Starting phenix.real_space_refine on Sun Feb 18 12:58:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c6l_7348/02_2024/6c6l_7348.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c6l_7348/02_2024/6c6l_7348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c6l_7348/02_2024/6c6l_7348.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c6l_7348/02_2024/6c6l_7348.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c6l_7348/02_2024/6c6l_7348.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c6l_7348/02_2024/6c6l_7348.pdb" } resolution = 3.5 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= 0.008 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: 4 Type Number sf(0) Gaussians S 136 5.16 5 C 14483 2.51 5 N 3547 2.21 5 O 3944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 125": "NH1" <-> "NH2" Residue "D ARG 161": "NH1" <-> "NH2" Residue "C PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 95": "NH1" <-> "NH2" Residue "E ARG 46": "NH1" <-> "NH2" Residue "E ARG 117": "NH1" <-> "NH2" Residue "E ARG 124": "NH1" <-> "NH2" Residue "E ARG 153": "NH1" <-> "NH2" Residue "B TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 117": "NH1" <-> "NH2" Residue "F ARG 124": "NH1" <-> "NH2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "G ARG 117": "NH1" <-> "NH2" Residue "G ARG 124": "NH1" <-> "NH2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "H ARG 117": "NH1" <-> "NH2" Residue "H ARG 124": "NH1" <-> "NH2" Residue "H ARG 153": "NH1" <-> "NH2" Residue "I ARG 117": "NH1" <-> "NH2" Residue "I ARG 124": "NH1" <-> "NH2" Residue "I ARG 153": "NH1" <-> "NH2" Residue "J ARG 117": "NH1" <-> "NH2" Residue "J ARG 124": "NH1" <-> "NH2" Residue "J ARG 153": "NH1" <-> "NH2" Residue "K ARG 117": "NH1" <-> "NH2" Residue "K ARG 124": "NH1" <-> "NH2" Residue "K ARG 153": "NH1" <-> "NH2" Residue "L ARG 117": "NH1" <-> "NH2" Residue "L ARG 124": "NH1" <-> "NH2" Residue "L ARG 153": "NH1" <-> "NH2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A ARG 352": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 2": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22110 Number of models: 1 Model: "" Number of chains: 15 Chain: "D" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1139 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 6, 'TRANS': 150} Chain: "C" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1488 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 197} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 395 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 50} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "M" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 550 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 64} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 2793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2793 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 9, 'TRANS': 334} Chain: "F" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1143 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "J" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "K" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1143 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "L" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 6054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 6054 Classifications: {'peptide': 746} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 724} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "O" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 583 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Time building chain proxies: 11.59, per 1000 atoms: 0.52 Number of scatterers: 22110 At special positions: 0 Unit cell: (130.38, 116.85, 123, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 136 16.00 O 3944 8.00 N 3547 7.00 C 14483 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Time building additional restraints: 9.16 Conformation dependent library (CDL) restraints added in 4.1 seconds 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5258 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 4 sheets defined 75.5% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'D' and resid 14 through 49 removed outlier: 4.148A pdb=" N PHE D 18 " --> pdb=" O TYR D 14 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS D 23 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA D 24 " --> pdb=" O PHE D 20 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 60 through 81 removed outlier: 3.522A pdb=" N ILE D 68 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU D 69 " --> pdb=" O MET D 65 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA D 70 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D 80 " --> pdb=" O VAL D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 124 removed outlier: 3.687A pdb=" N MET D 97 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS D 98 " --> pdb=" O ASN D 94 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU D 99 " --> pdb=" O GLY D 95 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 110 " --> pdb=" O GLY D 106 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL D 124 " --> pdb=" O GLY D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 129 removed outlier: 4.272A pdb=" N MET D 128 " --> pdb=" O ARG D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 160 removed outlier: 3.530A pdb=" N ILE D 142 " --> pdb=" O VAL D 138 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU D 147 " --> pdb=" O PHE D 143 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLY D 148 " --> pdb=" O SER D 144 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY D 151 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET D 152 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL D 154 " --> pdb=" O TYR D 150 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE D 157 " --> pdb=" O ILE D 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 39 removed outlier: 3.546A pdb=" N VAL C 28 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 54 removed outlier: 3.557A pdb=" N PHE C 50 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 90 removed outlier: 4.013A pdb=" N TRP C 59 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA C 60 " --> pdb=" O PRO C 56 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 62 " --> pdb=" O MET C 58 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL C 68 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL C 72 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 73 " --> pdb=" O GLY C 69 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER C 84 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA C 89 " --> pdb=" O SER C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 100 removed outlier: 3.557A pdb=" N LYS C 99 " --> pdb=" O ARG C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 123 removed outlier: 3.848A pdb=" N ILE C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS C 107 " --> pdb=" O SER C 103 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL C 110 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ALA C 111 " --> pdb=" O CYS C 107 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 118 " --> pdb=" O GLY C 114 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER C 123 " --> pdb=" O ILE C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 173 removed outlier: 3.637A pdb=" N PHE C 146 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE C 172 " --> pdb=" O ALA C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 185 through 192 Processing helix chain 'C' and resid 192 through 208 removed outlier: 3.514A pdb=" N GLY C 202 " --> pdb=" O GLY C 198 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS C 208 " --> pdb=" O LEU C 204 " (cutoff:3.500A) Processing helix chain 'N' and resid 223 through 245 removed outlier: 3.834A pdb=" N VAL N 229 " --> pdb=" O MET N 225 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER N 230 " --> pdb=" O CYS N 226 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER N 242 " --> pdb=" O ILE N 238 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TRP N 243 " --> pdb=" O VAL N 239 " (cutoff:3.500A) Processing helix chain 'N' and resid 250 through 254 removed outlier: 3.580A pdb=" N ALA N 253 " --> pdb=" O THR N 250 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 24 removed outlier: 4.183A pdb=" N VAL M 8 " --> pdb=" O PHE M 4 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL M 13 " --> pdb=" O GLY M 9 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU M 20 " --> pdb=" O ALA M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 51 removed outlier: 3.517A pdb=" N SER M 35 " --> pdb=" O ALA M 31 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL M 37 " --> pdb=" O TRP M 33 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU M 41 " --> pdb=" O VAL M 37 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA M 42 " --> pdb=" O ILE M 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 43 removed outlier: 3.915A pdb=" N GLY E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE E 21 " --> pdb=" O CYS E 17 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE E 23 " --> pdb=" O SER E 19 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR E 24 " --> pdb=" O ALA E 20 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY E 38 " --> pdb=" O LYS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 54 removed outlier: 3.632A pdb=" N ASN E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 76 removed outlier: 3.632A pdb=" N ILE E 63 " --> pdb=" O MET E 59 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA E 64 " --> pdb=" O ALA E 60 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL E 70 " --> pdb=" O TYR E 66 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER E 71 " --> pdb=" O GLY E 67 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU E 73 " --> pdb=" O VAL E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 122 removed outlier: 3.681A pdb=" N PHE E 88 " --> pdb=" O LEU E 84 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE E 89 " --> pdb=" O TYR E 85 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL E 97 " --> pdb=" O ALA E 93 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER E 120 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN E 121 " --> pdb=" O ARG E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 153 removed outlier: 3.523A pdb=" N ILE E 130 " --> pdb=" O PHE E 126 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU E 131 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE E 135 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA E 136 " --> pdb=" O ILE E 132 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU E 139 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY E 140 " --> pdb=" O ALA E 136 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU E 144 " --> pdb=" O GLY E 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 9 removed outlier: 4.234A pdb=" N ASN B 7 " --> pdb=" O VAL B 4 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE B 8 " --> pdb=" O TYR B 5 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP B 9 " --> pdb=" O PHE B 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4 through 9' Processing helix chain 'B' and resid 10 through 22 removed outlier: 3.570A pdb=" N ARG B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY B 19 " --> pdb=" O GLY B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 35 removed outlier: 3.756A pdb=" N TYR B 30 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE B 31 " --> pdb=" O ASN B 27 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN B 35 " --> pdb=" O ILE B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 47 Processing helix chain 'B' and resid 64 through 86 removed outlier: 3.718A pdb=" N LEU B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN B 86 " --> pdb=" O TYR B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 116 removed outlier: 3.529A pdb=" N TYR B 102 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE B 104 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ASP B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 107 " --> pdb=" O MET B 103 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR B 114 " --> pdb=" O MET B 110 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE B 115 " --> pdb=" O ILE B 111 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N HIS B 116 " --> pdb=" O THR B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.560A pdb=" N ILE B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLN B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 156 removed outlier: 4.168A pdb=" N GLU B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N THR B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP B 155 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B 156 " --> pdb=" O VAL B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 199 removed outlier: 3.598A pdb=" N ASN B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 231 removed outlier: 4.397A pdb=" N GLU B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N CYS B 207 " --> pdb=" O PRO B 203 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER B 230 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 242 removed outlier: 3.862A pdb=" N LEU B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 247 removed outlier: 4.185A pdb=" N GLY B 246 " --> pdb=" O PRO B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 258 removed outlier: 3.685A pdb=" N HIS B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN B 258 " --> pdb=" O PHE B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 269 Processing helix chain 'B' and resid 283 through 300 removed outlier: 4.191A pdb=" N HIS B 287 " --> pdb=" O ASN B 283 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 332 removed outlier: 3.676A pdb=" N LYS B 314 " --> pdb=" O TRP B 310 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 321 " --> pdb=" O GLU B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 341 removed outlier: 3.552A pdb=" N ILE B 338 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASN B 339 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR B 341 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 43 removed outlier: 4.204A pdb=" N PHE F 12 " --> pdb=" O TYR F 8 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY F 13 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE F 21 " --> pdb=" O CYS F 17 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE F 23 " --> pdb=" O SER F 19 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR F 24 " --> pdb=" O ALA F 20 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS F 34 " --> pdb=" O TYR F 30 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER F 35 " --> pdb=" O GLY F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 76 removed outlier: 3.688A pdb=" N GLY F 67 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL F 70 " --> pdb=" O TYR F 66 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR F 76 " --> pdb=" O VAL F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 122 removed outlier: 3.961A pdb=" N GLN F 90 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU F 91 " --> pdb=" O GLY F 87 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL F 97 " --> pdb=" O ALA F 93 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP F 113 " --> pdb=" O GLY F 109 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA F 114 " --> pdb=" O ILE F 110 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER F 120 " --> pdb=" O VAL F 116 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN F 121 " --> pdb=" O ARG F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 153 removed outlier: 4.421A pdb=" N GLY F 128 " --> pdb=" O ARG F 124 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU F 131 " --> pdb=" O VAL F 127 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE F 135 " --> pdb=" O LEU F 131 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU F 139 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY F 140 " --> pdb=" O ALA F 136 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY F 143 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU F 144 " --> pdb=" O GLY F 140 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU F 149 " --> pdb=" O ILE F 145 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG F 153 " --> pdb=" O LEU F 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 43 removed outlier: 3.786A pdb=" N GLY G 13 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY G 16 " --> pdb=" O PHE G 12 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA G 18 " --> pdb=" O ALA G 14 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE G 21 " --> pdb=" O CYS G 17 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE G 23 " --> pdb=" O SER G 19 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 51 removed outlier: 4.102A pdb=" N PHE G 51 " --> pdb=" O ASP G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 76 removed outlier: 3.752A pdb=" N GLY G 67 " --> pdb=" O ILE G 63 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL G 70 " --> pdb=" O TYR G 66 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU G 73 " --> pdb=" O VAL G 69 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR G 76 " --> pdb=" O VAL G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 122 removed outlier: 3.780A pdb=" N ILE G 89 " --> pdb=" O TYR G 85 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN G 90 " --> pdb=" O THR G 86 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU G 91 " --> pdb=" O GLY G 87 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA G 114 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN G 121 " --> pdb=" O ARG G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 153 removed outlier: 4.392A pdb=" N LEU G 131 " --> pdb=" O VAL G 127 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE G 132 " --> pdb=" O GLY G 128 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU G 133 " --> pdb=" O MET G 129 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE G 135 " --> pdb=" O LEU G 131 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU G 139 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY G 140 " --> pdb=" O ALA G 136 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY G 143 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU G 144 " --> pdb=" O GLY G 140 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG G 153 " --> pdb=" O LEU G 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 43 removed outlier: 3.769A pdb=" N GLY H 13 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY H 16 " --> pdb=" O PHE H 12 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS H 17 " --> pdb=" O GLY H 13 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE H 21 " --> pdb=" O CYS H 17 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE H 23 " --> pdb=" O SER H 19 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY H 38 " --> pdb=" O LYS H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 50 removed outlier: 3.732A pdb=" N LEU H 49 " --> pdb=" O ARG H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 76 removed outlier: 3.795A pdb=" N ILE H 63 " --> pdb=" O MET H 59 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA H 64 " --> pdb=" O ALA H 60 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE H 65 " --> pdb=" O GLY H 61 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU H 73 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS H 75 " --> pdb=" O SER H 71 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR H 76 " --> pdb=" O VAL H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 122 removed outlier: 3.509A pdb=" N PHE H 88 " --> pdb=" O LEU H 84 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE H 89 " --> pdb=" O TYR H 85 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP H 113 " --> pdb=" O GLY H 109 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA H 114 " --> pdb=" O ILE H 110 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER H 120 " --> pdb=" O VAL H 116 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLN H 121 " --> pdb=" O ARG H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 155 removed outlier: 4.328A pdb=" N GLY H 128 " --> pdb=" O ARG H 124 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU H 131 " --> pdb=" O VAL H 127 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE H 135 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA H 136 " --> pdb=" O ILE H 132 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU H 139 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY H 140 " --> pdb=" O ALA H 136 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA H 147 " --> pdb=" O GLY H 143 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG H 153 " --> pdb=" O LEU H 149 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR H 155 " --> pdb=" O ASN H 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 43 removed outlier: 3.778A pdb=" N GLY I 13 " --> pdb=" O ALA I 9 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE I 23 " --> pdb=" O SER I 19 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS I 34 " --> pdb=" O TYR I 30 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER I 35 " --> pdb=" O GLY I 31 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY I 38 " --> pdb=" O LYS I 34 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR I 42 " --> pdb=" O GLY I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 45 No H-bonds generated for 'chain 'I' and resid 44 through 45' Processing helix chain 'I' and resid 46 through 50 removed outlier: 3.876A pdb=" N LEU I 49 " --> pdb=" O ARG I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 76 removed outlier: 3.811A pdb=" N MET I 59 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA I 64 " --> pdb=" O ALA I 60 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY I 67 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU I 73 " --> pdb=" O VAL I 69 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR I 76 " --> pdb=" O VAL I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 122 removed outlier: 3.574A pdb=" N ILE I 89 " --> pdb=" O TYR I 85 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER I 96 " --> pdb=" O GLY I 92 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL I 97 " --> pdb=" O ALA I 93 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE I 110 " --> pdb=" O PHE I 106 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER I 120 " --> pdb=" O VAL I 116 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN I 121 " --> pdb=" O ARG I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 153 removed outlier: 4.344A pdb=" N GLY I 128 " --> pdb=" O ARG I 124 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU I 131 " --> pdb=" O VAL I 127 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE I 132 " --> pdb=" O GLY I 128 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE I 135 " --> pdb=" O LEU I 131 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU I 139 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY I 143 " --> pdb=" O LEU I 139 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU I 144 " --> pdb=" O GLY I 140 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU I 149 " --> pdb=" O ILE I 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 43 removed outlier: 4.185A pdb=" N PHE J 12 " --> pdb=" O TYR J 8 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY J 13 " --> pdb=" O ALA J 9 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA J 18 " --> pdb=" O ALA J 14 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE J 21 " --> pdb=" O CYS J 17 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE J 23 " --> pdb=" O SER J 19 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY J 38 " --> pdb=" O LYS J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 54 Processing helix chain 'J' and resid 54 through 76 removed outlier: 3.563A pdb=" N ILE J 58 " --> pdb=" O ILE J 54 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE J 63 " --> pdb=" O MET J 59 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY J 67 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU J 73 " --> pdb=" O VAL J 69 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR J 76 " --> pdb=" O VAL J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 122 removed outlier: 3.647A pdb=" N ILE J 89 " --> pdb=" O TYR J 85 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN J 90 " --> pdb=" O THR J 86 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU J 91 " --> pdb=" O GLY J 87 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER J 96 " --> pdb=" O GLY J 92 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL J 97 " --> pdb=" O ALA J 93 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA J 114 " --> pdb=" O ILE J 110 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER J 120 " --> pdb=" O VAL J 116 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLN J 121 " --> pdb=" O ARG J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 155 removed outlier: 4.470A pdb=" N GLY J 128 " --> pdb=" O ARG J 124 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU J 131 " --> pdb=" O VAL J 127 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE J 135 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU J 139 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY J 140 " --> pdb=" O ALA J 136 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY J 143 " --> pdb=" O LEU J 139 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU J 144 " --> pdb=" O GLY J 140 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU J 149 " --> pdb=" O ILE J 145 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA J 154 " --> pdb=" O LEU J 150 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR J 155 " --> pdb=" O ASN J 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 43 removed outlier: 3.673A pdb=" N GLY K 13 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE K 21 " --> pdb=" O CYS K 17 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE K 23 " --> pdb=" O SER K 19 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR K 24 " --> pdb=" O ALA K 20 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR K 42 " --> pdb=" O GLY K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 50 removed outlier: 3.844A pdb=" N LEU K 49 " --> pdb=" O ARG K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 76 removed outlier: 3.811A pdb=" N ILE K 63 " --> pdb=" O MET K 59 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA K 64 " --> pdb=" O ALA K 60 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL K 70 " --> pdb=" O TYR K 66 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER K 71 " --> pdb=" O GLY K 67 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR K 76 " --> pdb=" O VAL K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 122 removed outlier: 3.538A pdb=" N VAL K 97 " --> pdb=" O ALA K 93 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE K 110 " --> pdb=" O PHE K 106 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG K 117 " --> pdb=" O ASP K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 155 removed outlier: 3.985A pdb=" N GLY K 128 " --> pdb=" O ARG K 124 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU K 131 " --> pdb=" O VAL K 127 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE K 132 " --> pdb=" O GLY K 128 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU K 133 " --> pdb=" O MET K 129 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE K 135 " --> pdb=" O LEU K 131 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA K 136 " --> pdb=" O ILE K 132 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU K 139 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY K 140 " --> pdb=" O ALA K 136 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N THR K 155 " --> pdb=" O ASN K 151 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 43 removed outlier: 4.369A pdb=" N PHE L 12 " --> pdb=" O TYR L 8 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY L 13 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE L 21 " --> pdb=" O CYS L 17 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR L 24 " --> pdb=" O ALA L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 54 through 77 removed outlier: 3.583A pdb=" N ILE L 62 " --> pdb=" O ILE L 58 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE L 63 " --> pdb=" O MET L 59 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE L 65 " --> pdb=" O GLY L 61 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL L 70 " --> pdb=" O TYR L 66 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU L 73 " --> pdb=" O VAL L 69 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS L 75 " --> pdb=" O SER L 71 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER L 77 " --> pdb=" O LEU L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 122 removed outlier: 3.803A pdb=" N ILE L 89 " --> pdb=" O TYR L 85 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN L 90 " --> pdb=" O THR L 86 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER L 96 " --> pdb=" O GLY L 92 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER L 100 " --> pdb=" O SER L 96 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG L 117 " --> pdb=" O ASP L 113 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER L 120 " --> pdb=" O VAL L 116 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN L 121 " --> pdb=" O ARG L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 134 removed outlier: 4.135A pdb=" N GLY L 128 " --> pdb=" O ARG L 124 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE L 130 " --> pdb=" O PHE L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 152 removed outlier: 3.553A pdb=" N VAL L 138 " --> pdb=" O ILE L 134 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU L 139 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLY L 140 " --> pdb=" O ALA L 136 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY L 143 " --> pdb=" O LEU L 139 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA L 147 " --> pdb=" O GLY L 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 36 removed outlier: 3.609A pdb=" N TYR A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR A 32 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 79 removed outlier: 3.559A pdb=" N ILE A 59 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG A 61 " --> pdb=" O ASN A 57 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 76 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS A 77 " --> pdb=" O TYR A 73 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 93 removed outlier: 3.546A pdb=" N TYR A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 145 removed outlier: 4.390A pdb=" N TYR A 116 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA A 127 " --> pdb=" O GLN A 123 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN A 134 " --> pdb=" O GLN A 130 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR A 141 " --> pdb=" O ASP A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 208 removed outlier: 3.619A pdb=" N GLN A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 205 " --> pdb=" O GLN A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 256 removed outlier: 3.821A pdb=" N LEU A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 303 removed outlier: 3.683A pdb=" N ASN A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 325 removed outlier: 4.196A pdb=" N PHE A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU A 321 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 359 removed outlier: 3.982A pdb=" N ALA A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR A 348 " --> pdb=" O ASP A 344 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY A 354 " --> pdb=" O GLN A 350 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLU A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET A 356 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 407 through 423 removed outlier: 4.589A pdb=" N VAL A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Proline residue: A 416 - end of helix removed outlier: 3.991A pdb=" N MET A 422 " --> pdb=" O MET A 418 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE A 423 " --> pdb=" O PHE A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 442 Processing helix chain 'A' and resid 442 through 447 Processing helix chain 'A' and resid 454 through 461 removed outlier: 3.776A pdb=" N ALA A 458 " --> pdb=" O ILE A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 480 removed outlier: 3.950A pdb=" N MET A 468 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 523 removed outlier: 3.724A pdb=" N TRP A 522 " --> pdb=" O ASP A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 554 removed outlier: 3.968A pdb=" N LEU A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 560 removed outlier: 4.148A pdb=" N ASN A 558 " --> pdb=" O PHE A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 596 removed outlier: 3.522A pdb=" N ILE A 573 " --> pdb=" O ILE A 569 " (cutoff:3.500A) Proline residue: A 574 - end of helix removed outlier: 3.667A pdb=" N TYR A 585 " --> pdb=" O GLY A 581 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 595 " --> pdb=" O VAL A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 618 removed outlier: 3.840A pdb=" N ILE A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN A 614 " --> pdb=" O ASN A 610 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N MET A 615 " --> pdb=" O MET A 611 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 652 removed outlier: 3.586A pdb=" N VAL A 633 " --> pdb=" O HIS A 629 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS A 644 " --> pdb=" O MET A 640 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A 645 " --> pdb=" O ALA A 641 " (cutoff:3.500A) Proline residue: A 646 - end of helix removed outlier: 3.688A pdb=" N LEU A 649 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL A 651 " --> pdb=" O TRP A 647 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 732 removed outlier: 3.935A pdb=" N ILE A 713 " --> pdb=" O GLY A 709 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A 720 " --> pdb=" O VAL A 716 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL A 727 " --> pdb=" O CYS A 723 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 731 " --> pdb=" O VAL A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 759 removed outlier: 3.858A pdb=" N TRP A 737 " --> pdb=" O TYR A 733 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 744 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN A 745 " --> pdb=" O LEU A 741 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN A 756 " --> pdb=" O THR A 752 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE A 757 " --> pdb=" O MET A 753 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A 758 " --> pdb=" O THR A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 804 removed outlier: 3.694A pdb=" N PHE A 768 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 771 " --> pdb=" O VAL A 767 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA A 779 " --> pdb=" O ALA A 775 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU A 780 " --> pdb=" O MET A 776 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A 785 " --> pdb=" O THR A 781 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 786 " --> pdb=" O CYS A 782 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 787 " --> pdb=" O ALA A 783 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A 789 " --> pdb=" O LEU A 785 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 795 " --> pdb=" O THR A 791 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU A 804 " --> pdb=" O LEU A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 810 Processing helix chain 'O' and resid 9 through 31 removed outlier: 3.829A pdb=" N CYS O 13 " --> pdb=" O LYS O 9 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL O 15 " --> pdb=" O TRP O 11 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU O 16 " --> pdb=" O CYS O 12 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER O 17 " --> pdb=" O CYS O 13 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL O 22 " --> pdb=" O ALA O 18 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU O 24 " --> pdb=" O GLY O 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER O 25 " --> pdb=" O VAL O 21 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL O 26 " --> pdb=" O VAL O 22 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE O 27 " --> pdb=" O ILE O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 75 removed outlier: 4.343A pdb=" N VAL O 55 " --> pdb=" O VAL O 51 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU O 57 " --> pdb=" O HIS O 53 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL O 64 " --> pdb=" O LEU O 60 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE O 65 " --> pdb=" O VAL O 61 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN O 72 " --> pdb=" O PHE O 68 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL O 73 " --> pdb=" O CYS O 69 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU O 75 " --> pdb=" O PHE O 71 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42 removed outlier: 3.936A pdb=" N GLN A 40 " --> pdb=" O TRP A 340 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU A 338 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE A 334 " --> pdb=" O ASP A 329 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP A 329 " --> pdb=" O ILE A 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 42 removed outlier: 3.936A pdb=" N GLN A 40 " --> pdb=" O TRP A 340 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU A 338 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A 341 " --> pdb=" O ALA A 15 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA A 15 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 212 through 217 removed outlier: 4.207A pdb=" N PHE A 212 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR A 188 " --> pdb=" O TYR A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 378 through 379 1395 hydrogen bonds defined for protein. 4152 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: 6.36 Time building geometry restraints manager: 9.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6511 1.34 - 1.46: 4887 1.46 - 1.58: 10956 1.58 - 1.70: 0 1.70 - 1.82: 204 Bond restraints: 22558 Sorted by residual: bond pdb=" C ALA D 15 " pdb=" N PRO D 16 " ideal model delta sigma weight residual 1.335 1.383 -0.049 1.19e-02 7.06e+03 1.67e+01 bond pdb=" CB MET A 468 " pdb=" CG MET A 468 " ideal model delta sigma weight residual 1.520 1.452 0.068 3.00e-02 1.11e+03 5.09e+00 bond pdb=" N ASN B 164 " pdb=" CA ASN B 164 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.74e+00 bond pdb=" C ASP O 44 " pdb=" N PRO O 45 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.55e+00 bond pdb=" CB VAL M 60 " pdb=" CG2 VAL M 60 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.44e+00 ... (remaining 22553 not shown) Histogram of bond angle deviations from ideal: 95.36 - 103.22: 157 103.22 - 111.07: 8058 111.07 - 118.93: 10010 118.93 - 126.78: 12195 126.78 - 134.64: 218 Bond angle restraints: 30638 Sorted by residual: angle pdb=" C MET A 422 " pdb=" N PHE A 423 " pdb=" CA PHE A 423 " ideal model delta sigma weight residual 122.46 113.39 9.07 1.80e+00 3.09e-01 2.54e+01 angle pdb=" C GLN I 156 " pdb=" N ASP I 157 " pdb=" CA ASP I 157 " ideal model delta sigma weight residual 122.82 129.91 -7.09 1.42e+00 4.96e-01 2.50e+01 angle pdb=" C ASN A 384 " pdb=" N LYS A 385 " pdb=" CA LYS A 385 " ideal model delta sigma weight residual 121.54 130.50 -8.96 1.91e+00 2.74e-01 2.20e+01 angle pdb=" CA THR N 250 " pdb=" CB THR N 250 " pdb=" CG2 THR N 250 " ideal model delta sigma weight residual 110.50 118.28 -7.78 1.70e+00 3.46e-01 2.09e+01 angle pdb=" N GLY A 524 " pdb=" CA GLY A 524 " pdb=" C GLY A 524 " ideal model delta sigma weight residual 112.49 117.79 -5.30 1.21e+00 6.83e-01 1.92e+01 ... (remaining 30633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 12218 16.14 - 32.28: 676 32.28 - 48.42: 202 48.42 - 64.57: 6 64.57 - 80.71: 10 Dihedral angle restraints: 13112 sinusoidal: 4829 harmonic: 8283 Sorted by residual: dihedral pdb=" CA GLU L 137 " pdb=" C GLU L 137 " pdb=" N VAL L 138 " pdb=" CA VAL L 138 " ideal model delta harmonic sigma weight residual -180.00 -151.28 -28.72 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA MET A 422 " pdb=" C MET A 422 " pdb=" N PHE A 423 " pdb=" CA PHE A 423 " ideal model delta harmonic sigma weight residual 180.00 153.77 26.23 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA ARG B 276 " pdb=" C ARG B 276 " pdb=" N GLY B 277 " pdb=" CA GLY B 277 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 13109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2800 0.063 - 0.126: 705 0.126 - 0.189: 127 0.189 - 0.251: 12 0.251 - 0.314: 6 Chirality restraints: 3650 Sorted by residual: chirality pdb=" CB ILE N 218 " pdb=" CA ILE N 218 " pdb=" CG1 ILE N 218 " pdb=" CG2 ILE N 218 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA GLU A 818 " pdb=" N GLU A 818 " pdb=" C GLU A 818 " pdb=" CB GLU A 818 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CB ILE C 45 " pdb=" CA ILE C 45 " pdb=" CG1 ILE C 45 " pdb=" CG2 ILE C 45 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 3647 not shown) Planarity restraints: 3802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 200 " -0.045 5.00e-02 4.00e+02 6.72e-02 7.23e+00 pdb=" N PRO B 201 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 201 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 201 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 102 " 0.018 2.00e-02 2.50e+03 1.83e-02 6.70e+00 pdb=" CG TYR B 102 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR B 102 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR B 102 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR B 102 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR B 102 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 102 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 102 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 423 " -0.021 2.00e-02 2.50e+03 1.85e-02 6.00e+00 pdb=" CG PHE A 423 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE A 423 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 423 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 423 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 423 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A 423 " -0.001 2.00e-02 2.50e+03 ... (remaining 3799 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3933 2.76 - 3.29: 22511 3.29 - 3.83: 37010 3.83 - 4.36: 42844 4.36 - 4.90: 70870 Nonbonded interactions: 177168 Sorted by model distance: nonbonded pdb=" O VAL B 152 " pdb=" OG1 THR B 156 " model vdw 2.224 2.440 nonbonded pdb=" OH TYR A 31 " pdb=" OE1 GLU A 316 " model vdw 2.239 2.440 nonbonded pdb=" OD1 ASP C 44 " pdb=" OG SER N 216 " model vdw 2.269 2.440 nonbonded pdb=" O ASP B 298 " pdb=" OG1 THR B 301 " model vdw 2.289 2.440 nonbonded pdb=" ND2 ASN A 480 " pdb=" O LEU A 518 " model vdw 2.295 2.520 ... (remaining 177163 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = (chain 'H' and resid 1 through 159) selection = chain 'I' selection = chain 'J' selection = (chain 'K' and resid 1 through 159) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 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: 0.010 Extract box with map and model: 2.940 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 56.060 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 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 : 0.006 0.088 22558 Z= 0.406 Angle : 1.033 11.988 30638 Z= 0.543 Chirality : 0.057 0.314 3650 Planarity : 0.006 0.067 3802 Dihedral : 11.468 80.707 7854 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.34 % Allowed : 6.02 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.12), residues: 2884 helix: -2.93 (0.08), residues: 1916 sheet: -0.23 (0.77), residues: 43 loop : -2.14 (0.18), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP C 77 HIS 0.016 0.002 HIS A 559 PHE 0.041 0.003 PHE A 423 TYR 0.039 0.003 TYR A 300 ARG 0.013 0.001 ARG L 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 652 time to evaluate : 2.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 54 GLU cc_start: 0.7986 (tt0) cc_final: 0.7770 (tm-30) REVERT: D 58 LYS cc_start: 0.8090 (mmtt) cc_final: 0.7768 (mmmt) REVERT: D 59 SER cc_start: 0.8773 (t) cc_final: 0.8199 (p) REVERT: D 114 TYR cc_start: 0.8050 (t80) cc_final: 0.7844 (t80) REVERT: D 132 ARG cc_start: 0.7831 (ttp-110) cc_final: 0.7100 (tpp-160) REVERT: C 38 PHE cc_start: 0.8843 (m-10) cc_final: 0.8341 (m-80) REVERT: C 100 ASN cc_start: 0.9062 (t0) cc_final: 0.8766 (t0) REVERT: C 108 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8339 (tm-30) REVERT: C 211 GLU cc_start: 0.8473 (pm20) cc_final: 0.8199 (pm20) REVERT: N 256 LYS cc_start: 0.7920 (tmtm) cc_final: 0.7358 (pptt) REVERT: N 259 ASN cc_start: 0.6633 (t0) cc_final: 0.5326 (m110) REVERT: M 43 MET cc_start: 0.7804 (mmt) cc_final: 0.7204 (mmt) REVERT: M 44 MET cc_start: 0.7496 (ttp) cc_final: 0.6999 (tpp) REVERT: E 47 PRO cc_start: 0.8124 (Cg_endo) cc_final: 0.7921 (Cg_exo) REVERT: E 85 TYR cc_start: 0.8540 (t80) cc_final: 0.8093 (t80) REVERT: E 130 ILE cc_start: 0.7409 (pp) cc_final: 0.7142 (mt) REVERT: B 128 HIS cc_start: 0.8042 (t70) cc_final: 0.7366 (t-170) REVERT: B 188 TYR cc_start: 0.7755 (t80) cc_final: 0.7524 (t80) REVERT: B 202 GLU cc_start: 0.8041 (tp30) cc_final: 0.7745 (tp30) REVERT: B 230 SER cc_start: 0.8562 (t) cc_final: 0.8245 (p) REVERT: B 280 GLU cc_start: 0.8475 (mp0) cc_final: 0.7730 (tp30) REVERT: B 328 GLU cc_start: 0.8173 (tt0) cc_final: 0.7860 (tm-30) REVERT: F 48 ASP cc_start: 0.8639 (m-30) cc_final: 0.8146 (p0) REVERT: F 52 LYS cc_start: 0.7660 (tppp) cc_final: 0.7364 (tptp) REVERT: F 121 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8383 (mp10) REVERT: F 124 ARG cc_start: 0.8391 (mtp85) cc_final: 0.7811 (ttm170) REVERT: F 155 THR cc_start: 0.8067 (m) cc_final: 0.7702 (p) REVERT: G 48 ASP cc_start: 0.8391 (m-30) cc_final: 0.8165 (m-30) REVERT: G 52 LYS cc_start: 0.7394 (mmpt) cc_final: 0.7155 (mmtt) REVERT: G 122 GLN cc_start: 0.8251 (tp-100) cc_final: 0.7995 (tp-100) REVERT: G 129 MET cc_start: 0.7423 (tmm) cc_final: 0.7095 (tmm) REVERT: G 137 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7374 (tm-30) REVERT: G 139 LEU cc_start: 0.8336 (mp) cc_final: 0.8071 (tt) REVERT: G 156 GLN cc_start: 0.7436 (pp30) cc_final: 0.7179 (pp30) REVERT: H 43 CYS cc_start: 0.8481 (m) cc_final: 0.8271 (m) REVERT: H 85 TYR cc_start: 0.8562 (t80) cc_final: 0.8336 (t80) REVERT: I 3 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7680 (pm20) REVERT: I 50 LEU cc_start: 0.7854 (pt) cc_final: 0.6692 (tp) REVERT: I 51 PHE cc_start: 0.8718 (m-80) cc_final: 0.7821 (t80) REVERT: I 55 VAL cc_start: 0.7894 (m) cc_final: 0.7571 (t) REVERT: I 76 TYR cc_start: 0.8511 (m-80) cc_final: 0.8162 (m-80) REVERT: I 80 GLN cc_start: 0.8991 (pm20) cc_final: 0.8651 (tt0) REVERT: I 81 LYS cc_start: 0.9214 (mttm) cc_final: 0.8782 (mmmt) REVERT: J 47 PRO cc_start: 0.8448 (Cg_endo) cc_final: 0.8024 (Cg_exo) REVERT: J 48 ASP cc_start: 0.8911 (m-30) cc_final: 0.8635 (t0) REVERT: J 52 LYS cc_start: 0.8057 (tttt) cc_final: 0.7790 (tptt) REVERT: K 46 ARG cc_start: 0.8031 (ttt180) cc_final: 0.7795 (mtp180) REVERT: K 153 ARG cc_start: 0.7502 (ttm-80) cc_final: 0.7098 (ttm-80) REVERT: K 157 ASP cc_start: 0.8271 (t0) cc_final: 0.7635 (t0) REVERT: L 121 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8386 (mm-40) REVERT: L 137 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8139 (mt-10) REVERT: A 130 GLN cc_start: 0.7105 (tt0) cc_final: 0.6739 (tm-30) REVERT: A 200 GLU cc_start: 0.8852 (tp30) cc_final: 0.8603 (tp30) REVERT: A 223 TYR cc_start: 0.7786 (m-10) cc_final: 0.7584 (m-80) REVERT: A 254 GLU cc_start: 0.8924 (tt0) cc_final: 0.8281 (tp30) REVERT: A 270 ARG cc_start: 0.6527 (ttp80) cc_final: 0.6317 (ttp-110) REVERT: A 287 VAL cc_start: 0.7932 (m) cc_final: 0.7726 (p) REVERT: A 338 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8209 (mt-10) REVERT: A 489 ILE cc_start: 0.7894 (tp) cc_final: 0.7641 (tt) REVERT: A 764 PHE cc_start: 0.4968 (t80) cc_final: 0.4349 (m-80) REVERT: A 769 MET cc_start: 0.8338 (tpp) cc_final: 0.8086 (ttm) REVERT: A 776 MET cc_start: 0.6910 (mtt) cc_final: 0.6555 (tpp) REVERT: A 788 MET cc_start: 0.7847 (mmp) cc_final: 0.7642 (tpp) REVERT: A 817 TYR cc_start: 0.7612 (t80) cc_final: 0.7312 (t80) REVERT: A 823 GLU cc_start: 0.8611 (tt0) cc_final: 0.8252 (mp0) REVERT: O 14 THR cc_start: 0.6839 (m) cc_final: 0.6422 (p) REVERT: O 36 GLU cc_start: 0.7977 (pt0) cc_final: 0.7303 (pp20) REVERT: O 65 PHE cc_start: 0.7944 (m-80) cc_final: 0.7730 (m-10) REVERT: O 72 GLN cc_start: 0.7827 (pt0) cc_final: 0.7278 (pp30) outliers start: 8 outliers final: 1 residues processed: 659 average time/residue: 0.3571 time to fit residues: 361.6476 Evaluate side-chains 403 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 402 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 238 optimal weight: 7.9990 chunk 214 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 221 optimal weight: 0.4980 chunk 85 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 chunk 165 optimal weight: 0.9990 chunk 256 optimal weight: 2.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 GLN E 156 GLN B 128 HIS F 90 GLN F 156 GLN ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 GLN I 90 GLN I 151 ASN J 80 GLN ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN A 391 GLN ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22558 Z= 0.283 Angle : 0.720 9.472 30638 Z= 0.377 Chirality : 0.043 0.206 3650 Planarity : 0.005 0.058 3802 Dihedral : 5.300 33.664 3117 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.14 % Allowed : 13.40 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.14), residues: 2884 helix: -1.25 (0.10), residues: 2041 sheet: 0.12 (0.75), residues: 43 loop : -2.20 (0.19), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 751 HIS 0.007 0.001 HIS A 559 PHE 0.033 0.002 PHE A 423 TYR 0.020 0.002 TYR D 72 ARG 0.004 0.001 ARG D 125 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 454 time to evaluate : 2.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 54 GLU cc_start: 0.7744 (tt0) cc_final: 0.7414 (tm-30) REVERT: D 59 SER cc_start: 0.8944 (t) cc_final: 0.8422 (p) REVERT: D 114 TYR cc_start: 0.7969 (t80) cc_final: 0.7759 (t80) REVERT: D 145 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7531 (tm-30) REVERT: C 38 PHE cc_start: 0.9228 (m-10) cc_final: 0.8721 (m-80) REVERT: C 108 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8303 (tm-30) REVERT: C 129 THR cc_start: 0.8008 (OUTLIER) cc_final: 0.7336 (p) REVERT: C 203 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8198 (mp) REVERT: N 256 LYS cc_start: 0.7791 (tmtm) cc_final: 0.7333 (pptt) REVERT: N 259 ASN cc_start: 0.6473 (t0) cc_final: 0.5342 (m110) REVERT: M 66 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8194 (m-30) REVERT: E 84 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8229 (tm) REVERT: E 85 TYR cc_start: 0.8321 (t80) cc_final: 0.8031 (t80) REVERT: E 152 SER cc_start: 0.9097 (t) cc_final: 0.8838 (m) REVERT: B 79 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8588 (tm-30) REVERT: B 153 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7729 (tp) REVERT: B 178 GLU cc_start: 0.8154 (tp30) cc_final: 0.7910 (mt-10) REVERT: B 230 SER cc_start: 0.8131 (t) cc_final: 0.7800 (p) REVERT: B 258 GLN cc_start: 0.6491 (pp30) cc_final: 0.6258 (pp30) REVERT: B 279 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7070 (mp) REVERT: F 48 ASP cc_start: 0.8746 (m-30) cc_final: 0.8351 (p0) REVERT: F 52 LYS cc_start: 0.8079 (tppp) cc_final: 0.7599 (tptp) REVERT: F 121 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8480 (mp10) REVERT: F 124 ARG cc_start: 0.8448 (mtp85) cc_final: 0.7859 (ttp-170) REVERT: F 155 THR cc_start: 0.8363 (m) cc_final: 0.8104 (p) REVERT: G 122 GLN cc_start: 0.8284 (tp-100) cc_final: 0.8054 (tp-100) REVERT: H 43 CYS cc_start: 0.8742 (m) cc_final: 0.8466 (t) REVERT: H 85 TYR cc_start: 0.8489 (t80) cc_final: 0.8256 (t80) REVERT: H 149 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7840 (tt) REVERT: I 3 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7846 (pm20) REVERT: I 50 LEU cc_start: 0.7998 (pt) cc_final: 0.6735 (tp) REVERT: I 51 PHE cc_start: 0.8791 (m-80) cc_final: 0.8038 (t80) REVERT: I 76 TYR cc_start: 0.8450 (m-80) cc_final: 0.8175 (m-80) REVERT: I 80 GLN cc_start: 0.9095 (pm20) cc_final: 0.8729 (tt0) REVERT: I 81 LYS cc_start: 0.9252 (mttm) cc_final: 0.8755 (mmmt) REVERT: J 47 PRO cc_start: 0.8665 (Cg_endo) cc_final: 0.8443 (Cg_exo) REVERT: J 48 ASP cc_start: 0.9039 (m-30) cc_final: 0.8647 (t0) REVERT: J 52 LYS cc_start: 0.8157 (tttt) cc_final: 0.7855 (tptt) REVERT: J 78 LEU cc_start: 0.8941 (mp) cc_final: 0.8701 (mm) REVERT: K 153 ARG cc_start: 0.7755 (ttm-80) cc_final: 0.7097 (ttm-80) REVERT: K 157 ASP cc_start: 0.8056 (t0) cc_final: 0.7849 (t0) REVERT: L 121 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8133 (mm-40) REVERT: A 130 GLN cc_start: 0.7132 (tt0) cc_final: 0.6733 (tm-30) REVERT: A 200 GLU cc_start: 0.8684 (tp30) cc_final: 0.8451 (tp30) REVERT: A 287 VAL cc_start: 0.8195 (m) cc_final: 0.7953 (p) REVERT: A 552 TYR cc_start: 0.7657 (t80) cc_final: 0.7354 (t80) REVERT: A 721 GLU cc_start: 0.8475 (tm-30) cc_final: 0.7987 (tt0) REVERT: A 764 PHE cc_start: 0.5240 (t80) cc_final: 0.4242 (m-80) REVERT: A 777 TRP cc_start: 0.8402 (t60) cc_final: 0.6719 (t60) REVERT: O 4 VAL cc_start: 0.1714 (OUTLIER) cc_final: 0.1163 (t) REVERT: O 14 THR cc_start: 0.6578 (m) cc_final: 0.6198 (p) REVERT: O 72 GLN cc_start: 0.7707 (pt0) cc_final: 0.7135 (tm-30) outliers start: 97 outliers final: 54 residues processed: 522 average time/residue: 0.2975 time to fit residues: 250.6899 Evaluate side-chains 444 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 382 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 66 ASP Chi-restraints excluded: chain E residue 5 CYS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 51 PHE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain K residue 17 CYS Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 63 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 142 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 213 optimal weight: 6.9990 chunk 174 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 257 optimal weight: 4.9990 chunk 278 optimal weight: 0.8980 chunk 229 optimal weight: 2.9990 chunk 255 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN ** M 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN K 90 GLN ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22558 Z= 0.203 Angle : 0.641 9.804 30638 Z= 0.326 Chirality : 0.040 0.184 3650 Planarity : 0.004 0.055 3802 Dihedral : 4.814 19.614 3115 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.82 % Allowed : 16.35 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.15), residues: 2884 helix: -0.50 (0.11), residues: 2080 sheet: 0.75 (0.85), residues: 37 loop : -1.98 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 751 HIS 0.005 0.001 HIS A 796 PHE 0.022 0.001 PHE A 423 TYR 0.018 0.001 TYR N 251 ARG 0.004 0.000 ARG D 125 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 441 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 54 GLU cc_start: 0.7780 (tt0) cc_final: 0.7380 (tm-30) REVERT: D 114 TYR cc_start: 0.8172 (t80) cc_final: 0.7965 (t80) REVERT: D 125 ARG cc_start: 0.7891 (tpp80) cc_final: 0.7143 (tpp80) REVERT: D 127 TYR cc_start: 0.6607 (t80) cc_final: 0.6309 (t80) REVERT: D 145 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7583 (tm-30) REVERT: C 129 THR cc_start: 0.7950 (OUTLIER) cc_final: 0.7288 (p) REVERT: C 188 GLU cc_start: 0.8611 (tt0) cc_final: 0.8399 (tt0) REVERT: N 256 LYS cc_start: 0.7573 (tmtm) cc_final: 0.7052 (pptt) REVERT: N 259 ASN cc_start: 0.6402 (t0) cc_final: 0.5349 (m110) REVERT: M 43 MET cc_start: 0.7430 (mmt) cc_final: 0.6731 (mmt) REVERT: M 66 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7460 (m-30) REVERT: B 149 TYR cc_start: 0.8105 (t80) cc_final: 0.7572 (t80) REVERT: B 178 GLU cc_start: 0.8164 (tp30) cc_final: 0.7904 (mt-10) REVERT: B 230 SER cc_start: 0.8088 (t) cc_final: 0.7777 (p) REVERT: B 279 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.5928 (mt) REVERT: B 280 GLU cc_start: 0.8471 (mp0) cc_final: 0.7283 (tm-30) REVERT: F 48 ASP cc_start: 0.8708 (m-30) cc_final: 0.8173 (p0) REVERT: F 52 LYS cc_start: 0.8296 (tppp) cc_final: 0.7890 (tptp) REVERT: F 121 GLN cc_start: 0.8635 (mm-40) cc_final: 0.8429 (mp10) REVERT: F 124 ARG cc_start: 0.8535 (mtp85) cc_final: 0.7931 (ttm170) REVERT: F 155 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8170 (p) REVERT: G 45 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7773 (mt) REVERT: G 122 GLN cc_start: 0.8203 (tp-100) cc_final: 0.7327 (tm-30) REVERT: G 142 TYR cc_start: 0.7776 (m-80) cc_final: 0.7549 (m-80) REVERT: G 157 ASP cc_start: 0.6109 (m-30) cc_final: 0.5550 (m-30) REVERT: H 43 CYS cc_start: 0.8725 (m) cc_final: 0.8470 (t) REVERT: H 149 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7927 (tt) REVERT: I 3 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7846 (pm20) REVERT: I 50 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7531 (tp) REVERT: I 80 GLN cc_start: 0.9071 (pm20) cc_final: 0.8655 (tt0) REVERT: I 81 LYS cc_start: 0.9274 (mttm) cc_final: 0.8757 (mmmt) REVERT: J 47 PRO cc_start: 0.8673 (Cg_endo) cc_final: 0.8200 (Cg_exo) REVERT: J 48 ASP cc_start: 0.9069 (m-30) cc_final: 0.8770 (t0) REVERT: J 52 LYS cc_start: 0.8052 (tttt) cc_final: 0.7619 (tptt) REVERT: J 78 LEU cc_start: 0.8878 (mp) cc_final: 0.8586 (mm) REVERT: K 157 ASP cc_start: 0.8113 (t0) cc_final: 0.7768 (t0) REVERT: K 158 VAL cc_start: 0.8186 (t) cc_final: 0.7954 (t) REVERT: L 121 GLN cc_start: 0.8534 (mm-40) cc_final: 0.8122 (mm-40) REVERT: A 130 GLN cc_start: 0.7136 (tt0) cc_final: 0.6808 (tm-30) REVERT: A 481 ASP cc_start: 0.7666 (m-30) cc_final: 0.7275 (m-30) REVERT: A 514 TYR cc_start: 0.8454 (t80) cc_final: 0.8198 (t80) REVERT: A 552 TYR cc_start: 0.7775 (t80) cc_final: 0.7516 (t80) REVERT: A 565 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.6352 (ppp) REVERT: A 721 GLU cc_start: 0.8553 (tm-30) cc_final: 0.7950 (tt0) REVERT: A 769 MET cc_start: 0.8098 (tpp) cc_final: 0.7489 (ptt) REVERT: A 777 TRP cc_start: 0.8259 (t60) cc_final: 0.7934 (t60) REVERT: A 817 TYR cc_start: 0.7122 (t80) cc_final: 0.6888 (t80) REVERT: O 14 THR cc_start: 0.6595 (m) cc_final: 0.6266 (p) outliers start: 113 outliers final: 64 residues processed: 511 average time/residue: 0.2900 time to fit residues: 241.4106 Evaluate side-chains 447 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 375 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 223 LEU Chi-restraints excluded: chain N residue 226 CYS Chi-restraints excluded: chain M residue 66 ASP Chi-restraints excluded: chain E residue 5 CYS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 51 PHE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain F residue 17 CYS Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 126 PHE Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain J residue 17 CYS Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain L residue 17 CYS Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain O residue 47 ASP Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 71 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 254 optimal weight: 9.9990 chunk 193 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 172 optimal weight: 2.9990 chunk 258 optimal weight: 7.9990 chunk 273 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN G 53 ASN ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 GLN I 151 ASN ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22558 Z= 0.216 Angle : 0.646 11.277 30638 Z= 0.325 Chirality : 0.040 0.175 3650 Planarity : 0.004 0.050 3802 Dihedral : 4.652 19.387 3115 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 5.51 % Allowed : 17.80 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.15), residues: 2884 helix: -0.16 (0.11), residues: 2077 sheet: 0.97 (0.85), residues: 37 loop : -1.90 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 751 HIS 0.008 0.001 HIS A 796 PHE 0.028 0.002 PHE E 88 TYR 0.017 0.001 TYR C 140 ARG 0.007 0.000 ARG K 153 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 400 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 54 GLU cc_start: 0.7755 (tt0) cc_final: 0.7242 (tm-30) REVERT: D 59 SER cc_start: 0.8893 (t) cc_final: 0.8675 (p) REVERT: D 114 TYR cc_start: 0.8144 (t80) cc_final: 0.7932 (t80) REVERT: D 125 ARG cc_start: 0.7965 (tpp80) cc_final: 0.7248 (tpp80) REVERT: D 127 TYR cc_start: 0.6641 (t80) cc_final: 0.6377 (t80) REVERT: D 145 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7562 (tm-30) REVERT: C 129 THR cc_start: 0.7863 (OUTLIER) cc_final: 0.7291 (p) REVERT: C 188 GLU cc_start: 0.8575 (tt0) cc_final: 0.8337 (tt0) REVERT: N 256 LYS cc_start: 0.7467 (tmtm) cc_final: 0.6955 (pptt) REVERT: N 259 ASN cc_start: 0.6634 (t0) cc_final: 0.5600 (m110) REVERT: M 43 MET cc_start: 0.7383 (mmt) cc_final: 0.6839 (mmt) REVERT: M 66 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7313 (m-30) REVERT: E 85 TYR cc_start: 0.8147 (t80) cc_final: 0.7835 (t80) REVERT: E 122 GLN cc_start: 0.7755 (tp-100) cc_final: 0.7379 (tp40) REVERT: B 149 TYR cc_start: 0.8000 (t80) cc_final: 0.7446 (t80) REVERT: B 178 GLU cc_start: 0.8147 (tp30) cc_final: 0.7868 (mt-10) REVERT: B 236 ASP cc_start: 0.8001 (m-30) cc_final: 0.7513 (t0) REVERT: B 279 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6742 (mt) REVERT: B 317 GLU cc_start: 0.7611 (pp20) cc_final: 0.7342 (tp30) REVERT: F 48 ASP cc_start: 0.8741 (m-30) cc_final: 0.8194 (p0) REVERT: F 52 LYS cc_start: 0.8331 (tppp) cc_final: 0.7970 (tptp) REVERT: F 124 ARG cc_start: 0.8532 (mtp85) cc_final: 0.8043 (ttp-170) REVERT: F 155 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8218 (p) REVERT: G 45 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7726 (mt) REVERT: G 88 PHE cc_start: 0.8061 (m-80) cc_final: 0.7836 (m-80) REVERT: G 122 GLN cc_start: 0.8107 (tp-100) cc_final: 0.7896 (tp-100) REVERT: G 157 ASP cc_start: 0.6053 (m-30) cc_final: 0.5506 (m-30) REVERT: H 149 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7928 (tt) REVERT: I 3 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7763 (pm20) REVERT: I 50 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7463 (tp) REVERT: I 80 GLN cc_start: 0.9084 (pm20) cc_final: 0.8674 (tt0) REVERT: I 81 LYS cc_start: 0.9289 (mttm) cc_final: 0.8788 (mmmt) REVERT: J 47 PRO cc_start: 0.8614 (Cg_endo) cc_final: 0.8410 (Cg_exo) REVERT: J 48 ASP cc_start: 0.9105 (m-30) cc_final: 0.8792 (t0) REVERT: J 52 LYS cc_start: 0.8185 (tttt) cc_final: 0.7825 (tptt) REVERT: K 157 ASP cc_start: 0.8156 (t0) cc_final: 0.7845 (t0) REVERT: K 158 VAL cc_start: 0.8155 (t) cc_final: 0.7869 (t) REVERT: L 121 GLN cc_start: 0.8510 (mm-40) cc_final: 0.8087 (mm-40) REVERT: A 307 ASP cc_start: 0.8250 (t0) cc_final: 0.8022 (t0) REVERT: A 481 ASP cc_start: 0.7721 (m-30) cc_final: 0.7329 (m-30) REVERT: A 565 MET cc_start: 0.6959 (OUTLIER) cc_final: 0.6546 (ppp) REVERT: A 647 TRP cc_start: 0.6550 (t60) cc_final: 0.6115 (t60) REVERT: A 769 MET cc_start: 0.8145 (tpp) cc_final: 0.7515 (ptt) REVERT: A 817 TYR cc_start: 0.7286 (t80) cc_final: 0.7024 (t80) outliers start: 129 outliers final: 85 residues processed: 486 average time/residue: 0.2798 time to fit residues: 221.4972 Evaluate side-chains 468 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 375 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 223 LEU Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 66 ASP Chi-restraints excluded: chain E residue 5 CYS Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 51 PHE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 106 PHE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 126 PHE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain K residue 17 CYS Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain L residue 17 CYS Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 75 CYS Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain O residue 47 ASP Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 71 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 227 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 233 optimal weight: 6.9990 chunk 189 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 139 optimal weight: 0.6980 chunk 245 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 GLN G 53 ASN ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN K 90 GLN ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 151 ASN ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22558 Z= 0.256 Angle : 0.665 8.699 30638 Z= 0.336 Chirality : 0.041 0.179 3650 Planarity : 0.004 0.046 3802 Dihedral : 4.644 19.454 3115 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 6.15 % Allowed : 19.38 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.15), residues: 2884 helix: -0.02 (0.11), residues: 2067 sheet: 0.95 (0.84), residues: 37 loop : -1.89 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 751 HIS 0.009 0.001 HIS A 796 PHE 0.034 0.002 PHE L 126 TYR 0.016 0.001 TYR C 140 ARG 0.004 0.000 ARG K 153 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 391 time to evaluate : 2.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 54 GLU cc_start: 0.7777 (tt0) cc_final: 0.7259 (tp30) REVERT: D 59 SER cc_start: 0.8808 (t) cc_final: 0.8601 (p) REVERT: D 114 TYR cc_start: 0.8119 (t80) cc_final: 0.7918 (t80) REVERT: D 127 TYR cc_start: 0.6786 (t80) cc_final: 0.6453 (t80) REVERT: D 145 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7661 (tm-30) REVERT: C 129 THR cc_start: 0.7886 (OUTLIER) cc_final: 0.7263 (p) REVERT: C 188 GLU cc_start: 0.8556 (tt0) cc_final: 0.8333 (tt0) REVERT: N 259 ASN cc_start: 0.6864 (t0) cc_final: 0.5817 (m110) REVERT: M 43 MET cc_start: 0.7380 (mmt) cc_final: 0.6804 (mmt) REVERT: M 66 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7248 (m-30) REVERT: E 85 TYR cc_start: 0.8190 (t80) cc_final: 0.7739 (t80) REVERT: B 149 TYR cc_start: 0.8057 (t80) cc_final: 0.7520 (t80) REVERT: B 178 GLU cc_start: 0.8200 (tp30) cc_final: 0.7915 (tt0) REVERT: B 236 ASP cc_start: 0.7981 (m-30) cc_final: 0.7483 (t0) REVERT: B 279 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6321 (mm) REVERT: B 280 GLU cc_start: 0.8614 (mp0) cc_final: 0.7252 (tm-30) REVERT: F 48 ASP cc_start: 0.8696 (m-30) cc_final: 0.8127 (p0) REVERT: F 53 ASN cc_start: 0.8880 (m-40) cc_final: 0.8379 (t0) REVERT: F 124 ARG cc_start: 0.8527 (mtp85) cc_final: 0.8056 (ttp-170) REVERT: G 45 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7646 (mt) REVERT: G 157 ASP cc_start: 0.6092 (m-30) cc_final: 0.5560 (m-30) REVERT: H 149 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7941 (tt) REVERT: I 3 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7772 (pm20) REVERT: I 50 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7423 (tp) REVERT: I 80 GLN cc_start: 0.9097 (pm20) cc_final: 0.8720 (tt0) REVERT: I 81 LYS cc_start: 0.9304 (mttm) cc_final: 0.8842 (mmmt) REVERT: J 47 PRO cc_start: 0.8600 (Cg_endo) cc_final: 0.8376 (Cg_exo) REVERT: J 48 ASP cc_start: 0.9166 (m-30) cc_final: 0.8814 (t0) REVERT: J 52 LYS cc_start: 0.8246 (tttt) cc_final: 0.7842 (tptt) REVERT: K 157 ASP cc_start: 0.8229 (t0) cc_final: 0.7938 (t0) REVERT: K 158 VAL cc_start: 0.8334 (t) cc_final: 0.8046 (t) REVERT: L 121 GLN cc_start: 0.8493 (mm-40) cc_final: 0.8079 (mm-40) REVERT: A 307 ASP cc_start: 0.8321 (t0) cc_final: 0.8117 (t0) REVERT: A 481 ASP cc_start: 0.7756 (m-30) cc_final: 0.7374 (m-30) REVERT: A 721 GLU cc_start: 0.8455 (tm-30) cc_final: 0.7793 (tt0) REVERT: A 769 MET cc_start: 0.8078 (tpp) cc_final: 0.7368 (ptt) REVERT: A 817 TYR cc_start: 0.7407 (t80) cc_final: 0.7140 (t80) REVERT: O 5 VAL cc_start: 0.2550 (OUTLIER) cc_final: 0.1907 (m) outliers start: 144 outliers final: 103 residues processed: 489 average time/residue: 0.2951 time to fit residues: 235.5244 Evaluate side-chains 482 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 372 time to evaluate : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 223 LEU Chi-restraints excluded: chain N residue 224 LEU Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 66 ASP Chi-restraints excluded: chain E residue 5 CYS Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 51 PHE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain F residue 17 CYS Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 106 PHE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 126 PHE Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 148 LEU Chi-restraints excluded: chain I residue 151 ASN Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 17 CYS Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 75 CYS Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 47 ASP Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 61 VAL Chi-restraints excluded: chain O residue 71 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 92 optimal weight: 1.9990 chunk 246 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 chunk 160 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 273 optimal weight: 1.9990 chunk 227 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 GLN F 90 GLN ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 GLN I 151 ASN J 90 GLN K 122 GLN ** K 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 22558 Z= 0.173 Angle : 0.625 8.870 30638 Z= 0.310 Chirality : 0.039 0.204 3650 Planarity : 0.004 0.045 3802 Dihedral : 4.450 19.700 3115 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.27 % Allowed : 22.15 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.15), residues: 2884 helix: 0.23 (0.11), residues: 2072 sheet: 1.08 (0.84), residues: 37 loop : -1.84 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 77 HIS 0.007 0.001 HIS A 796 PHE 0.023 0.001 PHE C 181 TYR 0.017 0.001 TYR N 251 ARG 0.005 0.000 ARG M 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 419 time to evaluate : 2.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 59 SER cc_start: 0.8555 (t) cc_final: 0.8343 (p) REVERT: D 121 ASP cc_start: 0.8700 (t0) cc_final: 0.8263 (t0) REVERT: D 125 ARG cc_start: 0.7645 (tpp80) cc_final: 0.7140 (tpp80) REVERT: D 145 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7746 (tm-30) REVERT: C 129 THR cc_start: 0.7894 (OUTLIER) cc_final: 0.7374 (p) REVERT: C 131 GLU cc_start: 0.8470 (pt0) cc_final: 0.8087 (pt0) REVERT: N 259 ASN cc_start: 0.7089 (t0) cc_final: 0.6028 (m110) REVERT: M 43 MET cc_start: 0.7349 (mmt) cc_final: 0.6895 (mmt) REVERT: M 66 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7177 (m-30) REVERT: E 85 TYR cc_start: 0.8204 (t80) cc_final: 0.7858 (t80) REVERT: E 122 GLN cc_start: 0.8229 (mm-40) cc_final: 0.7883 (mm-40) REVERT: B 149 TYR cc_start: 0.7999 (t80) cc_final: 0.7524 (t80) REVERT: B 178 GLU cc_start: 0.8148 (tp30) cc_final: 0.7845 (tt0) REVERT: B 229 GLN cc_start: 0.8332 (tm-30) cc_final: 0.7382 (mt0) REVERT: B 236 ASP cc_start: 0.7987 (m-30) cc_final: 0.7492 (t0) REVERT: B 279 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.5825 (mp) REVERT: B 280 GLU cc_start: 0.8633 (mp0) cc_final: 0.7309 (tm-30) REVERT: F 48 ASP cc_start: 0.8737 (m-30) cc_final: 0.8215 (p0) REVERT: F 124 ARG cc_start: 0.8462 (mtp85) cc_final: 0.7962 (ttp-170) REVERT: G 45 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7569 (mt) REVERT: G 157 ASP cc_start: 0.6416 (m-30) cc_final: 0.5963 (m-30) REVERT: H 149 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7961 (tt) REVERT: I 3 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7797 (pm20) REVERT: I 50 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7226 (tp) REVERT: I 80 GLN cc_start: 0.9081 (pm20) cc_final: 0.8751 (tt0) REVERT: I 81 LYS cc_start: 0.9303 (mttm) cc_final: 0.8848 (mmmt) REVERT: J 47 PRO cc_start: 0.8553 (Cg_endo) cc_final: 0.8323 (Cg_exo) REVERT: J 48 ASP cc_start: 0.9169 (m-30) cc_final: 0.8814 (t0) REVERT: J 52 LYS cc_start: 0.8235 (tttt) cc_final: 0.7821 (tptt) REVERT: K 157 ASP cc_start: 0.8221 (t0) cc_final: 0.7922 (t0) REVERT: K 158 VAL cc_start: 0.8284 (t) cc_final: 0.7965 (t) REVERT: L 121 GLN cc_start: 0.8506 (mm-40) cc_final: 0.8107 (mm-40) REVERT: A 307 ASP cc_start: 0.8200 (t0) cc_final: 0.7984 (t0) REVERT: A 472 SER cc_start: 0.8721 (t) cc_final: 0.8473 (p) REVERT: A 481 ASP cc_start: 0.7679 (m-30) cc_final: 0.7272 (m-30) REVERT: A 490 PHE cc_start: 0.7043 (m-80) cc_final: 0.6572 (m-10) REVERT: A 552 TYR cc_start: 0.7764 (t80) cc_final: 0.7279 (t80) REVERT: A 721 GLU cc_start: 0.8407 (tm-30) cc_final: 0.7789 (tt0) REVERT: O 5 VAL cc_start: 0.2934 (OUTLIER) cc_final: 0.2252 (m) outliers start: 100 outliers final: 68 residues processed: 482 average time/residue: 0.2887 time to fit residues: 229.0240 Evaluate side-chains 466 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 391 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain M residue 66 ASP Chi-restraints excluded: chain E residue 51 PHE Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 106 PHE Chi-restraints excluded: chain G residue 126 PHE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 148 LEU Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 17 CYS Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 75 CYS Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 47 ASP Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 71 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 263 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 156 optimal weight: 9.9990 chunk 199 optimal weight: 7.9990 chunk 154 optimal weight: 0.7980 chunk 230 optimal weight: 7.9990 chunk 152 optimal weight: 10.0000 chunk 272 optimal weight: 0.7980 chunk 170 optimal weight: 3.9990 chunk 166 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN J 80 GLN K 90 GLN ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 22558 Z= 0.299 Angle : 0.705 11.190 30638 Z= 0.355 Chirality : 0.042 0.193 3650 Planarity : 0.004 0.042 3802 Dihedral : 4.632 18.871 3115 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 5.85 % Allowed : 21.81 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.15), residues: 2884 helix: 0.06 (0.11), residues: 2085 sheet: 0.81 (0.79), residues: 43 loop : -1.90 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 22 HIS 0.010 0.001 HIS A 796 PHE 0.032 0.002 PHE E 88 TYR 0.023 0.002 TYR D 114 ARG 0.004 0.000 ARG I 117 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 389 time to evaluate : 2.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 59 SER cc_start: 0.8766 (t) cc_final: 0.8562 (p) REVERT: D 121 ASP cc_start: 0.8744 (t0) cc_final: 0.8390 (t0) REVERT: D 125 ARG cc_start: 0.7491 (tpp80) cc_final: 0.7278 (tpp80) REVERT: D 145 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7686 (tm-30) REVERT: C 129 THR cc_start: 0.7755 (OUTLIER) cc_final: 0.7211 (p) REVERT: C 188 GLU cc_start: 0.8548 (tt0) cc_final: 0.8323 (tt0) REVERT: N 259 ASN cc_start: 0.7360 (t0) cc_final: 0.6709 (m-40) REVERT: M 43 MET cc_start: 0.7415 (mmt) cc_final: 0.6963 (mmt) REVERT: M 66 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7377 (m-30) REVERT: E 85 TYR cc_start: 0.8249 (t80) cc_final: 0.7779 (t80) REVERT: B 149 TYR cc_start: 0.7982 (t80) cc_final: 0.7508 (t80) REVERT: B 178 GLU cc_start: 0.8254 (tp30) cc_final: 0.7956 (tt0) REVERT: B 229 GLN cc_start: 0.8392 (tm-30) cc_final: 0.7339 (mp10) REVERT: B 236 ASP cc_start: 0.7977 (m-30) cc_final: 0.7489 (t0) REVERT: B 276 ARG cc_start: 0.8078 (mmt90) cc_final: 0.7834 (mmm160) REVERT: B 279 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6883 (mt) REVERT: F 53 ASN cc_start: 0.8717 (t0) cc_final: 0.8246 (t0) REVERT: F 124 ARG cc_start: 0.8617 (mtp85) cc_final: 0.8156 (ttp-170) REVERT: G 45 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7659 (mt) REVERT: G 157 ASP cc_start: 0.6315 (m-30) cc_final: 0.5806 (m-30) REVERT: H 149 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7958 (tt) REVERT: I 3 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7850 (pm20) REVERT: I 50 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7148 (tp) REVERT: I 81 LYS cc_start: 0.9357 (mttm) cc_final: 0.8933 (mmmt) REVERT: J 47 PRO cc_start: 0.8581 (Cg_endo) cc_final: 0.8332 (Cg_exo) REVERT: J 48 ASP cc_start: 0.9182 (m-30) cc_final: 0.8831 (t0) REVERT: J 52 LYS cc_start: 0.8279 (tttt) cc_final: 0.7838 (tptt) REVERT: J 106 PHE cc_start: 0.8046 (m-10) cc_final: 0.7434 (t80) REVERT: K 157 ASP cc_start: 0.8213 (t0) cc_final: 0.7907 (t0) REVERT: K 158 VAL cc_start: 0.8265 (t) cc_final: 0.7965 (t) REVERT: L 121 GLN cc_start: 0.8382 (mm-40) cc_final: 0.7861 (mm-40) REVERT: A 203 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8285 (tt) REVERT: A 211 LEU cc_start: 0.7147 (pp) cc_final: 0.6921 (pt) REVERT: A 385 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.7011 (ttpt) REVERT: A 481 ASP cc_start: 0.7772 (m-30) cc_final: 0.7394 (m-30) REVERT: A 487 MET cc_start: 0.8486 (mmm) cc_final: 0.8255 (mmm) REVERT: A 627 TYR cc_start: 0.5940 (t80) cc_final: 0.5740 (t80) REVERT: O 5 VAL cc_start: 0.2708 (OUTLIER) cc_final: 0.1976 (m) outliers start: 137 outliers final: 103 residues processed: 476 average time/residue: 0.2906 time to fit residues: 224.9809 Evaluate side-chains 485 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 373 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 223 LEU Chi-restraints excluded: chain N residue 224 LEU Chi-restraints excluded: chain N residue 236 ILE Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 66 ASP Chi-restraints excluded: chain E residue 5 CYS Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 51 PHE Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 106 PHE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 126 PHE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 132 ILE Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 148 LEU Chi-restraints excluded: chain I residue 151 ASN Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 17 CYS Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 75 CYS Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 47 ASP Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 61 VAL Chi-restraints excluded: chain O residue 71 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 168 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 173 optimal weight: 0.9990 chunk 185 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 214 optimal weight: 0.0370 overall best weight: 0.9264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN A 745 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22558 Z= 0.171 Angle : 0.652 10.543 30638 Z= 0.318 Chirality : 0.040 0.223 3650 Planarity : 0.004 0.044 3802 Dihedral : 4.431 19.109 3115 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.84 % Allowed : 24.33 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.16), residues: 2884 helix: 0.33 (0.12), residues: 2087 sheet: 1.09 (0.83), residues: 37 loop : -1.87 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 77 HIS 0.007 0.001 HIS A 796 PHE 0.021 0.001 PHE L 126 TYR 0.018 0.001 TYR F 30 ARG 0.004 0.000 ARG M 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 422 time to evaluate : 2.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 59 SER cc_start: 0.8497 (t) cc_final: 0.8281 (p) REVERT: D 132 ARG cc_start: 0.7846 (ttp80) cc_final: 0.7297 (tpp-160) REVERT: D 145 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7745 (tm-30) REVERT: C 129 THR cc_start: 0.7887 (OUTLIER) cc_final: 0.7342 (p) REVERT: C 131 GLU cc_start: 0.8509 (pt0) cc_final: 0.8166 (pt0) REVERT: N 212 ASP cc_start: 0.6875 (OUTLIER) cc_final: 0.6671 (p0) REVERT: N 259 ASN cc_start: 0.7287 (t0) cc_final: 0.6674 (m-40) REVERT: M 43 MET cc_start: 0.7394 (mmt) cc_final: 0.6907 (mmt) REVERT: E 85 TYR cc_start: 0.8250 (t80) cc_final: 0.7790 (t80) REVERT: B 149 TYR cc_start: 0.7929 (t80) cc_final: 0.7362 (t80) REVERT: B 178 GLU cc_start: 0.8169 (tp30) cc_final: 0.7854 (mt-10) REVERT: B 229 GLN cc_start: 0.8350 (tm-30) cc_final: 0.7359 (mt0) REVERT: B 236 ASP cc_start: 0.7904 (m-30) cc_final: 0.7421 (t0) REVERT: B 279 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6404 (mm) REVERT: B 280 GLU cc_start: 0.8775 (mp0) cc_final: 0.7238 (tm-30) REVERT: F 53 ASN cc_start: 0.8440 (t0) cc_final: 0.7991 (t0) REVERT: F 124 ARG cc_start: 0.8593 (mtp85) cc_final: 0.8026 (ttp-170) REVERT: G 45 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7618 (mt) REVERT: G 156 GLN cc_start: 0.6908 (pp30) cc_final: 0.6652 (pp30) REVERT: H 149 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7944 (tt) REVERT: I 3 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7779 (pm20) REVERT: I 50 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7062 (tp) REVERT: I 81 LYS cc_start: 0.9309 (mttm) cc_final: 0.8860 (mmmt) REVERT: J 47 PRO cc_start: 0.8539 (Cg_endo) cc_final: 0.8283 (Cg_exo) REVERT: J 48 ASP cc_start: 0.9136 (m-30) cc_final: 0.8854 (t0) REVERT: J 52 LYS cc_start: 0.8251 (tttt) cc_final: 0.7809 (tptt) REVERT: J 106 PHE cc_start: 0.7945 (m-10) cc_final: 0.7361 (t80) REVERT: K 157 ASP cc_start: 0.8243 (t0) cc_final: 0.7915 (t0) REVERT: K 158 VAL cc_start: 0.8284 (t) cc_final: 0.7968 (t) REVERT: L 121 GLN cc_start: 0.8371 (mm-40) cc_final: 0.8014 (mm-40) REVERT: A 257 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.8015 (m-30) REVERT: A 472 SER cc_start: 0.8683 (t) cc_final: 0.8426 (p) REVERT: A 481 ASP cc_start: 0.7662 (m-30) cc_final: 0.7276 (m-30) REVERT: A 490 PHE cc_start: 0.6976 (m-80) cc_final: 0.6639 (m-10) REVERT: A 552 TYR cc_start: 0.7766 (t80) cc_final: 0.7338 (t80) REVERT: A 721 GLU cc_start: 0.8436 (tm-30) cc_final: 0.7886 (tt0) REVERT: O 5 VAL cc_start: 0.2428 (OUTLIER) cc_final: 0.1926 (m) outliers start: 90 outliers final: 69 residues processed: 477 average time/residue: 0.2932 time to fit residues: 226.8389 Evaluate side-chains 470 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 393 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain N residue 212 ASP Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 223 LEU Chi-restraints excluded: chain N residue 224 LEU Chi-restraints excluded: chain N residue 238 ILE Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain E residue 51 PHE Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 126 PHE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 148 LEU Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 17 CYS Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 75 CYS Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 47 ASP Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 61 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 248 optimal weight: 0.8980 chunk 261 optimal weight: 6.9990 chunk 238 optimal weight: 4.9990 chunk 254 optimal weight: 1.9990 chunk 152 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 199 optimal weight: 0.0040 chunk 78 optimal weight: 9.9990 chunk 229 optimal weight: 3.9990 chunk 240 optimal weight: 0.8980 chunk 253 optimal weight: 0.8980 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN ** K 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22558 Z= 0.169 Angle : 0.655 10.408 30638 Z= 0.315 Chirality : 0.039 0.226 3650 Planarity : 0.004 0.046 3802 Dihedral : 4.293 17.185 3115 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.59 % Allowed : 24.71 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 2884 helix: 0.48 (0.12), residues: 2043 sheet: 1.10 (0.83), residues: 37 loop : -1.75 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 77 HIS 0.008 0.001 HIS A 796 PHE 0.021 0.001 PHE H 106 TYR 0.021 0.001 TYR D 127 ARG 0.005 0.000 ARG I 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 430 time to evaluate : 2.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 43 ILE cc_start: 0.8413 (mt) cc_final: 0.8212 (tt) REVERT: D 59 SER cc_start: 0.8682 (t) cc_final: 0.8392 (p) REVERT: D 145 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7774 (tm-30) REVERT: C 129 THR cc_start: 0.7838 (OUTLIER) cc_final: 0.7327 (p) REVERT: C 185 LEU cc_start: 0.7362 (mt) cc_final: 0.6790 (pp) REVERT: N 259 ASN cc_start: 0.7301 (t0) cc_final: 0.6748 (m-40) REVERT: E 85 TYR cc_start: 0.8218 (t80) cc_final: 0.7829 (t80) REVERT: B 149 TYR cc_start: 0.7906 (t80) cc_final: 0.7427 (t80) REVERT: B 178 GLU cc_start: 0.8154 (tp30) cc_final: 0.7812 (mt-10) REVERT: B 229 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7003 (mt0) REVERT: B 236 ASP cc_start: 0.7907 (m-30) cc_final: 0.7425 (t0) REVERT: B 279 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6064 (mp) REVERT: B 280 GLU cc_start: 0.8814 (mp0) cc_final: 0.7244 (tm-30) REVERT: F 53 ASN cc_start: 0.8318 (t0) cc_final: 0.7830 (t0) REVERT: F 124 ARG cc_start: 0.8601 (mtp85) cc_final: 0.8223 (ttp-170) REVERT: G 45 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7656 (mt) REVERT: G 142 TYR cc_start: 0.7624 (m-80) cc_final: 0.7380 (m-80) REVERT: G 156 GLN cc_start: 0.6944 (pp30) cc_final: 0.6681 (pp30) REVERT: G 158 VAL cc_start: 0.7926 (t) cc_final: 0.7681 (m) REVERT: I 3 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7813 (pm20) REVERT: I 50 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7158 (tp) REVERT: I 81 LYS cc_start: 0.9289 (mttm) cc_final: 0.8846 (mmmt) REVERT: I 88 PHE cc_start: 0.8831 (m-80) cc_final: 0.8387 (m-80) REVERT: J 48 ASP cc_start: 0.9157 (m-30) cc_final: 0.8850 (t0) REVERT: J 52 LYS cc_start: 0.8241 (tttt) cc_final: 0.7823 (tptt) REVERT: J 106 PHE cc_start: 0.7778 (m-10) cc_final: 0.7220 (t80) REVERT: K 142 TYR cc_start: 0.8099 (m-10) cc_final: 0.7886 (m-10) REVERT: K 157 ASP cc_start: 0.8248 (t0) cc_final: 0.7842 (t0) REVERT: K 158 VAL cc_start: 0.8207 (t) cc_final: 0.7923 (t) REVERT: L 121 GLN cc_start: 0.8383 (mm-40) cc_final: 0.8154 (mm110) REVERT: A 108 ASP cc_start: 0.8326 (t0) cc_final: 0.8121 (t0) REVERT: A 385 LYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6768 (ttpt) REVERT: A 472 SER cc_start: 0.8715 (t) cc_final: 0.8474 (p) REVERT: A 490 PHE cc_start: 0.6978 (m-80) cc_final: 0.6647 (m-10) REVERT: A 721 GLU cc_start: 0.8428 (tm-30) cc_final: 0.7906 (tt0) REVERT: O 5 VAL cc_start: 0.1044 (OUTLIER) cc_final: 0.0694 (m) outliers start: 84 outliers final: 64 residues processed: 480 average time/residue: 0.2972 time to fit residues: 232.6000 Evaluate side-chains 473 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 403 time to evaluate : 2.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain N residue 213 ASP Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 223 LEU Chi-restraints excluded: chain N residue 224 LEU Chi-restraints excluded: chain N residue 238 ILE Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain E residue 51 PHE Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 126 PHE Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 17 CYS Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 75 CYS Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 47 ASP Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 61 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 166 optimal weight: 9.9990 chunk 268 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 186 optimal weight: 6.9990 chunk 281 optimal weight: 0.7980 chunk 259 optimal weight: 5.9990 chunk 224 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 173 optimal weight: 0.9990 chunk 137 optimal weight: 7.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 22558 Z= 0.233 Angle : 0.697 10.650 30638 Z= 0.338 Chirality : 0.041 0.302 3650 Planarity : 0.004 0.046 3802 Dihedral : 4.393 18.545 3115 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.41 % Allowed : 25.27 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.16), residues: 2884 helix: 0.41 (0.12), residues: 2047 sheet: 1.13 (0.83), residues: 37 loop : -1.70 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 147 HIS 0.008 0.001 HIS A 796 PHE 0.022 0.001 PHE G 88 TYR 0.024 0.001 TYR D 72 ARG 0.005 0.000 ARG J 117 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 384 time to evaluate : 2.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 59 SER cc_start: 0.8498 (t) cc_final: 0.8273 (p) REVERT: D 145 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7769 (tm-30) REVERT: C 129 THR cc_start: 0.7757 (OUTLIER) cc_final: 0.7288 (p) REVERT: C 183 LYS cc_start: 0.7841 (mmmt) cc_final: 0.7632 (tptt) REVERT: C 185 LEU cc_start: 0.7445 (mt) cc_final: 0.6911 (pp) REVERT: C 188 GLU cc_start: 0.8523 (tt0) cc_final: 0.8254 (tt0) REVERT: N 259 ASN cc_start: 0.7497 (t0) cc_final: 0.6597 (t0) REVERT: E 85 TYR cc_start: 0.8241 (t80) cc_final: 0.7801 (t80) REVERT: B 85 ASP cc_start: 0.8078 (t70) cc_final: 0.7833 (t0) REVERT: B 149 TYR cc_start: 0.7908 (t80) cc_final: 0.7464 (t80) REVERT: B 178 GLU cc_start: 0.8213 (tp30) cc_final: 0.7888 (mt-10) REVERT: B 229 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7080 (mt0) REVERT: B 236 ASP cc_start: 0.7913 (m-30) cc_final: 0.7427 (t0) REVERT: B 280 GLU cc_start: 0.8800 (mp0) cc_final: 0.7530 (tm-30) REVERT: F 53 ASN cc_start: 0.8534 (t0) cc_final: 0.8038 (t0) REVERT: F 124 ARG cc_start: 0.8573 (mtp85) cc_final: 0.8204 (ttp-170) REVERT: G 45 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7548 (mt) REVERT: G 156 GLN cc_start: 0.7017 (pp30) cc_final: 0.6765 (pp30) REVERT: I 3 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7861 (pm20) REVERT: I 50 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7190 (tp) REVERT: I 81 LYS cc_start: 0.9306 (mttm) cc_final: 0.8886 (mmmt) REVERT: J 48 ASP cc_start: 0.9180 (m-30) cc_final: 0.8944 (t0) REVERT: J 52 LYS cc_start: 0.8273 (tttt) cc_final: 0.7833 (tptt) REVERT: J 106 PHE cc_start: 0.7827 (m-10) cc_final: 0.7282 (t80) REVERT: K 137 GLU cc_start: 0.7017 (tm-30) cc_final: 0.6640 (tm-30) REVERT: K 157 ASP cc_start: 0.8296 (t0) cc_final: 0.7935 (t0) REVERT: K 158 VAL cc_start: 0.8224 (t) cc_final: 0.7857 (t) REVERT: L 121 GLN cc_start: 0.8354 (mm-40) cc_final: 0.8108 (mm110) REVERT: A 345 GLU cc_start: 0.8863 (pt0) cc_final: 0.8501 (mm-30) REVERT: A 385 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6955 (ttpt) REVERT: A 490 PHE cc_start: 0.7185 (m-80) cc_final: 0.6711 (m-10) REVERT: A 721 GLU cc_start: 0.8450 (tm-30) cc_final: 0.7906 (tt0) REVERT: A 776 MET cc_start: 0.7116 (tpp) cc_final: 0.6911 (tpp) REVERT: O 5 VAL cc_start: 0.1556 (OUTLIER) cc_final: 0.1091 (m) outliers start: 80 outliers final: 71 residues processed: 434 average time/residue: 0.2842 time to fit residues: 201.8000 Evaluate side-chains 457 residues out of total 2357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 381 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain N residue 213 ASP Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 223 LEU Chi-restraints excluded: chain N residue 224 LEU Chi-restraints excluded: chain N residue 238 ILE Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 51 PHE Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 126 PHE Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 17 CYS Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 75 CYS Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 47 ASP Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 61 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 178 optimal weight: 3.9990 chunk 239 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 224 optimal weight: 0.2980 chunk 94 optimal weight: 9.9990 chunk 230 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.143275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.125833 restraints weight = 38216.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.129419 restraints weight = 16385.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.131709 restraints weight = 8837.206| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 22558 Z= 0.202 Angle : 0.687 11.142 30638 Z= 0.331 Chirality : 0.040 0.289 3650 Planarity : 0.004 0.047 3802 Dihedral : 4.385 21.290 3115 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.29 % Allowed : 25.48 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.16), residues: 2884 helix: 0.43 (0.12), residues: 2047 sheet: 1.22 (0.84), residues: 37 loop : -1.72 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 312 HIS 0.004 0.001 HIS A 559 PHE 0.049 0.001 PHE A 572 TYR 0.028 0.001 TYR D 72 ARG 0.005 0.000 ARG J 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4671.96 seconds wall clock time: 85 minutes 41.38 seconds (5141.38 seconds total)