Starting phenix.real_space_refine on Fri Feb 14 17:48:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8amf_15525/02_2025/8amf_15525.cif Found real_map, /net/cci-nas-00/data/ceres_data/8amf_15525/02_2025/8amf_15525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8amf_15525/02_2025/8amf_15525.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8amf_15525/02_2025/8amf_15525.map" model { file = "/net/cci-nas-00/data/ceres_data/8amf_15525/02_2025/8amf_15525.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8amf_15525/02_2025/8amf_15525.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 31 5.49 5 S 32 5.16 5 C 6520 2.51 5 N 1798 2.21 5 O 2126 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10507 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2504 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 322} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 207 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Chain: "D" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 200 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "B" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2504 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 322} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2504 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 322} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2504 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 322} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'AGS:plan-2': 1, 'AGS:plan-1': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'AGS:plan-2': 1, 'AGS:plan-1': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'AGS:plan-2': 1, 'AGS:plan-1': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'AGS:plan-2': 1, 'AGS:plan-1': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 6.49, per 1000 atoms: 0.62 Number of scatterers: 10507 At special positions: 0 Unit cell: (126.48, 119.04, 141.36, 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 32 16.00 P 31 15.00 O 2126 8.00 N 1798 7.00 C 6520 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 - 3.00 Amino acid : True - 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 1.5 seconds 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2376 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 15 sheets defined 37.4% alpha, 25.0% beta 5 base pairs and 7 stacking pairs defined. Time for finding SS restraints: 3.76 Creating SS restraints... Processing helix chain 'A' and resid 21 through 34 removed outlier: 3.898A pdb=" N ASP A 25 " --> pdb=" O LYS A 21 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 49 removed outlier: 5.518A pdb=" N ALA A 46 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N GLU A 47 " --> pdb=" O GLU A 44 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN A 48 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS A 49 " --> pdb=" O ALA A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 43 through 49' Processing helix chain 'A' and resid 85 through 98 removed outlier: 3.724A pdb=" N ALA A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 120 Processing helix chain 'A' and resid 134 through 148 removed outlier: 3.774A pdb=" N GLY A 138 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP A 147 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER A 148 " --> pdb=" O LYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.532A pdb=" N ILE A 168 " --> pdb=" O PRO A 164 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 164 through 169' Processing helix chain 'A' and resid 179 through 196 removed outlier: 3.628A pdb=" N MET A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ALA A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASN A 196 " --> pdb=" O GLY A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 232 removed outlier: 4.182A pdb=" N PHE A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.698A pdb=" N GLN A 250 " --> pdb=" O THR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.813A pdb=" N LEU A 292 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 327 removed outlier: 3.746A pdb=" N ALA A 327 " --> pdb=" O LYS A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 337 removed outlier: 3.673A pdb=" N ILE A 336 " --> pdb=" O PHE A 333 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP A 337 " --> pdb=" O ASP A 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 333 through 337' Processing helix chain 'B' and resid 21 through 34 removed outlier: 3.804A pdb=" N ASP B 25 " --> pdb=" O LYS B 21 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.761A pdb=" N LYS B 49 " --> pdb=" O ALA B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 84 through 98 removed outlier: 3.913A pdb=" N ALA B 89 " --> pdb=" O LYS B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 134 through 148 removed outlier: 3.989A pdb=" N SER B 148 " --> pdb=" O LYS B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 removed outlier: 3.853A pdb=" N ASP B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 198 removed outlier: 3.825A pdb=" N LYS B 190 " --> pdb=" O GLN B 186 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ALA B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN B 196 " --> pdb=" O GLY B 192 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS B 197 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 232 removed outlier: 3.920A pdb=" N PHE B 230 " --> pdb=" O ARG B 226 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 296 removed outlier: 3.889A pdb=" N LEU B 292 " --> pdb=" O THR B 288 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 293 " --> pdb=" O GLY B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 327 Processing helix chain 'B' and resid 329 through 336 removed outlier: 4.008A pdb=" N ILE B 332 " --> pdb=" O HIS B 329 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASP B 334 " --> pdb=" O GLU B 331 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B 335 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE B 336 " --> pdb=" O PHE B 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 34 removed outlier: 3.896A pdb=" N ASP F 25 " --> pdb=" O LYS F 21 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA F 26 " --> pdb=" O ALA F 22 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP F 33 " --> pdb=" O LEU F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 49 removed outlier: 3.756A pdb=" N LYS F 49 " --> pdb=" O ALA F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 64 removed outlier: 3.716A pdb=" N ASP F 61 " --> pdb=" O SER F 57 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA F 63 " --> pdb=" O ALA F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 98 removed outlier: 4.024A pdb=" N ALA F 89 " --> pdb=" O LYS F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 120 Processing helix chain 'F' and resid 134 through 149 removed outlier: 3.619A pdb=" N ASP F 147 " --> pdb=" O GLY F 143 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER F 148 " --> pdb=" O LYS F 144 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY F 149 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 169 removed outlier: 3.811A pdb=" N ASP F 169 " --> pdb=" O ARG F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 198 removed outlier: 3.961A pdb=" N ARG F 182 " --> pdb=" O GLY F 178 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS F 190 " --> pdb=" O GLN F 186 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA F 193 " --> pdb=" O ARG F 189 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER F 194 " --> pdb=" O LYS F 190 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE F 195 " --> pdb=" O LEU F 191 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN F 196 " --> pdb=" O GLY F 192 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS F 197 " --> pdb=" O ALA F 193 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR F 198 " --> pdb=" O SER F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 232 removed outlier: 3.877A pdb=" N PHE F 230 " --> pdb=" O ARG F 226 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR F 231 " --> pdb=" O ALA F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 251 removed outlier: 3.692A pdb=" N GLN F 250 " --> pdb=" O THR F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 298 removed outlier: 3.617A pdb=" N LEU F 292 " --> pdb=" O THR F 288 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS F 293 " --> pdb=" O GLY F 289 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP F 297 " --> pdb=" O LYS F 293 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU F 298 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 327 Processing helix chain 'F' and resid 329 through 336 removed outlier: 3.765A pdb=" N ILE F 332 " --> pdb=" O HIS F 329 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE F 333 " --> pdb=" O PRO F 330 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASP F 334 " --> pdb=" O GLU F 331 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU F 335 " --> pdb=" O ILE F 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 34 removed outlier: 3.944A pdb=" N ASP G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA G 26 " --> pdb=" O ALA G 22 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 49 removed outlier: 3.623A pdb=" N GLN G 48 " --> pdb=" O ARG G 45 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS G 49 " --> pdb=" O ALA G 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 49' Processing helix chain 'G' and resid 57 through 62 Processing helix chain 'G' and resid 84 through 98 removed outlier: 3.852A pdb=" N ALA G 89 " --> pdb=" O LYS G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 120 removed outlier: 3.567A pdb=" N ALA G 117 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU G 120 " --> pdb=" O TYR G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 149 removed outlier: 4.385A pdb=" N SER G 148 " --> pdb=" O LYS G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 162 Processing helix chain 'G' and resid 164 through 169 removed outlier: 3.864A pdb=" N ASP G 169 " --> pdb=" O ARG G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 196 removed outlier: 3.996A pdb=" N LYS G 190 " --> pdb=" O GLN G 186 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ALA G 193 " --> pdb=" O ARG G 189 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER G 194 " --> pdb=" O LYS G 190 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN G 196 " --> pdb=" O GLY G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 232 removed outlier: 3.906A pdb=" N PHE G 230 " --> pdb=" O ARG G 226 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR G 231 " --> pdb=" O ALA G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 298 removed outlier: 4.014A pdb=" N LEU G 292 " --> pdb=" O THR G 288 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS G 293 " --> pdb=" O GLY G 289 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP G 297 " --> pdb=" O LYS G 293 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU G 298 " --> pdb=" O ILE G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 327 removed outlier: 3.845A pdb=" N ALA G 327 " --> pdb=" O LYS G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 332 removed outlier: 3.662A pdb=" N ILE G 332 " --> pdb=" O HIS G 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 329 through 332' Processing helix chain 'G' and resid 333 through 338 removed outlier: 3.873A pdb=" N ASP G 337 " --> pdb=" O PHE G 333 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS G 338 " --> pdb=" O ASP G 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 333 through 338' Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 removed outlier: 3.857A pdb=" N SER B 130 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL B 154 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ILE B 205 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL B 156 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 234 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS B 265 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP B 237 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL B 263 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLU B 252 " --> pdb=" O GLY B 248 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLY B 248 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASN B 254 " --> pdb=" O GLY B 246 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLY B 246 " --> pdb=" O ASN B 254 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 41 removed outlier: 3.857A pdb=" N SER B 130 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL B 154 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ILE B 205 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL B 156 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 234 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS B 265 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP B 237 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL B 263 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 277 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA4, first strand: chain 'A' and resid 127 through 130 removed outlier: 3.883A pdb=" N SER A 130 " --> pdb=" O PHE A 105 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE A 74 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N LEU A 236 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU A 76 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL A 238 " --> pdb=" O GLU A 76 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N TYR A 78 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARG A 235 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 127 through 130 removed outlier: 3.883A pdb=" N SER A 130 " --> pdb=" O PHE A 105 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE A 74 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N LEU A 236 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU A 76 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL A 238 " --> pdb=" O GLU A 76 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N TYR A 78 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARG A 235 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 209 through 210 Processing sheet with id=AA7, first strand: chain 'B' and resid 40 through 41 removed outlier: 3.588A pdb=" N MET B 40 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER F 130 " --> pdb=" O PHE F 105 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE F 75 " --> pdb=" O PHE F 204 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE F 74 " --> pdb=" O VAL F 234 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LEU F 236 " --> pdb=" O ILE F 74 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLU F 76 " --> pdb=" O LEU F 236 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N VAL F 238 " --> pdb=" O GLU F 76 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TYR F 78 " --> pdb=" O VAL F 238 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS F 265 " --> pdb=" O ARG F 235 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASP F 237 " --> pdb=" O VAL F 263 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N VAL F 263 " --> pdb=" O ASP F 237 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 40 through 41 removed outlier: 3.588A pdb=" N MET B 40 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER F 130 " --> pdb=" O PHE F 105 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE F 75 " --> pdb=" O PHE F 204 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE F 74 " --> pdb=" O VAL F 234 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LEU F 236 " --> pdb=" O ILE F 74 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLU F 76 " --> pdb=" O LEU F 236 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N VAL F 238 " --> pdb=" O GLU F 76 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TYR F 78 " --> pdb=" O VAL F 238 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS F 265 " --> pdb=" O ARG F 235 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASP F 237 " --> pdb=" O VAL F 263 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N VAL F 263 " --> pdb=" O ASP F 237 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 52 through 53 Processing sheet with id=AB1, first strand: chain 'F' and resid 40 through 41 removed outlier: 3.729A pdb=" N MET F 40 " --> pdb=" O LEU G 129 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU G 129 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER G 130 " --> pdb=" O PHE G 105 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ALA G 104 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE G 74 " --> pdb=" O VAL G 234 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N LEU G 236 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU G 76 " --> pdb=" O LEU G 236 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL G 238 " --> pdb=" O GLU G 76 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TYR G 78 " --> pdb=" O VAL G 238 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG G 235 " --> pdb=" O VAL G 264 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLU G 252 " --> pdb=" O GLY G 248 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLY G 248 " --> pdb=" O GLU G 252 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASN G 254 " --> pdb=" O GLY G 246 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY G 246 " --> pdb=" O ASN G 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 40 through 41 removed outlier: 3.729A pdb=" N MET F 40 " --> pdb=" O LEU G 129 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU G 129 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER G 130 " --> pdb=" O PHE G 105 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ALA G 104 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE G 74 " --> pdb=" O VAL G 234 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N LEU G 236 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU G 76 " --> pdb=" O LEU G 236 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL G 238 " --> pdb=" O GLU G 76 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TYR G 78 " --> pdb=" O VAL G 238 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG G 235 " --> pdb=" O VAL G 264 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 52 through 53 Processing sheet with id=AB4, first strand: chain 'F' and resid 209 through 210 Processing sheet with id=AB5, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AB6, first strand: chain 'G' and resid 209 through 210 361 hydrogen bonds defined for protein. 1011 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 7 stacking parallelities Total time for adding SS restraints: 3.54 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 3475 1.35 - 1.50: 2611 1.50 - 1.65: 4533 1.65 - 1.80: 45 1.80 - 1.95: 15 Bond restraints: 10679 Sorted by residual: bond pdb=" O1A AGS B 500 " pdb=" PA AGS B 500 " ideal model delta sigma weight residual 1.481 1.582 -0.101 2.70e-02 1.37e+03 1.40e+01 bond pdb=" O2B AGS A 500 " pdb=" PB AGS A 500 " ideal model delta sigma weight residual 1.531 1.472 0.059 1.60e-02 3.91e+03 1.38e+01 bond pdb=" O1A AGS F 500 " pdb=" PA AGS F 500 " ideal model delta sigma weight residual 1.481 1.571 -0.090 2.70e-02 1.37e+03 1.12e+01 bond pdb=" O2B AGS G 500 " pdb=" PB AGS G 500 " ideal model delta sigma weight residual 1.531 1.483 0.048 1.60e-02 3.91e+03 8.81e+00 bond pdb=" O2B AGS B 500 " pdb=" PB AGS B 500 " ideal model delta sigma weight residual 1.531 1.484 0.047 1.60e-02 3.91e+03 8.50e+00 ... (remaining 10674 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 13687 1.90 - 3.80: 640 3.80 - 5.70: 75 5.70 - 7.60: 29 7.60 - 9.50: 23 Bond angle restraints: 14454 Sorted by residual: angle pdb=" C LYS B 85 " pdb=" N THR B 86 " pdb=" CA THR B 86 " ideal model delta sigma weight residual 120.68 112.00 8.68 1.70e+00 3.46e-01 2.61e+01 angle pdb=" C LYS F 85 " pdb=" N THR F 86 " pdb=" CA THR F 86 " ideal model delta sigma weight residual 121.52 112.43 9.09 1.84e+00 2.95e-01 2.44e+01 angle pdb=" C ASP B 249 " pdb=" N GLN B 250 " pdb=" CA GLN B 250 " ideal model delta sigma weight residual 121.54 129.39 -7.85 1.91e+00 2.74e-01 1.69e+01 angle pdb=" C ASP A 249 " pdb=" N GLN A 250 " pdb=" CA GLN A 250 " ideal model delta sigma weight residual 121.54 129.30 -7.76 1.91e+00 2.74e-01 1.65e+01 angle pdb=" C ASP G 249 " pdb=" N GLN G 250 " pdb=" CA GLN G 250 " ideal model delta sigma weight residual 121.54 129.20 -7.66 1.91e+00 2.74e-01 1.61e+01 ... (remaining 14449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.38: 6052 28.38 - 56.75: 428 56.75 - 85.13: 51 85.13 - 113.50: 4 113.50 - 141.88: 4 Dihedral angle restraints: 6539 sinusoidal: 2803 harmonic: 3736 Sorted by residual: dihedral pdb=" CA LYS B 14 " pdb=" C LYS B 14 " pdb=" N PHE B 15 " pdb=" CA PHE B 15 " ideal model delta harmonic sigma weight residual 180.00 141.87 38.13 0 5.00e+00 4.00e-02 5.82e+01 dihedral pdb=" CA GLY G 84 " pdb=" C GLY G 84 " pdb=" N LYS G 85 " pdb=" CA LYS G 85 " ideal model delta harmonic sigma weight residual 180.00 152.61 27.39 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA GLY F 84 " pdb=" C GLY F 84 " pdb=" N LYS F 85 " pdb=" CA LYS F 85 " ideal model delta harmonic sigma weight residual 180.00 152.67 27.33 0 5.00e+00 4.00e-02 2.99e+01 ... (remaining 6536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 1621 0.160 - 0.321: 14 0.321 - 0.481: 0 0.481 - 0.641: 1 0.641 - 0.802: 3 Chirality restraints: 1639 Sorted by residual: chirality pdb=" PB AGS B 500 " pdb=" O2B AGS B 500 " pdb=" O3A AGS B 500 " pdb=" O3B AGS B 500 " both_signs ideal model delta sigma weight residual True 3.18 2.38 0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" PB AGS G 500 " pdb=" O2B AGS G 500 " pdb=" O3A AGS G 500 " pdb=" O3B AGS G 500 " both_signs ideal model delta sigma weight residual True 3.18 2.47 0.71 2.00e-01 2.50e+01 1.25e+01 chirality pdb=" PB AGS F 500 " pdb=" O2B AGS F 500 " pdb=" O3A AGS F 500 " pdb=" O3B AGS F 500 " both_signs ideal model delta sigma weight residual True 3.18 2.48 0.70 2.00e-01 2.50e+01 1.23e+01 ... (remaining 1636 not shown) Planarity restraints: 1800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 269 " 0.049 5.00e-02 4.00e+02 7.46e-02 8.89e+00 pdb=" N PRO B 270 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 269 " -0.049 5.00e-02 4.00e+02 7.33e-02 8.61e+00 pdb=" N PRO F 270 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO F 270 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO F 270 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 269 " -0.044 5.00e-02 4.00e+02 6.61e-02 6.99e+00 pdb=" N PRO G 270 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO G 270 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 270 " -0.036 5.00e-02 4.00e+02 ... (remaining 1797 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3041 2.80 - 3.33: 9499 3.33 - 3.85: 17033 3.85 - 4.38: 17939 4.38 - 4.90: 30428 Nonbonded interactions: 77940 Sorted by model distance: nonbonded pdb=" OG1 THR A 198 " pdb=" OG1 THR A 200 " model vdw 2.281 3.040 nonbonded pdb=" O1B AGS A 500 " pdb=" O2G AGS A 500 " model vdw 2.315 3.040 nonbonded pdb=" OG1 THR B 198 " pdb=" OG1 THR B 200 " model vdw 2.319 3.040 nonbonded pdb=" O SER A 83 " pdb=" OG SER A 83 " model vdw 2.326 3.040 nonbonded pdb=" OE1 GLU G 31 " pdb=" OG SER G 38 " model vdw 2.327 3.040 ... (remaining 77935 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'F' selection = chain 'G' } 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: 0.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.870 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 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 : 0.007 0.143 10679 Z= 0.441 Angle : 0.992 9.496 14454 Z= 0.538 Chirality : 0.065 0.802 1639 Planarity : 0.006 0.075 1800 Dihedral : 18.673 141.876 4163 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.77 % Allowed : 14.52 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.87 (0.18), residues: 1324 helix: -2.93 (0.21), residues: 328 sheet: -1.99 (0.31), residues: 212 loop : -2.66 (0.18), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 307 HIS 0.007 0.001 HIS F 176 PHE 0.021 0.003 PHE B 105 TYR 0.021 0.003 TYR B 78 ARG 0.004 0.000 ARG F 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 179 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.9408 (mt) cc_final: 0.8961 (mt) REVERT: A 176 HIS cc_start: 0.7897 (m-70) cc_final: 0.7670 (m90) REVERT: A 183 MET cc_start: 0.9020 (tmm) cc_final: 0.8594 (tmm) REVERT: A 258 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8127 (tm-30) REVERT: A 307 TRP cc_start: 0.8704 (m-90) cc_final: 0.8279 (m-90) REVERT: B 76 GLU cc_start: 0.8000 (pp20) cc_final: 0.7762 (pp20) REVERT: B 183 MET cc_start: 0.8690 (tmm) cc_final: 0.8295 (tmm) REVERT: B 215 MET cc_start: 0.5997 (mmm) cc_final: 0.5779 (mmm) REVERT: B 258 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8016 (tm-30) REVERT: B 274 GLU cc_start: 0.8732 (pp20) cc_final: 0.7907 (pp20) REVERT: F 140 GLU cc_start: 0.8905 (tp30) cc_final: 0.8598 (tp30) REVERT: F 141 ILE cc_start: 0.9301 (mt) cc_final: 0.8909 (mm) REVERT: F 183 MET cc_start: 0.8956 (tmm) cc_final: 0.8332 (tmm) REVERT: F 258 GLU cc_start: 0.8855 (tm-30) cc_final: 0.7791 (tm-30) REVERT: F 274 GLU cc_start: 0.8797 (pp20) cc_final: 0.8490 (pp20) REVERT: F 307 TRP cc_start: 0.8749 (m-90) cc_final: 0.8540 (m-90) REVERT: G 47 GLU cc_start: 0.8930 (pm20) cc_final: 0.8663 (pm20) REVERT: G 183 MET cc_start: 0.8708 (tmm) cc_final: 0.8128 (tmm) REVERT: G 186 GLN cc_start: 0.8691 (tm-30) cc_final: 0.7776 (tp40) REVERT: G 333 PHE cc_start: 0.8006 (m-10) cc_final: 0.7660 (m-80) outliers start: 8 outliers final: 2 residues processed: 187 average time/residue: 0.2283 time to fit residues: 59.9072 Evaluate side-chains 111 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain G residue 50 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 68 optimal weight: 30.0000 chunk 54 optimal weight: 5.9990 chunk 105 optimal weight: 30.0000 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 20.0000 chunk 78 optimal weight: 0.0000 chunk 121 optimal weight: 8.9990 overall best weight: 3.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS B 176 HIS B 196 ASN B 329 HIS F 176 HIS ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.115709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.087858 restraints weight = 27195.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.090569 restraints weight = 13300.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.092301 restraints weight = 8703.662| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 10679 Z= 0.256 Angle : 0.678 7.933 14454 Z= 0.362 Chirality : 0.047 0.199 1639 Planarity : 0.004 0.053 1800 Dihedral : 17.344 156.997 1717 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.21 % Allowed : 20.77 % Favored : 77.02 % 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: -2.64 (0.21), residues: 1324 helix: -1.26 (0.26), residues: 348 sheet: -1.52 (0.32), residues: 240 loop : -2.12 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 307 HIS 0.005 0.001 HIS B 329 PHE 0.019 0.001 PHE B 105 TYR 0.018 0.002 TYR A 78 ARG 0.002 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 MET cc_start: 0.9155 (tmm) cc_final: 0.8616 (tmm) REVERT: A 206 ASN cc_start: 0.8709 (t0) cc_final: 0.8219 (t0) REVERT: A 208 LEU cc_start: 0.8839 (tp) cc_final: 0.8464 (tp) REVERT: A 274 GLU cc_start: 0.8889 (pp20) cc_final: 0.8216 (pp20) REVERT: A 283 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8813 (tp30) REVERT: A 315 ILE cc_start: 0.4094 (OUTLIER) cc_final: 0.3659 (mp) REVERT: B 76 GLU cc_start: 0.7338 (pp20) cc_final: 0.7038 (pp20) REVERT: B 141 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8848 (mp) REVERT: B 183 MET cc_start: 0.9036 (tmm) cc_final: 0.8590 (tmm) REVERT: B 184 MET cc_start: 0.9239 (tpp) cc_final: 0.8910 (tpp) REVERT: B 206 ASN cc_start: 0.8649 (t0) cc_final: 0.8439 (t0) REVERT: B 258 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8633 (tm-30) REVERT: F 76 GLU cc_start: 0.8130 (pp20) cc_final: 0.7613 (pp20) REVERT: F 140 GLU cc_start: 0.8950 (tp30) cc_final: 0.8663 (tp30) REVERT: F 183 MET cc_start: 0.9103 (tmm) cc_final: 0.8396 (tmm) REVERT: F 188 MET cc_start: 0.8302 (ttm) cc_final: 0.7957 (ttp) REVERT: F 212 VAL cc_start: 0.8386 (OUTLIER) cc_final: 0.8067 (p) REVERT: G 183 MET cc_start: 0.8733 (tmm) cc_final: 0.8245 (tmm) REVERT: G 186 GLN cc_start: 0.8725 (tm-30) cc_final: 0.7804 (tp40) REVERT: G 206 ASN cc_start: 0.8860 (t0) cc_final: 0.8515 (t0) REVERT: G 307 TRP cc_start: 0.8362 (m100) cc_final: 0.7397 (m100) REVERT: G 333 PHE cc_start: 0.7900 (m-10) cc_final: 0.7698 (m-80) outliers start: 23 outliers final: 6 residues processed: 151 average time/residue: 0.1906 time to fit residues: 43.3542 Evaluate side-chains 111 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 325 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 38 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 29 optimal weight: 40.0000 chunk 125 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.108862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.078811 restraints weight = 27450.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.081194 restraints weight = 15055.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.082751 restraints weight = 10446.772| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.146 10679 Z= 0.467 Angle : 0.797 8.726 14454 Z= 0.416 Chirality : 0.049 0.249 1639 Planarity : 0.005 0.046 1800 Dihedral : 17.763 149.681 1717 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 2.79 % Allowed : 24.04 % Favored : 73.17 % 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: -1.86 (0.23), residues: 1324 helix: -0.38 (0.29), residues: 324 sheet: -1.16 (0.34), residues: 240 loop : -1.66 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 307 HIS 0.009 0.002 HIS F 329 PHE 0.022 0.002 PHE F 15 TYR 0.028 0.002 TYR A 231 ARG 0.003 0.000 ARG B 341 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 HIS cc_start: 0.7973 (m90) cc_final: 0.7707 (m90) REVERT: A 183 MET cc_start: 0.9106 (tmm) cc_final: 0.8509 (tmm) REVERT: A 188 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8460 (tmm) REVERT: A 208 LEU cc_start: 0.8836 (tp) cc_final: 0.8470 (tp) REVERT: A 274 GLU cc_start: 0.9046 (pp20) cc_final: 0.8544 (pp20) REVERT: A 280 MET cc_start: 0.9238 (tpp) cc_final: 0.8979 (mmm) REVERT: B 76 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7429 (pp20) REVERT: B 183 MET cc_start: 0.9019 (tmm) cc_final: 0.8580 (tmm) REVERT: B 206 ASN cc_start: 0.8871 (t0) cc_final: 0.8653 (t0) REVERT: B 258 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8621 (tm-30) REVERT: F 147 ASP cc_start: 0.8169 (p0) cc_final: 0.7520 (t0) REVERT: F 183 MET cc_start: 0.9053 (tmm) cc_final: 0.8183 (tmm) REVERT: F 184 MET cc_start: 0.9163 (tpp) cc_final: 0.8905 (tpp) REVERT: G 183 MET cc_start: 0.8865 (tmm) cc_final: 0.8308 (tmm) REVERT: G 206 ASN cc_start: 0.8849 (t0) cc_final: 0.8511 (t0) REVERT: G 215 MET cc_start: 0.7416 (mmm) cc_final: 0.7207 (mmm) REVERT: G 274 GLU cc_start: 0.9022 (pp20) cc_final: 0.8677 (pp20) REVERT: G 307 TRP cc_start: 0.8672 (m100) cc_final: 0.7838 (m100) REVERT: G 315 ILE cc_start: 0.6700 (OUTLIER) cc_final: 0.6343 (mp) REVERT: G 333 PHE cc_start: 0.7847 (m-10) cc_final: 0.7362 (m-80) outliers start: 29 outliers final: 15 residues processed: 123 average time/residue: 0.1793 time to fit residues: 33.7311 Evaluate side-chains 108 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 315 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 72 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 96 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 ASN ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 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 = 0.3825 r_free = 0.3825 target = 0.112941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.083019 restraints weight = 26839.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.085614 restraints weight = 14127.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.087285 restraints weight = 9580.713| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10679 Z= 0.214 Angle : 0.640 8.940 14454 Z= 0.335 Chirality : 0.046 0.204 1639 Planarity : 0.004 0.043 1800 Dihedral : 17.236 153.203 1717 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.88 % Allowed : 24.90 % Favored : 72.21 % 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 (0.23), residues: 1324 helix: -0.41 (0.28), residues: 376 sheet: -0.81 (0.36), residues: 216 loop : -1.74 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 307 HIS 0.004 0.001 HIS A 176 PHE 0.017 0.001 PHE B 105 TYR 0.019 0.002 TYR A 231 ARG 0.002 0.000 ARG B 239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: A 78 TYR cc_start: 0.9062 (p90) cc_final: 0.8698 (p90) REVERT: A 140 GLU cc_start: 0.9001 (tp30) cc_final: 0.8789 (mm-30) REVERT: A 141 ILE cc_start: 0.9539 (mt) cc_final: 0.9287 (tp) REVERT: A 183 MET cc_start: 0.9167 (tmm) cc_final: 0.8640 (tmm) REVERT: A 208 LEU cc_start: 0.8769 (tp) cc_final: 0.8442 (tp) REVERT: A 274 GLU cc_start: 0.9006 (pp20) cc_final: 0.8538 (pp20) REVERT: A 280 MET cc_start: 0.9221 (tpp) cc_final: 0.8949 (mmm) REVERT: A 283 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8777 (tp30) REVERT: A 307 TRP cc_start: 0.7834 (m100) cc_final: 0.7292 (m100) REVERT: B 183 MET cc_start: 0.9075 (tmm) cc_final: 0.8675 (tmm) REVERT: B 184 MET cc_start: 0.9156 (tpp) cc_final: 0.8786 (tpp) REVERT: B 206 ASN cc_start: 0.8744 (t0) cc_final: 0.8526 (t0) REVERT: B 212 VAL cc_start: 0.8979 (OUTLIER) cc_final: 0.8761 (p) REVERT: B 258 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8527 (tm-30) REVERT: F 76 GLU cc_start: 0.8165 (pp20) cc_final: 0.7802 (pp20) REVERT: F 147 ASP cc_start: 0.8041 (p0) cc_final: 0.7549 (t0) REVERT: F 183 MET cc_start: 0.9149 (tmm) cc_final: 0.8457 (tmm) REVERT: G 171 ASP cc_start: 0.8343 (t0) cc_final: 0.8042 (t0) REVERT: G 183 MET cc_start: 0.8930 (tmm) cc_final: 0.8315 (tmm) REVERT: G 206 ASN cc_start: 0.8772 (t0) cc_final: 0.8490 (t0) REVERT: G 274 GLU cc_start: 0.8938 (pp20) cc_final: 0.8547 (pp20) REVERT: G 307 TRP cc_start: 0.8689 (m100) cc_final: 0.7894 (m100) REVERT: G 315 ILE cc_start: 0.6318 (OUTLIER) cc_final: 0.5967 (mp) REVERT: G 333 PHE cc_start: 0.7892 (m-10) cc_final: 0.7391 (m-80) outliers start: 30 outliers final: 12 residues processed: 135 average time/residue: 0.1811 time to fit residues: 37.8250 Evaluate side-chains 114 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 315 ILE Chi-restraints excluded: chain G residue 325 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 111 optimal weight: 20.0000 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 112 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.111042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.080883 restraints weight = 26772.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.083512 restraints weight = 13940.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.085227 restraints weight = 9361.882| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 10679 Z= 0.325 Angle : 0.688 8.720 14454 Z= 0.359 Chirality : 0.047 0.216 1639 Planarity : 0.004 0.043 1800 Dihedral : 17.308 152.560 1717 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.37 % Allowed : 25.10 % Favored : 71.54 % 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: -1.45 (0.23), residues: 1324 helix: 0.09 (0.29), residues: 352 sheet: -0.76 (0.35), residues: 232 loop : -1.58 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 307 HIS 0.004 0.001 HIS A 176 PHE 0.020 0.002 PHE G 105 TYR 0.022 0.002 TYR A 231 ARG 0.002 0.000 ARG F 235 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 1.137 Fit side-chains REVERT: A 141 ILE cc_start: 0.9529 (mt) cc_final: 0.9299 (tp) REVERT: A 183 MET cc_start: 0.9203 (tmm) cc_final: 0.8592 (tmm) REVERT: A 188 MET cc_start: 0.8946 (tmm) cc_final: 0.8602 (tmm) REVERT: A 208 LEU cc_start: 0.8789 (tp) cc_final: 0.8426 (tp) REVERT: A 274 GLU cc_start: 0.9047 (pp20) cc_final: 0.8534 (pp20) REVERT: A 307 TRP cc_start: 0.7940 (m100) cc_final: 0.7419 (m100) REVERT: B 29 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9156 (tt) REVERT: B 183 MET cc_start: 0.9101 (tmm) cc_final: 0.8650 (tmm) REVERT: B 258 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8554 (tm-30) REVERT: F 76 GLU cc_start: 0.8295 (pp20) cc_final: 0.8046 (pp20) REVERT: F 140 GLU cc_start: 0.8971 (tp30) cc_final: 0.8516 (tp30) REVERT: F 183 MET cc_start: 0.9111 (tmm) cc_final: 0.8230 (tmm) REVERT: F 251 LYS cc_start: 0.8337 (tptt) cc_final: 0.8079 (tptt) REVERT: G 53 MET cc_start: 0.8869 (tmm) cc_final: 0.8513 (tmm) REVERT: G 171 ASP cc_start: 0.8420 (t0) cc_final: 0.8071 (t0) REVERT: G 183 MET cc_start: 0.8939 (tmm) cc_final: 0.8256 (tmm) REVERT: G 206 ASN cc_start: 0.8872 (t0) cc_final: 0.8480 (t0) REVERT: G 215 MET cc_start: 0.7328 (mmm) cc_final: 0.7077 (mmm) REVERT: G 274 GLU cc_start: 0.9071 (pp20) cc_final: 0.8623 (pp20) REVERT: G 307 TRP cc_start: 0.8804 (m100) cc_final: 0.8047 (m100) REVERT: G 315 ILE cc_start: 0.6303 (OUTLIER) cc_final: 0.5914 (mp) REVERT: G 333 PHE cc_start: 0.7994 (m-10) cc_final: 0.7497 (m-80) outliers start: 35 outliers final: 19 residues processed: 137 average time/residue: 0.1707 time to fit residues: 36.2081 Evaluate side-chains 118 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 315 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 100 optimal weight: 30.0000 chunk 115 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 129 optimal weight: 20.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.108880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.078846 restraints weight = 27120.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.081336 restraints weight = 14386.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.082964 restraints weight = 9759.242| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.135 10679 Z= 0.467 Angle : 0.782 8.906 14454 Z= 0.406 Chirality : 0.049 0.232 1639 Planarity : 0.005 0.043 1800 Dihedral : 17.687 151.788 1717 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 4.13 % Allowed : 25.48 % Favored : 70.38 % 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: -1.53 (0.23), residues: 1324 helix: -0.09 (0.28), residues: 352 sheet: -0.85 (0.34), residues: 240 loop : -1.55 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 307 HIS 0.007 0.001 HIS A 176 PHE 0.025 0.002 PHE G 105 TYR 0.025 0.003 TYR A 231 ARG 0.002 0.000 ARG F 226 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 95 time to evaluate : 1.324 Fit side-chains revert: symmetry clash REVERT: A 183 MET cc_start: 0.9189 (tmm) cc_final: 0.8593 (tmm) REVERT: A 188 MET cc_start: 0.8989 (tmm) cc_final: 0.8611 (tmt) REVERT: A 208 LEU cc_start: 0.8781 (tp) cc_final: 0.8422 (tp) REVERT: A 274 GLU cc_start: 0.9143 (pp20) cc_final: 0.8665 (pp20) REVERT: B 29 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9187 (tt) REVERT: B 183 MET cc_start: 0.9142 (tmm) cc_final: 0.8712 (tmm) REVERT: B 258 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8591 (tm-30) REVERT: F 140 GLU cc_start: 0.8978 (tp30) cc_final: 0.8739 (tp30) REVERT: F 183 MET cc_start: 0.9042 (tmm) cc_final: 0.8050 (tmm) REVERT: G 53 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8519 (tmm) REVERT: G 183 MET cc_start: 0.8977 (tmm) cc_final: 0.8316 (tmm) REVERT: G 206 ASN cc_start: 0.8874 (t0) cc_final: 0.8545 (m-40) REVERT: G 274 GLU cc_start: 0.9217 (pp20) cc_final: 0.8733 (pp20) REVERT: G 307 TRP cc_start: 0.8863 (m100) cc_final: 0.8132 (m100) REVERT: G 315 ILE cc_start: 0.6473 (OUTLIER) cc_final: 0.6061 (mp) REVERT: G 333 PHE cc_start: 0.7973 (m-10) cc_final: 0.7543 (m-80) outliers start: 43 outliers final: 29 residues processed: 131 average time/residue: 0.1785 time to fit residues: 36.5189 Evaluate side-chains 124 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 134 SER Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 234 VAL Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 315 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 72 optimal weight: 30.0000 chunk 121 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.114337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.084387 restraints weight = 26875.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.087047 restraints weight = 14102.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.088753 restraints weight = 9486.524| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10679 Z= 0.203 Angle : 0.635 8.919 14454 Z= 0.332 Chirality : 0.046 0.248 1639 Planarity : 0.004 0.048 1800 Dihedral : 17.168 156.452 1717 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.17 % Allowed : 26.63 % Favored : 70.19 % 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: -1.18 (0.24), residues: 1324 helix: 0.41 (0.29), residues: 352 sheet: -0.60 (0.36), residues: 220 loop : -1.46 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 307 HIS 0.005 0.001 HIS A 176 PHE 0.018 0.001 PHE B 105 TYR 0.013 0.002 TYR B 78 ARG 0.001 0.000 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 1.144 Fit side-chains revert: symmetry clash REVERT: A 141 ILE cc_start: 0.9545 (mt) cc_final: 0.9287 (tp) REVERT: A 157 ASP cc_start: 0.7901 (t0) cc_final: 0.7532 (t0) REVERT: A 183 MET cc_start: 0.9196 (tmm) cc_final: 0.8638 (tmm) REVERT: A 205 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8939 (pt) REVERT: A 208 LEU cc_start: 0.8798 (tp) cc_final: 0.8523 (tp) REVERT: A 274 GLU cc_start: 0.9057 (pp20) cc_final: 0.8648 (pp20) REVERT: A 307 TRP cc_start: 0.7942 (m100) cc_final: 0.7445 (m100) REVERT: A 315 ILE cc_start: 0.4658 (OUTLIER) cc_final: 0.3416 (mp) REVERT: B 29 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9106 (tt) REVERT: B 183 MET cc_start: 0.9165 (tmm) cc_final: 0.8715 (tmm) REVERT: B 184 MET cc_start: 0.9238 (tpp) cc_final: 0.8971 (tpp) REVERT: B 212 VAL cc_start: 0.9003 (OUTLIER) cc_final: 0.8776 (p) REVERT: B 258 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8431 (tm-30) REVERT: F 183 MET cc_start: 0.9171 (tmm) cc_final: 0.8397 (tmm) REVERT: F 212 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.8053 (p) REVERT: G 53 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8474 (tmm) REVERT: G 183 MET cc_start: 0.9048 (tmm) cc_final: 0.8415 (tmm) REVERT: G 206 ASN cc_start: 0.8889 (t0) cc_final: 0.8553 (m-40) REVERT: G 274 GLU cc_start: 0.9084 (pp20) cc_final: 0.8591 (pp20) REVERT: G 307 TRP cc_start: 0.8872 (m100) cc_final: 0.8168 (m100) REVERT: G 315 ILE cc_start: 0.6363 (OUTLIER) cc_final: 0.5783 (mp) outliers start: 33 outliers final: 15 residues processed: 133 average time/residue: 0.1734 time to fit residues: 35.9726 Evaluate side-chains 119 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 315 ILE Chi-restraints excluded: chain G residue 325 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 89 optimal weight: 7.9990 chunk 131 optimal weight: 7.9990 chunk 125 optimal weight: 0.5980 chunk 113 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 133 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 11 optimal weight: 0.2980 overall best weight: 4.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.111387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.081317 restraints weight = 27036.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.083881 restraints weight = 14470.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.085543 restraints weight = 9854.226| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 10679 Z= 0.307 Angle : 0.681 8.893 14454 Z= 0.353 Chirality : 0.046 0.215 1639 Planarity : 0.004 0.046 1800 Dihedral : 17.239 153.839 1717 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.17 % Allowed : 27.02 % Favored : 69.81 % 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: -1.17 (0.24), residues: 1324 helix: 0.45 (0.29), residues: 352 sheet: -0.70 (0.34), residues: 240 loop : -1.44 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 307 HIS 0.005 0.001 HIS A 176 PHE 0.016 0.002 PHE G 105 TYR 0.024 0.002 TYR A 325 ARG 0.002 0.000 ARG F 235 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 98 time to evaluate : 1.174 Fit side-chains revert: symmetry clash REVERT: A 141 ILE cc_start: 0.9566 (mt) cc_final: 0.9312 (tp) REVERT: A 157 ASP cc_start: 0.7349 (t0) cc_final: 0.7035 (t0) REVERT: A 183 MET cc_start: 0.9192 (tmm) cc_final: 0.8625 (tmm) REVERT: A 205 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8917 (pt) REVERT: A 206 ASN cc_start: 0.8714 (t0) cc_final: 0.8504 (t0) REVERT: A 208 LEU cc_start: 0.8717 (tp) cc_final: 0.8455 (tp) REVERT: A 274 GLU cc_start: 0.9102 (pp20) cc_final: 0.8642 (pp20) REVERT: A 307 TRP cc_start: 0.8037 (m100) cc_final: 0.7541 (m100) REVERT: A 315 ILE cc_start: 0.4733 (OUTLIER) cc_final: 0.3529 (mp) REVERT: B 29 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9160 (tt) REVERT: B 183 MET cc_start: 0.9203 (tmm) cc_final: 0.8849 (tmm) REVERT: B 258 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8485 (tm-30) REVERT: F 183 MET cc_start: 0.9031 (tmm) cc_final: 0.8030 (tmm) REVERT: G 53 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8499 (tmm) REVERT: G 171 ASP cc_start: 0.8143 (t0) cc_final: 0.7937 (t0) REVERT: G 183 MET cc_start: 0.9002 (tmm) cc_final: 0.8377 (tmm) REVERT: G 206 ASN cc_start: 0.8909 (t0) cc_final: 0.8581 (m-40) REVERT: G 274 GLU cc_start: 0.9114 (pp20) cc_final: 0.8634 (pp20) REVERT: G 307 TRP cc_start: 0.8935 (m100) cc_final: 0.8318 (m100) REVERT: G 315 ILE cc_start: 0.6409 (OUTLIER) cc_final: 0.5976 (mp) outliers start: 33 outliers final: 21 residues processed: 125 average time/residue: 0.1661 time to fit residues: 32.6230 Evaluate side-chains 121 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 134 SER Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 315 ILE Chi-restraints excluded: chain G residue 325 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 63 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 100 optimal weight: 30.0000 chunk 112 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS ** 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 = 0.3843 r_free = 0.3843 target = 0.114053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.084200 restraints weight = 26962.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.086881 restraints weight = 14150.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.088636 restraints weight = 9533.696| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10679 Z= 0.199 Angle : 0.639 8.568 14454 Z= 0.333 Chirality : 0.045 0.193 1639 Planarity : 0.004 0.049 1800 Dihedral : 16.937 154.905 1717 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.60 % Allowed : 27.88 % Favored : 69.52 % 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: -0.96 (0.24), residues: 1324 helix: 0.71 (0.30), residues: 352 sheet: -0.45 (0.36), residues: 220 loop : -1.39 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 307 HIS 0.004 0.001 HIS F 176 PHE 0.014 0.001 PHE G 333 TYR 0.021 0.002 TYR A 325 ARG 0.001 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ILE cc_start: 0.9519 (mt) cc_final: 0.9266 (tp) REVERT: A 157 ASP cc_start: 0.7212 (t0) cc_final: 0.6882 (t0) REVERT: A 183 MET cc_start: 0.9232 (tmm) cc_final: 0.8643 (tmm) REVERT: A 205 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8971 (pt) REVERT: A 206 ASN cc_start: 0.8619 (t0) cc_final: 0.8337 (t0) REVERT: A 208 LEU cc_start: 0.8661 (tp) cc_final: 0.8437 (tp) REVERT: A 274 GLU cc_start: 0.9058 (pp20) cc_final: 0.8606 (pp20) REVERT: A 307 TRP cc_start: 0.8177 (m100) cc_final: 0.7709 (m100) REVERT: A 315 ILE cc_start: 0.4659 (OUTLIER) cc_final: 0.3482 (mp) REVERT: B 29 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9118 (tt) REVERT: B 183 MET cc_start: 0.9221 (tmm) cc_final: 0.8808 (tmm) REVERT: B 184 MET cc_start: 0.9291 (tpp) cc_final: 0.9040 (tpp) REVERT: B 258 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8065 (tm-30) REVERT: F 183 MET cc_start: 0.9068 (tmm) cc_final: 0.8120 (tmm) REVERT: G 53 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8473 (tmm) REVERT: G 183 MET cc_start: 0.9058 (tmm) cc_final: 0.8436 (tmm) REVERT: G 206 ASN cc_start: 0.8878 (t0) cc_final: 0.8604 (m-40) REVERT: G 274 GLU cc_start: 0.9045 (pp20) cc_final: 0.8542 (pp20) REVERT: G 307 TRP cc_start: 0.8925 (m100) cc_final: 0.8303 (m100) REVERT: G 315 ILE cc_start: 0.6338 (OUTLIER) cc_final: 0.5884 (mp) outliers start: 27 outliers final: 18 residues processed: 135 average time/residue: 0.1785 time to fit residues: 37.3921 Evaluate side-chains 133 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 134 SER Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 315 ILE Chi-restraints excluded: chain G residue 325 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 101 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 130 optimal weight: 30.0000 chunk 79 optimal weight: 5.9990 chunk 29 optimal weight: 30.0000 chunk 17 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.108166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.080578 restraints weight = 27567.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.081391 restraints weight = 14354.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.082394 restraints weight = 10715.794| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.137 10679 Z= 0.443 Angle : 0.781 9.532 14454 Z= 0.404 Chirality : 0.048 0.215 1639 Planarity : 0.005 0.045 1800 Dihedral : 17.507 152.424 1717 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 2.88 % Allowed : 28.27 % Favored : 68.85 % 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: -1.14 (0.24), residues: 1324 helix: 0.44 (0.28), residues: 356 sheet: -0.62 (0.35), residues: 240 loop : -1.44 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 307 HIS 0.006 0.001 HIS A 176 PHE 0.020 0.002 PHE G 105 TYR 0.022 0.002 TYR F 231 ARG 0.002 0.000 ARG F 235 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 ILE cc_start: 0.9528 (mt) cc_final: 0.9314 (tp) REVERT: A 183 MET cc_start: 0.9188 (tmm) cc_final: 0.8640 (tmm) REVERT: A 206 ASN cc_start: 0.8786 (t0) cc_final: 0.8544 (t0) REVERT: A 208 LEU cc_start: 0.8721 (tp) cc_final: 0.8420 (tp) REVERT: A 274 GLU cc_start: 0.9157 (pp20) cc_final: 0.8667 (pp20) REVERT: A 307 TRP cc_start: 0.8041 (m100) cc_final: 0.7542 (m100) REVERT: A 315 ILE cc_start: 0.4868 (OUTLIER) cc_final: 0.3873 (mp) REVERT: B 29 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9192 (tt) REVERT: B 183 MET cc_start: 0.9233 (tmm) cc_final: 0.8865 (tmm) REVERT: B 258 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8506 (tm-30) REVERT: F 183 MET cc_start: 0.8978 (tmm) cc_final: 0.7908 (tmm) REVERT: G 53 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8509 (tmm) REVERT: G 183 MET cc_start: 0.8975 (tmm) cc_final: 0.8377 (tmm) REVERT: G 206 ASN cc_start: 0.8882 (t0) cc_final: 0.8634 (m-40) REVERT: G 251 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7695 (tmtt) REVERT: G 274 GLU cc_start: 0.9175 (pp20) cc_final: 0.8621 (pp20) REVERT: G 307 TRP cc_start: 0.9017 (m100) cc_final: 0.8394 (m100) REVERT: G 315 ILE cc_start: 0.6505 (OUTLIER) cc_final: 0.6080 (mp) outliers start: 30 outliers final: 20 residues processed: 130 average time/residue: 0.1990 time to fit residues: 39.0657 Evaluate side-chains 126 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 134 SER Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 251 LYS Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 315 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 133 optimal weight: 10.0000 chunk 130 optimal weight: 30.0000 chunk 55 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 15 optimal weight: 0.0020 chunk 94 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS ** 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 = 0.3860 r_free = 0.3860 target = 0.115163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.086246 restraints weight = 26355.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.088663 restraints weight = 14301.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.090368 restraints weight = 8916.616| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10679 Z= 0.188 Angle : 0.679 11.558 14454 Z= 0.350 Chirality : 0.046 0.262 1639 Planarity : 0.004 0.052 1800 Dihedral : 17.077 159.608 1717 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.40 % Allowed : 28.46 % Favored : 69.13 % 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: -0.95 (0.24), residues: 1324 helix: 0.71 (0.29), residues: 356 sheet: -0.49 (0.36), residues: 220 loop : -1.37 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 307 HIS 0.005 0.001 HIS F 176 PHE 0.015 0.001 PHE G 333 TYR 0.025 0.002 TYR F 231 ARG 0.001 0.000 ARG A 209 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2824.66 seconds wall clock time: 51 minutes 51.77 seconds (3111.77 seconds total)