Starting phenix.real_space_refine on Mon Jun 9 09:28:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8amf_15525/06_2025/8amf_15525.cif Found real_map, /net/cci-nas-00/data/ceres_data/8amf_15525/06_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_15525/06_2025/8amf_15525.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8amf_15525/06_2025/8amf_15525.map" model { file = "/net/cci-nas-00/data/ceres_data/8amf_15525/06_2025/8amf_15525.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8amf_15525/06_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 6.90, per 1000 atoms: 0.66 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: 2.82 Conformation dependent library (CDL) restraints added in 1.4 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: 4.05 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: 3.73 Time building geometry restraints manager: 3.31 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: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 31.240 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.450 ------------------------------------------------------------------------------- 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 10691 Z= 0.313 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 Details of bonding type rmsd hydrogen bonds : bond 0.26136 ( 318) hydrogen bonds : angle 8.01262 ( 1031) covalent geometry : bond 0.00706 (10679) covalent geometry : angle 0.99199 (14454) Misc. bond : bond 0.00693 ( 12) *********************** 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 : 1.194 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: 0.2301 time to fit residues: 60.5244 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 : 1.231 ------------------------------------------------------------------------------- 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 = 0.087857 restraints weight = 27195.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.090561 restraints weight = 13302.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.092307 restraints weight = 8693.362| |-----------------------------------------------------------------------------| 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 10691 Z= 0.170 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 Details of bonding type rmsd hydrogen bonds : bond 0.04676 ( 318) hydrogen bonds : angle 5.64824 ( 1031) covalent geometry : bond 0.00404 (10679) covalent geometry : angle 0.67781 (14454) Misc. bond : bond 0.00518 ( 12) *********************** 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 : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 MET cc_start: 0.9154 (tmm) cc_final: 0.8616 (tmm) REVERT: A 206 ASN cc_start: 0.8710 (t0) cc_final: 0.8218 (t0) REVERT: A 208 LEU cc_start: 0.8839 (tp) cc_final: 0.8464 (tp) REVERT: A 274 GLU cc_start: 0.8888 (pp20) cc_final: 0.8217 (pp20) REVERT: A 283 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8812 (tp30) REVERT: A 315 ILE cc_start: 0.4093 (OUTLIER) cc_final: 0.3656 (mp) REVERT: B 76 GLU cc_start: 0.7337 (pp20) cc_final: 0.7036 (pp20) REVERT: B 141 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8847 (mp) REVERT: B 183 MET cc_start: 0.9036 (tmm) cc_final: 0.8590 (tmm) REVERT: B 184 MET cc_start: 0.9238 (tpp) cc_final: 0.8910 (tpp) REVERT: B 206 ASN cc_start: 0.8649 (t0) cc_final: 0.8440 (t0) REVERT: B 258 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8633 (tm-30) REVERT: F 76 GLU cc_start: 0.8133 (pp20) cc_final: 0.7613 (pp20) REVERT: F 140 GLU cc_start: 0.8950 (tp30) cc_final: 0.8662 (tp30) REVERT: F 183 MET cc_start: 0.9104 (tmm) cc_final: 0.8398 (tmm) REVERT: F 188 MET cc_start: 0.8302 (ttm) cc_final: 0.7958 (ttp) REVERT: F 212 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.8073 (p) REVERT: G 183 MET cc_start: 0.8733 (tmm) cc_final: 0.8244 (tmm) REVERT: G 186 GLN cc_start: 0.8726 (tm-30) cc_final: 0.7805 (tp40) REVERT: G 206 ASN cc_start: 0.8860 (t0) cc_final: 0.8514 (t0) REVERT: G 307 TRP cc_start: 0.8363 (m100) cc_final: 0.7396 (m100) REVERT: G 333 PHE cc_start: 0.7898 (m-10) cc_final: 0.7696 (m-80) outliers start: 23 outliers final: 6 residues processed: 151 average time/residue: 0.1876 time to fit residues: 42.4822 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 : 1.109 ------------------------------------------------------------------------------- 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: 3.9990 chunk 115 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 29 optimal weight: 40.0000 chunk 125 optimal weight: 8.9990 chunk 35 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.109649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.079598 restraints weight = 27465.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.082014 restraints weight = 14974.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.083595 restraints weight = 10365.248| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.131 10691 Z= 0.277 Angle : 0.759 8.788 14454 Z= 0.396 Chirality : 0.048 0.223 1639 Planarity : 0.005 0.046 1800 Dihedral : 17.610 151.040 1717 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.60 % Allowed : 23.37 % Favored : 74.04 % 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: -1.85 (0.23), residues: 1324 helix: -0.31 (0.29), residues: 324 sheet: -1.17 (0.33), residues: 240 loop : -1.68 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 307 HIS 0.010 0.002 HIS F 329 PHE 0.022 0.002 PHE F 15 TYR 0.026 0.002 TYR A 231 ARG 0.003 0.000 ARG B 341 Details of bonding type rmsd hydrogen bonds : bond 0.04884 ( 318) hydrogen bonds : angle 5.55141 ( 1031) covalent geometry : bond 0.00654 (10679) covalent geometry : angle 0.75921 (14454) Misc. bond : bond 0.00535 ( 12) *********************** 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: 27 poor density : 104 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 ILE cc_start: 0.9585 (mt) cc_final: 0.9335 (tp) REVERT: A 176 HIS cc_start: 0.8002 (m90) cc_final: 0.7788 (m90) REVERT: A 183 MET cc_start: 0.9092 (tmm) cc_final: 0.8519 (tmm) REVERT: A 208 LEU cc_start: 0.8830 (tp) cc_final: 0.8517 (tp) REVERT: A 274 GLU cc_start: 0.9016 (pp20) cc_final: 0.8504 (pp20) REVERT: A 280 MET cc_start: 0.9226 (tpp) cc_final: 0.8988 (mmm) REVERT: B 183 MET cc_start: 0.9016 (tmm) cc_final: 0.8604 (tmm) REVERT: B 206 ASN cc_start: 0.8828 (t0) cc_final: 0.8617 (t0) REVERT: B 258 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8613 (tm-30) REVERT: F 147 ASP cc_start: 0.8185 (p0) cc_final: 0.7527 (t0) REVERT: F 183 MET cc_start: 0.9083 (tmm) cc_final: 0.8226 (tmm) REVERT: F 184 MET cc_start: 0.9075 (tpp) cc_final: 0.8850 (tpp) REVERT: G 183 MET cc_start: 0.8854 (tmm) cc_final: 0.8388 (tmm) REVERT: G 206 ASN cc_start: 0.8827 (t0) cc_final: 0.8546 (t0) REVERT: G 274 GLU cc_start: 0.8994 (pp20) cc_final: 0.8691 (pp20) REVERT: G 307 TRP cc_start: 0.8634 (m100) cc_final: 0.7808 (m100) REVERT: G 315 ILE cc_start: 0.6670 (OUTLIER) cc_final: 0.6338 (mp) REVERT: G 333 PHE cc_start: 0.7750 (m-10) cc_final: 0.7284 (m-80) outliers start: 27 outliers final: 14 residues processed: 125 average time/residue: 0.1754 time to fit residues: 34.0011 Evaluate side-chains 107 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 214 VAL Chi-restraints excluded: chain B residue 23 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: 10.0000 chunk 104 optimal weight: 0.0670 chunk 130 optimal weight: 50.0000 chunk 25 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 2 optimal weight: 20.0000 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN ** 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 = 0.3793 r_free = 0.3793 target = 0.110832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.080666 restraints weight = 27319.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.083308 restraints weight = 14060.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.085011 restraints weight = 9444.266| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 10691 Z= 0.187 Angle : 0.673 9.098 14454 Z= 0.352 Chirality : 0.046 0.207 1639 Planarity : 0.004 0.043 1800 Dihedral : 17.353 152.563 1717 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.46 % Allowed : 24.04 % Favored : 72.50 % 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: -1.63 (0.23), residues: 1324 helix: -0.10 (0.29), residues: 348 sheet: -0.82 (0.36), residues: 216 loop : -1.67 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 307 HIS 0.005 0.001 HIS F 329 PHE 0.021 0.001 PHE F 15 TYR 0.016 0.002 TYR A 78 ARG 0.002 0.000 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.04151 ( 318) hydrogen bonds : angle 5.28529 ( 1031) covalent geometry : bond 0.00443 (10679) covalent geometry : angle 0.67340 (14454) Misc. bond : bond 0.00503 ( 12) *********************** 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: 36 poor density : 105 time to evaluate : 2.398 Fit side-chains REVERT: A 141 ILE cc_start: 0.9558 (mt) cc_final: 0.9312 (tp) REVERT: A 183 MET cc_start: 0.9156 (tmm) cc_final: 0.8597 (tmm) REVERT: A 208 LEU cc_start: 0.8778 (tp) cc_final: 0.8445 (tp) REVERT: A 274 GLU cc_start: 0.9022 (pp20) cc_final: 0.8535 (pp20) REVERT: A 280 MET cc_start: 0.9224 (tpp) cc_final: 0.8955 (mmm) REVERT: A 283 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8772 (tp30) REVERT: A 307 TRP cc_start: 0.7890 (m100) cc_final: 0.7380 (m100) REVERT: B 183 MET cc_start: 0.9073 (tmm) cc_final: 0.8694 (tmm) REVERT: B 184 MET cc_start: 0.9192 (tpp) cc_final: 0.8802 (tpp) REVERT: B 206 ASN cc_start: 0.8755 (t0) cc_final: 0.8534 (t0) REVERT: B 212 VAL cc_start: 0.9053 (OUTLIER) cc_final: 0.8837 (p) REVERT: B 258 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8572 (tm-30) REVERT: B 310 TYR cc_start: 0.5882 (m-10) cc_final: 0.5485 (m-10) REVERT: F 76 GLU cc_start: 0.8258 (pp20) cc_final: 0.7889 (pp20) REVERT: F 147 ASP cc_start: 0.8021 (p0) cc_final: 0.7507 (t0) REVERT: F 183 MET cc_start: 0.9119 (tmm) cc_final: 0.8334 (tmm) REVERT: G 171 ASP cc_start: 0.8325 (t0) cc_final: 0.8034 (t0) REVERT: G 183 MET cc_start: 0.8918 (tmm) cc_final: 0.8365 (tmm) REVERT: G 206 ASN cc_start: 0.8780 (t0) cc_final: 0.8526 (t0) REVERT: G 274 GLU cc_start: 0.8979 (pp20) cc_final: 0.8601 (pp20) REVERT: G 307 TRP cc_start: 0.8694 (m100) cc_final: 0.7892 (m100) REVERT: G 315 ILE cc_start: 0.6372 (OUTLIER) cc_final: 0.5993 (mp) REVERT: G 333 PHE cc_start: 0.7928 (m-10) cc_final: 0.7454 (m-80) outliers start: 36 outliers final: 15 residues processed: 134 average time/residue: 0.2605 time to fit residues: 54.1767 Evaluate side-chains 115 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 1.346 ------------------------------------------------------------------------------- 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 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 201 ILE Chi-restraints excluded: chain B residue 212 VAL 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 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 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: 1.9990 chunk 63 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 65 optimal weight: 0.3980 chunk 42 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 112 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 overall best weight: 4.6788 ------------------------------------------------------------------------------- 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 ** 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 = 0.3788 r_free = 0.3788 target = 0.110454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.080578 restraints weight = 27207.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.083137 restraints weight = 14346.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.084759 restraints weight = 9754.715| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 10691 Z= 0.195 Angle : 0.677 7.891 14454 Z= 0.353 Chirality : 0.046 0.200 1639 Planarity : 0.004 0.043 1800 Dihedral : 17.286 152.902 1717 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 3.37 % Allowed : 25.58 % Favored : 71.06 % 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: -1.47 (0.23), residues: 1324 helix: 0.08 (0.29), residues: 352 sheet: -0.75 (0.35), residues: 232 loop : -1.60 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 307 HIS 0.010 0.001 HIS F 329 PHE 0.020 0.002 PHE A 105 TYR 0.022 0.002 TYR A 231 ARG 0.002 0.000 ARG F 235 Details of bonding type rmsd hydrogen bonds : bond 0.04016 ( 318) hydrogen bonds : angle 5.25829 ( 1031) covalent geometry : bond 0.00468 (10679) covalent geometry : angle 0.67691 (14454) Misc. bond : bond 0.00504 ( 12) *********************** 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 143 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 1.317 Fit side-chains REVERT: A 140 GLU cc_start: 0.8880 (tp30) cc_final: 0.8653 (mm-30) REVERT: A 141 ILE cc_start: 0.9554 (mt) cc_final: 0.9293 (tp) REVERT: A 157 ASP cc_start: 0.8005 (t0) cc_final: 0.7803 (t0) REVERT: A 183 MET cc_start: 0.9194 (tmm) cc_final: 0.8581 (tmm) REVERT: A 206 ASN cc_start: 0.8564 (t0) cc_final: 0.8173 (t0) REVERT: A 208 LEU cc_start: 0.8787 (tp) cc_final: 0.8435 (tp) REVERT: A 274 GLU cc_start: 0.9030 (pp20) cc_final: 0.8558 (pp20) REVERT: A 283 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8794 (tp30) REVERT: A 307 TRP cc_start: 0.7927 (m100) cc_final: 0.7438 (m100) REVERT: B 29 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9128 (tt) REVERT: B 183 MET cc_start: 0.9117 (tmm) cc_final: 0.8707 (tmm) REVERT: B 212 VAL cc_start: 0.9086 (OUTLIER) cc_final: 0.8859 (p) REVERT: B 258 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8557 (tm-30) REVERT: F 140 GLU cc_start: 0.8923 (tp30) cc_final: 0.8454 (tp30) REVERT: F 147 ASP cc_start: 0.8128 (p0) cc_final: 0.7558 (t0) REVERT: F 183 MET cc_start: 0.9136 (tmm) cc_final: 0.8253 (tmm) REVERT: F 212 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8384 (p) REVERT: F 251 LYS cc_start: 0.8329 (tptt) cc_final: 0.7784 (tptp) REVERT: G 53 MET cc_start: 0.8833 (tmm) cc_final: 0.8495 (tmm) REVERT: G 171 ASP cc_start: 0.8401 (t0) cc_final: 0.8072 (t0) REVERT: G 183 MET cc_start: 0.8941 (tmm) cc_final: 0.8336 (tmm) REVERT: G 206 ASN cc_start: 0.8821 (t0) cc_final: 0.8451 (t0) REVERT: G 274 GLU cc_start: 0.9042 (pp20) cc_final: 0.8596 (pp20) REVERT: G 307 TRP cc_start: 0.8790 (m100) cc_final: 0.8035 (m100) REVERT: G 315 ILE cc_start: 0.6316 (OUTLIER) cc_final: 0.5917 (mp) REVERT: G 333 PHE cc_start: 0.7966 (m-10) cc_final: 0.7493 (m-80) outliers start: 35 outliers final: 21 residues processed: 137 average time/residue: 0.1790 time to fit residues: 38.1506 Evaluate side-chains 125 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 201 ILE Chi-restraints excluded: chain B residue 212 VAL 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 179 LEU Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 212 VAL 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: 9.9990 chunk 93 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 ** 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 = 0.3777 r_free = 0.3777 target = 0.109750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.079876 restraints weight = 27257.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.082353 restraints weight = 14631.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.083930 restraints weight = 10049.425| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 10691 Z= 0.240 Angle : 0.713 8.324 14454 Z= 0.372 Chirality : 0.047 0.224 1639 Planarity : 0.004 0.044 1800 Dihedral : 17.463 153.189 1717 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % 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: -1.43 (0.23), residues: 1324 helix: 0.09 (0.29), residues: 352 sheet: -0.83 (0.34), residues: 240 loop : -1.53 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 307 HIS 0.008 0.001 HIS F 329 PHE 0.021 0.002 PHE G 105 TYR 0.020 0.002 TYR A 231 ARG 0.002 0.000 ARG F 226 Details of bonding type rmsd hydrogen bonds : bond 0.04298 ( 318) hydrogen bonds : angle 5.41884 ( 1031) covalent geometry : bond 0.00571 (10679) covalent geometry : angle 0.71342 (14454) Misc. bond : bond 0.00504 ( 12) *********************** 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 145 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 102 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: A 140 GLU cc_start: 0.8810 (tp30) cc_final: 0.8588 (mm-30) REVERT: A 141 ILE cc_start: 0.9578 (mt) cc_final: 0.9323 (tp) REVERT: A 183 MET cc_start: 0.9184 (tmm) cc_final: 0.8606 (tmm) REVERT: A 206 ASN cc_start: 0.8606 (t0) cc_final: 0.8202 (t0) REVERT: A 208 LEU cc_start: 0.8800 (tp) cc_final: 0.8437 (tp) REVERT: A 274 GLU cc_start: 0.9107 (pp20) cc_final: 0.8634 (pp20) REVERT: A 307 TRP cc_start: 0.7914 (m100) cc_final: 0.7638 (m-90) REVERT: B 29 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9162 (tt) REVERT: B 183 MET cc_start: 0.9151 (tmm) cc_final: 0.8738 (tmm) REVERT: B 258 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8603 (tm-30) REVERT: F 140 GLU cc_start: 0.8888 (tp30) cc_final: 0.8429 (tp30) REVERT: F 183 MET cc_start: 0.9035 (tmm) cc_final: 0.8067 (tmm) REVERT: G 53 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8515 (tmm) REVERT: G 171 ASP cc_start: 0.8363 (t0) cc_final: 0.8064 (t0) REVERT: G 183 MET cc_start: 0.8945 (tmm) cc_final: 0.8370 (tmm) REVERT: G 206 ASN cc_start: 0.8852 (t0) cc_final: 0.8483 (m-40) REVERT: G 274 GLU cc_start: 0.9108 (pp20) cc_final: 0.8649 (pp20) REVERT: G 307 TRP cc_start: 0.8860 (m100) cc_final: 0.8142 (m100) REVERT: G 315 ILE cc_start: 0.6438 (OUTLIER) cc_final: 0.5899 (mp) REVERT: G 333 PHE cc_start: 0.8016 (m-10) cc_final: 0.7550 (m-80) outliers start: 43 outliers final: 29 residues processed: 136 average time/residue: 0.1685 time to fit residues: 35.9671 Evaluate side-chains 129 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 1.186 ------------------------------------------------------------------------------- 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 76 GLU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 201 ILE 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 128 LEU Chi-restraints excluded: chain G residue 191 LEU 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: 4.9990 chunk 3 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.111076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.080963 restraints weight = 27426.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.083615 restraints weight = 14064.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.085340 restraints weight = 9414.516| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 10691 Z= 0.180 Angle : 0.668 9.422 14454 Z= 0.348 Chirality : 0.046 0.250 1639 Planarity : 0.004 0.046 1800 Dihedral : 17.300 155.193 1717 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 3.85 % Allowed : 26.35 % 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: -1.27 (0.24), residues: 1324 helix: 0.32 (0.29), residues: 352 sheet: -0.73 (0.34), residues: 240 loop : -1.49 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 307 HIS 0.007 0.001 HIS F 329 PHE 0.016 0.001 PHE G 105 TYR 0.019 0.002 TYR A 231 ARG 0.001 0.000 ARG F 226 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 318) hydrogen bonds : angle 5.25403 ( 1031) covalent geometry : bond 0.00434 (10679) covalent geometry : angle 0.66814 (14454) Misc. bond : bond 0.00519 ( 12) *********************** 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 144 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 104 time to evaluate : 1.341 Fit side-chains revert: symmetry clash REVERT: A 140 GLU cc_start: 0.8820 (tp30) cc_final: 0.8576 (mm-30) REVERT: A 141 ILE cc_start: 0.9564 (mt) cc_final: 0.9311 (tp) REVERT: A 183 MET cc_start: 0.9179 (tmm) cc_final: 0.8660 (tmm) REVERT: A 206 ASN cc_start: 0.8548 (t0) cc_final: 0.8117 (t0) REVERT: A 208 LEU cc_start: 0.8779 (tp) cc_final: 0.8439 (tp) REVERT: A 274 GLU cc_start: 0.9082 (pp20) cc_final: 0.8659 (pp20) REVERT: A 307 TRP cc_start: 0.7907 (m100) cc_final: 0.7403 (m100) REVERT: A 315 ILE cc_start: 0.4593 (OUTLIER) cc_final: 0.3475 (mp) REVERT: B 29 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9148 (tt) REVERT: B 183 MET cc_start: 0.9168 (tmm) cc_final: 0.8824 (tmm) REVERT: B 212 VAL cc_start: 0.9066 (OUTLIER) cc_final: 0.8828 (p) REVERT: B 220 GLU cc_start: 0.8854 (pm20) cc_final: 0.8533 (pt0) REVERT: B 258 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8534 (tm-30) REVERT: B 307 TRP cc_start: 0.8567 (m-90) cc_final: 0.8104 (m100) REVERT: F 183 MET cc_start: 0.9115 (tmm) cc_final: 0.8212 (tmm) REVERT: F 212 VAL cc_start: 0.8672 (OUTLIER) cc_final: 0.8348 (p) REVERT: G 53 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8483 (tmm) REVERT: G 171 ASP cc_start: 0.8358 (t0) cc_final: 0.8053 (t0) REVERT: G 183 MET cc_start: 0.8982 (tmm) cc_final: 0.8424 (tmm) REVERT: G 206 ASN cc_start: 0.8859 (t0) cc_final: 0.8454 (t0) REVERT: G 255 VAL cc_start: 0.8527 (OUTLIER) cc_final: 0.8238 (p) REVERT: G 274 GLU cc_start: 0.9091 (pp20) cc_final: 0.8620 (pp20) REVERT: G 307 TRP cc_start: 0.8880 (m100) cc_final: 0.8165 (m100) REVERT: G 315 ILE cc_start: 0.6419 (OUTLIER) cc_final: 0.5862 (mp) outliers start: 40 outliers final: 24 residues processed: 134 average time/residue: 0.2170 time to fit residues: 46.2051 Evaluate side-chains 128 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 1.443 ------------------------------------------------------------------------------- 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 315 ILE 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 212 VAL 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 179 LEU Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 212 VAL 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 93 VAL Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 255 VAL 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: 30.0000 chunk 131 optimal weight: 9.9990 chunk 125 optimal weight: 0.2980 chunk 113 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 133 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- 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 = 0.3833 r_free = 0.3833 target = 0.113306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.083255 restraints weight = 26739.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.085955 restraints weight = 13679.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.087689 restraints weight = 9089.967| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10691 Z= 0.154 Angle : 0.650 8.800 14454 Z= 0.336 Chirality : 0.045 0.196 1639 Planarity : 0.004 0.044 1800 Dihedral : 17.069 154.854 1717 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.94 % Allowed : 27.21 % 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: -1.04 (0.24), residues: 1324 helix: 0.59 (0.30), residues: 344 sheet: -0.53 (0.35), residues: 220 loop : -1.38 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 307 HIS 0.007 0.001 HIS F 329 PHE 0.013 0.001 PHE G 105 TYR 0.017 0.002 TYR F 231 ARG 0.001 0.000 ARG F 235 Details of bonding type rmsd hydrogen bonds : bond 0.03541 ( 318) hydrogen bonds : angle 5.06869 ( 1031) covalent geometry : bond 0.00370 (10679) covalent geometry : angle 0.64964 (14454) Misc. bond : bond 0.00477 ( 12) *********************** 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 151 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 110 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 HIS cc_start: 0.8477 (OUTLIER) cc_final: 0.8027 (m-70) REVERT: A 140 GLU cc_start: 0.8958 (tp30) cc_final: 0.8663 (mm-30) REVERT: A 141 ILE cc_start: 0.9491 (mt) cc_final: 0.9284 (tp) REVERT: A 157 ASP cc_start: 0.7974 (t0) cc_final: 0.7569 (m-30) REVERT: A 183 MET cc_start: 0.9230 (tmm) cc_final: 0.8623 (tmm) REVERT: A 206 ASN cc_start: 0.8556 (t0) cc_final: 0.8021 (t0) REVERT: A 208 LEU cc_start: 0.8739 (tp) cc_final: 0.8416 (tp) REVERT: A 274 GLU cc_start: 0.9110 (pp20) cc_final: 0.8680 (pp20) REVERT: A 307 TRP cc_start: 0.7981 (m100) cc_final: 0.7513 (m100) REVERT: A 315 ILE cc_start: 0.4661 (OUTLIER) cc_final: 0.3572 (mp) REVERT: B 29 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9164 (tt) REVERT: B 183 MET cc_start: 0.9248 (tmm) cc_final: 0.8893 (tmm) REVERT: B 212 VAL cc_start: 0.9057 (OUTLIER) cc_final: 0.8851 (p) REVERT: B 258 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8163 (tm-30) REVERT: F 183 MET cc_start: 0.9143 (tmm) cc_final: 0.8360 (tmm) REVERT: F 188 MET cc_start: 0.8319 (tmm) cc_final: 0.8094 (ttm) REVERT: F 206 ASN cc_start: 0.9031 (t0) cc_final: 0.8742 (t0) REVERT: F 212 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8409 (p) REVERT: F 283 GLU cc_start: 0.8872 (mm-30) cc_final: 0.7866 (tp30) REVERT: G 53 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8523 (tmm) REVERT: G 171 ASP cc_start: 0.8411 (t0) cc_final: 0.7977 (t0) REVERT: G 183 MET cc_start: 0.9008 (tmm) cc_final: 0.8401 (tmm) REVERT: G 206 ASN cc_start: 0.8914 (t0) cc_final: 0.8444 (t0) REVERT: G 274 GLU cc_start: 0.9077 (pp20) cc_final: 0.8567 (pp20) REVERT: G 280 MET cc_start: 0.9040 (mmm) cc_final: 0.8718 (mmm) REVERT: G 307 TRP cc_start: 0.8909 (m100) cc_final: 0.8266 (m100) REVERT: G 315 ILE cc_start: 0.6373 (OUTLIER) cc_final: 0.5810 (mp) outliers start: 41 outliers final: 23 residues processed: 141 average time/residue: 0.2022 time to fit residues: 43.9173 Evaluate side-chains 137 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 1.608 ------------------------------------------------------------------------------- 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 110 HIS 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 179 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 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 212 VAL 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 128 LEU Chi-restraints excluded: chain G residue 214 VAL 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: 10.0000 chunk 21 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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 = 0.3790 r_free = 0.3790 target = 0.110562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.080380 restraints weight = 27551.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.082996 restraints weight = 14231.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.084712 restraints weight = 9563.718| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 10691 Z= 0.203 Angle : 0.700 11.767 14454 Z= 0.362 Chirality : 0.046 0.296 1639 Planarity : 0.004 0.047 1800 Dihedral : 17.294 158.043 1717 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 3.85 % Allowed : 27.21 % Favored : 68.94 % 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: -1.08 (0.24), residues: 1324 helix: 0.53 (0.29), residues: 356 sheet: -0.60 (0.34), residues: 240 loop : -1.41 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 307 HIS 0.007 0.001 HIS F 329 PHE 0.021 0.002 PHE B 15 TYR 0.026 0.002 TYR A 325 ARG 0.001 0.000 ARG F 226 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 318) hydrogen bonds : angle 5.22236 ( 1031) covalent geometry : bond 0.00491 (10679) covalent geometry : angle 0.69983 (14454) Misc. bond : bond 0.00509 ( 12) *********************** 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 148 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 1.631 Fit side-chains revert: symmetry clash REVERT: A 140 GLU cc_start: 0.8846 (tp30) cc_final: 0.8617 (mm-30) REVERT: A 141 ILE cc_start: 0.9538 (mt) cc_final: 0.9319 (tp) REVERT: A 183 MET cc_start: 0.9179 (tmm) cc_final: 0.8654 (tmm) REVERT: A 206 ASN cc_start: 0.8571 (t0) cc_final: 0.8065 (t0) REVERT: A 208 LEU cc_start: 0.8764 (tp) cc_final: 0.8437 (tp) REVERT: A 274 GLU cc_start: 0.9099 (pp20) cc_final: 0.8642 (pp20) REVERT: A 307 TRP cc_start: 0.7976 (m100) cc_final: 0.7524 (m100) REVERT: A 315 ILE cc_start: 0.4722 (OUTLIER) cc_final: 0.3680 (mp) REVERT: B 29 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9149 (tt) REVERT: B 183 MET cc_start: 0.9219 (tmm) cc_final: 0.8921 (tmm) REVERT: B 258 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8478 (tm-30) REVERT: F 183 MET cc_start: 0.9122 (tmm) cc_final: 0.8203 (tmm) REVERT: F 212 VAL cc_start: 0.8822 (OUTLIER) cc_final: 0.8498 (p) REVERT: F 280 MET cc_start: 0.9327 (tpp) cc_final: 0.9078 (mmm) REVERT: F 283 GLU cc_start: 0.8842 (mm-30) cc_final: 0.7924 (tp30) REVERT: G 53 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8491 (tmm) REVERT: G 183 MET cc_start: 0.8973 (tmm) cc_final: 0.8417 (tmm) REVERT: G 206 ASN cc_start: 0.8877 (t0) cc_final: 0.8457 (t0) REVERT: G 215 MET cc_start: 0.7003 (mmm) cc_final: 0.5974 (mpp) REVERT: G 245 LYS cc_start: 0.9164 (mttp) cc_final: 0.8832 (mttt) REVERT: G 254 ASN cc_start: 0.5414 (m-40) cc_final: 0.4927 (m-40) REVERT: G 255 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8259 (p) REVERT: G 274 GLU cc_start: 0.9089 (pp20) cc_final: 0.8605 (pp20) REVERT: G 307 TRP cc_start: 0.8948 (m100) cc_final: 0.8336 (m100) REVERT: G 315 ILE cc_start: 0.6425 (OUTLIER) cc_final: 0.5992 (mp) outliers start: 40 outliers final: 29 residues processed: 136 average time/residue: 0.2677 time to fit residues: 57.2985 Evaluate side-chains 137 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 102 time to evaluate : 2.953 ------------------------------------------------------------------------------- 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 110 HIS 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 53 MET Chi-restraints excluded: chain B residue 76 GLU 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 201 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain F residue 23 LEU 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 212 VAL 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 93 VAL Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 255 VAL 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: 6.9990 chunk 10 optimal weight: 9.9990 chunk 130 optimal weight: 30.0000 chunk 79 optimal weight: 8.9990 chunk 29 optimal weight: 30.0000 chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 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** ** 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 = 0.3835 r_free = 0.3835 target = 0.116956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.084752 restraints weight = 27360.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.087497 restraints weight = 14164.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.089300 restraints weight = 9607.071| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 10691 Z= 0.208 Angle : 0.716 11.627 14454 Z= 0.369 Chirality : 0.047 0.284 1639 Planarity : 0.004 0.048 1800 Dihedral : 17.309 155.811 1717 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 3.46 % Allowed : 27.69 % 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: -1.01 (0.24), residues: 1324 helix: 0.55 (0.29), residues: 356 sheet: -0.28 (0.36), residues: 216 loop : -1.43 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 307 HIS 0.007 0.001 HIS F 329 PHE 0.019 0.002 PHE B 15 TYR 0.023 0.002 TYR A 325 ARG 0.001 0.000 ARG F 189 Details of bonding type rmsd hydrogen bonds : bond 0.03945 ( 318) hydrogen bonds : angle 5.27939 ( 1031) covalent geometry : bond 0.00498 (10679) covalent geometry : angle 0.71630 (14454) Misc. bond : bond 0.00521 ( 12) ********************** 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 140 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 HIS cc_start: 0.8535 (OUTLIER) cc_final: 0.8059 (m-70) REVERT: A 140 GLU cc_start: 0.8935 (tp30) cc_final: 0.8645 (mm-30) REVERT: A 183 MET cc_start: 0.9252 (tmm) cc_final: 0.8562 (tmm) REVERT: A 206 ASN cc_start: 0.8620 (t0) cc_final: 0.8151 (t0) REVERT: A 208 LEU cc_start: 0.8740 (tp) cc_final: 0.8384 (tp) REVERT: A 274 GLU cc_start: 0.9125 (pp20) cc_final: 0.8643 (pp20) REVERT: A 307 TRP cc_start: 0.8201 (m100) cc_final: 0.7705 (m100) REVERT: A 315 ILE cc_start: 0.5097 (OUTLIER) cc_final: 0.4161 (mp) REVERT: B 29 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9108 (tt) REVERT: B 183 MET cc_start: 0.9243 (tmm) cc_final: 0.8905 (tmm) REVERT: B 258 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8494 (tm-30) REVERT: F 183 MET cc_start: 0.9153 (tmm) cc_final: 0.8362 (tmm) REVERT: F 212 VAL cc_start: 0.8704 (OUTLIER) cc_final: 0.8392 (p) REVERT: F 280 MET cc_start: 0.9427 (tpp) cc_final: 0.9122 (mmm) REVERT: F 283 GLU cc_start: 0.8945 (mm-30) cc_final: 0.7981 (tp30) REVERT: G 53 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8532 (tmm) REVERT: G 183 MET cc_start: 0.8967 (tmm) cc_final: 0.8394 (tmm) REVERT: G 206 ASN cc_start: 0.8876 (t0) cc_final: 0.8415 (t0) REVERT: G 215 MET cc_start: 0.7087 (mmm) cc_final: 0.6041 (mpp) REVERT: G 274 GLU cc_start: 0.9133 (pp20) cc_final: 0.8637 (pp20) REVERT: G 280 MET cc_start: 0.8919 (mmm) cc_final: 0.8450 (mmm) REVERT: G 307 TRP cc_start: 0.8993 (m100) cc_final: 0.8366 (m100) REVERT: G 315 ILE cc_start: 0.6417 (OUTLIER) cc_final: 0.5987 (mp) outliers start: 36 outliers final: 28 residues processed: 131 average time/residue: 0.2365 time to fit residues: 48.4168 Evaluate side-chains 134 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 110 HIS 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 53 MET Chi-restraints excluded: chain B residue 76 GLU 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 201 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain F residue 23 LEU 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 212 VAL 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 93 VAL Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 214 VAL 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 133 optimal weight: 20.0000 chunk 130 optimal weight: 30.0000 chunk 55 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 chunk 15 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.112533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.082368 restraints weight = 26557.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.085026 restraints weight = 13708.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.086748 restraints weight = 9180.206| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 10691 Z= 0.169 Angle : 0.688 11.770 14454 Z= 0.354 Chirality : 0.046 0.246 1639 Planarity : 0.004 0.049 1800 Dihedral : 17.180 156.648 1717 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.94 % Allowed : 27.50 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.24), residues: 1324 helix: 0.63 (0.29), residues: 356 sheet: -0.33 (0.36), residues: 216 loop : -1.41 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 307 HIS 0.006 0.001 HIS F 329 PHE 0.017 0.001 PHE B 15 TYR 0.023 0.002 TYR A 325 ARG 0.001 0.000 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.03667 ( 318) hydrogen bonds : angle 5.13025 ( 1031) covalent geometry : bond 0.00408 (10679) covalent geometry : angle 0.68808 (14454) Misc. bond : bond 0.00495 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3607.38 seconds wall clock time: 66 minutes 54.40 seconds (4014.40 seconds total)