded: chain 1 residue 9 LEU Chi-restraints excluded: chain 1 residue 24 VAL Chi-restraints excluded: chain 1 residue 74 VAL Chi-restraints excluded: chain 1 residue 79 ILE Chi-restraints excluded: chain 1 residue 147 GLU Chi-restraints excluded: chain 1 residue 156 ILE Chi-restraints excluded: chain 1 residue 276 LEU Chi-restraints excluded: chain 1 residue 296 VAL Chi-restraints excluded: chain 1 residue 339 THR Chi-restraints excluded: chain 2 residue 9 LEU Chi-restraints excluded: chain 2 residue 46 PHE Chi-restraints excluded: chain 2 residue 118 VAL Chi-restraints excluded: chain 2 residue 125 THR Chi-restraints excluded: chain 2 residue 166 ILE Chi-restraints excluded: chain 2 residue 192 ILE Chi-restraints excluded: chain 2 residue 194 THR Chi-restraints excluded: chain 2 residue 285 LEU Chi-restraints excluded: chain 2 residue 288 SER Chi-restraints excluded: chain 2 residue 386 ILE Chi-restraints excluded: chain 2 residue 390 ILE Chi-restraints excluded: chain 2 residue 419 VAL Chi-restraints excluded: chain 2 residue 459 LEU Chi-restraints excluded: chain 3 residue 92 LEU Chi-restraints excluded: chain 4 residue 62 SER Chi-restraints excluded: chain 4 residue 75 ASN Chi-restraints excluded: chain 4 residue 91 LEU Chi-restraints excluded: chain 4 residue 209 ILE Chi-restraints excluded: chain 4 residue 296 ILE Chi-restraints excluded: chain 4 residue 317 VAL Chi-restraints excluded: chain 4 residue 450 GLU Chi-restraints excluded: chain 4 residue 454 MET Chi-restraints excluded: chain 5 residue 10 ILE Chi-restraints excluded: chain 5 residue 89 LEU Chi-restraints excluded: chain 5 residue 92 ILE Chi-restraints excluded: chain 5 residue 129 ILE Chi-restraints excluded: chain 5 residue 154 ILE Chi-restraints excluded: chain 5 residue 161 LEU Chi-restraints excluded: chain 5 residue 227 SER Chi-restraints excluded: chain 5 residue 232 LEU Chi-restraints excluded: chain 5 residue 234 ASN Chi-restraints excluded: chain 5 residue 255 LEU Chi-restraints excluded: chain 5 residue 289 LEU Chi-restraints excluded: chain 5 residue 351 HIS Chi-restraints excluded: chain 5 residue 352 SER Chi-restraints excluded: chain 5 residue 368 SER Chi-restraints excluded: chain 5 residue 395 THR Chi-restraints excluded: chain 5 residue 421 SER Chi-restraints excluded: chain 5 residue 432 ILE Chi-restraints excluded: chain 5 residue 439 SER Chi-restraints excluded: chain 5 residue 447 THR Chi-restraints excluded: chain 5 residue 483 VAL Chi-restraints excluded: chain 5 residue 488 VAL Chi-restraints excluded: chain 5 residue 495 ASN Chi-restraints excluded: chain 5 residue 498 SER Chi-restraints excluded: chain 5 residue 502 THR Chi-restraints excluded: chain 5 residue 519 ILE Chi-restraints excluded: chain 5 residue 548 SER Chi-restraints excluded: chain 5 residue 554 LEU Chi-restraints excluded: chain 5 residue 606 LEU Chi-restraints excluded: chain 5 residue 621 ILE Chi-restraints excluded: chain 5 residue 634 VAL Chi-restraints excluded: chain 6 residue 75 ILE Chi-restraints excluded: chain 6 residue 86 SER Chi-restraints excluded: chain 6 residue 100 SER Chi-restraints excluded: chain 8 residue 4 PHE Chi-restraints excluded: chain 8 residue 12 ASP Chi-restraints excluded: chain 8 residue 24 ASP Chi-restraints excluded: chain 9 residue 2 THR Chi-restraints excluded: chain 9 residue 13 ASN Chi-restraints excluded: chain 9 residue 38 LEU Chi-restraints excluded: chain 9 residue 48 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 695 optimal weight: 0.0470 chunk 81 optimal weight: 1.9990 chunk 411 optimal weight: 2.9990 chunk 527 optimal weight: 0.5980 chunk 408 optimal weight: 0.5980 chunk 607 optimal weight: 3.9990 chunk 403 optimal weight: 0.0010 chunk 719 optimal weight: 0.9990 chunk 449 optimal weight: 3.9990 chunk 438 optimal weight: 3.9990 chunk 331 optimal weight: 6.9990 overall best weight: 0.4486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 517 ASN A 680 ASN ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 HIS C 163 ASN E 188 GLN F 58 GLN G 136 ASN K 193 GLN K 195 GLN S 238 GLN ** X 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 130 GLN ** g 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 11 GLN ** 1 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 391 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.249 63492 Z= 0.504 Angle : 1.505 50.716 85985 Z= 0.968 Chirality : 0.290 6.366 9595 Planarity : 0.004 0.092 10740 Dihedral : 11.767 177.081 9742 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.53 % Favored : 95.45 % Rotamer: Outliers : 3.17 % Allowed : 17.97 % Favored : 78.86 % 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: -0.53 (0.10), residues: 7531 helix: 0.72 (0.08), residues: 3943 sheet: -1.01 (0.27), residues: 356 loop : -1.63 (0.10), residues: 3232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 106 HIS 0.008 0.001 HIS 4 228 PHE 0.019 0.001 PHE C 83 TYR 0.022 0.001 TYR F 67 ARG 0.009 0.000 ARG Y 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 1249 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1042 time to evaluate : 5.973 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: A 326 ASP cc_start: 0.7165 (t0) cc_final: 0.6303 (p0) REVERT: A 549 MET cc_start: 0.7559 (ttm) cc_final: 0.7350 (ttm) REVERT: C 68 ASP cc_start: 0.7764 (t0) cc_final: 0.7492 (t0) REVERT: C 275 THR cc_start: 0.7646 (m) cc_final: 0.7247 (p) REVERT: D 6 GLU cc_start: 0.7054 (tp30) cc_final: 0.6322 (tt0) REVERT: D 47 SER cc_start: 0.9063 (t) cc_final: 0.8649 (m) REVERT: E 133 TYR cc_start: 0.8068 (p90) cc_final: 0.7758 (p90) REVERT: F 93 ASN cc_start: 0.8501 (m-40) cc_final: 0.8172 (t0) REVERT: H 99 MET cc_start: 0.7026 (mtt) cc_final: 0.6741 (mtt) REVERT: H 133 GLN cc_start: 0.8190 (tp40) cc_final: 0.7709 (tp40) REVERT: I 107 LYS cc_start: 0.8008 (mmtt) cc_final: 0.7661 (mmtp) REVERT: J 70 ILE cc_start: 0.8106 (mt) cc_final: 0.7799 (mt) REVERT: K 41 MET cc_start: 0.3330 (ptp) cc_final: 0.1804 (ttm) REVERT: L 38 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8592 (mt) REVERT: O 97 GLN cc_start: 0.6113 (mp10) cc_final: 0.5856 (mp10) REVERT: P 59 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: P 99 TYR cc_start: 0.7499 (m-80) cc_final: 0.7266 (m-80) REVERT: Q 56 GLN cc_start: 0.8657 (tp40) cc_final: 0.8414 (tp40) REVERT: Q 57 GLU cc_start: 0.8006 (pt0) cc_final: 0.7715 (mt-10) REVERT: Q 106 GLU cc_start: 0.8099 (pp20) cc_final: 0.7888 (pp20) REVERT: Q 120 GLN cc_start: 0.7715 (mt0) cc_final: 0.7494 (mt0) REVERT: R 18 MET cc_start: 0.7757 (ttm) cc_final: 0.7497 (mtp) REVERT: W 93 LYS cc_start: 0.8522 (ttmp) cc_final: 0.8320 (ttmm) REVERT: X 23 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7876 (m-30) REVERT: Y 55 ASN cc_start: 0.7398 (t0) cc_final: 0.6898 (t0) REVERT: Y 110 MET cc_start: 0.7999 (mtp) cc_final: 0.7721 (mtp) REVERT: Y 119 ILE cc_start: 0.8634 (tp) cc_final: 0.8060 (pt) REVERT: Y 128 ASP cc_start: 0.7739 (p0) cc_final: 0.7130 (p0) REVERT: Y 148 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.7500 (p90) REVERT: Z 147 VAL cc_start: 0.8663 (OUTLIER) cc_final: 0.8380 (m) REVERT: a 94 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9000 (tp) REVERT: a 133 GLU cc_start: 0.7997 (mp0) cc_final: 0.7616 (mp0) REVERT: c 15 TRP cc_start: 0.6134 (p90) cc_final: 0.4942 (p90) REVERT: d 34 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7980 (mt0) REVERT: d 92 LYS cc_start: 0.7002 (ttmm) cc_final: 0.6522 (ttpt) REVERT: e 41 ARG cc_start: 0.8263 (mmm160) cc_final: 0.7996 (mmp-170) REVERT: k 106 ARG cc_start: 0.6776 (ttp80) cc_final: 0.6443 (ttp80) REVERT: n 107 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.7134 (mt0) REVERT: 1 310 ASN cc_start: 0.7942 (t0) cc_final: 0.7648 (m-40) REVERT: 3 1 MET cc_start: 0.5092 (tpt) cc_final: 0.3824 (mtp) REVERT: 4 82 ASP cc_start: 0.8099 (p0) cc_final: 0.7888 (p0) REVERT: 4 169 MET cc_start: 0.8498 (mmt) cc_final: 0.8271 (mmm) REVERT: 4 209 ILE cc_start: 0.8927 (pt) cc_final: 0.8716 (mt) REVERT: 4 273 TYR cc_start: 0.5974 (m-10) cc_final: 0.5738 (m-10) REVERT: 4 296 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8466 (pp) REVERT: 4 352 ASP cc_start: 0.7528 (t0) cc_final: 0.7255 (t0) REVERT: 4 369 MET cc_start: 0.8381 (mtm) cc_final: 0.8059 (mtm) REVERT: 4 454 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7631 (mpp) REVERT: 5 40 ILE cc_start: 0.9021 (mm) cc_final: 0.8807 (mt) REVERT: 5 144 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7514 (mm-30) REVERT: 8 61 ASP cc_start: 0.8323 (t70) cc_final: 0.8039 (t0) REVERT: 9 58 ARG cc_start: 0.7685 (ttt90) cc_final: 0.7252 (ttm110) outliers start: 207 outliers final: 142 residues processed: 1182 average time/residue: 0.6029 time to fit residues: 1213.9661 Evaluate side-chains 1133 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 981 time to evaluate : 6.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 674 HIS Chi-restraints excluded: chain A residue 680 ASN Chi-restraints excluded: chain A residue 699 MET Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 372 ASN Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 201 ARG Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 161 GLU Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain H residue 217 ASP Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 136 CYS Chi-restraints excluded: chain I residue 175 CYS Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain J residue 186 ASN Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 85 CYS Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 195 GLN Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 58 GLN Chi-restraints excluded: chain P residue 59 GLU Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain S residue 163 ASP Chi-restraints excluded: chain U residue 25 VAL Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 59 GLU Chi-restraints excluded: chain U residue 112 ARG Chi-restraints excluded: chain W residue 67 ILE Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 23 ASP Chi-restraints excluded: chain X residue 50 LEU Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain X residue 135 LEU Chi-restraints excluded: chain Y residue 44 ILE Chi-restraints excluded: chain Y residue 70 SER Chi-restraints excluded: chain Y residue 148 PHE Chi-restraints excluded: chain Z residue 66 THR Chi-restraints excluded: chain Z residue 147 VAL Chi-restraints excluded: chain Z residue 180 THR Chi-restraints excluded: chain a residue 74 ASP Chi-restraints excluded: chain a residue 94 LEU Chi-restraints excluded: chain c residue 17 TYR Chi-restraints excluded: chain d residue 34 GLN Chi-restraints excluded: chain e residue 46 TYR Chi-restraints excluded: chain f residue 8 ILE Chi-restraints excluded: chain f residue 40 THR Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain g residue 56 SER Chi-restraints excluded: chain i residue 13 ILE Chi-restraints excluded: chain j residue 80 PHE Chi-restraints excluded: chain j residue 83 LYS Chi-restraints excluded: chain n residue 107 GLN Chi-restraints excluded: chain 1 residue 4 ASN Chi-restraints excluded: chain 1 residue 9 LEU Chi-restraints excluded: chain 1 residue 74 VAL Chi-restraints excluded: chain 1 residue 79 ILE Chi-restraints excluded: chain 1 residue 137 ILE Chi-restraints excluded: chain 1 residue 147 GLU Chi-restraints excluded: chain 1 residue 156 ILE Chi-restraints excluded: chain 1 residue 157 ILE Chi-restraints excluded: chain 1 residue 276 LEU Chi-restraints excluded: chain 1 residue 339 THR Chi-restraints excluded: chain 2 residue 9 LEU Chi-restraints excluded: chain 2 residue 46 PHE Chi-restraints excluded: chain 2 residue 125 THR Chi-restraints excluded: chain 2 residue 288 SER Chi-restraints excluded: chain 2 residue 386 ILE Chi-restraints excluded: chain 2 residue 390 ILE Chi-restraints excluded: chain 2 residue 419 VAL Chi-restraints excluded: chain 2 residue 459 LEU Chi-restraints excluded: chain 4 residue 62 SER Chi-restraints excluded: chain 4 residue 68 LEU Chi-restraints excluded: chain 4 residue 265 LEU Chi-restraints excluded: chain 4 residue 296 ILE Chi-restraints excluded: chain 4 residue 317 VAL Chi-restraints excluded: chain 4 residue 450 GLU Chi-restraints excluded: chain 4 residue 454 MET Chi-restraints excluded: chain 5 residue 5 ILE Chi-restraints excluded: chain 5 residue 10 ILE Chi-restraints excluded: chain 5 residue 89 LEU Chi-restraints excluded: chain 5 residue 92 ILE Chi-restraints excluded: chain 5 residue 129 ILE Chi-restraints excluded: chain 5 residue 232 LEU Chi-restraints excluded: chain 5 residue 234 ASN Chi-restraints excluded: chain 5 residue 289 LEU Chi-restraints excluded: chain 5 residue 351 HIS Chi-restraints excluded: chain 5 residue 395 THR Chi-restraints excluded: chain 5 residue 400 ILE Chi-restraints excluded: chain 5 residue 421 SER Chi-restraints excluded: chain 5 residue 432 ILE Chi-restraints excluded: chain 5 residue 483 VAL Chi-restraints excluded: chain 5 residue 488 VAL Chi-restraints excluded: chain 5 residue 495 ASN Chi-restraints excluded: chain 5 residue 519 ILE Chi-restraints excluded: chain 5 residue 554 LEU Chi-restraints excluded: chain 5 residue 634 VAL Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain 6 residue 75 ILE Chi-restraints excluded: chain 6 residue 86 SER Chi-restraints excluded: chain 6 residue 100 SER Chi-restraints excluded: chain 8 residue 4 PHE Chi-restraints excluded: chain 9 residue 13 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 444 optimal weight: 0.3980 chunk 287 optimal weight: 0.9990 chunk 429 optimal weight: 0.9990 chunk 216 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 457 optimal weight: 3.9990 chunk 489 optimal weight: 0.9990 chunk 355 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 565 optimal weight: 0.0870 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 HIS H 33 HIS H 145 GLN K 195 GLN P 73 ASN S 238 GLN ** U 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 85 GLN ** g 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 34 GLN ** 2 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.5429 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= 0.508 Angle : 1.508 50.700 85985 Z= 0.968 Chirality : 0.290 6.365 9595 Planarity : 0.004 0.095 10740 Dihedral : 11.532 176.710 9742 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.65 % Favored : 95.33 % Rotamer: Outliers : 3.17 % Allowed : 18.20 % Favored : 78.63 % 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: 3928 sheet: -0.99 (0.27), residues: 361 loop : -1.56 (0.10), residues: 3242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 106 HIS 0.009 0.001 HIS 4 228 PHE 0.020 0.001 PHE Y 129 TYR 0.024 0.001 TYR F 67 ARG 0.015 0.000 ARG K 196 *********************** 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 1212 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1005 time to evaluate : 5.442 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: A 326 ASP cc_start: 0.7116 (t0) cc_final: 0.6263 (p0) REVERT: A 549 MET cc_start: 0.7613 (ttm) cc_final: 0.7315 (ttm) REVERT: B 171 LEU cc_start: 0.8153 (mt) cc_final: 0.7914 (mt) REVERT: C 58 MET cc_start: 0.6874 (mtp) cc_final: 0.6471 (mtp) REVERT: C 68 ASP cc_start: 0.7768 (t0) cc_final: 0.7497 (t0) REVERT: C 275 THR cc_start: 0.7625 (m) cc_final: 0.7202 (p) REVERT: D 6 GLU cc_start: 0.6951 (tp30) cc_final: 0.6719 (tt0) REVERT: D 47 SER cc_start: 0.9074 (t) cc_final: 0.8652 (m) REVERT: E 133 TYR cc_start: 0.8078 (p90) cc_final: 0.7778 (p90) REVERT: F 25 MET cc_start: 0.7458 (ptp) cc_final: 0.7182 (ptp) REVERT: F 93 ASN cc_start: 0.8500 (m-40) cc_final: 0.8175 (t0) REVERT: H 99 MET cc_start: 0.7033 (mtt) cc_final: 0.6734 (mtt) REVERT: H 119 MET cc_start: 0.7039 (pmm) cc_final: 0.6114 (ptt) REVERT: H 133 GLN cc_start: 0.8358 (tp40) cc_final: 0.7842 (tp40) REVERT: I 107 LYS cc_start: 0.8061 (mmtt) cc_final: 0.7739 (mmtp) REVERT: J 96 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8460 (m-40) REVERT: K 41 MET cc_start: 0.3390 (ptp) cc_final: 0.1894 (ttm) REVERT: K 197 LYS cc_start: 0.8523 (ttmm) cc_final: 0.7991 (tttp) REVERT: L 38 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8614 (mt) REVERT: O 62 LEU cc_start: 0.5878 (mp) cc_final: 0.5577 (mp) REVERT: P 59 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7240 (mp0) REVERT: Q 56 GLN cc_start: 0.8663 (tp40) cc_final: 0.8342 (tp40) REVERT: Q 57 GLU cc_start: 0.8035 (pt0) cc_final: 0.7598 (mt-10) REVERT: Q 120 GLN cc_start: 0.7817 (mt0) cc_final: 0.7577 (mt0) REVERT: Q 123 ASP cc_start: 0.8090 (m-30) cc_final: 0.7879 (m-30) REVERT: R 21 GLN cc_start: 0.8446 (tt0) cc_final: 0.8193 (mt0) REVERT: R 49 GLN cc_start: 0.8152 (tt0) cc_final: 0.7891 (mt0) REVERT: U 126 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8729 (mm) REVERT: W 93 LYS cc_start: 0.8576 (ttmp) cc_final: 0.8347 (ttmm) REVERT: X 23 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.7869 (m-30) REVERT: Y 55 ASN cc_start: 0.7388 (t0) cc_final: 0.6898 (t0) REVERT: Y 110 MET cc_start: 0.7998 (mtp) cc_final: 0.7715 (mtp) REVERT: Y 128 ASP cc_start: 0.7748 (p0) cc_final: 0.7149 (p0) REVERT: Y 148 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.7394 (p90) REVERT: Z 147 VAL cc_start: 0.8713 (OUTLIER) cc_final: 0.8477 (m) REVERT: a 94 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9027 (tp) REVERT: a 133 GLU cc_start: 0.7989 (mp0) cc_final: 0.7506 (mp0) REVERT: d 34 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8047 (mt0) REVERT: e 41 ARG cc_start: 0.8268 (mmm160) cc_final: 0.7999 (mmp-170) REVERT: k 106 ARG cc_start: 0.6700 (ttp80) cc_final: 0.6374 (ttp80) REVERT: n 65 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7446 (mt-10) REVERT: n 107 GLN cc_start: 0.7415 (OUTLIER) cc_final: 0.7091 (mt0) REVERT: 1 310 ASN cc_start: 0.7820 (t0) cc_final: 0.7545 (m-40) REVERT: 3 1 MET cc_start: 0.5098 (tpt) cc_final: 0.3866 (mtp) REVERT: 4 82 ASP cc_start: 0.8083 (p0) cc_final: 0.7848 (p0) REVERT: 4 169 MET cc_start: 0.8488 (mmt) cc_final: 0.8276 (mmm) REVERT: 4 273 TYR cc_start: 0.5985 (m-10) cc_final: 0.5774 (m-10) REVERT: 4 296 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8522 (pp) REVERT: 4 352 ASP cc_start: 0.7590 (t0) cc_final: 0.7305 (t0) REVERT: 4 369 MET cc_start: 0.8369 (mtm) cc_final: 0.8089 (mtm) REVERT: 4 439 TYR cc_start: 0.8844 (OUTLIER) cc_final: 0.8370 (m-80) REVERT: 4 454 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7649 (mpp) REVERT: 5 40 ILE cc_start: 0.8993 (mm) cc_final: 0.8790 (mt) REVERT: 5 606 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8005 (tp) REVERT: 5 616 MET cc_start: 0.7394 (tpp) cc_final: 0.7126 (ttm) REVERT: 8 61 ASP cc_start: 0.8427 (t70) cc_final: 0.8032 (t0) REVERT: 9 58 ARG cc_start: 0.7686 (ttt90) cc_final: 0.7255 (ttm110) outliers start: 207 outliers final: 157 residues processed: 1137 average time/residue: 0.6065 time to fit residues: 1172.9013 Evaluate side-chains 1133 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 962 time to evaluate : 5.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 674 HIS Chi-restraints excluded: chain A residue 680 ASN Chi-restraints excluded: chain A residue 699 MET Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 372 ASN Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 161 GLU Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 136 CYS Chi-restraints excluded: chain I residue 175 CYS Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain J residue 186 ASN Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 85 CYS Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 147 MET Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 58 GLN Chi-restraints excluded: chain P residue 59 GLU Chi-restraints excluded: chain P residue 61 GLU Chi-restraints excluded: chain P residue 73 ASN Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 163 ASP Chi-restraints excluded: chain U residue 25 VAL Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 59 GLU Chi-restraints excluded: chain U residue 112 ARG Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain W residue 67 ILE Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 23 ASP Chi-restraints excluded: chain X residue 50 LEU Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain X residue 135 LEU Chi-restraints excluded: chain Y residue 44 ILE Chi-restraints excluded: chain Y residue 70 SER Chi-restraints excluded: chain Y residue 148 PHE Chi-restraints excluded: chain Z residue 66 THR Chi-restraints excluded: chain Z residue 147 VAL Chi-restraints excluded: chain Z residue 180 THR Chi-restraints excluded: chain a residue 74 ASP Chi-restraints excluded: chain a residue 94 LEU Chi-restraints excluded: chain d residue 34 GLN Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain e residue 46 TYR Chi-restraints excluded: chain e residue 52 LEU Chi-restraints excluded: chain f residue 8 ILE Chi-restraints excluded: chain f residue 40 THR Chi-restraints excluded: chain g residue 56 SER Chi-restraints excluded: chain g residue 61 SER Chi-restraints excluded: chain i residue 13 ILE Chi-restraints excluded: chain j residue 83 LYS Chi-restraints excluded: chain k residue 90 THR Chi-restraints excluded: chain n residue 107 GLN Chi-restraints excluded: chain 1 residue 4 ASN Chi-restraints excluded: chain 1 residue 74 VAL Chi-restraints excluded: chain 1 residue 79 ILE Chi-restraints excluded: chain 1 residue 115 LEU Chi-restraints excluded: chain 1 residue 147 GLU Chi-restraints excluded: chain 1 residue 156 ILE Chi-restraints excluded: chain 1 residue 157 ILE Chi-restraints excluded: chain 1 residue 276 LEU Chi-restraints excluded: chain 1 residue 296 VAL Chi-restraints excluded: chain 1 residue 339 THR Chi-restraints excluded: chain 2 residue 9 LEU Chi-restraints excluded: chain 2 residue 46 PHE Chi-restraints excluded: chain 2 residue 125 THR Chi-restraints excluded: chain 2 residue 288 SER Chi-restraints excluded: chain 2 residue 386 ILE Chi-restraints excluded: chain 2 residue 390 ILE Chi-restraints excluded: chain 2 residue 419 VAL Chi-restraints excluded: chain 2 residue 459 LEU Chi-restraints excluded: chain 4 residue 36 LEU Chi-restraints excluded: chain 4 residue 62 SER Chi-restraints excluded: chain 4 residue 68 LEU Chi-restraints excluded: chain 4 residue 75 ASN Chi-restraints excluded: chain 4 residue 94 LEU Chi-restraints excluded: chain 4 residue 265 LEU Chi-restraints excluded: chain 4 residue 296 ILE Chi-restraints excluded: chain 4 residue 315 LEU Chi-restraints excluded: chain 4 residue 317 VAL Chi-restraints excluded: chain 4 residue 439 TYR Chi-restraints excluded: chain 4 residue 450 GLU Chi-restraints excluded: chain 4 residue 454 MET Chi-restraints excluded: chain 5 residue 5 ILE Chi-restraints excluded: chain 5 residue 10 ILE Chi-restraints excluded: chain 5 residue 92 ILE Chi-restraints excluded: chain 5 residue 129 ILE Chi-restraints excluded: chain 5 residue 154 ILE Chi-restraints excluded: chain 5 residue 232 LEU Chi-restraints excluded: chain 5 residue 234 ASN Chi-restraints excluded: chain 5 residue 255 LEU Chi-restraints excluded: chain 5 residue 289 LEU Chi-restraints excluded: chain 5 residue 351 HIS Chi-restraints excluded: chain 5 residue 395 THR Chi-restraints excluded: chain 5 residue 400 ILE Chi-restraints excluded: chain 5 residue 421 SER Chi-restraints excluded: chain 5 residue 432 ILE Chi-restraints excluded: chain 5 residue 483 VAL Chi-restraints excluded: chain 5 residue 488 VAL Chi-restraints excluded: chain 5 residue 519 ILE Chi-restraints excluded: chain 5 residue 548 SER Chi-restraints excluded: chain 5 residue 606 LEU Chi-restraints excluded: chain 5 residue 634 VAL Chi-restraints excluded: chain 6 residue 18 LEU Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain 6 residue 75 ILE Chi-restraints excluded: chain 6 residue 100 SER Chi-restraints excluded: chain 8 residue 4 PHE Chi-restraints excluded: chain 8 residue 31 VAL Chi-restraints excluded: chain 9 residue 2 THR Chi-restraints excluded: chain 9 residue 13 ASN Chi-restraints excluded: chain 9 residue 48 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 654 optimal weight: 3.9990 chunk 688 optimal weight: 0.6980 chunk 628 optimal weight: 0.6980 chunk 670 optimal weight: 0.2980 chunk 403 optimal weight: 2.9990 chunk 291 optimal weight: 6.9990 chunk 526 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 605 optimal weight: 2.9990 chunk 633 optimal weight: 0.8980 chunk 667 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 680 ASN ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 GLN K 195 GLN P 73 ASN S 238 GLN ** U 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 88 ASN f 48 ASN ** g 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.5541 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= 0.512 Angle : 1.513 50.698 85985 Z= 0.970 Chirality : 0.290 6.368 9595 Planarity : 0.004 0.094 10740 Dihedral : 11.393 176.449 9742 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.71 % Favored : 95.26 % Rotamer: Outliers : 3.09 % Allowed : 18.45 % Favored : 78.46 % 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: -0.31 (0.10), residues: 7531 helix: 0.89 (0.09), residues: 3932 sheet: -0.91 (0.27), residues: 351 loop : -1.51 (0.10), residues: 3248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP B 106 HIS 0.008 0.001 HIS 4 228 PHE 0.024 0.001 PHE Y 129 TYR 0.027 0.001 TYR F 67 ARG 0.009 0.000 ARG Y 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 1199 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 997 time to evaluate : 5.428 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: A 326 ASP cc_start: 0.7192 (t0) cc_final: 0.6344 (p0) REVERT: A 549 MET cc_start: 0.7641 (ttm) cc_final: 0.7331 (ttm) REVERT: C 58 MET cc_start: 0.6912 (mtp) cc_final: 0.6516 (mtp) REVERT: C 68 ASP cc_start: 0.7799 (t0) cc_final: 0.7504 (t0) REVERT: C 149 THR cc_start: 0.8323 (m) cc_final: 0.8059 (p) REVERT: C 275 THR cc_start: 0.7702 (m) cc_final: 0.7282 (p) REVERT: D 47 SER cc_start: 0.9074 (t) cc_final: 0.8658 (m) REVERT: D 69 THR cc_start: 0.8828 (p) cc_final: 0.8540 (m) REVERT: E 133 TYR cc_start: 0.8087 (p90) cc_final: 0.7747 (p90) REVERT: F 25 MET cc_start: 0.7445 (ptp) cc_final: 0.7205 (ptp) REVERT: F 93 ASN cc_start: 0.8507 (m-40) cc_final: 0.8182 (t0) REVERT: H 99 MET cc_start: 0.7034 (mtt) cc_final: 0.6747 (mtt) REVERT: H 119 MET cc_start: 0.6984 (pmm) cc_final: 0.5964 (ptt) REVERT: H 133 GLN cc_start: 0.8371 (tp40) cc_final: 0.7843 (tp40) REVERT: I 107 LYS cc_start: 0.8119 (mmtt) cc_final: 0.7762 (mmtp) REVERT: J 76 ILE cc_start: 0.8778 (mp) cc_final: 0.8559 (mt) REVERT: J 96 ASN cc_start: 0.8892 (OUTLIER) cc_final: 0.8446 (m-40) REVERT: K 41 MET cc_start: 0.3371 (ptp) cc_final: 0.1884 (ttm) REVERT: L 38 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8650 (mt) REVERT: O 62 LEU cc_start: 0.6011 (mp) cc_final: 0.5687 (mp) REVERT: P 59 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: Q 57 GLU cc_start: 0.7985 (pt0) cc_final: 0.7662 (mt-10) REVERT: R 21 GLN cc_start: 0.8406 (tt0) cc_final: 0.8168 (mt0) REVERT: R 49 GLN cc_start: 0.8145 (tt0) cc_final: 0.7843 (mt0) REVERT: R 89 LYS cc_start: 0.9062 (mmmm) cc_final: 0.8815 (mtpt) REVERT: U 54 MET cc_start: 0.8378 (mmt) cc_final: 0.8085 (mmp) REVERT: W 93 LYS cc_start: 0.8625 (ttmp) cc_final: 0.8388 (ttmm) REVERT: X 23 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.7866 (m-30) REVERT: Y 55 ASN cc_start: 0.7335 (t0) cc_final: 0.6840 (t0) REVERT: Y 110 MET cc_start: 0.8009 (mtp) cc_final: 0.7729 (mtp) REVERT: Y 128 ASP cc_start: 0.7534 (p0) cc_final: 0.7018 (p0) REVERT: Y 148 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.7438 (p90) REVERT: a 94 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9060 (tp) REVERT: d 5 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.7287 (mt0) REVERT: d 34 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8153 (mt0) REVERT: d 68 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7304 (mm-30) REVERT: e 41 ARG cc_start: 0.8257 (mmm160) cc_final: 0.7977 (mmp-170) REVERT: f 24 GLN cc_start: 0.7388 (tp-100) cc_final: 0.7148 (mm-40) REVERT: n 107 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.7060 (mt0) REVERT: 1 310 ASN cc_start: 0.7801 (t0) cc_final: 0.7571 (m-40) REVERT: 3 1 MET cc_start: 0.5134 (tpt) cc_final: 0.3860 (mtp) REVERT: 3 122 ASP cc_start: 0.6403 (p0) cc_final: 0.5991 (p0) REVERT: 4 169 MET cc_start: 0.8477 (mmt) cc_final: 0.8245 (mmm) REVERT: 4 352 ASP cc_start: 0.7594 (t0) cc_final: 0.7282 (t0) REVERT: 4 369 MET cc_start: 0.8402 (mtm) cc_final: 0.8094 (mtm) REVERT: 4 454 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7665 (mpp) REVERT: 5 40 ILE cc_start: 0.9001 (mm) cc_final: 0.8798 (mt) REVERT: 5 606 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8064 (tp) REVERT: 5 616 MET cc_start: 0.7434 (tpp) cc_final: 0.7114 (ttm) REVERT: 8 61 ASP cc_start: 0.8410 (t70) cc_final: 0.8063 (t0) REVERT: 8 69 MET cc_start: 0.6563 (tpt) cc_final: 0.6280 (tpt) REVERT: 9 58 ARG cc_start: 0.7651 (ttt90) cc_final: 0.7191 (ttm110) outliers start: 202 outliers final: 168 residues processed: 1125 average time/residue: 0.5911 time to fit residues: 1132.8948 Evaluate side-chains 1138 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 959 time to evaluate : 5.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 674 HIS Chi-restraints excluded: chain A residue 680 ASN Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 372 ASN Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 161 GLU Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 217 ASP Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 136 CYS Chi-restraints excluded: chain I residue 175 CYS Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain J residue 186 ASN Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 85 CYS Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 147 MET Chi-restraints excluded: chain K residue 195 GLN Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 58 GLN Chi-restraints excluded: chain P residue 59 GLU Chi-restraints excluded: chain P residue 61 GLU Chi-restraints excluded: chain P residue 73 ASN Chi-restraints excluded: chain S residue 54 GLU Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain U residue 25 VAL Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 59 GLU Chi-restraints excluded: chain U residue 112 ARG Chi-restraints excluded: chain W residue 67 ILE Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 23 ASP Chi-restraints excluded: chain X residue 50 LEU Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain X residue 135 LEU Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain Y residue 44 ILE Chi-restraints excluded: chain Y residue 70 SER Chi-restraints excluded: chain Y residue 148 PHE Chi-restraints excluded: chain Z residue 66 THR Chi-restraints excluded: chain Z residue 116 LYS Chi-restraints excluded: chain Z residue 180 THR Chi-restraints excluded: chain a residue 74 ASP Chi-restraints excluded: chain a residue 94 LEU Chi-restraints excluded: chain c residue 17 TYR Chi-restraints excluded: chain d residue 5 GLN Chi-restraints excluded: chain d residue 34 GLN Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain e residue 46 TYR Chi-restraints excluded: chain e residue 52 LEU Chi-restraints excluded: chain f residue 8 ILE Chi-restraints excluded: chain f residue 40 THR Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain g residue 56 SER Chi-restraints excluded: chain g residue 61 SER Chi-restraints excluded: chain i residue 13 ILE Chi-restraints excluded: chain j residue 83 LYS Chi-restraints excluded: chain n residue 107 GLN Chi-restraints excluded: chain 1 residue 4 ASN Chi-restraints excluded: chain 1 residue 74 VAL Chi-restraints excluded: chain 1 residue 79 ILE Chi-restraints excluded: chain 1 residue 147 GLU Chi-restraints excluded: chain 1 residue 156 ILE Chi-restraints excluded: chain 1 residue 157 ILE Chi-restraints excluded: chain 1 residue 276 LEU Chi-restraints excluded: chain 1 residue 296 VAL Chi-restraints excluded: chain 1 residue 339 THR Chi-restraints excluded: chain 2 residue 9 LEU Chi-restraints excluded: chain 2 residue 46 PHE Chi-restraints excluded: chain 2 residue 125 THR Chi-restraints excluded: chain 2 residue 166 ILE Chi-restraints excluded: chain 2 residue 288 SER Chi-restraints excluded: chain 2 residue 386 ILE Chi-restraints excluded: chain 2 residue 419 VAL Chi-restraints excluded: chain 2 residue 459 LEU Chi-restraints excluded: chain 3 residue 92 LEU Chi-restraints excluded: chain 4 residue 36 LEU Chi-restraints excluded: chain 4 residue 62 SER Chi-restraints excluded: chain 4 residue 68 LEU Chi-restraints excluded: chain 4 residue 75 ASN Chi-restraints excluded: chain 4 residue 94 LEU Chi-restraints excluded: chain 4 residue 265 LEU Chi-restraints excluded: chain 4 residue 315 LEU Chi-restraints excluded: chain 4 residue 317 VAL Chi-restraints excluded: chain 4 residue 450 GLU Chi-restraints excluded: chain 4 residue 454 MET Chi-restraints excluded: chain 5 residue 5 ILE Chi-restraints excluded: chain 5 residue 10 ILE Chi-restraints excluded: chain 5 residue 92 ILE Chi-restraints excluded: chain 5 residue 129 ILE Chi-restraints excluded: chain 5 residue 154 ILE Chi-restraints excluded: chain 5 residue 232 LEU Chi-restraints excluded: chain 5 residue 234 ASN Chi-restraints excluded: chain 5 residue 255 LEU Chi-restraints excluded: chain 5 residue 289 LEU Chi-restraints excluded: chain 5 residue 351 HIS Chi-restraints excluded: chain 5 residue 395 THR Chi-restraints excluded: chain 5 residue 400 ILE Chi-restraints excluded: chain 5 residue 421 SER Chi-restraints excluded: chain 5 residue 432 ILE Chi-restraints excluded: chain 5 residue 439 SER Chi-restraints excluded: chain 5 residue 483 VAL Chi-restraints excluded: chain 5 residue 488 VAL Chi-restraints excluded: chain 5 residue 502 THR Chi-restraints excluded: chain 5 residue 519 ILE Chi-restraints excluded: chain 5 residue 548 SER Chi-restraints excluded: chain 5 residue 554 LEU Chi-restraints excluded: chain 5 residue 606 LEU Chi-restraints excluded: chain 5 residue 634 VAL Chi-restraints excluded: chain 6 residue 18 LEU Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain 6 residue 74 ILE Chi-restraints excluded: chain 6 residue 75 ILE Chi-restraints excluded: chain 6 residue 100 SER Chi-restraints excluded: chain 8 residue 4 PHE Chi-restraints excluded: chain 8 residue 7 LEU Chi-restraints excluded: chain 8 residue 31 VAL Chi-restraints excluded: chain 9 residue 2 THR Chi-restraints excluded: chain 9 residue 13 ASN Chi-restraints excluded: chain 9 residue 48 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 439 optimal weight: 3.9990 chunk 708 optimal weight: 6.9990 chunk 432 optimal weight: 0.9990 chunk 336 optimal weight: 0.7980 chunk 492 optimal weight: 0.9990 chunk 743 optimal weight: 0.0970 chunk 684 optimal weight: 0.7980 chunk 591 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 457 optimal weight: 3.9990 chunk 362 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 680 ASN C 115 HIS K 195 GLN P 73 ASN ** U 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 24 GLN f 48 ASN ** g 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 537 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.5625 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= 0.508 Angle : 1.510 50.706 85985 Z= 0.969 Chirality : 0.290 6.366 9595 Planarity : 0.004 0.095 10740 Dihedral : 11.258 176.214 9742 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.61 % Favored : 95.37 % Rotamer: Outliers : 2.94 % Allowed : 18.74 % Favored : 78.32 % 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: -0.22 (0.10), residues: 7531 helix: 0.96 (0.09), residues: 3927 sheet: -0.98 (0.26), residues: 372 loop : -1.44 (0.11), residues: 3232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 106 HIS 0.008 0.001 HIS 4 228 PHE 0.032 0.001 PHE Y 129 TYR 0.033 0.001 TYR F 67 ARG 0.009 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 1196 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1004 time to evaluate : 5.497 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: A 228 ASN cc_start: 0.8569 (OUTLIER) cc_final: 0.7933 (t160) REVERT: A 326 ASP cc_start: 0.7143 (t0) cc_final: 0.6328 (p0) REVERT: A 338 GLN cc_start: 0.6943 (mp10) cc_final: 0.6714 (mp10) REVERT: A 549 MET cc_start: 0.7668 (ttm) cc_final: 0.7341 (ttm) REVERT: C 58 MET cc_start: 0.6928 (mtp) cc_final: 0.6551 (mtp) REVERT: C 68 ASP cc_start: 0.7789 (t0) cc_final: 0.7488 (t0) REVERT: C 149 THR cc_start: 0.8263 (m) cc_final: 0.8005 (p) REVERT: C 275 THR cc_start: 0.7662 (m) cc_final: 0.7246 (p) REVERT: D 47 SER cc_start: 0.9033 (t) cc_final: 0.8623 (m) REVERT: D 69 THR cc_start: 0.8831 (p) cc_final: 0.8541 (m) REVERT: E 133 TYR cc_start: 0.8155 (p90) cc_final: 0.7780 (p90) REVERT: F 25 MET cc_start: 0.7474 (ptp) cc_final: 0.7238 (ptp) REVERT: F 93 ASN cc_start: 0.8500 (m-40) cc_final: 0.8180 (t0) REVERT: G 203 TYR cc_start: 0.7292 (m-80) cc_final: 0.7071 (m-80) REVERT: H 99 MET cc_start: 0.7042 (mtt) cc_final: 0.6774 (mtt) REVERT: H 119 MET cc_start: 0.6969 (pmm) cc_final: 0.5921 (ptt) REVERT: H 133 GLN cc_start: 0.8354 (tp40) cc_final: 0.7824 (tp40) REVERT: I 107 LYS cc_start: 0.8103 (mmtt) cc_final: 0.7820 (mmtp) REVERT: J 76 ILE cc_start: 0.8746 (mp) cc_final: 0.8524 (mt) REVERT: J 96 ASN cc_start: 0.8880 (OUTLIER) cc_final: 0.8434 (m-40) REVERT: K 41 MET cc_start: 0.3349 (ptp) cc_final: 0.1852 (ttm) REVERT: K 197 LYS cc_start: 0.8622 (ttmm) cc_final: 0.8104 (tttp) REVERT: L 38 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8654 (mt) REVERT: O 62 LEU cc_start: 0.6021 (mp) cc_final: 0.5657 (mp) REVERT: P 59 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7146 (mp0) REVERT: P 62 ARG cc_start: 0.8124 (mtm110) cc_final: 0.7741 (mtm110) REVERT: Q 56 GLN cc_start: 0.8674 (tp40) cc_final: 0.8405 (tp40) REVERT: Q 57 GLU cc_start: 0.7956 (pt0) cc_final: 0.7630 (mt-10) REVERT: R 21 GLN cc_start: 0.8424 (tt0) cc_final: 0.8201 (mt0) REVERT: R 49 GLN cc_start: 0.8108 (tt0) cc_final: 0.7845 (mt0) REVERT: R 65 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7196 (tt0) REVERT: R 89 LYS cc_start: 0.9058 (mmmm) cc_final: 0.8812 (mtpt) REVERT: U 54 MET cc_start: 0.8373 (mmt) cc_final: 0.8032 (mmp) REVERT: W 93 LYS cc_start: 0.8644 (ttmp) cc_final: 0.8408 (ttmm) REVERT: X 23 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.7848 (m-30) REVERT: Y 55 ASN cc_start: 0.7337 (t0) cc_final: 0.6843 (t0) REVERT: Y 110 MET cc_start: 0.7997 (mtp) cc_final: 0.7716 (mtp) REVERT: Y 128 ASP cc_start: 0.7323 (p0) cc_final: 0.6928 (p0) REVERT: Y 148 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.7301 (p90) REVERT: a 94 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9021 (tp) REVERT: a 118 LYS cc_start: 0.8707 (ttmm) cc_final: 0.8340 (mmtm) REVERT: d 5 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7351 (mt0) REVERT: d 34 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8186 (mt0) REVERT: e 41 ARG cc_start: 0.8248 (mmm160) cc_final: 0.7981 (mmp-170) REVERT: f 24 GLN cc_start: 0.7269 (tp40) cc_final: 0.7065 (mm-40) REVERT: n 107 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.7027 (mt0) REVERT: 1 310 ASN cc_start: 0.7767 (t0) cc_final: 0.7545 (m-40) REVERT: 2 102 GLU cc_start: 0.8176 (pt0) cc_final: 0.7887 (pt0) REVERT: 3 122 ASP cc_start: 0.6361 (p0) cc_final: 0.5969 (p0) REVERT: 4 169 MET cc_start: 0.8445 (mmt) cc_final: 0.8236 (mmm) REVERT: 4 352 ASP cc_start: 0.7581 (t0) cc_final: 0.7292 (t0) REVERT: 4 369 MET cc_start: 0.8381 (mtm) cc_final: 0.8089 (mtm) REVERT: 4 454 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7651 (mpp) REVERT: 5 40 ILE cc_start: 0.8995 (mm) cc_final: 0.8794 (mt) REVERT: 5 606 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8053 (tp) REVERT: 5 616 MET cc_start: 0.7450 (tpp) cc_final: 0.7096 (ttm) REVERT: 8 61 ASP cc_start: 0.8409 (t70) cc_final: 0.8024 (t0) REVERT: 8 69 MET cc_start: 0.6583 (tpt) cc_final: 0.6304 (tpt) REVERT: 9 58 ARG cc_start: 0.7626 (ttt90) cc_final: 0.7177 (ttm110) outliers start: 192 outliers final: 160 residues processed: 1125 average time/residue: 0.6037 time to fit residues: 1156.6666 Evaluate side-chains 1147 residues out of total 6527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 975 time to evaluate : 5.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 497 PHE Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 674 HIS Chi-restraints excluded: chain A residue 680 ASN Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 372 ASN Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 161 GLU Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 136 CYS Chi-restraints excluded: chain I residue 175 CYS Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain J residue 186 ASN Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 85 CYS Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 147 MET Chi-restraints excluded: chain K residue 195 GLN Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 58 GLN Chi-restraints excluded: chain P residue 59 GLU Chi-restraints excluded: chain P residue 61 GLU Chi-restraints excluded: chain S residue 54 GLU Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain U residue 25 VAL Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 59 GLU Chi-restraints excluded: chain U residue 112 ARG Chi-restraints excluded: chain W residue 67 ILE Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 23 ASP Chi-restraints excluded: chain X residue 50 LEU Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain X residue 135 LEU Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain Y residue 44 ILE Chi-restraints excluded: chain Y residue 70 SER Chi-restraints excluded: chain Y residue 148 PHE Chi-restraints excluded: chain Z residue 116 LYS Chi-restraints excluded: chain Z residue 180 THR Chi-restraints excluded: chain a residue 74 ASP Chi-restraints excluded: chain a residue 94 LEU Chi-restraints excluded: chain c residue 17 TYR Chi-restraints excluded: chain d residue 5 GLN Chi-restraints excluded: chain d residue 34 GLN Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain e residue 46 TYR Chi-restraints excluded: chain e residue 52 LEU Chi-restraints excluded: chain f residue 8 ILE Chi-restraints excluded: chain f residue 40 THR Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain g residue 56 SER Chi-restraints excluded: chain g residue 61 SER Chi-restraints excluded: chain i residue 13 ILE Chi-restraints excluded: chain j residue 83 LYS Chi-restraints excluded: chain n residue 107 GLN Chi-restraints excluded: chain 1 residue 74 VAL Chi-restraints excluded: chain 1 residue 147 GLU Chi-restraints excluded: chain 1 residue 156 ILE Chi-restraints excluded: chain 1 residue 157 ILE Chi-restraints excluded: chain 1 residue 276 LEU Chi-restraints excluded: chain 1 residue 296 VAL Chi-restraints excluded: chain 1 residue 339 THR Chi-restraints excluded: chain 2 residue 9 LEU Chi-restraints excluded: chain 2 residue 46 PHE Chi-restraints excluded: chain 2 residue 118 VAL Chi-restraints excluded: chain 2 residue 125 THR Chi-restraints excluded: chain 2 residue 166 ILE Chi-restraints excluded: chain 2 residue 288 SER Chi-restraints excluded: chain 2 residue 386 ILE Chi-restraints excluded: chain 2 residue 419 VAL Chi-restraints excluded: chain 3 residue 92 LEU Chi-restraints excluded: chain 4 residue 36 LEU Chi-restraints excluded: chain 4 residue 62 SER Chi-restraints excluded: chain 4 residue 68 LEU Chi-restraints excluded: chain 4 residue 94 LEU Chi-restraints excluded: chain 4 residue 265 LEU Chi-restraints excluded: chain 4 residue 315 LEU Chi-restraints excluded: chain 4 residue 317 VAL Chi-restraints excluded: chain 4 residue 450 GLU Chi-restraints excluded: chain 4 residue 454 MET Chi-restraints excluded: chain 5 residue 5 ILE Chi-restraints excluded: chain 5 residue 10 ILE Chi-restraints excluded: chain 5 residue 89 LEU Chi-restraints excluded: chain 5 residue 92 ILE Chi-restraints excluded: chain 5 residue 129 ILE Chi-restraints excluded: chain 5 residue 154 ILE Chi-restraints excluded: chain 5 residue 232 LEU Chi-restraints excluded: chain 5 residue 234 ASN Chi-restraints excluded: chain 5 residue 255 LEU Chi-restraints excluded: chain 5 residue 289 LEU Chi-restraints excluded: chain 5 residue 351 HIS Chi-restraints excluded: chain 5 residue 395 THR Chi-restraints excluded: chain 5 residue 421 SER Chi-restraints excluded: chain 5 residue 432 ILE Chi-restraints excluded: chain 5 residue 483 VAL Chi-restraints excluded: chain 5 residue 488 VAL Chi-restraints excluded: chain 5 residue 502 THR Chi-restraints excluded: chain 5 residue 519 ILE Chi-restraints excluded: chain 5 residue 548 SER Chi-restraints excluded: chain 5 residue 554 LEU Chi-restraints excluded: chain 5 residue 606 LEU Chi-restraints excluded: chain 5 residue 634 VAL Chi-restraints excluded: chain 6 residue 18 LEU Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain 6 residue 74 ILE Chi-restraints excluded: chain 6 residue 75 ILE Chi-restraints excluded: chain 6 residue 100 SER Chi-restraints excluded: chain 8 residue 4 PHE Chi-restraints excluded: chain 8 residue 7 LEU Chi-restraints excluded: chain 8 residue 31 VAL Chi-restraints excluded: chain 9 residue 2 THR Chi-restraints excluded: chain 9 residue 48 LEU Chi-restraints excluded: chain 9 residue 64 LEU 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: 2.9990 chunk 545 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 592 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 608 optimal weight: 0.9980 chunk 75 optimal weight: 0.3980 chunk 109 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN B 43 ASN K 195 GLN P 73 ASN ** U 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 62 GLN a 146 GLN ** g 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.135455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.105411 restraints weight = 89354.548| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.52 r_work: 0.3133 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.5709 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= 0.532 Angle : 1.524 50.690 85985 Z= 0.975 Chirality : 0.291 6.375 9595 Planarity : 0.004 0.096 10740 Dihedral : 11.351 176.307 9742 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.95 % Favored : 95.02 % Rotamer: Outliers : 3.08 % Allowed : 18.88 % Favored : 78.05 % 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: -0.27 (0.10), residues: 7531 helix: 0.90 (0.09), residues: 3941 sheet: -0.96 (0.27), residues: 354 loop : -1.45 (0.11), residues: 3236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 106 HIS 0.009 0.001 HIS 2 185 PHE 0.030 0.001 PHE Y 129 TYR 0.033 0.002 TYR F 67 ARG 0.018 0.000 ARG K 196 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20177.92 seconds wall clock time: 351 minutes 52.46 seconds (21112.46 seconds total)