Starting phenix.real_space_refine on Wed Aug 7 00:58:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d06_30525/08_2024/7d06_30525.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d06_30525/08_2024/7d06_30525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d06_30525/08_2024/7d06_30525.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d06_30525/08_2024/7d06_30525.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d06_30525/08_2024/7d06_30525.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d06_30525/08_2024/7d06_30525.cif" } resolution = 3.1 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 88 5.16 5 C 11778 2.51 5 N 2978 2.21 5 O 3472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 13": "OE1" <-> "OE2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A GLU 95": "OE1" <-> "OE2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "B GLU 15": "OE1" <-> "OE2" Residue "B GLU 25": "OE1" <-> "OE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B GLU 135": "OE1" <-> "OE2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "C GLU 18": "OE1" <-> "OE2" Residue "C GLU 21": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 90": "OE1" <-> "OE2" Residue "D GLU 13": "OE1" <-> "OE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D GLU 95": "OE1" <-> "OE2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "D GLU 130": "OE1" <-> "OE2" Residue "E GLU 15": "OE1" <-> "OE2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "E GLU 135": "OE1" <-> "OE2" Residue "E GLU 236": "OE1" <-> "OE2" Residue "E GLU 270": "OE1" <-> "OE2" Residue "E ARG 272": "NH1" <-> "NH2" Residue "F GLU 18": "OE1" <-> "OE2" Residue "F GLU 21": "OE1" <-> "OE2" Residue "F GLU 47": "OE1" <-> "OE2" Residue "F PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 90": "OE1" <-> "OE2" Residue "G ARG 4": "NH1" <-> "NH2" Residue "G PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 100": "OE1" <-> "OE2" Residue "G GLU 186": "OE1" <-> "OE2" Residue "H ARG 4": "NH1" <-> "NH2" Residue "H GLU 7": "OE1" <-> "OE2" Residue "H PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 100": "OE1" <-> "OE2" Residue "H GLU 156": "OE1" <-> "OE2" Residue "I ARG 78": "NH1" <-> "NH2" Residue "I PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 4": "NH1" <-> "NH2" Residue "J GLU 142": "OE1" <-> "OE2" Residue "J GLU 156": "OE1" <-> "OE2" Residue "J GLU 186": "OE1" <-> "OE2" Residue "K ARG 4": "NH1" <-> "NH2" Residue "K GLU 96": "OE1" <-> "OE2" Residue "L GLU 96": "OE1" <-> "OE2" Residue "L GLU 100": "OE1" <-> "OE2" Residue "L GLU 142": "OE1" <-> "OE2" Residue "L GLU 186": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 18328 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1902 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "B" Number of atoms: 2032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2032 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 11, 'TRANS': 251} Chain: "C" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 763 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "D" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1902 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "E" Number of atoms: 2032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2032 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 11, 'TRANS': 251} Chain: "F" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 763 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "G" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1391 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "H" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1391 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "I" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1391 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "J" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1391 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "K" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1391 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "L" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1391 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "A" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 294 Unusual residues: {'PGV': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 243 Unusual residues: {'PGV': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.04, per 1000 atoms: 0.55 Number of scatterers: 18328 At special positions: 0 Unit cell: (134.788, 121.744, 153.267, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 P 12 15.00 O 3472 8.00 N 2978 7.00 C 11778 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: 6.63 Conformation dependent library (CDL) restraints added in 3.4 seconds 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4328 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 20 sheets defined 47.8% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 2 through 30 removed outlier: 3.514A pdb=" N PHE A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 49 removed outlier: 3.712A pdb=" N ARG A 40 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 76 removed outlier: 3.571A pdb=" N TYR A 72 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 83 through 95 removed outlier: 3.628A pdb=" N ARG A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 106 removed outlier: 3.589A pdb=" N VAL A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 102 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 123 removed outlier: 3.657A pdb=" N GLY A 118 " --> pdb=" O THR A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 140 through 172 removed outlier: 3.949A pdb=" N ARG A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Proline residue: A 153 - end of helix removed outlier: 3.806A pdb=" N VAL A 157 " --> pdb=" O PRO A 153 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 190 removed outlier: 3.530A pdb=" N ASN A 189 " --> pdb=" O GLY A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 196 Processing helix chain 'A' and resid 196 through 220 removed outlier: 3.534A pdb=" N LYS A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 214 " --> pdb=" O CYS A 210 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 255 removed outlier: 3.886A pdb=" N ALA A 229 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 231 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 236 " --> pdb=" O MET A 232 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 60 removed outlier: 3.624A pdb=" N ARG B 57 " --> pdb=" O THR B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.747A pdb=" N ALA B 87 " --> pdb=" O GLN B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 112 removed outlier: 3.535A pdb=" N VAL B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 118 Processing helix chain 'B' and resid 122 through 138 removed outlier: 3.733A pdb=" N GLU B 128 " --> pdb=" O ASN B 124 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA B 131 " --> pdb=" O ALA B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 163 removed outlier: 3.623A pdb=" N LEU B 160 " --> pdb=" O ARG B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 removed outlier: 3.656A pdb=" N ARG B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU B 197 " --> pdb=" O ARG B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 235 through 240 removed outlier: 3.802A pdb=" N ALA B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 251 Processing helix chain 'C' and resid 21 through 34 removed outlier: 3.687A pdb=" N GLY C 27 " --> pdb=" O GLN C 23 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE C 31 " --> pdb=" O GLY C 27 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 63 removed outlier: 3.673A pdb=" N GLN C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 86 removed outlier: 3.872A pdb=" N ILE C 82 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN C 84 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 30 removed outlier: 3.513A pdb=" N PHE D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 49 removed outlier: 3.712A pdb=" N ARG D 40 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS D 46 " --> pdb=" O VAL D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 76 removed outlier: 3.571A pdb=" N TYR D 72 " --> pdb=" O GLY D 68 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 82 No H-bonds generated for 'chain 'D' and resid 80 through 82' Processing helix chain 'D' and resid 83 through 95 removed outlier: 3.629A pdb=" N ARG D 94 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 106 removed outlier: 3.589A pdb=" N VAL D 99 " --> pdb=" O GLU D 95 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA D 102 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 123 removed outlier: 3.658A pdb=" N GLY D 118 " --> pdb=" O THR D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 133 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 140 through 172 removed outlier: 3.948A pdb=" N ARG D 144 " --> pdb=" O ILE D 140 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP D 146 " --> pdb=" O SER D 142 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY D 148 " --> pdb=" O ARG D 144 " (cutoff:3.500A) Proline residue: D 153 - end of helix removed outlier: 3.806A pdb=" N VAL D 157 " --> pdb=" O PRO D 153 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE D 158 " --> pdb=" O MET D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 190 removed outlier: 3.531A pdb=" N ASN D 189 " --> pdb=" O GLY D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 196 Processing helix chain 'D' and resid 196 through 220 removed outlier: 3.534A pdb=" N LYS D 202 " --> pdb=" O ASN D 198 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA D 214 " --> pdb=" O CYS D 210 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 255 removed outlier: 3.886A pdb=" N ALA D 229 " --> pdb=" O PRO D 225 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR D 230 " --> pdb=" O GLU D 226 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA D 231 " --> pdb=" O GLY D 227 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL D 236 " --> pdb=" O MET D 232 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE D 248 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 60 removed outlier: 3.624A pdb=" N ARG E 57 " --> pdb=" O THR E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 89 removed outlier: 3.747A pdb=" N ALA E 87 " --> pdb=" O GLN E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 112 removed outlier: 3.852A pdb=" N GLU E 109 " --> pdb=" O MET E 105 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL E 111 " --> pdb=" O VAL E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 118 Processing helix chain 'E' and resid 122 through 138 removed outlier: 3.733A pdb=" N GLU E 128 " --> pdb=" O ASN E 124 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 163 removed outlier: 3.624A pdb=" N LEU E 160 " --> pdb=" O ARG E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 199 removed outlier: 3.656A pdb=" N ARG E 193 " --> pdb=" O THR E 189 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU E 197 " --> pdb=" O ARG E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 214 Processing helix chain 'E' and resid 235 through 240 removed outlier: 3.801A pdb=" N ALA E 239 " --> pdb=" O GLU E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 251 Processing helix chain 'F' and resid 21 through 34 removed outlier: 3.687A pdb=" N GLY F 27 " --> pdb=" O GLN F 23 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE F 31 " --> pdb=" O GLY F 27 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS F 33 " --> pdb=" O ALA F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 63 removed outlier: 3.673A pdb=" N GLN F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN F 63 " --> pdb=" O GLN F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 86 removed outlier: 3.871A pdb=" N ILE F 82 " --> pdb=" O LYS F 78 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN F 84 " --> pdb=" O LEU F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 27 removed outlier: 3.788A pdb=" N VAL G 10 " --> pdb=" O SER G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 110 removed outlier: 3.728A pdb=" N VAL G 101 " --> pdb=" O GLN G 97 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN G 104 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP G 107 " --> pdb=" O LYS G 103 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG G 110 " --> pdb=" O LEU G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 116 removed outlier: 4.260A pdb=" N THR G 116 " --> pdb=" O SER G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 134 removed outlier: 3.903A pdb=" N ILE G 131 " --> pdb=" O GLU G 127 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER G 132 " --> pdb=" O GLN G 128 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN G 133 " --> pdb=" O GLN G 129 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 191 removed outlier: 3.680A pdb=" N LYS G 191 " --> pdb=" O ASP G 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 30 removed outlier: 3.893A pdb=" N ILE H 15 " --> pdb=" O GLY H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 92 Processing helix chain 'H' and resid 94 through 110 removed outlier: 3.608A pdb=" N LYS H 103 " --> pdb=" O LYS H 99 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN H 104 " --> pdb=" O GLU H 100 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA H 105 " --> pdb=" O VAL H 101 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU H 106 " --> pdb=" O GLN H 102 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG H 110 " --> pdb=" O LEU H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 116 removed outlier: 4.027A pdb=" N THR H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 135 removed outlier: 3.899A pdb=" N ILE H 131 " --> pdb=" O GLU H 127 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER H 132 " --> pdb=" O GLN H 128 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN H 133 " --> pdb=" O GLN H 129 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASN H 135 " --> pdb=" O ILE H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 193 removed outlier: 3.504A pdb=" N LEU H 188 " --> pdb=" O ASP H 184 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE H 189 " --> pdb=" O LEU H 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 26 removed outlier: 3.569A pdb=" N ALA I 9 " --> pdb=" O THR I 5 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE I 15 " --> pdb=" O GLY I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 92 removed outlier: 3.542A pdb=" N THR I 91 " --> pdb=" O ASP I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 110 removed outlier: 3.650A pdb=" N LYS I 99 " --> pdb=" O ALA I 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 118 removed outlier: 4.176A pdb=" N THR I 116 " --> pdb=" O SER I 112 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN I 117 " --> pdb=" O SER I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 135 removed outlier: 3.789A pdb=" N ILE I 131 " --> pdb=" O GLU I 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER I 132 " --> pdb=" O GLN I 128 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN I 135 " --> pdb=" O ILE I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 193 Processing helix chain 'J' and resid 5 through 27 Processing helix chain 'J' and resid 94 through 110 removed outlier: 3.612A pdb=" N LYS J 99 " --> pdb=" O ALA J 95 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN J 104 " --> pdb=" O GLU J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 132 removed outlier: 4.124A pdb=" N LEU J 130 " --> pdb=" O MET J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 193 removed outlier: 3.592A pdb=" N SER J 190 " --> pdb=" O GLU J 186 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE J 192 " --> pdb=" O LEU J 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 30 removed outlier: 3.605A pdb=" N VAL K 10 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE K 15 " --> pdb=" O GLY K 11 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE K 22 " --> pdb=" O GLY K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 110 removed outlier: 3.754A pdb=" N ASN K 104 " --> pdb=" O GLU K 100 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP K 107 " --> pdb=" O LYS K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 116 removed outlier: 4.453A pdb=" N THR K 116 " --> pdb=" O SER K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 132 removed outlier: 3.601A pdb=" N GLN K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU K 130 " --> pdb=" O MET K 126 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE K 131 " --> pdb=" O GLU K 127 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER K 132 " --> pdb=" O GLN K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 193 removed outlier: 3.833A pdb=" N ILE K 189 " --> pdb=" O LEU K 185 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS K 191 " --> pdb=" O ASP K 187 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE K 193 " --> pdb=" O ILE K 189 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 28 removed outlier: 3.515A pdb=" N ILE L 15 " --> pdb=" O GLY L 11 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE L 22 " --> pdb=" O GLY L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 109 removed outlier: 3.604A pdb=" N GLU L 100 " --> pdb=" O GLU L 96 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS L 103 " --> pdb=" O LYS L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 134 removed outlier: 4.056A pdb=" N GLN L 129 " --> pdb=" O THR L 125 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU L 130 " --> pdb=" O MET L 126 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE L 131 " --> pdb=" O GLU L 127 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER L 132 " --> pdb=" O GLN L 128 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET L 134 " --> pdb=" O LEU L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 192 Processing sheet with id=AA1, first strand: chain 'B' and resid 35 through 37 removed outlier: 6.696A pdb=" N ILE B 36 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS B 17 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU B 69 " --> pdb=" O LYS B 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 21 through 22 Processing sheet with id=AA3, first strand: chain 'B' and resid 92 through 95 removed outlier: 3.547A pdb=" N ASP B 174 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER B 207 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA B 43 " --> pdb=" O TYR B 221 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N VAL B 223 " --> pdb=" O ALA B 43 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N MET B 45 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B 220 " --> pdb=" O GLU B 231 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU B 231 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL B 222 " --> pdb=" O GLN B 229 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 10 through 13 removed outlier: 7.144A pdb=" N VAL C 11 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN C 45 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY C 13 " --> pdb=" O GLN C 45 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 35 through 37 removed outlier: 6.696A pdb=" N ILE E 36 " --> pdb=" O LEU E 13 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS E 17 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU E 69 " --> pdb=" O LYS E 17 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 21 through 22 Processing sheet with id=AA7, first strand: chain 'E' and resid 92 through 95 removed outlier: 3.547A pdb=" N ASP E 174 " --> pdb=" O LEU E 95 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER E 207 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA E 43 " --> pdb=" O TYR E 221 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N VAL E 223 " --> pdb=" O ALA E 43 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N MET E 45 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE E 220 " --> pdb=" O GLU E 231 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU E 231 " --> pdb=" O ILE E 220 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL E 222 " --> pdb=" O GLN E 229 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 10 through 13 removed outlier: 7.143A pdb=" N VAL F 11 " --> pdb=" O LEU F 43 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN F 45 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY F 13 " --> pdb=" O GLN F 45 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 175 through 176 removed outlier: 7.172A pdb=" N LYS G 43 " --> pdb=" O ILE G 176 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER G 70 " --> pdb=" O THR G 83 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASP G 85 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N VAL G 68 " --> pdb=" O ASP G 85 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL G 58 " --> pdb=" O ILE G 65 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LYS G 57 " --> pdb=" O LEU G 159 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ILE G 161 " --> pdb=" O LYS G 57 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR G 59 " --> pdb=" O ILE G 161 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL G 148 " --> pdb=" O GLN G 180 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 137 through 141 removed outlier: 5.491A pdb=" N ILE G 140 " --> pdb=" O LEU G 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 175 through 176 removed outlier: 8.801A pdb=" N ILE H 176 " --> pdb=" O THR H 41 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LYS H 43 " --> pdb=" O ILE H 176 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR H 81 " --> pdb=" O ILE H 71 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE H 71 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR H 83 " --> pdb=" O ASP H 69 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL H 58 " --> pdb=" O ILE H 65 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LYS H 57 " --> pdb=" O LEU H 159 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ILE H 161 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR H 59 " --> pdb=" O ILE H 161 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE H 146 " --> pdb=" O GLN H 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 137 through 141 removed outlier: 5.519A pdb=" N ILE H 140 " --> pdb=" O LEU H 170 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 175 through 176 removed outlier: 7.208A pdb=" N LYS I 43 " --> pdb=" O ILE I 176 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASP I 85 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL I 68 " --> pdb=" O ASP I 85 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL I 58 " --> pdb=" O ILE I 65 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LYS I 57 " --> pdb=" O LEU I 159 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ILE I 161 " --> pdb=" O LYS I 57 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR I 59 " --> pdb=" O ILE I 161 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL I 148 " --> pdb=" O GLN I 180 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 137 through 141 removed outlier: 5.509A pdb=" N ILE I 140 " --> pdb=" O LEU I 170 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 42 through 46 removed outlier: 6.665A pdb=" N ASP J 85 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL J 68 " --> pdb=" O ASP J 85 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL J 58 " --> pdb=" O ILE J 65 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LYS J 57 " --> pdb=" O LEU J 159 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ILE J 161 " --> pdb=" O LYS J 57 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR J 59 " --> pdb=" O ILE J 161 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 137 through 141 removed outlier: 6.082A pdb=" N ILE J 140 " --> pdb=" O LEU J 170 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 41 through 46 removed outlier: 6.453A pdb=" N THR K 81 " --> pdb=" O ILE K 71 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ILE K 71 " --> pdb=" O THR K 81 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR K 83 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL K 58 " --> pdb=" O ILE K 65 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS K 57 " --> pdb=" O LEU K 159 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE K 161 " --> pdb=" O LYS K 57 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR K 59 " --> pdb=" O ILE K 161 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL K 148 " --> pdb=" O GLN K 180 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 137 through 141 removed outlier: 5.714A pdb=" N ILE K 140 " --> pdb=" O LEU K 170 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 175 through 176 removed outlier: 8.865A pdb=" N ILE L 176 " --> pdb=" O THR L 41 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LYS L 43 " --> pdb=" O ILE L 176 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASP L 85 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N VAL L 68 " --> pdb=" O ASP L 85 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL L 58 " --> pdb=" O ILE L 65 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LYS L 57 " --> pdb=" O LEU L 159 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ILE L 161 " --> pdb=" O LYS L 57 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR L 59 " --> pdb=" O ILE L 161 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL L 148 " --> pdb=" O GLN L 180 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 137 through 141 removed outlier: 5.379A pdb=" N ILE L 140 " --> pdb=" O LEU L 170 " (cutoff:3.500A) 792 hydrogen bonds defined for protein. 2295 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: 5.14 Time building geometry restraints manager: 7.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3035 1.30 - 1.43: 4276 1.43 - 1.56: 10999 1.56 - 1.68: 76 1.68 - 1.81: 168 Bond restraints: 18554 Sorted by residual: bond pdb=" C11 PGV A 304 " pdb=" C12 PGV A 304 " ideal model delta sigma weight residual 1.332 1.553 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C11 PGV A 303 " pdb=" C12 PGV A 303 " ideal model delta sigma weight residual 1.332 1.552 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C11 PGV D 304 " pdb=" C12 PGV D 304 " ideal model delta sigma weight residual 1.332 1.552 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C11 PGV D 303 " pdb=" C12 PGV D 303 " ideal model delta sigma weight residual 1.332 1.552 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C11 PGV D 302 " pdb=" C12 PGV D 302 " ideal model delta sigma weight residual 1.332 1.552 -0.220 2.00e-02 2.50e+03 1.21e+02 ... (remaining 18549 not shown) Histogram of bond angle deviations from ideal: 80.19 - 90.96: 12 90.96 - 101.73: 79 101.73 - 112.50: 9914 112.50 - 123.27: 14271 123.27 - 134.03: 718 Bond angle restraints: 24994 Sorted by residual: angle pdb=" C19 PGV D 305 " pdb=" C20 PGV D 305 " pdb=" C21 PGV D 305 " ideal model delta sigma weight residual 113.71 80.19 33.52 3.00e+00 1.11e-01 1.25e+02 angle pdb=" C19 PGV A 301 " pdb=" C20 PGV A 301 " pdb=" C21 PGV A 301 " ideal model delta sigma weight residual 113.71 81.12 32.59 3.00e+00 1.11e-01 1.18e+02 angle pdb=" C19 PGV D 301 " pdb=" C20 PGV D 301 " pdb=" C21 PGV D 301 " ideal model delta sigma weight residual 113.71 81.14 32.57 3.00e+00 1.11e-01 1.18e+02 angle pdb=" C19 PGV A 305 " pdb=" C20 PGV A 305 " pdb=" C21 PGV A 305 " ideal model delta sigma weight residual 113.71 81.47 32.24 3.00e+00 1.11e-01 1.16e+02 angle pdb=" C19 PGV A 306 " pdb=" C20 PGV A 306 " pdb=" C21 PGV A 306 " ideal model delta sigma weight residual 113.71 82.13 31.58 3.00e+00 1.11e-01 1.11e+02 ... (remaining 24989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.10: 10561 30.10 - 60.19: 678 60.19 - 90.29: 64 90.29 - 120.39: 9 120.39 - 150.48: 12 Dihedral angle restraints: 11324 sinusoidal: 4582 harmonic: 6742 Sorted by residual: dihedral pdb=" CA GLU L 156 " pdb=" C GLU L 156 " pdb=" N LYS L 157 " pdb=" CA LYS L 157 " ideal model delta harmonic sigma weight residual 180.00 151.19 28.81 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA GLU I 156 " pdb=" C GLU I 156 " pdb=" N LYS I 157 " pdb=" CA LYS I 157 " ideal model delta harmonic sigma weight residual 180.00 152.00 28.00 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA THR B 119 " pdb=" C THR B 119 " pdb=" N LYS B 120 " pdb=" CA LYS B 120 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 11321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2563 0.087 - 0.174: 368 0.174 - 0.261: 46 0.261 - 0.348: 3 0.348 - 0.435: 2 Chirality restraints: 2982 Sorted by residual: chirality pdb=" CB THR B 119 " pdb=" CA THR B 119 " pdb=" OG1 THR B 119 " pdb=" CG2 THR B 119 " both_signs ideal model delta sigma weight residual False 2.55 2.12 0.43 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CB THR E 119 " pdb=" CA THR E 119 " pdb=" OG1 THR E 119 " pdb=" CG2 THR E 119 " both_signs ideal model delta sigma weight residual False 2.55 2.12 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CA ASN H 35 " pdb=" N ASN H 35 " pdb=" C ASN H 35 " pdb=" CB ASN H 35 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 2979 not shown) Planarity restraints: 3134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 PGV D 303 " 0.166 2.00e-02 2.50e+03 3.24e-01 1.05e+03 pdb=" C11 PGV D 303 " -0.428 2.00e-02 2.50e+03 pdb=" C12 PGV D 303 " 0.428 2.00e-02 2.50e+03 pdb=" C13 PGV D 303 " -0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PGV A 303 " -0.166 2.00e-02 2.50e+03 3.24e-01 1.05e+03 pdb=" C11 PGV A 303 " 0.428 2.00e-02 2.50e+03 pdb=" C12 PGV A 303 " -0.427 2.00e-02 2.50e+03 pdb=" C13 PGV A 303 " 0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PGV A 304 " 0.160 2.00e-02 2.50e+03 2.78e-01 7.73e+02 pdb=" C11 PGV A 304 " -0.360 2.00e-02 2.50e+03 pdb=" C12 PGV A 304 " 0.359 2.00e-02 2.50e+03 pdb=" C13 PGV A 304 " -0.159 2.00e-02 2.50e+03 ... (remaining 3131 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 212 2.60 - 3.17: 14250 3.17 - 3.75: 25968 3.75 - 4.32: 37448 4.32 - 4.90: 62645 Nonbonded interactions: 140523 Sorted by model distance: nonbonded pdb=" O MET E 105 " pdb=" OG SER E 106 " model vdw 2.021 3.040 nonbonded pdb=" O MET B 105 " pdb=" OG SER B 106 " model vdw 2.082 3.040 nonbonded pdb=" O06 PGV D 305 " pdb=" O12 PGV D 305 " model vdw 2.112 3.040 nonbonded pdb=" OD1 ASN G 94 " pdb=" N ALA G 95 " model vdw 2.129 3.120 nonbonded pdb=" O LEU L 73 " pdb=" O ASP L 74 " model vdw 2.143 3.040 ... (remaining 140518 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 256 or resid 301 through 305)) selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = (chain 'I' and resid 3 through 193) selection = chain 'J' selection = chain 'K' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.230 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: 0.000 Extract box with map and model: 0.750 Check model and map are aligned: 0.000 Set scattering table: 0.070 Process input model: 47.430 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 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 : 0.012 0.221 18554 Z= 0.833 Angle : 1.544 33.516 24994 Z= 0.713 Chirality : 0.063 0.435 2982 Planarity : 0.016 0.324 3134 Dihedral : 19.877 150.482 6996 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 1.02 % Allowed : 10.38 % Favored : 88.60 % Rotamer: Outliers : 4.91 % Allowed : 9.82 % Favored : 85.27 % 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: -5.86 (0.12), residues: 2350 helix: -4.75 (0.05), residues: 992 sheet: -2.06 (0.29), residues: 278 loop : -3.44 (0.15), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 212 HIS 0.005 0.002 HIS B 263 PHE 0.030 0.003 PHE C 17 TYR 0.039 0.003 TYR J 40 ARG 0.004 0.001 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 445 time to evaluate : 2.274 Fit side-chains REVERT: A 120 MET cc_start: 0.9144 (mtt) cc_final: 0.8916 (mtt) REVERT: A 188 ASN cc_start: 0.8657 (t0) cc_final: 0.8289 (t0) REVERT: B 17 LYS cc_start: 0.8533 (mtpt) cc_final: 0.8324 (mtmm) REVERT: B 120 LYS cc_start: 0.8653 (mppt) cc_final: 0.8397 (mmtt) REVERT: B 185 LYS cc_start: 0.9016 (ttmt) cc_final: 0.8732 (mtpt) REVERT: B 190 ARG cc_start: 0.7932 (mpp80) cc_final: 0.7698 (mtm180) REVERT: B 262 SER cc_start: 0.5448 (OUTLIER) cc_final: 0.4927 (m) REVERT: C 33 LYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6905 (pttp) REVERT: C 34 GLN cc_start: 0.7401 (tp-100) cc_final: 0.7158 (tp40) REVERT: C 67 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.7293 (tppt) REVERT: C 93 HIS cc_start: 0.6548 (m90) cc_final: 0.6303 (m-70) REVERT: E 17 LYS cc_start: 0.8570 (mtpt) cc_final: 0.8263 (mtpt) REVERT: E 25 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6615 (mt-10) REVERT: E 33 SER cc_start: 0.8859 (OUTLIER) cc_final: 0.8647 (p) REVERT: F 30 ILE cc_start: 0.7108 (mt) cc_final: 0.6828 (mp) REVERT: F 45 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6601 (mp10) REVERT: F 73 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8015 (ttmm) REVERT: G 141 ASP cc_start: 0.7866 (p0) cc_final: 0.7566 (p0) REVERT: G 160 LYS cc_start: 0.8785 (ttpt) cc_final: 0.8397 (tttp) REVERT: H 45 GLN cc_start: 0.8058 (mt0) cc_final: 0.7853 (mt0) REVERT: H 50 ASN cc_start: 0.8600 (t0) cc_final: 0.8280 (t0) REVERT: H 97 GLN cc_start: 0.8047 (mp10) cc_final: 0.7612 (mp10) REVERT: H 187 ASP cc_start: 0.7242 (t0) cc_final: 0.7035 (t0) REVERT: I 43 LYS cc_start: 0.8778 (ptpp) cc_final: 0.8525 (ptmm) REVERT: I 191 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8085 (tttt) REVERT: J 43 LYS cc_start: 0.8370 (ptpp) cc_final: 0.8067 (pttp) REVERT: J 133 ASN cc_start: 0.6886 (m-40) cc_final: 0.6615 (m-40) REVERT: J 134 MET cc_start: 0.6031 (pmm) cc_final: 0.5609 (pmm) REVERT: J 147 MET cc_start: 0.8458 (ptm) cc_final: 0.8256 (ptp) REVERT: K 135 ASN cc_start: 0.5731 (OUTLIER) cc_final: 0.5438 (p0) outliers start: 92 outliers final: 27 residues processed: 513 average time/residue: 0.3292 time to fit residues: 244.3147 Evaluate side-chains 363 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 327 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 235 GLU Chi-restraints excluded: chain E residue 246 LYS Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 45 GLN Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 ARG Chi-restraints excluded: chain I residue 191 LYS Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 135 ASN Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain L residue 190 SER Chi-restraints excluded: chain L residue 192 PHE Chi-restraints excluded: chain L residue 193 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 212 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 139 GLN A 191 GLN B 144 GLN C 66 GLN C 93 HIS D 46 HIS D 139 GLN D 191 GLN F 89 GLN G 45 GLN G 97 GLN H 35 ASN H 45 GLN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 GLN I 104 ASN L 102 GLN L 128 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18554 Z= 0.309 Angle : 0.771 10.690 24994 Z= 0.401 Chirality : 0.046 0.306 2982 Planarity : 0.005 0.060 3134 Dihedral : 17.446 172.014 3095 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.36 % Favored : 90.43 % Rotamer: Outliers : 3.58 % Allowed : 14.03 % Favored : 82.39 % 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: -3.85 (0.14), residues: 2350 helix: -2.24 (0.12), residues: 1044 sheet: -1.63 (0.30), residues: 278 loop : -3.11 (0.16), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 212 HIS 0.005 0.001 HIS B 263 PHE 0.024 0.002 PHE F 17 TYR 0.016 0.002 TYR B 173 ARG 0.005 0.001 ARG I 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 352 time to evaluate : 2.143 Fit side-chains revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8695 (mtpp) cc_final: 0.8461 (mmmm) REVERT: B 120 LYS cc_start: 0.8586 (mppt) cc_final: 0.8270 (mmtt) REVERT: B 135 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7802 (tm-30) REVERT: B 262 SER cc_start: 0.5102 (OUTLIER) cc_final: 0.4696 (m) REVERT: D 186 MET cc_start: 0.8971 (ttm) cc_final: 0.8767 (ttp) REVERT: E 17 LYS cc_start: 0.8762 (mtpt) cc_final: 0.8554 (mtpt) REVERT: F 23 GLN cc_start: 0.8403 (mt0) cc_final: 0.8159 (mm-40) REVERT: F 61 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7899 (tp) REVERT: F 67 LYS cc_start: 0.6988 (OUTLIER) cc_final: 0.6702 (mptp) REVERT: F 70 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6620 (mt) REVERT: G 85 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.8013 (p0) REVERT: H 50 ASN cc_start: 0.8805 (t0) cc_final: 0.8524 (t0) REVERT: H 60 MET cc_start: 0.8283 (tpp) cc_final: 0.7761 (ttt) REVERT: H 93 PHE cc_start: 0.6773 (OUTLIER) cc_final: 0.6032 (p90) REVERT: I 23 PHE cc_start: 0.7666 (m-10) cc_final: 0.7446 (t80) REVERT: I 78 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.7179 (mmt90) REVERT: I 185 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7723 (pp) REVERT: I 186 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7987 (mm-30) REVERT: I 191 LYS cc_start: 0.8691 (ttmt) cc_final: 0.8206 (tttt) REVERT: J 43 LYS cc_start: 0.8204 (ptpp) cc_final: 0.7972 (pttp) REVERT: J 73 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8043 (tt) REVERT: J 134 MET cc_start: 0.5990 (pmm) cc_final: 0.5656 (pmm) REVERT: J 147 MET cc_start: 0.8435 (ptm) cc_final: 0.7936 (ptp) REVERT: K 174 ASP cc_start: 0.8531 (m-30) cc_final: 0.8289 (m-30) REVERT: K 192 PHE cc_start: 0.7060 (t80) cc_final: 0.6835 (t80) REVERT: L 143 ASP cc_start: 0.8009 (m-30) cc_final: 0.7674 (m-30) outliers start: 67 outliers final: 35 residues processed: 398 average time/residue: 0.3035 time to fit residues: 179.8578 Evaluate side-chains 357 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 313 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 45 GLN Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 147 MET Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 93 PHE Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 ARG Chi-restraints excluded: chain I residue 136 SER Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 167 LEU Chi-restraints excluded: chain L residue 192 PHE Chi-restraints excluded: chain L residue 193 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 144 optimal weight: 0.7980 chunk 58 optimal weight: 7.9990 chunk 212 optimal weight: 20.0000 chunk 229 optimal weight: 9.9990 chunk 189 optimal weight: 4.9990 chunk 211 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 170 optimal weight: 20.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 155 ASN E 208 HIS ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18554 Z= 0.290 Angle : 0.681 11.691 24994 Z= 0.354 Chirality : 0.045 0.275 2982 Planarity : 0.004 0.055 3134 Dihedral : 16.451 164.449 3047 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.74 % Favored : 90.00 % Rotamer: Outliers : 3.74 % Allowed : 14.94 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.16), residues: 2350 helix: -0.71 (0.15), residues: 1048 sheet: -1.31 (0.31), residues: 278 loop : -2.88 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 212 HIS 0.010 0.001 HIS E 263 PHE 0.022 0.002 PHE F 17 TYR 0.017 0.002 TYR G 145 ARG 0.006 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 328 time to evaluate : 2.272 Fit side-chains REVERT: B 120 LYS cc_start: 0.8604 (mppt) cc_final: 0.8269 (mmtt) REVERT: B 135 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7789 (tp30) REVERT: B 262 SER cc_start: 0.4421 (OUTLIER) cc_final: 0.4150 (m) REVERT: E 17 LYS cc_start: 0.8884 (mtpt) cc_final: 0.8619 (mtpt) REVERT: E 105 MET cc_start: 0.8441 (mtt) cc_final: 0.8063 (mtt) REVERT: F 61 LEU cc_start: 0.8255 (mm) cc_final: 0.8024 (tp) REVERT: H 35 ASN cc_start: 0.7313 (OUTLIER) cc_final: 0.6669 (t0) REVERT: H 50 ASN cc_start: 0.8799 (t0) cc_final: 0.8424 (t0) REVERT: H 60 MET cc_start: 0.8297 (tpp) cc_final: 0.7860 (ttt) REVERT: H 93 PHE cc_start: 0.6718 (OUTLIER) cc_final: 0.6013 (p90) REVERT: I 191 LYS cc_start: 0.8593 (ttmt) cc_final: 0.8016 (tttt) REVERT: J 43 LYS cc_start: 0.8182 (ptpp) cc_final: 0.7919 (pttp) REVERT: J 73 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8010 (tt) REVERT: J 134 MET cc_start: 0.5961 (pmm) cc_final: 0.5659 (pmm) REVERT: J 147 MET cc_start: 0.8413 (ptm) cc_final: 0.7904 (ptp) REVERT: L 42 MET cc_start: 0.7951 (mmm) cc_final: 0.7705 (mtt) outliers start: 70 outliers final: 44 residues processed: 375 average time/residue: 0.3089 time to fit residues: 174.3598 Evaluate side-chains 357 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 309 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 93 PHE Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 ARG Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 136 SER Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 97 GLN Chi-restraints excluded: chain L residue 147 MET Chi-restraints excluded: chain L residue 167 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 110 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 142 optimal weight: 9.9990 chunk 213 optimal weight: 2.9990 chunk 226 optimal weight: 30.0000 chunk 111 optimal weight: 0.0670 chunk 202 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 GLN ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 ASN E 264 GLN G 45 GLN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18554 Z= 0.168 Angle : 0.619 12.246 24994 Z= 0.323 Chirality : 0.043 0.342 2982 Planarity : 0.004 0.052 3134 Dihedral : 15.525 153.046 3033 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.81 % Favored : 91.06 % Rotamer: Outliers : 3.42 % Allowed : 15.69 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.17), residues: 2350 helix: 0.18 (0.16), residues: 1054 sheet: -1.15 (0.32), residues: 264 loop : -2.64 (0.17), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 212 HIS 0.006 0.001 HIS B 118 PHE 0.015 0.001 PHE D 182 TYR 0.015 0.001 TYR G 145 ARG 0.007 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 336 time to evaluate : 2.065 Fit side-chains revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8647 (mtpp) cc_final: 0.8393 (mmmm) REVERT: B 135 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7721 (tp30) REVERT: D 186 MET cc_start: 0.8846 (ttm) cc_final: 0.8478 (ttp) REVERT: E 17 LYS cc_start: 0.8880 (mtpt) cc_final: 0.8645 (mtpt) REVERT: G 85 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.8064 (p0) REVERT: H 35 ASN cc_start: 0.7223 (OUTLIER) cc_final: 0.6759 (t0) REVERT: H 50 ASN cc_start: 0.8758 (t0) cc_final: 0.8412 (t0) REVERT: H 60 MET cc_start: 0.8259 (tpp) cc_final: 0.7767 (ttt) REVERT: I 16 ILE cc_start: 0.8424 (mm) cc_final: 0.8194 (mm) REVERT: I 78 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.6935 (mmt180) REVERT: I 191 LYS cc_start: 0.8540 (ttmt) cc_final: 0.8023 (tttt) REVERT: J 43 LYS cc_start: 0.8151 (ptpp) cc_final: 0.7937 (pttp) REVERT: J 147 MET cc_start: 0.8413 (ptm) cc_final: 0.8053 (ptp) REVERT: L 42 MET cc_start: 0.7847 (mmm) cc_final: 0.7647 (mtt) outliers start: 64 outliers final: 37 residues processed: 383 average time/residue: 0.2959 time to fit residues: 170.1170 Evaluate side-chains 356 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 316 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 147 MET Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 191 LYS Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 ARG Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 93 PHE Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 167 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 0.6980 chunk 128 optimal weight: 6.9990 chunk 3 optimal weight: 0.5980 chunk 168 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 193 optimal weight: 20.0000 chunk 156 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 203 optimal weight: 0.0270 chunk 57 optimal weight: 10.0000 overall best weight: 2.8642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 155 ASN F 87 HIS ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18554 Z= 0.272 Angle : 0.653 12.352 24994 Z= 0.337 Chirality : 0.044 0.297 2982 Planarity : 0.004 0.052 3134 Dihedral : 15.239 144.488 3031 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.40 % Favored : 90.47 % Rotamer: Outliers : 4.00 % Allowed : 16.38 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.17), residues: 2350 helix: 0.47 (0.17), residues: 1050 sheet: -1.07 (0.33), residues: 264 loop : -2.59 (0.17), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 212 HIS 0.007 0.001 HIS B 118 PHE 0.020 0.002 PHE F 17 TYR 0.015 0.002 TYR G 40 ARG 0.006 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 317 time to evaluate : 2.049 Fit side-chains revert: symmetry clash REVERT: B 63 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8326 (mt) REVERT: B 120 LYS cc_start: 0.8666 (mppt) cc_final: 0.8365 (mmtt) REVERT: B 135 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7722 (tp30) REVERT: D 186 MET cc_start: 0.8971 (ttm) cc_final: 0.8731 (ttp) REVERT: D 226 GLU cc_start: 0.7789 (pp20) cc_final: 0.7312 (pp20) REVERT: E 17 LYS cc_start: 0.8904 (mtpt) cc_final: 0.8663 (mtpt) REVERT: E 105 MET cc_start: 0.8497 (mtt) cc_final: 0.8203 (mtt) REVERT: H 35 ASN cc_start: 0.7282 (OUTLIER) cc_final: 0.6726 (t0) REVERT: H 50 ASN cc_start: 0.8794 (t0) cc_final: 0.8433 (t0) REVERT: H 60 MET cc_start: 0.8279 (tpp) cc_final: 0.7856 (ttt) REVERT: I 191 LYS cc_start: 0.8536 (ttmt) cc_final: 0.8060 (tttt) REVERT: J 43 LYS cc_start: 0.8157 (ptpp) cc_final: 0.7946 (pttp) REVERT: J 73 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.8013 (tt) REVERT: J 147 MET cc_start: 0.8427 (ptm) cc_final: 0.7992 (ptp) outliers start: 75 outliers final: 60 residues processed: 371 average time/residue: 0.3103 time to fit residues: 171.7340 Evaluate side-chains 370 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 307 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 147 MET Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 191 LYS Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 128 GLN Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 ARG Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 136 SER Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 93 PHE Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 97 GLN Chi-restraints excluded: chain L residue 147 MET Chi-restraints excluded: chain L residue 167 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 0.9990 chunk 203 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 226 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 194 HIS E 155 ASN F 87 HIS I 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18554 Z= 0.225 Angle : 0.624 12.545 24994 Z= 0.324 Chirality : 0.044 0.320 2982 Planarity : 0.004 0.052 3134 Dihedral : 14.864 137.729 3031 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.19 % Favored : 90.72 % Rotamer: Outliers : 4.32 % Allowed : 17.18 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.17), residues: 2350 helix: 0.76 (0.17), residues: 1050 sheet: -1.01 (0.33), residues: 264 loop : -2.52 (0.17), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 212 HIS 0.009 0.001 HIS B 118 PHE 0.016 0.001 PHE F 17 TYR 0.014 0.001 TYR G 145 ARG 0.005 0.000 ARG E 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 323 time to evaluate : 2.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 63 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8319 (mt) REVERT: B 120 LYS cc_start: 0.8584 (mppt) cc_final: 0.8316 (mmtt) REVERT: B 135 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7715 (tp30) REVERT: B 246 LYS cc_start: 0.8221 (tptm) cc_final: 0.7918 (ptpp) REVERT: C 14 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7581 (pttp) REVERT: E 17 LYS cc_start: 0.8892 (mtpt) cc_final: 0.8643 (mtpt) REVERT: E 105 MET cc_start: 0.8424 (mtt) cc_final: 0.8157 (mtt) REVERT: F 70 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6507 (mt) REVERT: H 35 ASN cc_start: 0.7237 (OUTLIER) cc_final: 0.6701 (t0) REVERT: H 50 ASN cc_start: 0.8785 (t0) cc_final: 0.8451 (t0) REVERT: H 60 MET cc_start: 0.8266 (tpp) cc_final: 0.7856 (ttt) REVERT: I 191 LYS cc_start: 0.8446 (ttmt) cc_final: 0.8082 (tttt) REVERT: J 42 MET cc_start: 0.8593 (mtp) cc_final: 0.8077 (mtp) REVERT: J 43 LYS cc_start: 0.8150 (ptpp) cc_final: 0.7943 (pttp) REVERT: J 73 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7935 (tt) REVERT: J 147 MET cc_start: 0.8438 (ptm) cc_final: 0.7945 (ptp) REVERT: K 69 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7836 (t0) REVERT: K 174 ASP cc_start: 0.8477 (m-30) cc_final: 0.8264 (m-30) outliers start: 81 outliers final: 57 residues processed: 378 average time/residue: 0.3231 time to fit residues: 183.0489 Evaluate side-chains 376 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 313 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 147 MET Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 128 GLN Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 ARG Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 136 SER Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 167 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 128 optimal weight: 0.3980 chunk 165 optimal weight: 8.9990 chunk 190 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 155 ASN I 102 GLN J 102 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 18554 Z= 0.365 Angle : 0.691 12.647 24994 Z= 0.357 Chirality : 0.047 0.306 2982 Planarity : 0.004 0.052 3134 Dihedral : 14.835 130.441 3030 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.09 % Favored : 89.74 % Rotamer: Outliers : 4.38 % Allowed : 17.34 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.17), residues: 2350 helix: 0.68 (0.17), residues: 1050 sheet: -1.03 (0.32), residues: 278 loop : -2.59 (0.17), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 212 HIS 0.009 0.001 HIS B 118 PHE 0.028 0.002 PHE F 17 TYR 0.018 0.002 TYR G 40 ARG 0.004 0.000 ARG J 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 317 time to evaluate : 2.129 Fit side-chains revert: symmetry clash REVERT: B 31 ASN cc_start: 0.6322 (t0) cc_final: 0.6008 (t0) REVERT: B 120 LYS cc_start: 0.8569 (mppt) cc_final: 0.8249 (mmtt) REVERT: B 135 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7738 (tp30) REVERT: B 246 LYS cc_start: 0.8267 (tptm) cc_final: 0.7944 (ptpp) REVERT: C 47 GLU cc_start: 0.7633 (pm20) cc_final: 0.7425 (pm20) REVERT: E 17 LYS cc_start: 0.8925 (mtpt) cc_final: 0.8670 (mtpt) REVERT: E 105 MET cc_start: 0.8540 (mtt) cc_final: 0.8230 (mtt) REVERT: F 70 LEU cc_start: 0.6612 (OUTLIER) cc_final: 0.6369 (mt) REVERT: H 35 ASN cc_start: 0.7367 (OUTLIER) cc_final: 0.6993 (t0) REVERT: H 50 ASN cc_start: 0.8843 (t0) cc_final: 0.8541 (t0) REVERT: H 60 MET cc_start: 0.8285 (tpp) cc_final: 0.7925 (ttt) REVERT: I 191 LYS cc_start: 0.8453 (ttmt) cc_final: 0.8099 (tttt) REVERT: J 43 LYS cc_start: 0.8171 (ptpp) cc_final: 0.7916 (pttp) REVERT: J 73 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.8028 (tt) REVERT: J 147 MET cc_start: 0.8421 (ptm) cc_final: 0.7909 (ptp) REVERT: J 178 ASN cc_start: 0.8463 (m110) cc_final: 0.8197 (m110) REVERT: K 174 ASP cc_start: 0.8473 (m-30) cc_final: 0.8261 (m-30) outliers start: 82 outliers final: 60 residues processed: 374 average time/residue: 0.3183 time to fit residues: 178.4289 Evaluate side-chains 371 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 308 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 142 GLU Chi-restraints excluded: chain G residue 147 MET Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 128 GLN Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 ARG Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 136 SER Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 97 GLN Chi-restraints excluded: chain L residue 147 MET Chi-restraints excluded: chain L residue 167 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 0.7980 chunk 134 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 111 optimal weight: 0.0970 chunk 21 optimal weight: 0.7980 chunk 177 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 155 ASN F 89 GLN G 45 GLN I 45 GLN I 102 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18554 Z= 0.159 Angle : 0.605 12.334 24994 Z= 0.317 Chirality : 0.042 0.323 2982 Planarity : 0.004 0.054 3134 Dihedral : 14.084 126.762 3030 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.60 % Favored : 91.32 % Rotamer: Outliers : 3.31 % Allowed : 19.16 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.18), residues: 2350 helix: 1.20 (0.17), residues: 1050 sheet: -1.05 (0.33), residues: 264 loop : -2.42 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 6 HIS 0.007 0.001 HIS B 118 PHE 0.016 0.001 PHE L 13 TYR 0.014 0.001 TYR G 145 ARG 0.005 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4700 Ramachandran restraints generated. 2350 Oldfield, 0 Emsley, 2350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 326 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8614 (mtpp) cc_final: 0.8357 (mmmm) REVERT: B 31 ASN cc_start: 0.6071 (t0) cc_final: 0.5781 (t0) REVERT: B 63 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8184 (mt) REVERT: B 135 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7716 (tp30) REVERT: B 246 LYS cc_start: 0.8201 (tptm) cc_final: 0.7916 (ptpt) REVERT: E 17 LYS cc_start: 0.8877 (mtpt) cc_final: 0.8632 (mtpt) REVERT: F 7 GLN cc_start: 0.6594 (pp30) cc_final: 0.6306 (pm20) REVERT: G 85 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8097 (p0) REVERT: H 35 ASN cc_start: 0.7002 (OUTLIER) cc_final: 0.6636 (t0) REVERT: H 50 ASN cc_start: 0.8781 (t0) cc_final: 0.8435 (t0) REVERT: H 60 MET cc_start: 0.8250 (tpp) cc_final: 0.7817 (ttt) REVERT: H 128 GLN cc_start: 0.5387 (OUTLIER) cc_final: 0.5140 (mp10) REVERT: I 191 LYS cc_start: 0.8422 (ttmt) cc_final: 0.8063 (tttt) REVERT: J 43 LYS cc_start: 0.8106 (ptpp) cc_final: 0.7880 (pttp) REVERT: J 73 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7801 (tt) REVERT: J 147 MET cc_start: 0.8429 (ptm) cc_final: 0.7929 (ptp) outliers start: 62 outliers final: 45 residues processed: 373 average time/residue: 0.2944 time to fit residues: 165.8322 Evaluate side-chains 355 residues out of total 1994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 305 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 147 MET Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 128 GLN Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 78 ARG Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 93 PHE Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 167 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.606 > 50: distance: 23 - 46: 15.614 distance: 28 - 57: 3.453 distance: 31 - 35: 5.517 distance: 32 - 65: 10.596 distance: 35 - 36: 8.734 distance: 36 - 37: 3.280 distance: 37 - 46: 4.413 distance: 38 - 70: 16.910 distance: 40 - 41: 6.475 distance: 40 - 42: 4.692 distance: 41 - 43: 7.476 distance: 42 - 44: 6.071 distance: 43 - 45: 9.667 distance: 44 - 45: 7.030 distance: 46 - 47: 6.577 distance: 47 - 48: 5.912 distance: 47 - 50: 8.086 distance: 48 - 49: 15.139 distance: 48 - 57: 10.985 distance: 49 - 78: 21.546 distance: 50 - 51: 5.583 distance: 51 - 52: 8.759 distance: 51 - 53: 5.410 distance: 52 - 54: 5.839 distance: 53 - 55: 10.635 distance: 54 - 56: 7.460 distance: 55 - 56: 8.234 distance: 57 - 58: 3.792 distance: 58 - 59: 3.046 distance: 58 - 61: 8.284 distance: 59 - 65: 3.788 distance: 60 - 87: 8.243 distance: 61 - 62: 5.918 distance: 62 - 63: 6.860 distance: 62 - 64: 13.557 distance: 66 - 67: 4.449 distance: 66 - 69: 5.877 distance: 67 - 70: 7.521 distance: 68 - 94: 14.705 distance: 70 - 71: 11.123 distance: 71 - 74: 18.809 distance: 72 - 73: 8.995 distance: 72 - 78: 6.206 distance: 73 - 100: 17.020 distance: 74 - 75: 7.845 distance: 75 - 76: 12.669 distance: 76 - 77: 12.437 distance: 78 - 79: 9.848 distance: 79 - 80: 11.117 distance: 79 - 82: 12.542 distance: 82 - 83: 7.898 distance: 83 - 84: 7.623 distance: 84 - 85: 11.940 distance: 85 - 86: 14.034 distance: 87 - 88: 13.684 distance: 88 - 89: 18.303 distance: 88 - 91: 30.023 distance: 89 - 90: 8.008 distance: 89 - 94: 3.425 distance: 91 - 92: 16.452 distance: 91 - 93: 6.007 distance: 94 - 95: 7.168 distance: 95 - 96: 5.881 distance: 95 - 98: 9.411 distance: 96 - 97: 12.920 distance: 96 - 100: 16.158 distance: 98 - 99: 8.454 distance: 100 - 101: 20.785 distance: 101 - 102: 23.896 distance: 102 - 103: 4.119 distance: 102 - 104: 16.538 distance: 104 - 105: 3.115 distance: 105 - 106: 21.307 distance: 105 - 108: 6.684 distance: 106 - 107: 12.564 distance: 106 - 112: 13.844 distance: 108 - 109: 3.309 distance: 109 - 110: 32.055 distance: 109 - 111: 17.320