Starting phenix.real_space_refine on Tue Aug 6 06:42:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch0_30367/08_2024/7ch0_30367.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch0_30367/08_2024/7ch0_30367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch0_30367/08_2024/7ch0_30367.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch0_30367/08_2024/7ch0_30367.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch0_30367/08_2024/7ch0_30367.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch0_30367/08_2024/7ch0_30367.cif" } resolution = 3.7 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= 0.001 sd= 0.010 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 6 5.49 5 S 68 5.16 5 C 10164 2.51 5 N 2666 2.21 5 O 2952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 18": "NH1" <-> "NH2" Residue "A GLU 36": "OE1" <-> "OE2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A ARG 141": "NH1" <-> "NH2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B ARG 33": "NH1" <-> "NH2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B ARG 135": "NH1" <-> "NH2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "B ARG 157": "NH1" <-> "NH2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B GLU 189": "OE1" <-> "OE2" Residue "B ARG 255": "NH1" <-> "NH2" Residue "B ASP 260": "OD1" <-> "OD2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "E ARG 33": "NH1" <-> "NH2" Residue "E GLU 64": "OE1" <-> "OE2" Residue "E ARG 135": "NH1" <-> "NH2" Residue "E GLU 144": "OE1" <-> "OE2" Residue "E ARG 157": "NH1" <-> "NH2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E GLU 189": "OE1" <-> "OE2" Residue "E ARG 255": "NH1" <-> "NH2" Residue "D ARG 18": "NH1" <-> "NH2" Residue "D GLU 36": "OE1" <-> "OE2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "D ARG 111": "NH1" <-> "NH2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D ARG 141": "NH1" <-> "NH2" Residue "D ARG 196": "NH1" <-> "NH2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C ARG 97": "NH1" <-> "NH2" Residue "F GLU 30": "OE1" <-> "OE2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F ARG 97": "NH1" <-> "NH2" Residue "G GLU 37": "OE1" <-> "OE2" Residue "G ARG 55": "NH1" <-> "NH2" Residue "G GLU 109": "OE1" <-> "OE2" Residue "G GLU 119": "OE1" <-> "OE2" Residue "H ARG 67": "NH1" <-> "NH2" Residue "H GLU 122": "OE1" <-> "OE2" Residue "I ARG 55": "NH1" <-> "NH2" Residue "I GLU 122": "OE1" <-> "OE2" Residue "I GLU 144": "OE1" <-> "OE2" Residue "J ARG 55": "NH1" <-> "NH2" Residue "J TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 109": "OE1" <-> "OE2" Residue "K GLU 37": "OE1" <-> "OE2" Residue "K ARG 55": "NH1" <-> "NH2" Residue "K ARG 89": "NH1" <-> "NH2" Residue "K GLU 122": "OE1" <-> "OE2" Residue "K GLU 144": "OE1" <-> "OE2" Residue "L ARG 55": "NH1" <-> "NH2" Residue "L GLU 87": "OE1" <-> "OE2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 15856 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1934 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain: "B" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1995 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 244} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1995 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 244} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1934 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain: "C" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 725 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "F" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 725 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "G" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "H" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "I" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1033 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "J" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "K" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "L" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1033 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.55, per 1000 atoms: 0.54 Number of scatterers: 15856 At special positions: 0 Unit cell: (108.7, 105.439, 150.006, 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 68 16.00 P 6 15.00 O 2952 8.00 N 2666 7.00 C 10164 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: 5.66 Conformation dependent library (CDL) restraints added in 2.8 seconds 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3824 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 22 sheets defined 38.9% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 3 through 32 removed outlier: 3.538A pdb=" N SER A 8 " --> pdb=" O ASN A 4 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU A 9 " --> pdb=" O ALA A 5 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A 10 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 52 removed outlier: 3.617A pdb=" N VAL A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG A 46 " --> pdb=" O PRO A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 77 removed outlier: 3.623A pdb=" N ILE A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 70 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 71 " --> pdb=" O GLY A 67 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL A 77 " --> pdb=" O GLN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 82 removed outlier: 3.617A pdb=" N TYR A 81 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 86 Processing helix chain 'A' and resid 87 through 98 removed outlier: 4.001A pdb=" N LEU A 93 " --> pdb=" O MET A 89 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 126 removed outlier: 3.538A pdb=" N VAL A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 removed outlier: 3.523A pdb=" N GLU A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 144 through 174 removed outlier: 3.586A pdb=" N TRP A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 155 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Proline residue: A 156 - end of helix removed outlier: 4.034A pdb=" N VAL A 160 " --> pdb=" O PRO A 156 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 173 " --> pdb=" O GLY A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 191 removed outlier: 3.913A pdb=" N ASN A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 220 removed outlier: 3.806A pdb=" N LYS A 205 " --> pdb=" O ASN A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 243 removed outlier: 3.868A pdb=" N ILE A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 257 removed outlier: 3.950A pdb=" N LEU A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.733A pdb=" N ILE B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 84 removed outlier: 3.795A pdb=" N TYR B 81 " --> pdb=" O ARG B 77 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR B 82 " --> pdb=" O SER B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 124 through 132 removed outlier: 4.013A pdb=" N GLU B 130 " --> pdb=" O MET B 126 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 132 " --> pdb=" O LYS B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 157 removed outlier: 3.756A pdb=" N ARG B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 156 " --> pdb=" O ARG B 152 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 189 removed outlier: 3.681A pdb=" N ILE B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 211 Processing helix chain 'B' and resid 229 through 233 Processing helix chain 'B' and resid 261 through 266 Processing helix chain 'E' and resid 47 through 55 removed outlier: 3.732A pdb=" N ILE E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 84 removed outlier: 3.794A pdb=" N TYR E 81 " --> pdb=" O ARG E 77 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR E 82 " --> pdb=" O SER E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 107 Processing helix chain 'E' and resid 124 through 132 removed outlier: 4.014A pdb=" N GLU E 130 " --> pdb=" O MET E 126 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL E 132 " --> pdb=" O LYS E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 157 removed outlier: 3.756A pdb=" N ARG E 152 " --> pdb=" O GLY E 148 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA E 154 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA E 156 " --> pdb=" O ARG E 152 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 removed outlier: 3.680A pdb=" N ILE E 187 " --> pdb=" O LEU E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 211 Processing helix chain 'D' and resid 4 through 32 removed outlier: 3.537A pdb=" N SER D 8 " --> pdb=" O ASN D 4 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU D 9 " --> pdb=" O ALA D 5 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY D 10 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR D 16 " --> pdb=" O LYS D 12 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 27 " --> pdb=" O ALA D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 52 removed outlier: 3.617A pdb=" N VAL D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG D 46 " --> pdb=" O PRO D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 77 removed outlier: 3.622A pdb=" N ILE D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE D 66 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D 70 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY D 71 " --> pdb=" O GLY D 67 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY D 74 " --> pdb=" O LEU D 70 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL D 77 " --> pdb=" O GLN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 82 removed outlier: 3.618A pdb=" N TYR D 81 " --> pdb=" O LEU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 86 Processing helix chain 'D' and resid 87 through 98 removed outlier: 4.001A pdb=" N LEU D 93 " --> pdb=" O MET D 89 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU D 96 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 126 removed outlier: 3.538A pdb=" N VAL D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA D 105 " --> pdb=" O PRO D 101 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY D 113 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR D 117 " --> pdb=" O GLY D 113 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 134 removed outlier: 3.523A pdb=" N GLU D 133 " --> pdb=" O LEU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 144 through 174 removed outlier: 3.586A pdb=" N TRP D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY D 151 " --> pdb=" O ARG D 147 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER D 154 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 155 " --> pdb=" O GLY D 151 " (cutoff:3.500A) Proline residue: D 156 - end of helix removed outlier: 4.034A pdb=" N VAL D 160 " --> pdb=" O PRO D 156 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL D 173 " --> pdb=" O GLY D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 191 removed outlier: 3.913A pdb=" N ASN D 191 " --> pdb=" O SER D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 220 removed outlier: 3.805A pdb=" N LYS D 205 " --> pdb=" O ASN D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 243 removed outlier: 3.868A pdb=" N ILE D 231 " --> pdb=" O THR D 227 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER D 232 " --> pdb=" O SER D 228 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR D 236 " --> pdb=" O SER D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 257 removed outlier: 3.950A pdb=" N LEU D 247 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 31 removed outlier: 4.022A pdb=" N MET C 31 " --> pdb=" O PRO C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 62 removed outlier: 5.122A pdb=" N LEU C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU C 58 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS C 60 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 removed outlier: 3.723A pdb=" N LYS C 67 " --> pdb=" O ASP C 63 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 31 removed outlier: 4.022A pdb=" N MET F 31 " --> pdb=" O PRO F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 62 removed outlier: 5.121A pdb=" N LEU F 57 " --> pdb=" O GLY F 53 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU F 58 " --> pdb=" O GLY F 54 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 68 removed outlier: 3.723A pdb=" N LYS F 67 " --> pdb=" O ASP F 63 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN F 68 " --> pdb=" O LEU F 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 28 removed outlier: 4.001A pdb=" N TRP G 9 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL G 10 " --> pdb=" O ASN G 6 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU G 15 " --> pdb=" O GLY G 11 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA G 28 " --> pdb=" O VAL G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 152 removed outlier: 3.606A pdb=" N ILE G 147 " --> pdb=" O LEU G 143 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN G 149 " --> pdb=" O ASP G 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 24 removed outlier: 3.658A pdb=" N TRP H 9 " --> pdb=" O LYS H 5 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY H 11 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE H 13 " --> pdb=" O TRP H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 151 Processing helix chain 'I' and resid 8 through 28 removed outlier: 4.015A pdb=" N LEU I 14 " --> pdb=" O VAL I 10 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA I 28 " --> pdb=" O VAL I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 151 removed outlier: 3.694A pdb=" N LEU I 146 " --> pdb=" O VAL I 142 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY I 148 " --> pdb=" O GLU I 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 28 removed outlier: 3.796A pdb=" N GLY J 11 " --> pdb=" O GLU J 7 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE J 13 " --> pdb=" O TRP J 9 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU J 18 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA J 21 " --> pdb=" O ALA J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 152 removed outlier: 3.526A pdb=" N GLY J 148 " --> pdb=" O GLU J 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 28 removed outlier: 4.494A pdb=" N PHE K 13 " --> pdb=" O TRP K 9 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU K 15 " --> pdb=" O GLY K 11 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA K 21 " --> pdb=" O ALA K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 152 removed outlier: 3.618A pdb=" N LEU K 146 " --> pdb=" O VAL K 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 18 removed outlier: 3.700A pdb=" N ALA L 17 " --> pdb=" O PHE L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 28 removed outlier: 4.190A pdb=" N CYS L 25 " --> pdb=" O ALA L 21 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU L 26 " --> pdb=" O LEU L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 152 Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 32 removed outlier: 3.587A pdb=" N VAL B 9 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 14 through 18 removed outlier: 3.723A pdb=" N ILE B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N PHE B 16 " --> pdb=" O ASP B 25 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASP B 25 " --> pdb=" O PHE B 16 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG B 18 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ILE B 23 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 37 through 39 removed outlier: 6.309A pdb=" N THR B 37 " --> pdb=" O VAL B 200 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 217 through 218 removed outlier: 3.840A pdb=" N ALA B 225 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 30 through 32 removed outlier: 3.587A pdb=" N VAL E 9 " --> pdb=" O VAL E 31 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 14 through 18 removed outlier: 3.723A pdb=" N ILE E 27 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N PHE E 16 " --> pdb=" O ASP E 25 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASP E 25 " --> pdb=" O PHE E 16 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG E 18 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ILE E 23 " --> pdb=" O ARG E 18 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 37 through 39 removed outlier: 6.310A pdb=" N THR E 37 " --> pdb=" O VAL E 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 215 through 218 removed outlier: 3.653A pdb=" N ALA E 215 " --> pdb=" O GLY E 227 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY E 227 " --> pdb=" O ALA E 215 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA E 225 " --> pdb=" O ILE E 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 6 through 9 removed outlier: 3.665A pdb=" N MET C 8 " --> pdb=" O ALA C 15 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA C 15 " --> pdb=" O MET C 8 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N ARG C 46 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU C 16 " --> pdb=" O ARG C 46 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N SER C 48 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N GLY C 18 " --> pdb=" O SER C 48 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL C 50 " --> pdb=" O GLY C 18 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU C 20 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 41 through 42 Processing sheet with id=AB2, first strand: chain 'F' and resid 6 through 9 removed outlier: 3.665A pdb=" N MET F 8 " --> pdb=" O ALA F 15 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA F 15 " --> pdb=" O MET F 8 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N ARG F 46 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU F 16 " --> pdb=" O ARG F 46 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N SER F 48 " --> pdb=" O LEU F 16 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N GLY F 18 " --> pdb=" O SER F 48 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL F 50 " --> pdb=" O GLY F 18 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU F 20 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 41 through 42 Processing sheet with id=AB4, first strand: chain 'G' and resid 39 through 45 removed outlier: 3.588A pdb=" N ALA G 44 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR G 83 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N VAL G 65 " --> pdb=" O GLU G 87 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N VAL G 64 " --> pdb=" O ILE G 60 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE G 60 " --> pdb=" O VAL G 64 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY G 66 " --> pdb=" O VAL G 58 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N SER G 59 " --> pdb=" O LEU G 114 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 39 through 40 Processing sheet with id=AB6, first strand: chain 'H' and resid 81 through 83 removed outlier: 6.809A pdb=" N TYR H 43 " --> pdb=" O ILE H 134 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 63 through 64 removed outlier: 3.510A pdb=" N SER H 59 " --> pdb=" O LEU H 112 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 39 through 43 removed outlier: 3.531A pdb=" N ARG I 67 " --> pdb=" O GLU I 85 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N VAL I 65 " --> pdb=" O GLU I 87 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL I 63 " --> pdb=" O ILE I 60 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL I 58 " --> pdb=" O VAL I 65 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU I 99 " --> pdb=" O LYS I 138 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 57 through 60 removed outlier: 3.994A pdb=" N GLY J 66 " --> pdb=" O VAL J 58 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE J 60 " --> pdb=" O VAL J 64 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL J 64 " --> pdb=" O ILE J 60 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N VAL J 65 " --> pdb=" O GLU J 87 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR J 83 " --> pdb=" O ALA J 69 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA J 44 " --> pdb=" O VAL J 82 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP J 132 " --> pdb=" O THR J 41 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 98 through 100 Processing sheet with id=AC2, first strand: chain 'K' and resid 39 through 40 Processing sheet with id=AC3, first strand: chain 'K' and resid 43 through 45 removed outlier: 6.744A pdb=" N THR K 83 " --> pdb=" O ALA K 69 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL K 64 " --> pdb=" O ILE K 60 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE K 60 " --> pdb=" O VAL K 64 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL K 58 " --> pdb=" O GLY K 66 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU K 114 " --> pdb=" O PRO K 57 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N SER K 59 " --> pdb=" O LEU K 114 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG K 102 " --> pdb=" O TYR K 111 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN K 115 " --> pdb=" O SER K 98 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER K 98 " --> pdb=" O ASN K 115 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU K 99 " --> pdb=" O LYS K 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 133 through 134 removed outlier: 8.787A pdb=" N ILE L 134 " --> pdb=" O THR L 41 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TYR L 43 " --> pdb=" O ILE L 134 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG L 67 " --> pdb=" O GLU L 85 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N VAL L 65 " --> pdb=" O GLU L 87 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LEU L 114 " --> pdb=" O PRO L 57 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER L 59 " --> pdb=" O LEU L 114 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU L 99 " --> pdb=" O LYS L 138 " (cutoff:3.500A) 522 hydrogen bonds defined for protein. 1482 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: 3.87 Time building geometry restraints manager: 6.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5082 1.34 - 1.46: 2652 1.46 - 1.57: 8266 1.57 - 1.69: 10 1.69 - 1.81: 124 Bond restraints: 16134 Sorted by residual: bond pdb=" C4 ATP E 301 " pdb=" C5 ATP E 301 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.26e+01 bond pdb=" C4 ATP B 301 " pdb=" C5 ATP B 301 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.17e+01 bond pdb=" C5 ATP B 301 " pdb=" C6 ATP B 301 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.48e+01 bond pdb=" C5 ATP E 301 " pdb=" C6 ATP E 301 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.44e+01 bond pdb=" C5 ATP E 301 " pdb=" N7 ATP E 301 " ideal model delta sigma weight residual 1.387 1.339 0.048 1.00e-02 1.00e+04 2.31e+01 ... (remaining 16129 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.49: 495 106.49 - 113.77: 9291 113.77 - 121.04: 7498 121.04 - 128.32: 4551 128.32 - 135.60: 117 Bond angle restraints: 21952 Sorted by residual: angle pdb=" PB ATP E 301 " pdb=" O3B ATP E 301 " pdb=" PG ATP E 301 " ideal model delta sigma weight residual 139.87 120.92 18.95 1.00e+00 1.00e+00 3.59e+02 angle pdb=" PB ATP B 301 " pdb=" O3B ATP B 301 " pdb=" PG ATP B 301 " ideal model delta sigma weight residual 139.87 120.94 18.93 1.00e+00 1.00e+00 3.58e+02 angle pdb=" PA ATP E 301 " pdb=" O3A ATP E 301 " pdb=" PB ATP E 301 " ideal model delta sigma weight residual 136.83 119.25 17.58 1.00e+00 1.00e+00 3.09e+02 angle pdb=" PA ATP B 301 " pdb=" O3A ATP B 301 " pdb=" PB ATP B 301 " ideal model delta sigma weight residual 136.83 119.31 17.52 1.00e+00 1.00e+00 3.07e+02 angle pdb=" C5 ATP E 301 " pdb=" C4 ATP E 301 " pdb=" N3 ATP E 301 " ideal model delta sigma weight residual 126.80 118.28 8.52 1.00e+00 1.00e+00 7.26e+01 ... (remaining 21947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8532 17.94 - 35.88: 847 35.88 - 53.82: 226 53.82 - 71.77: 57 71.77 - 89.71: 12 Dihedral angle restraints: 9674 sinusoidal: 3720 harmonic: 5954 Sorted by residual: dihedral pdb=" CA THR J 77 " pdb=" C THR J 77 " pdb=" N TYR J 78 " pdb=" CA TYR J 78 " ideal model delta harmonic sigma weight residual -180.00 -153.22 -26.78 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA ASP G 95 " pdb=" C ASP G 95 " pdb=" N THR G 96 " pdb=" CA THR G 96 " ideal model delta harmonic sigma weight residual 180.00 154.56 25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA THR L 77 " pdb=" C THR L 77 " pdb=" N TYR L 78 " pdb=" CA TYR L 78 " ideal model delta harmonic sigma weight residual 180.00 154.90 25.10 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 9671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2335 0.083 - 0.165: 298 0.165 - 0.248: 13 0.248 - 0.331: 3 0.331 - 0.414: 3 Chirality restraints: 2652 Sorted by residual: chirality pdb=" CB ILE L 71 " pdb=" CA ILE L 71 " pdb=" CG1 ILE L 71 " pdb=" CG2 ILE L 71 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CB ILE I 71 " pdb=" CA ILE I 71 " pdb=" CG1 ILE I 71 " pdb=" CG2 ILE I 71 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CB ILE H 71 " pdb=" CA ILE H 71 " pdb=" CG1 ILE H 71 " pdb=" CG2 ILE H 71 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 2649 not shown) Planarity restraints: 2764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 26 " 0.053 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO C 27 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO C 27 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 27 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 26 " 0.053 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO F 27 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO F 27 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO F 27 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 41 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.40e+00 pdb=" N PRO D 42 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 42 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 42 " -0.036 5.00e-02 4.00e+02 ... (remaining 2761 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 80 2.51 - 3.11: 10055 3.11 - 3.70: 22639 3.70 - 4.30: 31649 4.30 - 4.90: 53836 Nonbonded interactions: 118259 Sorted by model distance: nonbonded pdb=" O GLY B 259 " pdb=" O ASP B 260 " model vdw 1.910 3.040 nonbonded pdb=" N GLN E 230 " pdb=" OE1 GLN E 230 " model vdw 2.036 3.120 nonbonded pdb=" O HIS B 226 " pdb=" ND1 HIS B 226 " model vdw 2.129 3.120 nonbonded pdb=" OD1 ASP B 260 " pdb=" N TYR B 261 " model vdw 2.232 3.120 nonbonded pdb=" O TYR E 261 " pdb=" N ALA E 263 " model vdw 2.272 3.120 ... (remaining 118254 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' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = (chain 'G' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 152)) selection = (chain 'H' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 152)) selection = chain 'I' selection = (chain 'J' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 152)) selection = (chain 'K' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 152)) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 40.640 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 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:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 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 : 0.008 0.079 16134 Z= 0.509 Angle : 1.105 18.950 21952 Z= 0.658 Chirality : 0.056 0.414 2652 Planarity : 0.007 0.079 2764 Dihedral : 16.223 89.707 5850 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.75 % Favored : 89.01 % Rotamer: Outliers : 6.24 % Allowed : 10.34 % Favored : 83.41 % 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: -6.21 (0.12), residues: 2056 helix: -4.84 (0.06), residues: 811 sheet: -3.29 (0.26), residues: 290 loop : -3.65 (0.16), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 7 HIS 0.003 0.001 HIS E 122 PHE 0.020 0.002 PHE B 254 TYR 0.036 0.002 TYR J 111 ARG 0.008 0.001 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 387 time to evaluate : 1.744 Fit side-chains revert: symmetry clash REVERT: A 9 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6980 (tp) REVERT: A 72 LEU cc_start: 0.8444 (mm) cc_final: 0.8040 (mt) REVERT: A 111 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8629 (tmm160) REVERT: A 122 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8317 (tp) REVERT: A 203 LEU cc_start: 0.8732 (mt) cc_final: 0.8437 (mt) REVERT: B 130 GLU cc_start: 0.8649 (mm-30) cc_final: 0.7888 (tt0) REVERT: B 176 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8417 (p0) REVERT: B 222 LYS cc_start: 0.8345 (pttt) cc_final: 0.7548 (ptmm) REVERT: B 242 GLN cc_start: 0.6892 (tm-30) cc_final: 0.6486 (tm-30) REVERT: E 139 LYS cc_start: 0.8589 (mmtt) cc_final: 0.8325 (mmtp) REVERT: E 207 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7847 (mm-30) REVERT: E 222 LYS cc_start: 0.8292 (pttt) cc_final: 0.7908 (ptpp) REVERT: D 38 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6491 (mmt180) REVERT: D 129 LEU cc_start: 0.9296 (mt) cc_final: 0.9079 (mt) REVERT: D 134 MET cc_start: 0.8799 (tpt) cc_final: 0.8585 (tpt) REVERT: C 32 ARG cc_start: 0.6746 (ptt90) cc_final: 0.6545 (ptt-90) REVERT: C 81 VAL cc_start: 0.8849 (OUTLIER) cc_final: 0.8649 (m) REVERT: F 83 THR cc_start: 0.8914 (t) cc_final: 0.8714 (m) REVERT: G 74 ASP cc_start: 0.7947 (t0) cc_final: 0.7712 (t0) REVERT: G 134 ILE cc_start: 0.8664 (mt) cc_final: 0.8450 (mp) REVERT: H 102 ARG cc_start: 0.8339 (mtt180) cc_final: 0.7910 (mtm-85) REVERT: J 30 ASN cc_start: 0.6046 (OUTLIER) cc_final: 0.5539 (m-40) REVERT: J 85 GLU cc_start: 0.8111 (tt0) cc_final: 0.7564 (tt0) REVERT: K 48 ASN cc_start: 0.8274 (m110) cc_final: 0.8013 (t0) outliers start: 105 outliers final: 21 residues processed: 457 average time/residue: 0.2992 time to fit residues: 193.6310 Evaluate side-chains 330 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 301 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 262 HIS Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 230 GLN Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain J residue 30 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 8.9990 chunk 154 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 185 optimal weight: 7.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 29 ASN A 73 GLN A 128 GLN ** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 GLN B 230 GLN E 57 GLN E 62 HIS E 203 HIS D 4 ASN D 29 ASN D 73 GLN D 191 ASN D 241 HIS C 70 ASN F 70 ASN G 91 ASN H 149 GLN I 91 ASN K 6 ASN K 48 ASN K 115 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16134 Z= 0.236 Angle : 0.679 8.881 21952 Z= 0.353 Chirality : 0.043 0.182 2652 Planarity : 0.006 0.061 2764 Dihedral : 8.936 87.562 2350 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.88 % Favored : 92.07 % Rotamer: Outliers : 3.33 % Allowed : 16.41 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.80 (0.15), residues: 2056 helix: -3.14 (0.13), residues: 836 sheet: -2.93 (0.27), residues: 288 loop : -3.22 (0.17), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 216 HIS 0.015 0.001 HIS E 62 PHE 0.018 0.002 PHE G 13 TYR 0.017 0.001 TYR K 40 ARG 0.006 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 323 time to evaluate : 1.800 Fit side-chains REVERT: A 26 MET cc_start: 0.9046 (ttt) cc_final: 0.8801 (ttp) REVERT: A 72 LEU cc_start: 0.8409 (mm) cc_final: 0.8160 (mt) REVERT: A 111 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8312 (tmm160) REVERT: A 127 GLU cc_start: 0.7511 (tt0) cc_final: 0.7310 (tt0) REVERT: A 158 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8802 (mp) REVERT: B 141 MET cc_start: 0.8283 (mmm) cc_final: 0.7875 (mmm) REVERT: B 222 LYS cc_start: 0.8388 (pttt) cc_final: 0.7513 (ptmm) REVERT: B 230 GLN cc_start: 0.7473 (mp-120) cc_final: 0.7239 (mp10) REVERT: B 242 GLN cc_start: 0.7038 (tm-30) cc_final: 0.6538 (tm-30) REVERT: E 40 MET cc_start: 0.8189 (mtp) cc_final: 0.7903 (mtt) REVERT: E 222 LYS cc_start: 0.8288 (pttt) cc_final: 0.7877 (ptpp) REVERT: D 38 ARG cc_start: 0.7172 (mtt180) cc_final: 0.6741 (mmt180) REVERT: D 75 TYR cc_start: 0.8810 (t80) cc_final: 0.8533 (t80) REVERT: D 231 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8629 (mp) REVERT: C 22 GLN cc_start: 0.7647 (pt0) cc_final: 0.7348 (pt0) REVERT: F 8 MET cc_start: 0.5547 (ttp) cc_final: 0.5205 (pmm) REVERT: G 74 ASP cc_start: 0.7788 (t0) cc_final: 0.7547 (t0) REVERT: G 134 ILE cc_start: 0.8696 (mt) cc_final: 0.8492 (mp) REVERT: H 88 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7575 (mm-40) REVERT: I 138 LYS cc_start: 0.8471 (mttt) cc_final: 0.8169 (mttt) REVERT: J 19 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8481 (mt) REVERT: J 30 ASN cc_start: 0.6285 (OUTLIER) cc_final: 0.5684 (m-40) REVERT: J 77 THR cc_start: 0.8556 (t) cc_final: 0.8337 (t) REVERT: J 85 GLU cc_start: 0.7999 (tt0) cc_final: 0.7783 (tt0) REVERT: K 6 ASN cc_start: 0.7567 (t0) cc_final: 0.7267 (t0) REVERT: K 9 TRP cc_start: 0.7688 (t-100) cc_final: 0.6605 (t60) outliers start: 56 outliers final: 32 residues processed: 366 average time/residue: 0.2661 time to fit residues: 143.5796 Evaluate side-chains 314 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 277 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 91 ASN Chi-restraints excluded: chain I residue 92 HIS Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 91 ASN Chi-restraints excluded: chain J residue 111 TYR Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 134 ILE Chi-restraints excluded: chain L residue 100 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 154 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 185 optimal weight: 8.9990 chunk 200 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 148 optimal weight: 30.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 233 GLN E 62 HIS D 191 ASN K 6 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16134 Z= 0.279 Angle : 0.666 9.130 21952 Z= 0.342 Chirality : 0.044 0.277 2652 Planarity : 0.005 0.055 2764 Dihedral : 7.705 68.523 2315 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 4.52 % Allowed : 19.32 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.16), residues: 2056 helix: -2.23 (0.16), residues: 844 sheet: -2.68 (0.28), residues: 286 loop : -3.03 (0.18), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 216 HIS 0.013 0.001 HIS E 62 PHE 0.019 0.002 PHE G 13 TYR 0.019 0.002 TYR K 40 ARG 0.006 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 288 time to evaluate : 1.822 Fit side-chains REVERT: A 26 MET cc_start: 0.9075 (ttt) cc_final: 0.8755 (ttp) REVERT: A 72 LEU cc_start: 0.8531 (mm) cc_final: 0.8270 (mt) REVERT: A 111 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8454 (tmm160) REVERT: B 141 MET cc_start: 0.8253 (mmm) cc_final: 0.7873 (mmm) REVERT: B 170 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8756 (mp10) REVERT: B 222 LYS cc_start: 0.8514 (pttt) cc_final: 0.7644 (ptmm) REVERT: B 242 GLN cc_start: 0.7047 (tm-30) cc_final: 0.6623 (tm-30) REVERT: E 222 LYS cc_start: 0.8381 (pttt) cc_final: 0.7920 (ptpp) REVERT: D 38 ARG cc_start: 0.7390 (mtt180) cc_final: 0.6798 (mmt180) REVERT: D 75 TYR cc_start: 0.8984 (t80) cc_final: 0.8673 (t80) REVERT: C 22 GLN cc_start: 0.7763 (pt0) cc_final: 0.7482 (pt0) REVERT: C 57 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8070 (tp) REVERT: F 22 GLN cc_start: 0.8603 (mt0) cc_final: 0.8258 (mt0) REVERT: G 74 ASP cc_start: 0.7780 (t0) cc_final: 0.7538 (t0) REVERT: G 134 ILE cc_start: 0.8737 (mt) cc_final: 0.8519 (mp) REVERT: H 88 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7596 (mm-40) REVERT: I 85 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.5889 (mp0) REVERT: I 138 LYS cc_start: 0.8475 (mttt) cc_final: 0.8211 (mttt) REVERT: J 30 ASN cc_start: 0.6491 (OUTLIER) cc_final: 0.5749 (m-40) REVERT: J 85 GLU cc_start: 0.7938 (tt0) cc_final: 0.7701 (tt0) REVERT: J 111 TYR cc_start: 0.8847 (OUTLIER) cc_final: 0.8375 (p90) REVERT: K 9 TRP cc_start: 0.7675 (t-100) cc_final: 0.6436 (t60) REVERT: K 151 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.6707 (pp) outliers start: 76 outliers final: 52 residues processed: 337 average time/residue: 0.2684 time to fit residues: 133.6934 Evaluate side-chains 328 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 269 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 89 ARG Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 55 ARG Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain I residue 92 HIS Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 91 ASN Chi-restraints excluded: chain J residue 111 TYR Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 141 MET Chi-restraints excluded: chain K residue 8 ILE Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 134 ILE Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 91 ASN Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 142 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 124 optimal weight: 20.0000 chunk 186 optimal weight: 2.9990 chunk 197 optimal weight: 0.0370 chunk 97 optimal weight: 0.6980 chunk 176 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 overall best weight: 1.5062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 HIS D 191 ASN K 6 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16134 Z= 0.173 Angle : 0.588 8.649 21952 Z= 0.302 Chirality : 0.042 0.209 2652 Planarity : 0.004 0.048 2764 Dihedral : 7.063 65.578 2309 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 4.22 % Allowed : 20.63 % Favored : 75.15 % 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: -3.41 (0.17), residues: 2056 helix: -1.57 (0.18), residues: 833 sheet: -2.41 (0.29), residues: 286 loop : -2.83 (0.18), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 216 HIS 0.003 0.001 HIS K 92 PHE 0.011 0.001 PHE A 185 TYR 0.015 0.001 TYR J 152 ARG 0.004 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 295 time to evaluate : 1.923 Fit side-chains REVERT: A 18 ARG cc_start: 0.7220 (mpt180) cc_final: 0.7008 (mtm-85) REVERT: A 72 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8303 (mt) REVERT: B 222 LYS cc_start: 0.8490 (pttt) cc_final: 0.7688 (ptmm) REVERT: B 242 GLN cc_start: 0.6925 (tm-30) cc_final: 0.6451 (tm-30) REVERT: E 162 GLU cc_start: 0.8258 (mp0) cc_final: 0.8049 (mp0) REVERT: E 222 LYS cc_start: 0.8384 (pttt) cc_final: 0.7845 (ptpp) REVERT: D 38 ARG cc_start: 0.7354 (mtt180) cc_final: 0.6772 (mmt180) REVERT: D 75 TYR cc_start: 0.8923 (t80) cc_final: 0.8448 (t80) REVERT: D 134 MET cc_start: 0.8448 (tpt) cc_final: 0.8225 (mmm) REVERT: D 231 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8774 (mp) REVERT: C 22 GLN cc_start: 0.7759 (pt0) cc_final: 0.7462 (pt0) REVERT: F 37 LYS cc_start: 0.5682 (OUTLIER) cc_final: 0.5403 (pttp) REVERT: G 74 ASP cc_start: 0.7882 (t0) cc_final: 0.7670 (t0) REVERT: G 134 ILE cc_start: 0.8709 (mt) cc_final: 0.8494 (mp) REVERT: H 70 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8108 (t0) REVERT: H 88 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7540 (mm-40) REVERT: I 85 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6079 (mp0) REVERT: I 138 LYS cc_start: 0.8403 (mttt) cc_final: 0.8153 (mttt) REVERT: J 30 ASN cc_start: 0.6364 (OUTLIER) cc_final: 0.5732 (m-40) REVERT: J 111 TYR cc_start: 0.8648 (OUTLIER) cc_final: 0.8405 (p90) REVERT: K 6 ASN cc_start: 0.7547 (t0) cc_final: 0.7214 (t0) REVERT: K 22 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6866 (mm) REVERT: K 151 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6585 (pp) outliers start: 71 outliers final: 40 residues processed: 342 average time/residue: 0.2798 time to fit residues: 142.5521 Evaluate side-chains 316 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 267 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 62 HIS Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 37 LYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 55 ARG Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain I residue 92 HIS Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 91 ASN Chi-restraints excluded: chain J residue 111 TYR Chi-restraints excluded: chain K residue 8 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 142 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 81 optimal weight: 0.9980 chunk 168 optimal weight: 20.0000 chunk 136 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 176 optimal weight: 0.1980 chunk 49 optimal weight: 0.3980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 233 GLN D 128 GLN D 191 ASN I 91 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16134 Z= 0.156 Angle : 0.572 8.624 21952 Z= 0.294 Chirality : 0.041 0.160 2652 Planarity : 0.004 0.044 2764 Dihedral : 6.658 64.526 2305 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 3.92 % Allowed : 21.40 % Favored : 74.67 % 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: -3.05 (0.18), residues: 2056 helix: -1.19 (0.18), residues: 834 sheet: -2.20 (0.30), residues: 286 loop : -2.72 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 216 HIS 0.008 0.001 HIS B 62 PHE 0.014 0.001 PHE A 219 TYR 0.014 0.001 TYR K 40 ARG 0.003 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 285 time to evaluate : 1.913 Fit side-chains REVERT: A 72 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8284 (mt) REVERT: B 11 MET cc_start: 0.7965 (mmm) cc_final: 0.7543 (mmm) REVERT: B 141 MET cc_start: 0.8255 (mmm) cc_final: 0.7861 (mmm) REVERT: B 222 LYS cc_start: 0.8396 (pttt) cc_final: 0.7570 (ptmm) REVERT: B 242 GLN cc_start: 0.6921 (tm-30) cc_final: 0.6453 (tm-30) REVERT: E 222 LYS cc_start: 0.8295 (pttt) cc_final: 0.7776 (ptpp) REVERT: D 26 MET cc_start: 0.8831 (ttp) cc_final: 0.8380 (tmm) REVERT: D 38 ARG cc_start: 0.7263 (mtt180) cc_final: 0.6719 (mmt180) REVERT: D 75 TYR cc_start: 0.8887 (t80) cc_final: 0.8401 (t80) REVERT: D 142 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7959 (mmt-90) REVERT: D 231 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8759 (mp) REVERT: F 37 LYS cc_start: 0.5676 (OUTLIER) cc_final: 0.5418 (pttp) REVERT: G 74 ASP cc_start: 0.7843 (t0) cc_final: 0.7639 (t0) REVERT: H 70 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8174 (t0) REVERT: H 88 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7583 (mm-40) REVERT: I 84 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8468 (mt) REVERT: I 85 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6189 (mp0) REVERT: I 91 ASN cc_start: 0.7889 (OUTLIER) cc_final: 0.7625 (p0) REVERT: J 30 ASN cc_start: 0.6329 (OUTLIER) cc_final: 0.5792 (m-40) REVERT: K 6 ASN cc_start: 0.7559 (t0) cc_final: 0.7251 (t0) REVERT: K 22 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6829 (mm) REVERT: K 79 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7395 (pp) REVERT: K 151 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6465 (pp) outliers start: 66 outliers final: 39 residues processed: 327 average time/residue: 0.2790 time to fit residues: 135.8760 Evaluate side-chains 321 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 270 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain E residue 7 ASN Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 37 LYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 55 ARG Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain I residue 91 ASN Chi-restraints excluded: chain I residue 92 HIS Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 91 ASN Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain K residue 8 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 134 ILE Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 142 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 115 optimal weight: 0.0030 chunk 48 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 163 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 20.0000 overall best weight: 1.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 HIS D 191 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16134 Z= 0.189 Angle : 0.584 9.053 21952 Z= 0.299 Chirality : 0.042 0.160 2652 Planarity : 0.004 0.043 2764 Dihedral : 6.560 64.867 2304 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 4.64 % Allowed : 21.58 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.18), residues: 2056 helix: -0.95 (0.19), residues: 828 sheet: -2.04 (0.31), residues: 286 loop : -2.62 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 216 HIS 0.002 0.001 HIS E 122 PHE 0.013 0.001 PHE A 185 TYR 0.015 0.001 TYR K 40 ARG 0.004 0.000 ARG J 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 275 time to evaluate : 1.805 Fit side-chains REVERT: A 72 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8315 (mt) REVERT: B 141 MET cc_start: 0.8274 (mmm) cc_final: 0.7893 (mmm) REVERT: B 222 LYS cc_start: 0.8408 (pttt) cc_final: 0.7580 (ptmm) REVERT: B 242 GLN cc_start: 0.7322 (tm-30) cc_final: 0.6835 (tm-30) REVERT: E 162 GLU cc_start: 0.8398 (mp0) cc_final: 0.8172 (mp0) REVERT: E 222 LYS cc_start: 0.8308 (pttt) cc_final: 0.7780 (ptpp) REVERT: D 26 MET cc_start: 0.8857 (ttp) cc_final: 0.8412 (tmm) REVERT: D 38 ARG cc_start: 0.7277 (mtt180) cc_final: 0.6775 (mmt180) REVERT: D 142 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7919 (mmt-90) REVERT: D 231 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8723 (mp) REVERT: C 8 MET cc_start: 0.5622 (mmt) cc_final: 0.5366 (mmt) REVERT: F 37 LYS cc_start: 0.5768 (OUTLIER) cc_final: 0.5512 (pttp) REVERT: G 74 ASP cc_start: 0.7923 (t0) cc_final: 0.7701 (t0) REVERT: I 84 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8504 (mt) REVERT: I 85 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6125 (mp0) REVERT: I 91 ASN cc_start: 0.8301 (OUTLIER) cc_final: 0.8025 (p0) REVERT: J 30 ASN cc_start: 0.6373 (OUTLIER) cc_final: 0.5851 (m-40) REVERT: K 6 ASN cc_start: 0.7587 (t0) cc_final: 0.7273 (t0) REVERT: K 22 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6930 (mm) REVERT: K 79 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7396 (pp) REVERT: K 151 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6512 (pp) outliers start: 78 outliers final: 45 residues processed: 325 average time/residue: 0.2680 time to fit residues: 131.0813 Evaluate side-chains 322 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 266 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 177 TRP Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain E residue 7 ASN Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain C residue 31 MET Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 37 LYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 89 ARG Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 55 ARG Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain I residue 91 ASN Chi-restraints excluded: chain I residue 92 HIS Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 91 ASN Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain K residue 8 ILE Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain L residue 142 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- 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: 72.416 > 50: distance: 10 - 14: 33.876 distance: 14 - 15: 57.290 distance: 15 - 16: 57.300 distance: 15 - 18: 55.092 distance: 16 - 17: 57.332 distance: 16 - 22: 55.266 distance: 18 - 19: 57.797 distance: 19 - 20: 56.205 distance: 19 - 21: 14.431 distance: 22 - 23: 39.500 distance: 23 - 24: 70.756 distance: 23 - 26: 45.858 distance: 24 - 25: 55.889 distance: 24 - 30: 57.131 distance: 26 - 27: 28.344 distance: 26 - 28: 21.856 distance: 27 - 29: 18.491 distance: 30 - 31: 39.097 distance: 32 - 33: 56.027 distance: 32 - 34: 39.651 distance: 34 - 35: 70.212 distance: 35 - 36: 11.969 distance: 36 - 37: 10.988 distance: 36 - 38: 45.394 distance: 38 - 39: 35.887 distance: 39 - 40: 4.081 distance: 39 - 42: 57.062 distance: 40 - 41: 57.489 distance: 40 - 46: 40.680 distance: 42 - 43: 48.110 distance: 43 - 44: 39.680 distance: 43 - 45: 56.702 distance: 46 - 47: 70.029 distance: 47 - 48: 39.553 distance: 47 - 50: 41.088 distance: 48 - 49: 37.326 distance: 48 - 55: 40.758 distance: 50 - 51: 38.657 distance: 51 - 52: 56.624 distance: 52 - 53: 57.247 distance: 53 - 54: 56.493 distance: 55 - 56: 43.105 distance: 56 - 57: 43.338 distance: 56 - 59: 43.987 distance: 57 - 58: 57.319 distance: 57 - 60: 53.851 distance: 60 - 61: 5.652 distance: 61 - 62: 42.572 distance: 61 - 64: 55.121 distance: 62 - 63: 39.605 distance: 62 - 71: 40.811 distance: 64 - 65: 40.322 distance: 65 - 66: 67.802 distance: 67 - 68: 40.661 distance: 68 - 69: 3.459 distance: 68 - 70: 40.535 distance: 71 - 72: 70.121 distance: 72 - 73: 39.505 distance: 72 - 75: 39.394 distance: 73 - 74: 40.248 distance: 73 - 77: 55.481 distance: 77 - 78: 40.126 distance: 77 - 83: 70.412 distance: 78 - 79: 64.742 distance: 78 - 81: 42.521 distance: 79 - 80: 55.886 distance: 79 - 84: 34.351 distance: 81 - 82: 39.571 distance: 82 - 83: 55.992