Starting phenix.real_space_refine (version: dev) on Sat Feb 25 19:17:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m9a_23721/02_2023/7m9a_23721_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m9a_23721/02_2023/7m9a_23721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m9a_23721/02_2023/7m9a_23721.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m9a_23721/02_2023/7m9a_23721.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m9a_23721/02_2023/7m9a_23721_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m9a_23721/02_2023/7m9a_23721_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 245": "OD1" <-> "OD2" Residue "D TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 144": "OD1" <-> "OD2" Residue "E PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 270": "OE1" <-> "OE2" Residue "F TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 270": "OE1" <-> "OE2" Residue "H TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "H TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 245": "OD1" <-> "OD2" Residue "H TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 116": "NH1" <-> "NH2" Residue "J PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 139": "OE1" <-> "OE2" Residue "J PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 57": "NH1" <-> "NH2" Residue "K TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 183": "OD1" <-> "OD2" Residue "K PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 26139 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "B" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "C" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "D" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "E" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "F" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2060 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 247} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "H" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2054 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 247} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "I" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "J" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2058 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 247} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "K" Number of atoms: 2062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2062 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 247} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "M" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 567 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "N" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 540 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.91, per 1000 atoms: 0.53 Number of scatterers: 26139 At special positions: 0 Unit cell: (144.97, 144.97, 171.57, 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 96 16.00 P 74 15.00 O 4919 8.00 N 4756 7.00 C 16294 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.39 Conformation dependent library (CDL) restraints added in 3.8 seconds 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5784 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 151 helices and 14 sheets defined 55.2% alpha, 7.0% beta 24 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 8.26 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 removed outlier: 3.504A pdb=" N LEU A 28 " --> pdb=" O GLU A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 52 Processing helix chain 'A' and resid 66 through 76 removed outlier: 3.537A pdb=" N ASP A 71 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 112 Processing helix chain 'A' and resid 122 through 135 removed outlier: 3.527A pdb=" N LYS A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.537A pdb=" N PHE A 154 " --> pdb=" O PRO A 151 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG A 158 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA A 161 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP A 163 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 182 Processing helix chain 'A' and resid 184 through 187 No H-bonds generated for 'chain 'A' and resid 184 through 187' Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.893A pdb=" N ILE A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 258 Processing helix chain 'A' and resid 265 through 273 removed outlier: 3.564A pdb=" N ALA A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS A 273 " --> pdb=" O GLN A 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 28 Processing helix chain 'B' and resid 37 through 52 Processing helix chain 'B' and resid 66 through 76 removed outlier: 3.569A pdb=" N TYR B 75 " --> pdb=" O ASP B 71 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 112 Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 151 through 163 removed outlier: 3.533A pdb=" N ALA B 155 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 180 Processing helix chain 'B' and resid 184 through 187 No H-bonds generated for 'chain 'B' and resid 184 through 187' Processing helix chain 'B' and resid 201 through 214 removed outlier: 3.709A pdb=" N LYS B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU B 212 " --> pdb=" O VAL B 208 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN B 213 " --> pdb=" O GLU B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 237 removed outlier: 4.779A pdb=" N ILE B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B 236 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 257 Processing helix chain 'B' and resid 265 through 274 removed outlier: 4.251A pdb=" N GLN B 269 " --> pdb=" O LYS B 265 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU B 274 " --> pdb=" O GLU B 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 28 Processing helix chain 'C' and resid 37 through 52 Processing helix chain 'C' and resid 66 through 76 Processing helix chain 'C' and resid 102 through 113 removed outlier: 3.616A pdb=" N LEU C 113 " --> pdb=" O ILE C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 135 Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 151 through 163 removed outlier: 3.980A pdb=" N ALA C 155 " --> pdb=" O PRO C 151 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 182 removed outlier: 4.893A pdb=" N ARG C 182 " --> pdb=" O ALA C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 189 removed outlier: 3.848A pdb=" N GLU C 188 " --> pdb=" O GLU C 184 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG C 189 " --> pdb=" O GLN C 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 184 through 189' Processing helix chain 'C' and resid 201 through 214 Processing helix chain 'C' and resid 227 through 237 Processing helix chain 'C' and resid 241 through 258 removed outlier: 4.035A pdb=" N GLU C 246 " --> pdb=" O GLY C 242 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE C 247 " --> pdb=" O ARG C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 274 Processing helix chain 'D' and resid 20 through 29 removed outlier: 3.614A pdb=" N GLU D 24 " --> pdb=" O TRP D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 52 Processing helix chain 'D' and resid 66 through 77 removed outlier: 3.517A pdb=" N HIS D 77 " --> pdb=" O TYR D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 112 Processing helix chain 'D' and resid 122 through 136 Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 174 through 180 Processing helix chain 'D' and resid 184 through 189 Processing helix chain 'D' and resid 201 through 214 Processing helix chain 'D' and resid 227 through 237 removed outlier: 3.729A pdb=" N ARG D 231 " --> pdb=" O LYS D 227 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA D 236 " --> pdb=" O ILE D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 257 Processing helix chain 'D' and resid 265 through 274 Processing helix chain 'E' and resid 20 through 28 Processing helix chain 'E' and resid 37 through 52 Processing helix chain 'E' and resid 66 through 76 Processing helix chain 'E' and resid 102 through 112 Processing helix chain 'E' and resid 122 through 135 Processing helix chain 'E' and resid 146 through 148 No H-bonds generated for 'chain 'E' and resid 146 through 148' Processing helix chain 'E' and resid 152 through 163 removed outlier: 3.649A pdb=" N ALA E 155 " --> pdb=" O GLU E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 182 removed outlier: 3.802A pdb=" N LYS E 181 " --> pdb=" O ALA E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'E' and resid 201 through 214 Processing helix chain 'E' and resid 227 through 237 removed outlier: 4.454A pdb=" N ILE E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 257 Processing helix chain 'E' and resid 265 through 274 Processing helix chain 'F' and resid 20 through 28 removed outlier: 3.934A pdb=" N LEU F 28 " --> pdb=" O GLU F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 52 removed outlier: 3.555A pdb=" N ASP F 44 " --> pdb=" O LYS F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 76 Processing helix chain 'F' and resid 102 through 112 Processing helix chain 'F' and resid 122 through 135 removed outlier: 3.509A pdb=" N ASP F 127 " --> pdb=" O SER F 123 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR F 129 " --> pdb=" O PHE F 125 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE F 130 " --> pdb=" O ARG F 126 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS F 134 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY F 135 " --> pdb=" O GLU F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 163 removed outlier: 3.865A pdb=" N ALA F 155 " --> pdb=" O PRO F 151 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASP F 156 " --> pdb=" O GLU F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 181 Processing helix chain 'F' and resid 184 through 189 Processing helix chain 'F' and resid 202 through 214 Processing helix chain 'F' and resid 227 through 237 Processing helix chain 'F' and resid 241 through 258 removed outlier: 3.765A pdb=" N ARG F 258 " --> pdb=" O ARG F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 274 Processing helix chain 'G' and resid 20 through 28 Processing helix chain 'G' and resid 37 through 52 Processing helix chain 'G' and resid 66 through 76 removed outlier: 3.551A pdb=" N ARG G 76 " --> pdb=" O ALA G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 112 Processing helix chain 'G' and resid 122 through 135 Processing helix chain 'G' and resid 154 through 163 Processing helix chain 'G' and resid 174 through 182 removed outlier: 3.955A pdb=" N ALA G 178 " --> pdb=" O ASP G 174 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL G 179 " --> pdb=" O ARG G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 189 Processing helix chain 'G' and resid 201 through 214 Processing helix chain 'G' and resid 227 through 237 removed outlier: 3.904A pdb=" N ARG G 231 " --> pdb=" O LYS G 227 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 257 Processing helix chain 'G' and resid 265 through 274 removed outlier: 3.907A pdb=" N GLN G 269 " --> pdb=" O LYS G 265 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU G 270 " --> pdb=" O ALA G 266 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL G 271 " --> pdb=" O VAL G 267 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA G 272 " --> pdb=" O LEU G 268 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS G 273 " --> pdb=" O GLN G 269 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU G 274 " --> pdb=" O GLU G 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 265 through 274' Processing helix chain 'H' and resid 20 through 29 removed outlier: 3.515A pdb=" N GLU H 24 " --> pdb=" O TRP H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 52 removed outlier: 3.822A pdb=" N GLY H 48 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS H 49 " --> pdb=" O TRP H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 76 removed outlier: 3.685A pdb=" N ARG H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 112 Processing helix chain 'H' and resid 122 through 135 Processing helix chain 'H' and resid 153 through 164 Processing helix chain 'H' and resid 174 through 182 removed outlier: 3.639A pdb=" N ILE H 180 " --> pdb=" O ASP H 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 189 Processing helix chain 'H' and resid 201 through 214 Processing helix chain 'H' and resid 227 through 237 removed outlier: 3.756A pdb=" N ARG H 231 " --> pdb=" O LYS H 227 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE H 232 " --> pdb=" O GLU H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 258 removed outlier: 4.186A pdb=" N LEU H 256 " --> pdb=" O ALA H 252 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER H 257 " --> pdb=" O ILE H 253 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG H 258 " --> pdb=" O ARG H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 274 removed outlier: 3.553A pdb=" N VAL H 271 " --> pdb=" O VAL H 267 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA H 272 " --> pdb=" O LEU H 268 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS H 273 " --> pdb=" O GLN H 269 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU H 274 " --> pdb=" O GLU H 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 29 Processing helix chain 'I' and resid 37 through 52 Processing helix chain 'I' and resid 66 through 76 Processing helix chain 'I' and resid 104 through 112 Processing helix chain 'I' and resid 122 through 135 Processing helix chain 'I' and resid 146 through 148 No H-bonds generated for 'chain 'I' and resid 146 through 148' Processing helix chain 'I' and resid 151 through 163 removed outlier: 3.575A pdb=" N ALA I 155 " --> pdb=" O GLU I 152 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU I 162 " --> pdb=" O ASP I 159 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP I 163 " --> pdb=" O ILE I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 182 removed outlier: 4.033A pdb=" N ARG I 182 " --> pdb=" O ALA I 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 189 Processing helix chain 'I' and resid 201 through 214 removed outlier: 3.657A pdb=" N GLN I 213 " --> pdb=" O GLU I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 237 removed outlier: 3.505A pdb=" N ILE I 232 " --> pdb=" O GLU I 228 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER I 235 " --> pdb=" O ARG I 231 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA I 236 " --> pdb=" O ILE I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 257 Processing helix chain 'I' and resid 265 through 274 Processing helix chain 'J' and resid 20 through 29 Processing helix chain 'J' and resid 37 through 52 Processing helix chain 'J' and resid 66 through 76 Processing helix chain 'J' and resid 102 through 113 removed outlier: 3.535A pdb=" N LEU J 113 " --> pdb=" O ILE J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 135 Processing helix chain 'J' and resid 146 through 148 No H-bonds generated for 'chain 'J' and resid 146 through 148' Processing helix chain 'J' and resid 151 through 163 removed outlier: 3.978A pdb=" N ALA J 155 " --> pdb=" O PRO J 151 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP J 156 " --> pdb=" O GLU J 152 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP J 159 " --> pdb=" O ALA J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 174 through 182 removed outlier: 4.291A pdb=" N ARG J 182 " --> pdb=" O ALA J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 189 Processing helix chain 'J' and resid 201 through 214 Processing helix chain 'J' and resid 227 through 237 removed outlier: 3.555A pdb=" N ILE J 232 " --> pdb=" O GLU J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 241 through 257 Processing helix chain 'J' and resid 265 through 274 removed outlier: 3.654A pdb=" N ALA J 272 " --> pdb=" O LEU J 268 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS J 273 " --> pdb=" O GLN J 269 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU J 274 " --> pdb=" O GLU J 270 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 28 Processing helix chain 'K' and resid 37 through 52 Processing helix chain 'K' and resid 66 through 76 removed outlier: 3.709A pdb=" N ARG K 74 " --> pdb=" O CYS K 70 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 112 Processing helix chain 'K' and resid 122 through 135 Processing helix chain 'K' and resid 146 through 148 No H-bonds generated for 'chain 'K' and resid 146 through 148' Processing helix chain 'K' and resid 153 through 163 Processing helix chain 'K' and resid 174 through 182 removed outlier: 3.880A pdb=" N ARG K 182 " --> pdb=" O ALA K 178 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 189 Processing helix chain 'K' and resid 201 through 215 Processing helix chain 'K' and resid 227 through 237 Processing helix chain 'K' and resid 241 through 257 removed outlier: 4.372A pdb=" N GLU K 246 " --> pdb=" O GLY K 242 " (cutoff:3.500A) Processing helix chain 'K' and resid 265 through 274 Processing helix chain 'L' and resid 20 through 29 Processing helix chain 'L' and resid 37 through 52 Processing helix chain 'L' and resid 66 through 76 removed outlier: 3.613A pdb=" N ARG L 76 " --> pdb=" O ALA L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 112 Processing helix chain 'L' and resid 122 through 135 Processing helix chain 'L' and resid 146 through 148 No H-bonds generated for 'chain 'L' and resid 146 through 148' Processing helix chain 'L' and resid 151 through 163 Processing helix chain 'L' and resid 174 through 182 removed outlier: 4.066A pdb=" N ASP L 177 " --> pdb=" O ASP L 174 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG L 182 " --> pdb=" O VAL L 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 189 Processing helix chain 'L' and resid 202 through 214 Processing helix chain 'L' and resid 227 through 237 removed outlier: 4.376A pdb=" N ILE L 232 " --> pdb=" O GLU L 228 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU L 233 " --> pdb=" O MET L 229 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 257 Processing helix chain 'L' and resid 265 through 274 removed outlier: 3.646A pdb=" N VAL L 271 " --> pdb=" O VAL L 267 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA L 272 " --> pdb=" O LEU L 268 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS L 273 " --> pdb=" O GLN L 269 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 193 through 195 removed outlier: 6.602A pdb=" N ARG A 57 " --> pdb=" O LEU A 194 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 193 through 195 removed outlier: 6.645A pdb=" N ARG B 57 " --> pdb=" O LEU B 194 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 193 through 196 removed outlier: 7.313A pdb=" N ARG C 57 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N PHE C 196 " --> pdb=" O ARG C 57 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL C 59 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 170 " --> pdb=" O CYS C 56 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 193 through 195 removed outlier: 6.538A pdb=" N ARG D 57 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU D 170 " --> pdb=" O CYS D 56 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 193 through 195 removed outlier: 6.742A pdb=" N ARG E 57 " --> pdb=" O LEU E 194 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 169 through 172 removed outlier: 7.354A pdb=" N CYS F 56 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N GLY F 172 " --> pdb=" O CYS F 56 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N VAL F 58 " --> pdb=" O GLY F 172 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 91 through 95 removed outlier: 6.681A pdb=" N MET F 140 " --> pdb=" O VAL F 92 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ILE F 94 " --> pdb=" O MET F 140 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE F 142 " --> pdb=" O ILE F 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'G' and resid 193 through 195 removed outlier: 6.137A pdb=" N ARG G 57 " --> pdb=" O LEU G 194 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 193 through 195 removed outlier: 6.746A pdb=" N ARG H 57 " --> pdb=" O LEU H 194 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'I' and resid 193 through 196 removed outlier: 7.567A pdb=" N ARG I 57 " --> pdb=" O LEU I 194 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N PHE I 196 " --> pdb=" O ARG I 57 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL I 59 " --> pdb=" O PHE I 196 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'J' and resid 169 through 172 removed outlier: 6.986A pdb=" N CYS J 56 " --> pdb=" O LEU J 170 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N GLY J 172 " --> pdb=" O CYS J 56 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL J 58 " --> pdb=" O GLY J 172 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'J' and resid 91 through 95 removed outlier: 6.502A pdb=" N MET J 140 " --> pdb=" O VAL J 92 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ILE J 94 " --> pdb=" O MET J 140 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE J 142 " --> pdb=" O ILE J 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'K' and resid 193 through 195 removed outlier: 6.892A pdb=" N ARG K 57 " --> pdb=" O LEU K 194 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'L' and resid 193 through 195 removed outlier: 6.557A pdb=" N ARG L 57 " --> pdb=" O LEU L 194 " (cutoff:3.500A) 1134 hydrogen bonds defined for protein. 3240 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 7.91 Time building geometry restraints manager: 12.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7507 1.34 - 1.45: 3784 1.45 - 1.57: 15093 1.57 - 1.69: 136 1.69 - 1.81: 144 Bond restraints: 26664 Sorted by residual: bond pdb=" N PRO K 90 " pdb=" CD PRO K 90 " ideal model delta sigma weight residual 1.473 1.554 -0.081 1.40e-02 5.10e+03 3.38e+01 bond pdb=" N LYS D 78 " pdb=" CA LYS D 78 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.41e-02 5.03e+03 4.48e+00 bond pdb=" CA LYS D 78 " pdb=" C LYS D 78 " ideal model delta sigma weight residual 1.524 1.549 -0.025 1.26e-02 6.30e+03 3.92e+00 bond pdb=" CB CYS H 56 " pdb=" SG CYS H 56 " ideal model delta sigma weight residual 1.808 1.762 0.046 3.30e-02 9.18e+02 1.98e+00 bond pdb=" CA ARG C 85 " pdb=" C ARG C 85 " ideal model delta sigma weight residual 1.524 1.539 -0.015 1.26e-02 6.30e+03 1.42e+00 ... (remaining 26659 not shown) Histogram of bond angle deviations from ideal: 92.04 - 101.00: 50 101.00 - 109.97: 3656 109.97 - 118.93: 18790 118.93 - 127.90: 13418 127.90 - 136.87: 215 Bond angle restraints: 36129 Sorted by residual: angle pdb=" N ASP C 174 " pdb=" CA ASP C 174 " pdb=" C ASP C 174 " ideal model delta sigma weight residual 114.75 98.32 16.43 1.26e+00 6.30e-01 1.70e+02 angle pdb=" N ARG C 85 " pdb=" CA ARG C 85 " pdb=" C ARG C 85 " ideal model delta sigma weight residual 109.81 136.87 -27.06 2.21e+00 2.05e-01 1.50e+02 angle pdb=" N THR C 173 " pdb=" CA THR C 173 " pdb=" C THR C 173 " ideal model delta sigma weight residual 110.56 132.86 -22.30 1.94e+00 2.66e-01 1.32e+02 angle pdb=" N LYS C 217 " pdb=" CA LYS C 217 " pdb=" C LYS C 217 " ideal model delta sigma weight residual 109.96 92.97 16.99 1.49e+00 4.50e-01 1.30e+02 angle pdb=" N ARG C 85 " pdb=" CA ARG C 85 " pdb=" CB ARG C 85 " ideal model delta sigma weight residual 110.37 92.04 18.33 1.78e+00 3.16e-01 1.06e+02 ... (remaining 36124 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 15875 35.09 - 70.17: 423 70.17 - 105.26: 13 105.26 - 140.34: 9 140.34 - 175.43: 6 Dihedral angle restraints: 16326 sinusoidal: 7386 harmonic: 8940 Sorted by residual: dihedral pdb=" O2A ADP L 301 " pdb=" O3A ADP L 301 " pdb=" PA ADP L 301 " pdb=" PB ADP L 301 " ideal model delta sinusoidal sigma weight residual -60.00 115.43 -175.43 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP J 301 " pdb=" O3A ADP J 301 " pdb=" PA ADP J 301 " pdb=" PB ADP J 301 " ideal model delta sinusoidal sigma weight residual 300.00 128.25 171.75 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O1B ADP K 301 " pdb=" O3A ADP K 301 " pdb=" PB ADP K 301 " pdb=" PA ADP K 301 " ideal model delta sinusoidal sigma weight residual -60.00 101.86 -161.86 1 2.00e+01 2.50e-03 4.68e+01 ... (remaining 16323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 4056 0.160 - 0.319: 13 0.319 - 0.479: 1 0.479 - 0.638: 1 0.638 - 0.798: 1 Chirality restraints: 4072 Sorted by residual: chirality pdb=" CA THR C 173 " pdb=" N THR C 173 " pdb=" C THR C 173 " pdb=" CB THR C 173 " both_signs ideal model delta sigma weight residual False 2.53 1.73 0.80 2.00e-01 2.50e+01 1.59e+01 chirality pdb=" CA ARG C 85 " pdb=" N ARG C 85 " pdb=" C ARG C 85 " pdb=" CB ARG C 85 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.02e+00 chirality pdb=" CA GLN C 81 " pdb=" N GLN C 81 " pdb=" C GLN C 81 " pdb=" CB GLN C 81 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 4069 not shown) Planarity restraints: 4356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 85 " -0.044 5.00e-02 4.00e+02 6.60e-02 6.96e+00 pdb=" N PRO C 86 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 86 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 86 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 85 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.29e+00 pdb=" N PRO D 86 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO D 86 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 86 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 85 " 0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO H 86 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO H 86 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 86 " 0.024 5.00e-02 4.00e+02 ... (remaining 4353 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.08: 6 2.08 - 2.79: 5333 2.79 - 3.49: 35271 3.49 - 4.20: 58327 4.20 - 4.90: 102506 Nonbonded interactions: 201443 Sorted by model distance: nonbonded pdb=" OE2 GLU A 212 " pdb=" OG SER A 222 " model vdw 1.381 2.440 nonbonded pdb=" OE1 GLU C 212 " pdb=" CB LEU C 224 " model vdw 1.821 3.440 nonbonded pdb=" NE ARG F 53 " pdb=" OE2 GLU F 139 " model vdw 2.046 2.520 nonbonded pdb=" O VAL K 89 " pdb=" N VAL K 138 " model vdw 2.059 2.520 nonbonded pdb=" OE1 GLU E 61 " pdb=" OH TYR E 240 " model vdw 2.063 2.440 ... (remaining 201438 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' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) selection = (chain 'B' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) selection = (chain 'C' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) selection = (chain 'D' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) selection = (chain 'E' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) selection = (chain 'F' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 80 or (resid 81 and (name N or nam \ e CA or name C or name O or name CB )) or resid 82 through 118 or (resid 119 and \ (name N or name CA or name C or name O or name CB )) or resid 120 through 211 o \ r (resid 212 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 13 through 216 or (resid 217 and (name N or name CA or name C or name O or name \ CB )) or resid 218 through 224 or (resid 225 and (name N or name CA or name C or \ name O or name CB )) or resid 226 through 275)) selection = (chain 'G' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) selection = (chain 'H' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 211 or ( \ resid 212 and (name N or name CA or name C or name O or name CB )) or resid 213 \ through 275)) selection = (chain 'I' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) selection = (chain 'J' and (resid 19 through 75 or (resid 76 and (name N or name CA or name \ C or name O or name CB )) or resid 77 through 80 or (resid 81 and (name N or nam \ e CA or name C or name O or name CB )) or resid 82 through 118 or (resid 119 and \ (name N or name CA or name C or name O or name CB )) or resid 120 through 216 o \ r (resid 217 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 18 through 224 or (resid 225 and (name N or name CA or name C or name O or name \ CB )) or resid 226 through 275)) selection = (chain 'K' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 118 or (resid 119 and \ (name N or name CA or name C or name O or name CB )) or resid 120 through 211 o \ r (resid 212 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 13 through 216 or (resid 217 and (name N or name CA or name C or name O or name \ CB )) or resid 218 through 224 or (resid 225 and (name N or name CA or name C or \ name O or name CB )) or resid 226 through 275)) selection = (chain 'L' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 74 5.49 5 S 96 5.16 5 C 16294 2.51 5 N 4756 2.21 5 O 4919 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.690 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: 0.030 Extract box with map and model: 6.300 Check model and map are aligned: 0.420 Process input model: 70.060 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.230 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 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 : 0.003 0.081 26664 Z= 0.173 Angle : 0.658 27.056 36129 Z= 0.379 Chirality : 0.044 0.798 4072 Planarity : 0.004 0.066 4356 Dihedral : 14.894 175.428 10542 Min Nonbonded Distance : 1.381 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.65 % Favored : 97.25 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.14), residues: 3060 helix: 0.25 (0.11), residues: 1810 sheet: 0.73 (0.36), residues: 204 loop : -0.05 (0.18), residues: 1046 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 913 time to evaluate : 3.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 916 average time/residue: 0.4914 time to fit residues: 644.9376 Evaluate side-chains 389 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 389 time to evaluate : 3.219 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 0.0570 chunk 230 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 177 optimal weight: 0.6980 chunk 276 optimal weight: 5.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 HIS B 185 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 GLN D 269 GLN E 213 GLN F 223 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 223 ASN K 38 GLN K 185 GLN L 38 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 26664 Z= 0.218 Angle : 0.654 8.384 36129 Z= 0.322 Chirality : 0.041 0.180 4072 Planarity : 0.005 0.052 4356 Dihedral : 15.855 177.073 4087 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.86 % Favored : 98.07 % Rotamer Outliers : 3.17 % 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: 1.21 (0.15), residues: 3060 helix: 1.09 (0.12), residues: 1809 sheet: 1.05 (0.37), residues: 204 loop : 0.47 (0.19), residues: 1047 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 426 time to evaluate : 3.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 51 residues processed: 488 average time/residue: 0.4678 time to fit residues: 349.0058 Evaluate side-chains 379 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 328 time to evaluate : 3.238 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.2529 time to fit residues: 28.8214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 229 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 276 optimal weight: 7.9990 chunk 298 optimal weight: 6.9990 chunk 246 optimal weight: 5.9990 chunk 274 optimal weight: 8.9990 chunk 94 optimal weight: 0.0020 chunk 221 optimal weight: 6.9990 overall best weight: 1.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 HIS ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN H 38 GLN H 185 GLN L 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 26664 Z= 0.288 Angle : 0.642 7.149 36129 Z= 0.320 Chirality : 0.041 0.202 4072 Planarity : 0.004 0.048 4356 Dihedral : 15.886 178.873 4087 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.42 % Favored : 97.52 % Rotamer Outliers : 2.65 % 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: 1.22 (0.15), residues: 3060 helix: 1.20 (0.12), residues: 1821 sheet: 0.84 (0.35), residues: 204 loop : 0.30 (0.19), residues: 1035 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 360 time to evaluate : 3.194 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 outliers start: 71 outliers final: 38 residues processed: 413 average time/residue: 0.4051 time to fit residues: 259.2554 Evaluate side-chains 337 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 299 time to evaluate : 3.156 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.2508 time to fit residues: 21.9999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 131 optimal weight: 0.2980 chunk 185 optimal weight: 2.9990 chunk 277 optimal weight: 6.9990 chunk 293 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 263 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 GLN L 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 26664 Z= 0.285 Angle : 0.631 9.953 36129 Z= 0.313 Chirality : 0.041 0.219 4072 Planarity : 0.004 0.065 4356 Dihedral : 15.833 178.712 4087 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.39 % Favored : 97.55 % Rotamer Outliers : 2.20 % 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: 1.19 (0.15), residues: 3060 helix: 1.31 (0.12), residues: 1794 sheet: 0.74 (0.34), residues: 205 loop : 0.04 (0.19), residues: 1061 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 349 time to evaluate : 3.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 33 residues processed: 388 average time/residue: 0.4087 time to fit residues: 244.4402 Evaluate side-chains 325 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 292 time to evaluate : 3.057 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.2582 time to fit residues: 20.0356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 4 optimal weight: 0.0010 chunk 218 optimal weight: 0.9980 chunk 121 optimal weight: 0.0870 chunk 250 optimal weight: 8.9990 chunk 203 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 150 optimal weight: 20.0000 chunk 263 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN I 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 26664 Z= 0.166 Angle : 0.570 7.449 36129 Z= 0.281 Chirality : 0.039 0.201 4072 Planarity : 0.004 0.059 4356 Dihedral : 15.581 178.236 4087 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.39 % Favored : 97.55 % Rotamer Outliers : 1.45 % 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: 1.42 (0.15), residues: 3060 helix: 1.53 (0.12), residues: 1795 sheet: 0.84 (0.34), residues: 205 loop : 0.07 (0.18), residues: 1060 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 320 time to evaluate : 3.220 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 outliers start: 39 outliers final: 18 residues processed: 342 average time/residue: 0.4056 time to fit residues: 216.4283 Evaluate side-chains 310 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 292 time to evaluate : 3.135 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2493 time to fit residues: 12.5204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 4.9990 chunk 264 optimal weight: 5.9990 chunk 58 optimal weight: 0.0060 chunk 172 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 294 optimal weight: 7.9990 chunk 244 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 24 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 overall best weight: 2.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN C 98 GLN G 193 HIS H 38 GLN I 185 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.5751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 26664 Z= 0.345 Angle : 0.679 9.594 36129 Z= 0.338 Chirality : 0.043 0.212 4072 Planarity : 0.005 0.065 4356 Dihedral : 15.681 178.498 4087 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.50 % Favored : 96.44 % Rotamer Outliers : 2.28 % 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: 1.01 (0.15), residues: 3060 helix: 1.21 (0.12), residues: 1806 sheet: 0.54 (0.35), residues: 205 loop : -0.11 (0.18), residues: 1049 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 320 time to evaluate : 3.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 31 residues processed: 357 average time/residue: 0.4324 time to fit residues: 235.2018 Evaluate side-chains 313 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 282 time to evaluate : 3.151 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2651 time to fit residues: 19.1605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 167 optimal weight: 6.9990 chunk 214 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 247 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 293 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 185 GLN H 38 GLN I 185 GLN L 193 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.5970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 26664 Z= 0.260 Angle : 0.613 11.537 36129 Z= 0.304 Chirality : 0.041 0.220 4072 Planarity : 0.004 0.084 4356 Dihedral : 15.464 179.361 4087 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.61 % Favored : 97.29 % Rotamer Outliers : 1.38 % 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: 1.04 (0.15), residues: 3060 helix: 1.34 (0.12), residues: 1784 sheet: 0.52 (0.35), residues: 205 loop : -0.27 (0.18), residues: 1071 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 303 time to evaluate : 3.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 22 residues processed: 331 average time/residue: 0.3933 time to fit residues: 205.5825 Evaluate side-chains 302 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 280 time to evaluate : 3.172 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2371 time to fit residues: 14.4315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 0.0980 chunk 117 optimal weight: 3.9990 chunk 174 optimal weight: 20.0000 chunk 88 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 56 optimal weight: 0.0770 chunk 186 optimal weight: 1.9990 chunk 199 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 GLN I 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.6092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 26664 Z= 0.201 Angle : 0.601 10.545 36129 Z= 0.296 Chirality : 0.040 0.198 4072 Planarity : 0.004 0.049 4356 Dihedral : 15.320 179.184 4087 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.88 % Favored : 97.03 % Rotamer Outliers : 1.08 % 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: 1.16 (0.15), residues: 3060 helix: 1.44 (0.12), residues: 1794 sheet: 0.48 (0.34), residues: 213 loop : -0.24 (0.18), residues: 1053 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 299 time to evaluate : 3.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 12 residues processed: 317 average time/residue: 0.4006 time to fit residues: 197.7236 Evaluate side-chains 288 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 276 time to evaluate : 3.104 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2210 time to fit residues: 9.3233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 0.0170 chunk 280 optimal weight: 7.9990 chunk 256 optimal weight: 1.9990 chunk 273 optimal weight: 0.0770 chunk 164 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 246 optimal weight: 0.9990 chunk 258 optimal weight: 0.6980 chunk 272 optimal weight: 0.9980 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN F 185 GLN I 185 GLN L 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.6209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 26664 Z= 0.157 Angle : 0.590 10.916 36129 Z= 0.288 Chirality : 0.040 0.205 4072 Planarity : 0.004 0.050 4356 Dihedral : 15.100 176.778 4087 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.65 % Favored : 97.29 % Rotamer Outliers : 0.45 % 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: 1.34 (0.15), residues: 3060 helix: 1.70 (0.13), residues: 1729 sheet: 0.52 (0.33), residues: 213 loop : -0.25 (0.18), residues: 1118 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 292 time to evaluate : 3.213 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 outliers start: 12 outliers final: 5 residues processed: 300 average time/residue: 0.4114 time to fit residues: 193.3743 Evaluate side-chains 279 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 274 time to evaluate : 3.138 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2523 time to fit residues: 6.6007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 5.9990 chunk 288 optimal weight: 7.9990 chunk 176 optimal weight: 4.9990 chunk 136 optimal weight: 0.6980 chunk 200 optimal weight: 6.9990 chunk 302 optimal weight: 5.9990 chunk 278 optimal weight: 9.9990 chunk 241 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 186 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 ASN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 GLN ** I 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.6537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.070 26664 Z= 0.454 Angle : 0.750 12.141 36129 Z= 0.375 Chirality : 0.046 0.275 4072 Planarity : 0.006 0.106 4356 Dihedral : 15.423 175.150 4087 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.73 % Favored : 96.05 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.15), residues: 3060 helix: 1.07 (0.12), residues: 1795 sheet: 0.21 (0.34), residues: 212 loop : -0.49 (0.18), residues: 1053 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 300 time to evaluate : 3.199 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 outliers start: 15 outliers final: 9 residues processed: 311 average time/residue: 0.3930 time to fit residues: 194.0374 Evaluate side-chains 285 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 276 time to evaluate : 3.179 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2350 time to fit residues: 8.3352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 0.6980 chunk 256 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 222 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 241 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 GLN ** I 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.160130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.130291 restraints weight = 41940.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.133240 restraints weight = 83307.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.131871 restraints weight = 34352.827| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.6578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 26664 Z= 0.191 Angle : 0.621 9.745 36129 Z= 0.306 Chirality : 0.041 0.247 4072 Planarity : 0.004 0.098 4356 Dihedral : 15.106 177.145 4087 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.81 % Favored : 97.06 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.15), residues: 3060 helix: 1.19 (0.12), residues: 1839 sheet: 0.31 (0.33), residues: 212 loop : -0.31 (0.19), residues: 1009 =============================================================================== Job complete usr+sys time: 5195.70 seconds wall clock time: 95 minutes 53.51 seconds (5753.51 seconds total)