Starting phenix.real_space_refine on Sat Mar 16 22:23:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgn_30358/03_2024/7cgn_30358_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgn_30358/03_2024/7cgn_30358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgn_30358/03_2024/7cgn_30358.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgn_30358/03_2024/7cgn_30358.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgn_30358/03_2024/7cgn_30358_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgn_30358/03_2024/7cgn_30358_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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 2950 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 119": "OE1" <-> "OE2" Residue "A ARG 124": "NH1" <-> "NH2" 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 33": "NH1" <-> "NH2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B GLU 112": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ARG 157": "NH1" <-> "NH2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B ASP 176": "OD1" <-> "OD2" Residue "B PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "D ARG 18": "NH1" <-> "NH2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D ARG 141": "NH1" <-> "NH2" Residue "D ARG 196": "NH1" <-> "NH2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E ARG 33": "NH1" <-> "NH2" Residue "E GLU 64": "OE1" <-> "OE2" Residue "E GLU 112": "OE1" <-> "OE2" Residue "E GLU 130": "OE1" <-> "OE2" Residue "E ARG 157": "NH1" <-> "NH2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E ASP 176": "OD1" <-> "OD2" Residue "E PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "G GLU 37": "OE1" <-> "OE2" Residue "G ARG 55": "NH1" <-> "NH2" Residue "H ARG 55": "NH1" <-> "NH2" Residue "H ASP 70": "OD1" <-> "OD2" Residue "H GLU 85": "OE1" <-> "OE2" Residue "H GLU 144": "OE1" <-> "OE2" Residue "I ARG 55": "NH1" <-> "NH2" Residue "I GLU 119": "OE1" <-> "OE2" Residue "I GLU 144": "OE1" <-> "OE2" Residue "J ARG 55": "NH1" <-> "NH2" Residue "J GLU 144": "OE1" <-> "OE2" Residue "K ARG 55": "NH1" <-> "NH2" Residue "L ARG 55": "NH1" <-> "NH2" Residue "L ASP 70": "OD1" <-> "OD2" Residue "L GLU 119": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15854 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: "C" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 724 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} 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: "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: "F" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 724 Classifications: {'peptide': 94} 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: 9.27, per 1000 atoms: 0.58 Number of scatterers: 15854 At special positions: 0 Unit cell: (104.352, 116.309, 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 2950 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: 5.70 Conformation dependent library (CDL) restraints added in 3.2 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... running ksdssp... Secondary structure from input PDB file: 64 helices and 13 sheets defined 38.3% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'A' and resid 6 through 30 removed outlier: 3.789A pdb=" N LYS A 12 " --> pdb=" O SER A 8 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A 14 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU A 17 " --> pdb=" O GLY A 13 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR A 19 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.710A pdb=" N VAL A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG A 46 " --> pdb=" O PRO A 42 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR A 49 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 80 removed outlier: 4.171A pdb=" N PHE A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 77 " --> pdb=" O GLN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 95 removed outlier: 3.533A pdb=" N GLY A 88 " --> pdb=" O THR A 85 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL A 91 " --> pdb=" O GLY A 88 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ALA A 92 " --> pdb=" O MET A 89 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER A 94 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 95 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 125 removed outlier: 3.660A pdb=" N ALA A 104 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 139 through 142 No H-bonds generated for 'chain 'A' and resid 139 through 142' Processing helix chain 'A' and resid 145 through 152 removed outlier: 3.588A pdb=" N VAL A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 173 removed outlier: 3.866A pdb=" N ILE A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 164 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 173 " --> pdb=" O GLY A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.686A pdb=" N TRP A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 188 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET A 189 " --> pdb=" O PHE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 220 removed outlier: 4.022A pdb=" N LEU A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 211 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP A 215 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 257 removed outlier: 4.136A pdb=" N SER A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.769A pdb=" N LEU B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 74 No H-bonds generated for 'chain 'B' and resid 72 through 74' Processing helix chain 'B' and resid 77 through 85 removed outlier: 4.116A pdb=" N LYS B 85 " --> pdb=" O TYR B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 109 through 113 removed outlier: 3.733A pdb=" N HIS B 113 " --> pdb=" O LEU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 131 removed outlier: 3.878A pdb=" N LYS B 128 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU B 130 " --> pdb=" O MET B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 158 removed outlier: 4.013A pdb=" N ARG B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 192 removed outlier: 3.520A pdb=" N LYS B 185 " --> pdb=" O GLY B 181 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B 189 " --> pdb=" O LYS B 185 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN B 191 " --> pdb=" O ILE B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 210 removed outlier: 5.038A pdb=" N SER B 210 " --> pdb=" O PRO B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 232 No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'B' and resid 238 through 245 Processing helix chain 'C' and resid 26 through 30 Processing helix chain 'C' and resid 52 through 63 Processing helix chain 'C' and resid 81 through 87 removed outlier: 3.669A pdb=" N LYS C 86 " --> pdb=" O TYR C 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 30 removed outlier: 3.789A pdb=" N LYS D 12 " --> pdb=" O SER D 8 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE D 14 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU D 17 " --> pdb=" O GLY D 13 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR D 19 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 51 removed outlier: 3.710A pdb=" N VAL D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG D 46 " --> pdb=" O PRO D 42 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR D 49 " --> pdb=" O VAL D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 80 removed outlier: 4.171A pdb=" N PHE D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR D 75 " --> pdb=" O GLY D 71 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU D 76 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL D 77 " --> pdb=" O GLN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 95 removed outlier: 3.533A pdb=" N GLY D 88 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL D 91 " --> pdb=" O GLY D 88 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ALA D 92 " --> pdb=" O MET D 89 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER D 94 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU D 95 " --> pdb=" O ALA D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 125 removed outlier: 3.661A pdb=" N ALA D 104 " --> pdb=" O GLY D 100 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA D 105 " --> pdb=" O PRO D 101 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER D 114 " --> pdb=" O GLY D 110 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR D 117 " --> pdb=" O GLY D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 139 through 142 No H-bonds generated for 'chain 'D' and resid 139 through 142' Processing helix chain 'D' and resid 145 through 152 removed outlier: 3.589A pdb=" N VAL D 152 " --> pdb=" O PHE D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 173 removed outlier: 3.867A pdb=" N ILE D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA D 164 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL D 173 " --> pdb=" O GLY D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 190 removed outlier: 3.687A pdb=" N TRP D 186 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER D 187 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA D 188 " --> pdb=" O PHE D 184 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET D 189 " --> pdb=" O PHE D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 220 removed outlier: 4.021A pdb=" N LEU D 203 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL D 208 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D 211 " --> pdb=" O VAL D 207 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR D 212 " --> pdb=" O VAL D 208 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP D 215 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN D 220 " --> pdb=" O ILE D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 257 removed outlier: 4.137A pdb=" N SER D 232 " --> pdb=" O SER D 228 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL D 240 " --> pdb=" O THR D 236 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU D 244 " --> pdb=" O VAL D 240 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU D 247 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N MET D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 55 removed outlier: 3.769A pdb=" N LEU E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 74 No H-bonds generated for 'chain 'E' and resid 72 through 74' Processing helix chain 'E' and resid 77 through 85 removed outlier: 4.116A pdb=" N LYS E 85 " --> pdb=" O TYR E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 106 Processing helix chain 'E' and resid 109 through 113 removed outlier: 3.732A pdb=" N HIS E 113 " --> pdb=" O LEU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 131 removed outlier: 3.878A pdb=" N LYS E 128 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU E 130 " --> pdb=" O MET E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 158 removed outlier: 4.012A pdb=" N ARG E 152 " --> pdb=" O GLY E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 192 removed outlier: 3.520A pdb=" N LYS E 185 " --> pdb=" O GLY E 181 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN E 191 " --> pdb=" O ILE E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 210 removed outlier: 5.038A pdb=" N SER E 210 " --> pdb=" O PRO E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 232 No H-bonds generated for 'chain 'E' and resid 229 through 232' Processing helix chain 'E' and resid 238 through 245 Processing helix chain 'F' and resid 26 through 30 Processing helix chain 'F' and resid 52 through 63 Processing helix chain 'F' and resid 81 through 87 removed outlier: 3.669A pdb=" N LYS F 86 " --> pdb=" O TYR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 25 removed outlier: 3.540A pdb=" N TRP G 9 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY G 11 " --> pdb=" O GLU G 7 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU G 18 " --> pdb=" O LEU G 14 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS G 25 " --> pdb=" O ALA G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 149 No H-bonds generated for 'chain 'G' and resid 146 through 149' Processing helix chain 'H' and resid 10 through 29 removed outlier: 3.539A pdb=" N VAL H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS H 25 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS H 27 " --> pdb=" O PHE H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 151 removed outlier: 3.759A pdb=" N PHE H 150 " --> pdb=" O LEU H 146 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU H 151 " --> pdb=" O ILE H 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 27 removed outlier: 4.028A pdb=" N TRP I 9 " --> pdb=" O LYS I 5 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL I 10 " --> pdb=" O ASN I 6 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE I 13 " --> pdb=" O TRP I 9 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 151 removed outlier: 3.515A pdb=" N PHE I 150 " --> pdb=" O LEU I 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 28 removed outlier: 3.702A pdb=" N GLY J 11 " --> pdb=" O GLU J 7 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 151 removed outlier: 3.515A pdb=" N PHE J 150 " --> pdb=" O LEU J 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 28 removed outlier: 3.993A pdb=" N ALA K 28 " --> pdb=" O VAL K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 151 removed outlier: 3.732A pdb=" N LEU K 151 " --> pdb=" O ILE K 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 27 Processing helix chain 'L' and resid 144 through 150 removed outlier: 3.565A pdb=" N PHE L 150 " --> pdb=" O LEU L 146 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.448A pdb=" N VAL B 31 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP B 10 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU B 29 " --> pdb=" O ASP B 10 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 214 through 216 removed outlier: 4.360A pdb=" N HIS B 214 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA B 38 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N CYS B 198 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE B 39 " --> pdb=" O CYS B 198 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL B 200 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.449A pdb=" N VAL E 31 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP E 10 " --> pdb=" O LEU E 29 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU E 29 " --> pdb=" O ASP E 10 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 214 through 218 removed outlier: 4.360A pdb=" N HIS E 214 " --> pdb=" O ILE E 36 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA E 38 " --> pdb=" O HIS E 214 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS E 198 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE E 39 " --> pdb=" O CYS E 198 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL E 200 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N GLY E 41 " --> pdb=" O VAL E 200 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'G' and resid 39 through 45 removed outlier: 3.677A pdb=" N LEU G 42 " --> pdb=" O LEU G 84 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU G 85 " --> pdb=" O ARG G 67 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG G 67 " --> pdb=" O GLU G 85 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU G 87 " --> pdb=" O VAL G 65 " (cutoff:3.500A) removed outlier: 10.119A pdb=" N VAL G 65 " --> pdb=" O GLU G 87 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL G 58 " --> pdb=" O VAL G 65 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU G 112 " --> pdb=" O SER G 59 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 81 through 87 removed outlier: 5.593A pdb=" N ASP H 132 " --> pdb=" O TYR H 43 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N THR H 45 " --> pdb=" O ASP H 132 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE H 134 " --> pdb=" O THR H 45 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 112 through 114 removed outlier: 5.832A pdb=" N ILE H 60 " --> pdb=" O VAL H 64 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N VAL H 64 " --> pdb=" O ILE H 60 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'I' and resid 112 through 114 removed outlier: 3.951A pdb=" N SER I 56 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE I 60 " --> pdb=" O VAL I 64 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL I 64 " --> pdb=" O ILE I 60 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'J' and resid 39 through 45 removed outlier: 3.634A pdb=" N LEU J 42 " --> pdb=" O LEU J 84 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'J' and resid 112 through 114 removed outlier: 6.470A pdb=" N ILE J 60 " --> pdb=" O VAL J 64 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL J 64 " --> pdb=" O ILE J 60 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'K' and resid 43 through 46 Processing sheet with id= L, first strand: chain 'K' and resid 112 through 114 removed outlier: 5.790A pdb=" N ILE K 60 " --> pdb=" O VAL K 64 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N VAL K 64 " --> pdb=" O ILE K 60 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'L' and resid 112 through 114 removed outlier: 3.961A pdb=" N SER L 56 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE L 60 " --> pdb=" O VAL L 64 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N VAL L 64 " --> pdb=" O ILE L 60 " (cutoff:3.500A) 499 hydrogen bonds defined for protein. 1452 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: 3.44 Time building geometry restraints manager: 6.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5142 1.35 - 1.47: 3629 1.47 - 1.60: 7227 1.60 - 1.72: 10 1.72 - 1.84: 124 Bond restraints: 16132 Sorted by residual: bond pdb=" C4 ATP E 301 " pdb=" C5 ATP E 301 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.91e+01 bond pdb=" C4 ATP B 301 " pdb=" C5 ATP B 301 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.86e+01 bond pdb=" C5 ATP E 301 " pdb=" C6 ATP E 301 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.34e+01 bond pdb=" C5 ATP B 301 " pdb=" C6 ATP B 301 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.33e+01 bond pdb=" C8 ATP E 301 " pdb=" N7 ATP E 301 " ideal model delta sigma weight residual 1.310 1.358 -0.048 1.00e-02 1.00e+04 2.30e+01 ... (remaining 16127 not shown) Histogram of bond angle deviations from ideal: 98.84 - 106.30: 454 106.30 - 113.75: 9344 113.75 - 121.21: 7825 121.21 - 128.66: 4221 128.66 - 136.12: 104 Bond angle restraints: 21948 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 139.87 120.50 19.37 1.00e+00 1.00e+00 3.75e+02 angle pdb=" PB ATP B 301 " pdb=" O3B ATP B 301 " pdb=" PG ATP B 301 " ideal model delta sigma weight residual 139.87 120.56 19.31 1.00e+00 1.00e+00 3.73e+02 angle pdb=" PA ATP E 301 " pdb=" O3A ATP E 301 " pdb=" PB ATP E 301 " ideal model delta sigma weight residual 136.83 120.47 16.36 1.00e+00 1.00e+00 2.68e+02 angle pdb=" PA ATP B 301 " pdb=" O3A ATP B 301 " pdb=" PB ATP B 301 " ideal model delta sigma weight residual 136.83 120.51 16.32 1.00e+00 1.00e+00 2.66e+02 angle pdb=" C5 ATP E 301 " pdb=" C4 ATP E 301 " pdb=" N3 ATP E 301 " ideal model delta sigma weight residual 126.80 118.64 8.16 1.00e+00 1.00e+00 6.67e+01 ... (remaining 21943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 8421 17.12 - 34.23: 867 34.23 - 51.35: 267 51.35 - 68.47: 94 68.47 - 85.59: 23 Dihedral angle restraints: 9672 sinusoidal: 3718 harmonic: 5954 Sorted by residual: dihedral pdb=" CA GLN J 135 " pdb=" C GLN J 135 " pdb=" N ASP J 136 " pdb=" CA ASP J 136 " ideal model delta harmonic sigma weight residual 180.00 152.81 27.19 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA ALA K 140 " pdb=" C ALA K 140 " pdb=" N MET K 141 " pdb=" CA MET K 141 " ideal model delta harmonic sigma weight residual 180.00 155.54 24.46 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA VAL J 142 " pdb=" C VAL J 142 " pdb=" N LEU J 143 " pdb=" CA LEU J 143 " ideal model delta harmonic sigma weight residual -180.00 -155.55 -24.45 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 9669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2114 0.064 - 0.129: 443 0.129 - 0.193: 76 0.193 - 0.257: 15 0.257 - 0.321: 4 Chirality restraints: 2652 Sorted by residual: chirality pdb=" CB ILE B 223 " pdb=" CA ILE B 223 " pdb=" CG1 ILE B 223 " pdb=" CG2 ILE B 223 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CB ILE E 223 " pdb=" CA ILE E 223 " pdb=" CG1 ILE E 223 " pdb=" CG2 ILE E 223 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CB ILE J 60 " pdb=" CA ILE J 60 " pdb=" CG1 ILE J 60 " pdb=" CG2 ILE J 60 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 2649 not shown) Planarity restraints: 2762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 16 " -0.024 2.00e-02 2.50e+03 2.39e-02 9.99e+00 pdb=" CG PHE E 16 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE E 16 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE E 16 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE E 16 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE E 16 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE E 16 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 16 " 0.024 2.00e-02 2.50e+03 2.38e-02 9.94e+00 pdb=" CG PHE B 16 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE B 16 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE B 16 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 16 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 16 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE B 16 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 41 " -0.049 5.00e-02 4.00e+02 7.46e-02 8.89e+00 pdb=" N PRO B 42 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 42 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 42 " -0.040 5.00e-02 4.00e+02 ... (remaining 2759 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2699 2.76 - 3.30: 14956 3.30 - 3.83: 26182 3.83 - 4.37: 28955 4.37 - 4.90: 48259 Nonbonded interactions: 121051 Sorted by model distance: nonbonded pdb=" O ALA K 69 " pdb=" N ILE K 71 " model vdw 2.225 2.520 nonbonded pdb=" O GLY A 110 " pdb=" OG SER A 114 " model vdw 2.230 2.440 nonbonded pdb=" O GLY D 110 " pdb=" OG SER D 114 " model vdw 2.231 2.440 nonbonded pdb=" O PRO B 42 " pdb=" CG ASP E 176 " model vdw 2.242 3.270 nonbonded pdb=" OG SER I 100 " pdb=" O ALA I 113 " model vdw 2.252 2.440 ... (remaining 121046 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.770 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 41.910 Find NCS groups from input model: 1.010 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 16132 Z= 0.372 Angle : 1.118 19.367 21948 Z= 0.678 Chirality : 0.057 0.321 2652 Planarity : 0.007 0.075 2762 Dihedral : 16.920 85.586 5848 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.44 % Favored : 89.83 % Rotamer: Outliers : 6.36 % Allowed : 9.75 % Favored : 83.89 % 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: -5.60 (0.13), residues: 2056 helix: -4.23 (0.08), residues: 801 sheet: -3.05 (0.28), residues: 254 loop : -3.41 (0.16), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 216 HIS 0.006 0.001 HIS K 92 PHE 0.054 0.002 PHE B 16 TYR 0.020 0.002 TYR H 40 ARG 0.006 0.001 ARG E 18 *********************** 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 617 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 510 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 TYR cc_start: 0.7525 (m-80) cc_final: 0.7273 (m-80) REVERT: A 189 MET cc_start: 0.6996 (ttm) cc_final: 0.6657 (ttm) REVERT: A 201 ASN cc_start: 0.8626 (t0) cc_final: 0.8268 (t0) REVERT: A 251 PHE cc_start: 0.8406 (t80) cc_final: 0.7979 (t80) REVERT: B 10 ASP cc_start: 0.7381 (t0) cc_final: 0.6881 (t0) REVERT: B 20 ASN cc_start: 0.6980 (OUTLIER) cc_final: 0.6747 (p0) REVERT: B 89 MET cc_start: 0.7196 (mtp) cc_final: 0.6968 (mtp) REVERT: B 100 MET cc_start: 0.7869 (mtt) cc_final: 0.7148 (mtt) REVERT: B 172 PHE cc_start: 0.8292 (m-80) cc_final: 0.7811 (m-80) REVERT: B 224 VAL cc_start: 0.8201 (OUTLIER) cc_final: 0.7792 (p) REVERT: C 59 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.8884 (tt) REVERT: C 74 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7798 (mm) REVERT: C 80 LYS cc_start: 0.9057 (mmtp) cc_final: 0.8828 (mmmt) REVERT: D 14 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8827 (tp) REVERT: D 135 MET cc_start: 0.8936 (mmt) cc_final: 0.8686 (mmp) REVERT: D 243 SER cc_start: 0.9724 (OUTLIER) cc_final: 0.9288 (t) REVERT: E 28 SER cc_start: 0.7412 (OUTLIER) cc_final: 0.6859 (t) REVERT: E 29 LEU cc_start: 0.8551 (pp) cc_final: 0.8164 (pp) REVERT: E 85 LYS cc_start: 0.8750 (mppt) cc_final: 0.8261 (mtpt) REVERT: E 126 MET cc_start: 0.9343 (tpp) cc_final: 0.8889 (tpp) REVERT: E 167 MET cc_start: 0.6955 (mtt) cc_final: 0.5822 (mtt) REVERT: E 202 SER cc_start: 0.8747 (OUTLIER) cc_final: 0.8523 (p) REVERT: F 74 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7069 (tp) REVERT: F 79 ASP cc_start: 0.7664 (t0) cc_final: 0.7448 (t0) REVERT: F 86 LYS cc_start: 0.8700 (pttt) cc_final: 0.8336 (tmtt) REVERT: G 12 ILE cc_start: 0.8905 (mt) cc_final: 0.8276 (tp) REVERT: G 40 TYR cc_start: 0.3456 (p90) cc_final: 0.3077 (p90) REVERT: G 48 ASN cc_start: 0.4710 (t0) cc_final: 0.4157 (p0) REVERT: G 81 ARG cc_start: 0.7323 (tmm160) cc_final: 0.6836 (ttp80) REVERT: G 89 ARG cc_start: 0.7487 (ptt-90) cc_final: 0.7143 (mtm-85) REVERT: G 145 ASP cc_start: 0.8790 (t0) cc_final: 0.8133 (p0) REVERT: H 6 ASN cc_start: 0.8646 (p0) cc_final: 0.8217 (p0) REVERT: H 90 TYR cc_start: 0.4957 (m-80) cc_final: 0.4715 (m-10) REVERT: H 130 ASP cc_start: 0.8383 (p0) cc_final: 0.7818 (p0) REVERT: H 135 GLN cc_start: 0.6918 (mt0) cc_final: 0.6668 (mp-120) REVERT: I 52 LEU cc_start: 0.3370 (tt) cc_final: 0.2824 (tt) REVERT: I 78 TYR cc_start: 0.6560 (m-10) cc_final: 0.4693 (p90) REVERT: I 88 GLN cc_start: 0.6454 (mt0) cc_final: 0.5430 (tm-30) REVERT: J 53 LYS cc_start: 0.7304 (mptt) cc_final: 0.6973 (ptpt) REVERT: K 88 GLN cc_start: 0.6898 (tp-100) cc_final: 0.6549 (pp30) REVERT: K 109 GLU cc_start: 0.7961 (mp0) cc_final: 0.7685 (mp0) outliers start: 107 outliers final: 15 residues processed: 569 average time/residue: 0.3073 time to fit residues: 247.2642 Evaluate side-chains 335 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 311 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 7.9990 chunk 154 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 52 optimal weight: 20.0000 chunk 104 optimal weight: 0.9990 chunk 82 optimal weight: 0.0970 chunk 159 optimal weight: 0.5980 chunk 61 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 chunk 185 optimal weight: 40.0000 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 73 GLN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN A 241 HIS B 105 ASN B 122 HIS B 191 ASN C 60 HIS C 68 GLN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 HIS D 29 ASN D 220 ASN E 26 ASN E 105 ASN E 122 HIS E 191 ASN E 262 HIS F 9 GLN F 89 ASN H 88 GLN I 91 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16132 Z= 0.183 Angle : 0.696 9.337 21948 Z= 0.353 Chirality : 0.045 0.259 2652 Planarity : 0.005 0.058 2762 Dihedral : 7.822 88.706 2296 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.98 % Favored : 91.63 % Rotamer: Outliers : 0.24 % Allowed : 5.89 % Favored : 93.88 % 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: -3.84 (0.16), residues: 2056 helix: -1.81 (0.15), residues: 815 sheet: -2.61 (0.30), residues: 252 loop : -3.20 (0.17), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 168 HIS 0.007 0.001 HIS D 11 PHE 0.021 0.002 PHE E 16 TYR 0.018 0.001 TYR I 40 ARG 0.013 0.001 ARG B 18 *********************** 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 424 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 420 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ILE cc_start: 0.9350 (mm) cc_final: 0.9148 (mt) REVERT: B 10 ASP cc_start: 0.7249 (t0) cc_final: 0.6779 (t0) REVERT: B 29 LEU cc_start: 0.9064 (pp) cc_final: 0.8839 (pp) REVERT: B 89 MET cc_start: 0.7320 (mtp) cc_final: 0.6747 (mtp) REVERT: B 172 PHE cc_start: 0.8242 (m-80) cc_final: 0.7944 (m-80) REVERT: C 68 GLN cc_start: 0.7080 (OUTLIER) cc_final: 0.6445 (tm-30) REVERT: D 135 MET cc_start: 0.8788 (mmt) cc_final: 0.8540 (mmp) REVERT: E 85 LYS cc_start: 0.8605 (mppt) cc_final: 0.8391 (mtpt) REVERT: E 89 MET cc_start: 0.8539 (mmt) cc_final: 0.8308 (mmm) REVERT: F 86 LYS cc_start: 0.8753 (pttt) cc_final: 0.8405 (tmtt) REVERT: F 93 ASP cc_start: 0.7189 (p0) cc_final: 0.6553 (t70) REVERT: G 48 ASN cc_start: 0.4382 (t0) cc_final: 0.4048 (p0) REVERT: G 72 THR cc_start: 0.4652 (t) cc_final: 0.3909 (p) REVERT: G 81 ARG cc_start: 0.7316 (tmm160) cc_final: 0.6886 (ttp80) REVERT: G 103 THR cc_start: 0.6250 (m) cc_final: 0.5670 (t) REVERT: G 145 ASP cc_start: 0.8654 (t0) cc_final: 0.7935 (p0) REVERT: H 6 ASN cc_start: 0.8499 (p0) cc_final: 0.8058 (p0) REVERT: J 52 LEU cc_start: 0.5603 (tt) cc_final: 0.5087 (tt) REVERT: J 53 LYS cc_start: 0.7341 (mptt) cc_final: 0.7021 (ptpt) REVERT: K 88 GLN cc_start: 0.6916 (tp-100) cc_final: 0.6508 (pp30) REVERT: K 109 GLU cc_start: 0.7639 (mp0) cc_final: 0.6898 (mp0) REVERT: L 81 ARG cc_start: 0.6840 (ttp80) cc_final: 0.6364 (ttp80) outliers start: 4 outliers final: 0 residues processed: 423 average time/residue: 0.2652 time to fit residues: 164.0500 Evaluate side-chains 297 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 296 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 0.9990 chunk 57 optimal weight: 0.3980 chunk 154 optimal weight: 4.9990 chunk 126 optimal weight: 30.0000 chunk 51 optimal weight: 5.9990 chunk 185 optimal weight: 20.0000 chunk 200 optimal weight: 30.0000 chunk 165 optimal weight: 8.9990 chunk 184 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN C 9 GLN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 GLN E 226 HIS F 68 GLN H 135 GLN I 88 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16132 Z= 0.189 Angle : 0.656 8.478 21948 Z= 0.330 Chirality : 0.045 0.269 2652 Planarity : 0.005 0.105 2762 Dihedral : 7.289 87.242 2296 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.95 % Favored : 90.76 % Rotamer: Outliers : 0.12 % Allowed : 5.17 % Favored : 94.71 % 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: -2.81 (0.17), residues: 2056 helix: -0.48 (0.18), residues: 809 sheet: -2.20 (0.31), residues: 262 loop : -3.03 (0.18), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 215 HIS 0.006 0.001 HIS B 262 PHE 0.030 0.002 PHE E 16 TYR 0.016 0.001 TYR K 40 ARG 0.009 0.001 ARG J 81 *********************** 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 402 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 400 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 ASP cc_start: 0.7292 (t0) cc_final: 0.6759 (t0) REVERT: B 29 LEU cc_start: 0.9170 (pp) cc_final: 0.8934 (pp) REVERT: B 75 MET cc_start: 0.7439 (ptp) cc_final: 0.7098 (ptp) REVERT: B 89 MET cc_start: 0.7585 (mtp) cc_final: 0.7083 (mtp) REVERT: B 220 ASP cc_start: 0.8126 (t70) cc_final: 0.7910 (t0) REVERT: E 170 GLN cc_start: 0.8837 (tp-100) cc_final: 0.8373 (tm-30) REVERT: E 221 LYS cc_start: 0.8865 (mppt) cc_final: 0.8661 (mppt) REVERT: E 237 ASP cc_start: 0.7698 (t70) cc_final: 0.7309 (t0) REVERT: F 86 LYS cc_start: 0.8804 (pttt) cc_final: 0.8458 (tmtt) REVERT: F 93 ASP cc_start: 0.7268 (p0) cc_final: 0.6673 (t70) REVERT: G 72 THR cc_start: 0.4812 (t) cc_final: 0.3964 (p) REVERT: G 81 ARG cc_start: 0.7202 (tmm160) cc_final: 0.6866 (ttp80) REVERT: G 103 THR cc_start: 0.6197 (m) cc_final: 0.5732 (t) REVERT: G 145 ASP cc_start: 0.8634 (t0) cc_final: 0.7906 (p0) REVERT: H 6 ASN cc_start: 0.8525 (p0) cc_final: 0.8105 (p0) REVERT: I 43 TYR cc_start: 0.7320 (m-10) cc_final: 0.7095 (m-10) REVERT: J 53 LYS cc_start: 0.7261 (mptt) cc_final: 0.6970 (ptpt) REVERT: K 56 SER cc_start: 0.5906 (p) cc_final: 0.5466 (m) REVERT: K 88 GLN cc_start: 0.6895 (tp-100) cc_final: 0.6359 (pp30) REVERT: K 109 GLU cc_start: 0.7432 (mp0) cc_final: 0.6889 (mp0) REVERT: L 81 ARG cc_start: 0.6806 (ttp80) cc_final: 0.6286 (ttp80) outliers start: 2 outliers final: 0 residues processed: 402 average time/residue: 0.2765 time to fit residues: 162.2182 Evaluate side-chains 289 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 186 optimal weight: 50.0000 chunk 197 optimal weight: 30.0000 chunk 97 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN B 214 HIS C 60 HIS C 89 ASN E 175 GLN E 214 HIS ** G 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 GLN I 91 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16132 Z= 0.265 Angle : 0.719 7.052 21948 Z= 0.364 Chirality : 0.047 0.195 2652 Planarity : 0.005 0.054 2762 Dihedral : 7.257 78.769 2296 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.17 % Favored : 89.59 % Rotamer: Outliers : 0.06 % Allowed : 4.99 % Favored : 94.95 % 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: -2.43 (0.18), residues: 2056 helix: -0.08 (0.18), residues: 808 sheet: -2.14 (0.33), residues: 226 loop : -2.87 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 168 HIS 0.005 0.001 HIS B 122 PHE 0.038 0.002 PHE E 16 TYR 0.029 0.002 TYR B 261 ARG 0.009 0.001 ARG D 97 *********************** 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 364 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 363 time to evaluate : 1.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 ASP cc_start: 0.7770 (t0) cc_final: 0.7157 (t0) REVERT: B 29 LEU cc_start: 0.9314 (pp) cc_final: 0.9067 (pp) REVERT: B 75 MET cc_start: 0.7461 (ptp) cc_final: 0.7102 (ptp) REVERT: B 100 MET cc_start: 0.7883 (mtt) cc_final: 0.7294 (mtt) REVERT: D 73 GLN cc_start: 0.8847 (tp40) cc_final: 0.8560 (tp-100) REVERT: D 135 MET cc_start: 0.8777 (mmm) cc_final: 0.8415 (mmp) REVERT: E 126 MET cc_start: 0.9243 (tpp) cc_final: 0.8960 (tpp) REVERT: E 221 LYS cc_start: 0.8946 (mppt) cc_final: 0.8698 (mppt) REVERT: F 86 LYS cc_start: 0.8943 (pttt) cc_final: 0.8615 (tmtt) REVERT: F 93 ASP cc_start: 0.7467 (p0) cc_final: 0.6798 (t70) REVERT: G 72 THR cc_start: 0.5492 (t) cc_final: 0.4510 (p) REVERT: G 81 ARG cc_start: 0.7378 (tmm160) cc_final: 0.6770 (ttp80) REVERT: G 145 ASP cc_start: 0.8755 (t0) cc_final: 0.7933 (p0) REVERT: H 6 ASN cc_start: 0.8644 (p0) cc_final: 0.8438 (p0) REVERT: H 90 TYR cc_start: 0.4081 (m-10) cc_final: 0.3543 (m-10) REVERT: J 53 LYS cc_start: 0.7375 (mptt) cc_final: 0.7044 (ptpt) REVERT: K 57 PRO cc_start: 0.6327 (Cg_exo) cc_final: 0.5924 (Cg_endo) REVERT: K 88 GLN cc_start: 0.6593 (tp-100) cc_final: 0.6281 (pp30) REVERT: L 81 ARG cc_start: 0.6592 (ttp80) cc_final: 0.5981 (ttp80) REVERT: L 90 TYR cc_start: 0.2729 (m-10) cc_final: 0.2158 (m-80) outliers start: 1 outliers final: 0 residues processed: 364 average time/residue: 0.2758 time to fit residues: 146.6619 Evaluate side-chains 265 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 146 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 168 optimal weight: 20.0000 chunk 136 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 100 optimal weight: 0.0020 chunk 176 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN B 191 ASN D 40 HIS E 175 GLN G 48 ASN H 149 GLN I 92 HIS L 110 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16132 Z= 0.173 Angle : 0.646 8.901 21948 Z= 0.321 Chirality : 0.045 0.229 2652 Planarity : 0.004 0.051 2762 Dihedral : 6.888 78.804 2296 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.66 % Favored : 91.15 % Rotamer: Outliers : 0.06 % Allowed : 3.63 % Favored : 96.31 % 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: -2.08 (0.18), residues: 2056 helix: 0.32 (0.19), residues: 816 sheet: -1.97 (0.31), residues: 260 loop : -2.80 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 9 HIS 0.005 0.001 HIS C 60 PHE 0.025 0.002 PHE D 185 TYR 0.014 0.001 TYR K 40 ARG 0.004 0.000 ARG D 97 *********************** 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 373 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 372 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.7509 (pm20) cc_final: 0.7165 (pm20) REVERT: B 10 ASP cc_start: 0.7502 (t0) cc_final: 0.7002 (t0) REVERT: B 29 LEU cc_start: 0.9138 (pp) cc_final: 0.8927 (pp) REVERT: B 75 MET cc_start: 0.7449 (ptp) cc_final: 0.7171 (ptp) REVERT: C 73 THR cc_start: 0.7888 (p) cc_final: 0.7657 (p) REVERT: D 73 GLN cc_start: 0.8753 (tp40) cc_final: 0.8425 (tp-100) REVERT: D 122 LEU cc_start: 0.9003 (tp) cc_final: 0.8728 (tp) REVERT: E 126 MET cc_start: 0.9201 (tpp) cc_final: 0.8944 (tpp) REVERT: F 86 LYS cc_start: 0.8871 (pttt) cc_final: 0.8480 (tmtt) REVERT: F 93 ASP cc_start: 0.7464 (p0) cc_final: 0.6782 (t70) REVERT: G 81 ARG cc_start: 0.7374 (tmm160) cc_final: 0.6784 (ttp80) REVERT: G 112 LEU cc_start: 0.5968 (tp) cc_final: 0.5224 (tt) REVERT: G 145 ASP cc_start: 0.8705 (t0) cc_final: 0.7887 (p0) REVERT: H 90 TYR cc_start: 0.4209 (m-10) cc_final: 0.3674 (m-10) REVERT: J 53 LYS cc_start: 0.7312 (mptt) cc_final: 0.7023 (ptpt) REVERT: J 141 MET cc_start: 0.1937 (pmm) cc_final: -0.0157 (ptp) REVERT: K 37 GLU cc_start: 0.5090 (tm-30) cc_final: 0.4678 (tm-30) REVERT: K 68 VAL cc_start: 0.7300 (m) cc_final: 0.6892 (m) REVERT: K 88 GLN cc_start: 0.6781 (tp-100) cc_final: 0.6430 (pp30) REVERT: L 81 ARG cc_start: 0.6713 (ttp80) cc_final: 0.6189 (ttp80) outliers start: 1 outliers final: 0 residues processed: 373 average time/residue: 0.2587 time to fit residues: 143.0010 Evaluate side-chains 271 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 115 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 197 optimal weight: 8.9990 chunk 163 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 103 optimal weight: 0.0030 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN G 48 ASN H 149 GLN J 91 ASN ** K 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16132 Z= 0.153 Angle : 0.635 9.292 21948 Z= 0.311 Chirality : 0.044 0.198 2652 Planarity : 0.004 0.054 2762 Dihedral : 6.712 78.441 2296 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.71 % Favored : 91.10 % Rotamer: Outliers : 0.06 % Allowed : 2.50 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.19), residues: 2056 helix: 0.66 (0.19), residues: 811 sheet: -1.87 (0.31), residues: 266 loop : -2.67 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 195 HIS 0.005 0.001 HIS B 62 PHE 0.024 0.001 PHE B 16 TYR 0.021 0.001 TYR B 261 ARG 0.006 0.000 ARG A 124 *********************** 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 372 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 371 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 ASP cc_start: 0.7492 (t0) cc_final: 0.6952 (t0) REVERT: B 75 MET cc_start: 0.7388 (ptp) cc_final: 0.7164 (ptp) REVERT: C 59 LEU cc_start: 0.9152 (mm) cc_final: 0.8870 (pp) REVERT: D 73 GLN cc_start: 0.8764 (tp40) cc_final: 0.8451 (tp-100) REVERT: E 126 MET cc_start: 0.9174 (tpp) cc_final: 0.8899 (tpp) REVERT: E 261 TYR cc_start: 0.7077 (m-80) cc_final: 0.6875 (m-10) REVERT: F 31 MET cc_start: 0.7601 (mpp) cc_final: 0.7312 (mpp) REVERT: F 86 LYS cc_start: 0.8854 (pttt) cc_final: 0.8427 (tmtt) REVERT: F 93 ASP cc_start: 0.7611 (p0) cc_final: 0.6955 (t70) REVERT: G 81 ARG cc_start: 0.7261 (tmm160) cc_final: 0.6719 (ttp80) REVERT: G 112 LEU cc_start: 0.6141 (tp) cc_final: 0.5409 (tt) REVERT: G 145 ASP cc_start: 0.8637 (t0) cc_final: 0.7776 (p0) REVERT: H 6 ASN cc_start: 0.8099 (p0) cc_final: 0.7867 (p0) REVERT: J 53 LYS cc_start: 0.7226 (mptt) cc_final: 0.6803 (ptpp) REVERT: J 141 MET cc_start: 0.2299 (pmm) cc_final: 0.0254 (ptp) REVERT: K 37 GLU cc_start: 0.4830 (tm-30) cc_final: 0.4497 (tm-30) REVERT: K 57 PRO cc_start: 0.6161 (Cg_exo) cc_final: 0.5866 (Cg_endo) REVERT: L 81 ARG cc_start: 0.6820 (ttp80) cc_final: 0.6337 (ttp80) REVERT: L 141 MET cc_start: 0.4587 (pmm) cc_final: 0.4170 (pmm) outliers start: 1 outliers final: 0 residues processed: 372 average time/residue: 0.2709 time to fit residues: 147.9199 Evaluate side-chains 268 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 112 optimal weight: 20.0000 chunk 144 optimal weight: 20.0000 chunk 111 optimal weight: 8.9990 chunk 166 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 196 optimal weight: 0.0470 chunk 123 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN E 214 HIS ** G 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16132 Z= 0.196 Angle : 0.654 8.572 21948 Z= 0.324 Chirality : 0.045 0.288 2652 Planarity : 0.004 0.081 2762 Dihedral : 6.662 78.795 2296 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.24 % Favored : 90.56 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % 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: -1.65 (0.19), residues: 2056 helix: 0.78 (0.19), residues: 806 sheet: -1.82 (0.31), residues: 266 loop : -2.59 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 168 HIS 0.005 0.001 HIS C 60 PHE 0.023 0.002 PHE B 172 TYR 0.018 0.001 TYR B 261 ARG 0.004 0.000 ARG F 46 *********************** REFINEMENT MACRO_CYCLE 7 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 356 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 356 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 ASP cc_start: 0.7818 (t0) cc_final: 0.7249 (t0) REVERT: B 75 MET cc_start: 0.7422 (ptp) cc_final: 0.7180 (ptp) REVERT: B 127 MET cc_start: 0.8502 (tmm) cc_final: 0.8300 (tmm) REVERT: D 122 LEU cc_start: 0.9040 (tp) cc_final: 0.8816 (tp) REVERT: E 24 PHE cc_start: 0.8564 (m-80) cc_final: 0.8269 (m-80) REVERT: E 90 LEU cc_start: 0.9128 (tt) cc_final: 0.8841 (tt) REVERT: E 126 MET cc_start: 0.9169 (tpp) cc_final: 0.8884 (tpp) REVERT: F 31 MET cc_start: 0.7672 (mpp) cc_final: 0.7412 (mpp) REVERT: F 86 LYS cc_start: 0.8914 (pttt) cc_final: 0.8482 (tmtt) REVERT: G 72 THR cc_start: 0.4880 (t) cc_final: 0.3878 (p) REVERT: G 81 ARG cc_start: 0.7364 (tmm160) cc_final: 0.6813 (ttp80) REVERT: G 90 TYR cc_start: 0.6476 (m-80) cc_final: 0.6107 (m-80) REVERT: G 109 GLU cc_start: 0.7194 (mp0) cc_final: 0.6641 (tp30) REVERT: G 112 LEU cc_start: 0.6271 (tp) cc_final: 0.5468 (tt) REVERT: G 145 ASP cc_start: 0.8616 (t0) cc_final: 0.7753 (p0) REVERT: H 90 TYR cc_start: 0.4051 (m-10) cc_final: 0.3395 (m-10) REVERT: I 91 ASN cc_start: 0.8293 (p0) cc_final: 0.6967 (m-40) REVERT: J 53 LYS cc_start: 0.7261 (mptt) cc_final: 0.6921 (ptpt) REVERT: J 141 MET cc_start: 0.2338 (pmm) cc_final: 0.0530 (ptp) REVERT: K 37 GLU cc_start: 0.4751 (tm-30) cc_final: 0.4449 (tm-30) REVERT: L 81 ARG cc_start: 0.6940 (ttp80) cc_final: 0.6449 (ttp80) REVERT: L 84 LEU cc_start: 0.7510 (mm) cc_final: 0.7308 (mm) REVERT: L 141 MET cc_start: 0.4504 (pmm) cc_final: 0.4225 (pmm) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.2775 time to fit residues: 144.1529 Evaluate side-chains 269 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 117 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 38 optimal weight: 0.5980 chunk 125 optimal weight: 5.9990 chunk 133 optimal weight: 0.0770 chunk 97 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 154 optimal weight: 0.6980 chunk 178 optimal weight: 7.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN G 48 ASN H 92 HIS K 110 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16132 Z= 0.150 Angle : 0.638 9.683 21948 Z= 0.310 Chirality : 0.044 0.258 2652 Planarity : 0.004 0.067 2762 Dihedral : 6.521 79.717 2296 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.37 % Favored : 91.44 % Rotamer: Outliers : 0.06 % Allowed : 1.13 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.19), residues: 2056 helix: 0.93 (0.19), residues: 811 sheet: -1.70 (0.32), residues: 268 loop : -2.61 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 195 HIS 0.004 0.001 HIS B 62 PHE 0.025 0.001 PHE B 16 TYR 0.018 0.001 TYR B 81 ARG 0.005 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 8 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 362 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 361 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 ASP cc_start: 0.7654 (t0) cc_final: 0.7152 (t0) REVERT: B 75 MET cc_start: 0.7459 (ptp) cc_final: 0.7206 (ptp) REVERT: B 127 MET cc_start: 0.8481 (tmm) cc_final: 0.8238 (tmm) REVERT: C 59 LEU cc_start: 0.9127 (mm) cc_final: 0.8904 (pp) REVERT: E 24 PHE cc_start: 0.8416 (m-80) cc_final: 0.8102 (m-80) REVERT: E 90 LEU cc_start: 0.9135 (tt) cc_final: 0.8823 (tt) REVERT: E 126 MET cc_start: 0.9150 (tpp) cc_final: 0.8920 (tpp) REVERT: F 86 LYS cc_start: 0.8848 (pttt) cc_final: 0.8430 (tmtt) REVERT: F 93 ASP cc_start: 0.7659 (p0) cc_final: 0.7133 (t70) REVERT: G 81 ARG cc_start: 0.7330 (tmm160) cc_final: 0.6796 (ttp80) REVERT: G 90 TYR cc_start: 0.6605 (m-80) cc_final: 0.6151 (m-80) REVERT: G 109 GLU cc_start: 0.7255 (mp0) cc_final: 0.6714 (tp30) REVERT: G 112 LEU cc_start: 0.6268 (tp) cc_final: 0.5399 (tt) REVERT: G 145 ASP cc_start: 0.8571 (t0) cc_final: 0.7720 (p0) REVERT: H 6 ASN cc_start: 0.8176 (p0) cc_final: 0.7885 (p0) REVERT: H 90 TYR cc_start: 0.4093 (m-10) cc_final: 0.3521 (m-10) REVERT: I 91 ASN cc_start: 0.8179 (p0) cc_final: 0.6820 (m-40) REVERT: J 53 LYS cc_start: 0.7167 (mptt) cc_final: 0.6774 (ptpt) REVERT: J 141 MET cc_start: 0.2404 (pmm) cc_final: 0.0530 (ptp) REVERT: K 37 GLU cc_start: 0.4788 (tm-30) cc_final: 0.4482 (tm-30) REVERT: L 81 ARG cc_start: 0.7093 (ttp80) cc_final: 0.6631 (ttp80) REVERT: L 84 LEU cc_start: 0.7515 (mm) cc_final: 0.7312 (mm) REVERT: L 141 MET cc_start: 0.4825 (pmm) cc_final: 0.3969 (ttt) outliers start: 1 outliers final: 0 residues processed: 362 average time/residue: 0.2674 time to fit residues: 142.7539 Evaluate side-chains 273 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 6.9990 chunk 171 optimal weight: 0.0870 chunk 183 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 143 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 chunk 173 optimal weight: 9.9990 chunk 182 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 overall best weight: 4.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN C 60 HIS G 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.5409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16132 Z= 0.252 Angle : 0.697 8.569 21948 Z= 0.344 Chirality : 0.046 0.255 2652 Planarity : 0.005 0.067 2762 Dihedral : 6.710 80.378 2296 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.92 % Favored : 89.83 % Rotamer: Outliers : 0.06 % Allowed : 0.83 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.55 (0.19), residues: 2056 helix: 0.82 (0.19), residues: 807 sheet: -1.81 (0.31), residues: 272 loop : -2.48 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 216 HIS 0.004 0.001 HIS B 122 PHE 0.020 0.002 PHE J 13 TYR 0.021 0.002 TYR B 261 ARG 0.009 0.001 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 9 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 338 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 337 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 ASP cc_start: 0.7974 (t0) cc_final: 0.7482 (t0) REVERT: B 127 MET cc_start: 0.8556 (tmm) cc_final: 0.8328 (tmm) REVERT: C 8 MET cc_start: 0.7881 (tpt) cc_final: 0.7619 (tpt) REVERT: D 122 LEU cc_start: 0.9066 (tp) cc_final: 0.8852 (tp) REVERT: E 90 LEU cc_start: 0.9165 (tt) cc_final: 0.8849 (tt) REVERT: E 126 MET cc_start: 0.9174 (tpp) cc_final: 0.8883 (tpp) REVERT: F 86 LYS cc_start: 0.8958 (pttt) cc_final: 0.8574 (tmtt) REVERT: G 48 ASN cc_start: 0.3134 (OUTLIER) cc_final: 0.2932 (p0) REVERT: G 72 THR cc_start: 0.5122 (t) cc_final: 0.4199 (p) REVERT: G 81 ARG cc_start: 0.7461 (tmm160) cc_final: 0.7191 (ttp80) REVERT: G 109 GLU cc_start: 0.7875 (mp0) cc_final: 0.6881 (tp30) REVERT: G 112 LEU cc_start: 0.6413 (tp) cc_final: 0.5515 (tt) REVERT: G 145 ASP cc_start: 0.8706 (t0) cc_final: 0.7823 (p0) REVERT: G 146 LEU cc_start: 0.6851 (pt) cc_final: 0.6640 (pt) REVERT: H 90 TYR cc_start: 0.4074 (m-10) cc_final: 0.3514 (m-10) REVERT: H 152 TYR cc_start: 0.7954 (m-80) cc_final: 0.7543 (m-80) REVERT: J 53 LYS cc_start: 0.7252 (mptt) cc_final: 0.6918 (ptpt) REVERT: J 141 MET cc_start: 0.2584 (pmm) cc_final: 0.0787 (ptp) REVERT: K 37 GLU cc_start: 0.4894 (tm-30) cc_final: 0.4543 (tm-30) REVERT: K 141 MET cc_start: 0.4463 (pmm) cc_final: 0.4098 (pmm) REVERT: L 81 ARG cc_start: 0.6909 (ttp80) cc_final: 0.6470 (ttp80) REVERT: L 84 LEU cc_start: 0.7656 (mm) cc_final: 0.7451 (mm) REVERT: L 141 MET cc_start: 0.4894 (pmm) cc_final: 0.3994 (ttt) outliers start: 1 outliers final: 0 residues processed: 338 average time/residue: 0.2667 time to fit residues: 132.8834 Evaluate side-chains 267 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 266 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 203 optimal weight: 0.0370 chunk 187 optimal weight: 6.9990 chunk 161 optimal weight: 0.0040 chunk 16 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 overall best weight: 0.5470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS B 191 ASN ** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16132 Z= 0.154 Angle : 0.674 9.990 21948 Z= 0.322 Chirality : 0.045 0.247 2652 Planarity : 0.004 0.062 2762 Dihedral : 6.528 79.788 2296 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.93 % Favored : 91.88 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.39 (0.19), residues: 2056 helix: 0.97 (0.19), residues: 809 sheet: -1.70 (0.32), residues: 274 loop : -2.43 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 168 HIS 0.007 0.001 HIS C 60 PHE 0.024 0.001 PHE B 16 TYR 0.016 0.001 TYR K 40 ARG 0.003 0.000 ARG E 52 ********************** REFINEMENT MACRO_CYCLE 10 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 357 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 357 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 ASP cc_start: 0.7755 (t0) cc_final: 0.7171 (t0) REVERT: B 89 MET cc_start: 0.7801 (ttm) cc_final: 0.7521 (ttm) REVERT: D 73 GLN cc_start: 0.8333 (tp-100) cc_final: 0.8087 (tp-100) REVERT: E 90 LEU cc_start: 0.9121 (tt) cc_final: 0.8834 (tt) REVERT: E 108 TYR cc_start: 0.8494 (t80) cc_final: 0.8186 (t80) REVERT: E 126 MET cc_start: 0.9170 (tpp) cc_final: 0.8935 (tpp) REVERT: F 97 ARG cc_start: 0.5861 (tmt170) cc_final: 0.5367 (mmp80) REVERT: G 90 TYR cc_start: 0.6146 (m-10) cc_final: 0.5420 (m-80) REVERT: G 109 GLU cc_start: 0.7781 (mp0) cc_final: 0.6671 (tp30) REVERT: G 112 LEU cc_start: 0.6625 (tp) cc_final: 0.5770 (tt) REVERT: G 145 ASP cc_start: 0.8639 (t0) cc_final: 0.7760 (p0) REVERT: H 6 ASN cc_start: 0.8211 (p0) cc_final: 0.7906 (p0) REVERT: H 90 TYR cc_start: 0.4085 (m-10) cc_final: 0.3553 (m-10) REVERT: H 152 TYR cc_start: 0.7937 (m-80) cc_final: 0.7508 (m-80) REVERT: J 53 LYS cc_start: 0.7215 (mptt) cc_final: 0.6840 (ptpt) REVERT: J 141 MET cc_start: 0.3056 (pmm) cc_final: 0.1387 (ptp) REVERT: K 37 GLU cc_start: 0.4642 (tm-30) cc_final: 0.4302 (tm-30) REVERT: L 81 ARG cc_start: 0.7146 (ttp80) cc_final: 0.6692 (ttp80) REVERT: L 84 LEU cc_start: 0.7541 (mm) cc_final: 0.7331 (mm) REVERT: L 141 MET cc_start: 0.5004 (pmm) cc_final: 0.4229 (ttt) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.2564 time to fit residues: 136.2282 Evaluate side-chains 273 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 149 optimal weight: 50.0000 chunk 23 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 67 optimal weight: 0.0870 chunk 166 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 191 ASN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.111626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.082514 restraints weight = 53713.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.083866 restraints weight = 35369.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.084562 restraints weight = 24268.536| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.5722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16132 Z= 0.225 Angle : 0.692 8.575 21948 Z= 0.338 Chirality : 0.045 0.243 2652 Planarity : 0.005 0.086 2762 Dihedral : 6.603 79.766 2296 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.48 % Favored : 90.32 % Rotamer: Outliers : 0.06 % Allowed : 0.59 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.45 (0.19), residues: 2056 helix: 0.89 (0.19), residues: 807 sheet: -1.76 (0.32), residues: 276 loop : -2.41 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 216 HIS 0.003 0.001 HIS K 92 PHE 0.020 0.002 PHE J 13 TYR 0.016 0.001 TYR A 222 ARG 0.010 0.001 ARG G 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3559.90 seconds wall clock time: 64 minutes 45.92 seconds (3885.92 seconds total)