Starting phenix.real_space_refine on Thu Jun 12 10:49:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9njr_49488/06_2025/9njr_49488.cif Found real_map, /net/cci-nas-00/data/ceres_data/9njr_49488/06_2025/9njr_49488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9njr_49488/06_2025/9njr_49488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9njr_49488/06_2025/9njr_49488.map" model { file = "/net/cci-nas-00/data/ceres_data/9njr_49488/06_2025/9njr_49488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9njr_49488/06_2025/9njr_49488.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 3 5.21 5 S 76 5.16 5 C 8619 2.51 5 N 2437 2.21 5 O 2722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13863 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2278 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 285} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2313 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 290} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2333 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 293} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2273 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 285} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2269 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 284} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2313 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 290} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.45, per 1000 atoms: 0.68 Number of scatterers: 13863 At special positions: 0 Unit cell: (102.875, 108.636, 192.582, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 76 16.00 P 6 15.00 Mg 3 11.99 O 2722 8.00 N 2437 7.00 C 8619 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=0, symmetry=0 Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 2.3 seconds 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3244 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 11 sheets defined 50.9% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 18 through 26 removed outlier: 3.765A pdb=" N ASN A 24 " --> pdb=" O GLU A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 38 Processing helix chain 'A' and resid 42 through 49 Processing helix chain 'A' and resid 50 through 57 removed outlier: 3.520A pdb=" N ILE A 57 " --> pdb=" O HIS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 73 Processing helix chain 'A' and resid 85 through 91 Processing helix chain 'A' and resid 100 through 107 Processing helix chain 'A' and resid 126 through 138 Processing helix chain 'A' and resid 161 through 172 Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 190 through 200 Processing helix chain 'A' and resid 200 through 206 removed outlier: 4.166A pdb=" N GLU A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 226 removed outlier: 4.058A pdb=" N VAL A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 253 removed outlier: 3.515A pdb=" N GLN A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 28 through 38 Processing helix chain 'B' and resid 42 through 49 Processing helix chain 'B' and resid 50 through 56 Processing helix chain 'B' and resid 61 through 76 removed outlier: 3.527A pdb=" N LYS B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 91 Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 126 through 139 removed outlier: 4.209A pdb=" N GLN B 139 " --> pdb=" O CYS B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 175 through 183 removed outlier: 3.622A pdb=" N VAL B 183 " --> pdb=" O CYS B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 206 removed outlier: 4.190A pdb=" N GLY B 202 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLU B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU B 204 " --> pdb=" O GLN B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 226 removed outlier: 4.011A pdb=" N VAL B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 removed outlier: 3.670A pdb=" N LEU B 232 " --> pdb=" O ARG B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 235 No H-bonds generated for 'chain 'B' and resid 235 through 235' Processing helix chain 'B' and resid 238 through 254 Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'C' and resid 19 through 26 removed outlier: 4.048A pdb=" N ASN C 24 " --> pdb=" O GLU C 21 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY C 26 " --> pdb=" O GLN C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 38 Processing helix chain 'C' and resid 42 through 49 Processing helix chain 'C' and resid 50 through 56 removed outlier: 3.695A pdb=" N LYS C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 76 removed outlier: 3.824A pdb=" N LYS C 67 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS C 74 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 91 Processing helix chain 'C' and resid 100 through 107 Processing helix chain 'C' and resid 127 through 138 Processing helix chain 'C' and resid 161 through 172 Processing helix chain 'C' and resid 175 through 183 Processing helix chain 'C' and resid 190 through 201 Processing helix chain 'C' and resid 201 through 206 Processing helix chain 'C' and resid 219 through 226 Processing helix chain 'C' and resid 231 through 254 Processing helix chain 'C' and resid 283 through 291 Processing helix chain 'D' and resid 18 through 26 removed outlier: 3.700A pdb=" N GLU D 21 " --> pdb=" O SER D 18 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN D 24 " --> pdb=" O GLU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 38 Processing helix chain 'D' and resid 42 through 48 Processing helix chain 'D' and resid 50 through 56 Processing helix chain 'D' and resid 61 through 76 removed outlier: 4.163A pdb=" N GLU D 66 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS D 67 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 91 Processing helix chain 'D' and resid 100 through 107 Processing helix chain 'D' and resid 126 through 138 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 175 through 182 Processing helix chain 'D' and resid 190 through 200 Processing helix chain 'D' and resid 200 through 206 removed outlier: 4.544A pdb=" N GLU D 204 " --> pdb=" O GLN D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 226 removed outlier: 3.697A pdb=" N VAL D 224 " --> pdb=" O ALA D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 252 removed outlier: 3.780A pdb=" N GLU D 252 " --> pdb=" O ARG D 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 26 removed outlier: 3.554A pdb=" N GLU E 21 " --> pdb=" O SER E 18 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY E 26 " --> pdb=" O GLN E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 38 removed outlier: 3.657A pdb=" N LEU E 32 " --> pdb=" O ASN E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 48 Processing helix chain 'E' and resid 50 through 56 Processing helix chain 'E' and resid 61 through 76 Processing helix chain 'E' and resid 83 through 92 removed outlier: 3.781A pdb=" N ARG E 92 " --> pdb=" O ASP E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 107 Processing helix chain 'E' and resid 126 through 138 Processing helix chain 'E' and resid 161 through 172 removed outlier: 3.516A pdb=" N ILE E 165 " --> pdb=" O ARG E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 182 Processing helix chain 'E' and resid 190 through 206 removed outlier: 4.334A pdb=" N GLY E 202 " --> pdb=" O VAL E 198 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLU E 203 " --> pdb=" O GLU E 199 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU E 204 " --> pdb=" O GLN E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 226 Processing helix chain 'E' and resid 233 through 254 Processing helix chain 'F' and resid 18 through 23 Processing helix chain 'F' and resid 28 through 38 Processing helix chain 'F' and resid 42 through 49 Processing helix chain 'F' and resid 50 through 56 Processing helix chain 'F' and resid 61 through 76 removed outlier: 3.510A pdb=" N ILE F 76 " --> pdb=" O ALA F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 91 Processing helix chain 'F' and resid 100 through 107 Processing helix chain 'F' and resid 126 through 138 Processing helix chain 'F' and resid 161 through 172 Processing helix chain 'F' and resid 175 through 182 Processing helix chain 'F' and resid 190 through 206 removed outlier: 4.334A pdb=" N GLY F 202 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N GLU F 203 " --> pdb=" O GLU F 199 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU F 204 " --> pdb=" O GLN F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 226 Processing helix chain 'F' and resid 228 through 233 removed outlier: 4.297A pdb=" N SER F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 235 No H-bonds generated for 'chain 'F' and resid 235 through 235' Processing helix chain 'F' and resid 238 through 254 Processing helix chain 'F' and resid 286 through 291 Processing sheet with id=AA1, first strand: chain 'A' and resid 95 through 96 Processing sheet with id=AA2, first strand: chain 'A' and resid 328 through 331 removed outlier: 3.714A pdb=" N ARG A 305 " --> pdb=" O TYR A 322 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ALA A 307 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ARG A 298 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU A 309 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU A 296 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARG A 211 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N PHE A 258 " --> pdb=" O ARG A 211 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE A 213 " --> pdb=" O PHE A 258 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N THR A 260 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL A 215 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N GLN A 262 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LYS A 150 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 212 " --> pdb=" O LYS A 150 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL A 151 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ALA A 186 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TYR A 153 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 95 through 96 Processing sheet with id=AA4, first strand: chain 'B' and resid 328 through 330 removed outlier: 5.352A pdb=" N ALA B 307 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ARG B 298 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU B 309 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU B 296 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE B 116 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE B 295 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLU B 118 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU B 297 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE B 120 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N LYS B 299 " --> pdb=" O PHE B 120 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR B 117 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ASN B 261 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL B 119 " --> pdb=" O ASN B 261 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LYS B 150 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU B 212 " --> pdb=" O LYS B 150 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL B 151 " --> pdb=" O SER B 184 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ALA B 186 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TYR B 153 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 95 through 96 Processing sheet with id=AA6, first strand: chain 'C' and resid 186 through 187 removed outlier: 6.610A pdb=" N LYS C 150 " --> pdb=" O LEU C 212 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL C 214 " --> pdb=" O LYS C 150 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA C 152 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ASP C 216 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE C 154 " --> pdb=" O ASP C 216 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA C 256 " --> pdb=" O ARG C 211 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY C 121 " --> pdb=" O ASN C 261 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU C 296 " --> pdb=" O LEU C 309 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LEU C 309 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ARG C 298 " --> pdb=" O ALA C 307 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ALA C 307 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.325A pdb=" N ARG D 294 " --> pdb=" O GLN D 310 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER D 115 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N LEU D 259 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N THR D 117 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ASN D 261 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL D 119 " --> pdb=" O ASN D 261 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LYS D 150 " --> pdb=" O TYR D 210 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU D 212 " --> pdb=" O LYS D 150 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL D 151 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N ALA D 186 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N TYR D 153 " --> pdb=" O ALA D 186 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 95 through 96 Processing sheet with id=AA9, first strand: chain 'E' and resid 328 through 331 removed outlier: 6.769A pdb=" N ARG E 294 " --> pdb=" O GLN E 310 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR E 117 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ASN E 261 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL E 119 " --> pdb=" O ASN E 261 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG E 211 " --> pdb=" O ALA E 256 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N PHE E 258 " --> pdb=" O ARG E 211 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE E 213 " --> pdb=" O PHE E 258 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N THR E 260 " --> pdb=" O ILE E 213 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL E 215 " --> pdb=" O THR E 260 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LYS E 150 " --> pdb=" O TYR E 210 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU E 212 " --> pdb=" O LYS E 150 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL E 151 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ALA E 186 " --> pdb=" O VAL E 151 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TYR E 153 " --> pdb=" O ALA E 186 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 95 through 96 Processing sheet with id=AB2, first strand: chain 'F' and resid 183 through 187 removed outlier: 7.120A pdb=" N LYS F 150 " --> pdb=" O ARG F 211 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE F 213 " --> pdb=" O LYS F 150 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA F 152 " --> pdb=" O ILE F 213 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N VAL F 215 " --> pdb=" O ALA F 152 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE F 154 " --> pdb=" O VAL F 215 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG F 211 " --> pdb=" O ALA F 256 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N PHE F 258 " --> pdb=" O ARG F 211 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE F 213 " --> pdb=" O PHE F 258 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR F 260 " --> pdb=" O ILE F 213 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL F 215 " --> pdb=" O THR F 260 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N GLN F 262 " --> pdb=" O VAL F 215 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY F 121 " --> pdb=" O ASN F 261 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG F 294 " --> pdb=" O GLN F 310 " (cutoff:3.500A) 675 hydrogen bonds defined for protein. 1878 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.41 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4693 1.34 - 1.46: 2232 1.46 - 1.58: 6969 1.58 - 1.70: 9 1.70 - 1.82: 118 Bond restraints: 14021 Sorted by residual: bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C5 ADP B 401 " pdb=" C6 ADP B 401 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" N THR E 42 " pdb=" CA THR E 42 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 7.10e+00 bond pdb=" N THR A 42 " pdb=" CA THR A 42 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.26e-02 6.30e+03 7.02e+00 bond pdb=" N THR C 138 " pdb=" CA THR C 138 " ideal model delta sigma weight residual 1.459 1.490 -0.032 1.28e-02 6.10e+03 6.07e+00 ... (remaining 14016 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 18594 2.24 - 4.49: 226 4.49 - 6.73: 36 6.73 - 8.97: 7 8.97 - 11.21: 6 Bond angle restraints: 18869 Sorted by residual: angle pdb=" PA ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sigma weight residual 120.50 131.71 -11.21 3.00e+00 1.11e-01 1.40e+01 angle pdb=" C GLU A 251 " pdb=" N GLU A 252 " pdb=" CA GLU A 252 " ideal model delta sigma weight residual 122.38 116.22 6.16 1.81e+00 3.05e-01 1.16e+01 angle pdb=" C1' ADP B 401 " pdb=" C2' ADP B 401 " pdb=" C3' ADP B 401 " ideal model delta sigma weight residual 111.00 101.52 9.48 3.00e+00 1.11e-01 9.99e+00 angle pdb=" C VAL F 198 " pdb=" N GLU F 199 " pdb=" CA GLU F 199 " ideal model delta sigma weight residual 122.38 116.75 5.63 1.81e+00 3.05e-01 9.69e+00 angle pdb=" N1 ADP B 401 " pdb=" C2 ADP B 401 " pdb=" N3 ADP B 401 " ideal model delta sigma weight residual 120.00 129.30 -9.30 3.00e+00 1.11e-01 9.60e+00 ... (remaining 18864 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.85: 8091 24.85 - 49.70: 451 49.70 - 74.55: 40 74.55 - 99.41: 6 99.41 - 124.26: 2 Dihedral angle restraints: 8590 sinusoidal: 3532 harmonic: 5058 Sorted by residual: dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 64.26 -124.26 1 2.00e+01 2.50e-03 3.75e+01 dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 42.26 -102.25 1 2.00e+01 2.50e-03 2.91e+01 dihedral pdb=" CA GLU F 199 " pdb=" C GLU F 199 " pdb=" N GLN F 200 " pdb=" CA GLN F 200 " ideal model delta harmonic sigma weight residual 180.00 158.94 21.06 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 8587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1563 0.043 - 0.086: 439 0.086 - 0.129: 150 0.129 - 0.172: 13 0.172 - 0.215: 7 Chirality restraints: 2172 Sorted by residual: chirality pdb=" CB ILE C 116 " pdb=" CA ILE C 116 " pdb=" CG1 ILE C 116 " pdb=" CG2 ILE C 116 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA GLU F 199 " pdb=" N GLU F 199 " pdb=" C GLU F 199 " pdb=" CB GLU F 199 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.40e-01 chirality pdb=" CA GLU D 70 " pdb=" N GLU D 70 " pdb=" C GLU D 70 " pdb=" CB GLU D 70 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.93e-01 ... (remaining 2169 not shown) Planarity restraints: 2434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET B 195 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" C MET B 195 " 0.038 2.00e-02 2.50e+03 pdb=" O MET B 195 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU B 196 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 241 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.84e+00 pdb=" C GLN C 241 " 0.029 2.00e-02 2.50e+03 pdb=" O GLN C 241 " -0.011 2.00e-02 2.50e+03 pdb=" N HIS C 242 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 142 " 0.146 9.50e-02 1.11e+02 6.54e-02 2.72e+00 pdb=" NE ARG E 142 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG E 142 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG E 142 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG E 142 " 0.007 2.00e-02 2.50e+03 ... (remaining 2431 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 200 2.59 - 3.17: 12261 3.17 - 3.75: 22452 3.75 - 4.32: 31260 4.32 - 4.90: 50834 Nonbonded interactions: 117007 Sorted by model distance: nonbonded pdb=" OG1 THR C 128 " pdb="MG MG C 402 " model vdw 2.014 2.170 nonbonded pdb=" O1B ADP A 401 " pdb="MG MG A 402 " model vdw 2.051 2.170 nonbonded pdb=" OG1 THR A 128 " pdb="MG MG A 402 " model vdw 2.097 2.170 nonbonded pdb=" O ARG B 235 " pdb=" N GLN B 237 " model vdw 2.221 3.120 nonbonded pdb=" O MET E 112 " pdb=" OG SER E 115 " model vdw 2.223 3.040 ... (remaining 117002 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' and (resid 16 through 200 or (resid 201 and (name N or name CA or nam \ e C or name O or name CB )) or resid 202 through 226 or resid 232 through 236 or \ resid 238 through 263 or resid 290 through 334)) selection = (chain 'B' and (resid 16 through 200 or (resid 201 and (name N or name CA or nam \ e C or name O or name CB )) or resid 202 through 226 or resid 232 through 263 or \ resid 290 through 334)) selection = (chain 'C' and (resid 16 through 226 or resid 232 through 236 or resid 238 throu \ gh 263 or resid 290 through 334)) selection = (chain 'D' and (resid 16 through 200 or (resid 201 and (name N or name CA or nam \ e C or name O or name CB )) or resid 202 through 226 or resid 232 through 236 or \ resid 238 through 334)) selection = (chain 'E' and (resid 16 through 200 or (resid 201 and (name N or name CA or nam \ e C or name O or name CB )) or resid 202 through 236 or resid 238 through 263 or \ resid 290 through 334)) selection = (chain 'F' and (resid 16 through 200 or (resid 201 and (name N or name CA or nam \ e C or name O or name CB )) or resid 202 through 226 or resid 232 through 263 or \ resid 290 through 334)) } 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 individual isotropic 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: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 33.990 Find NCS groups from input model: 0.760 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:14.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 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 : 0.004 0.109 14021 Z= 0.182 Angle : 0.653 11.213 18869 Z= 0.338 Chirality : 0.045 0.215 2172 Planarity : 0.004 0.065 2434 Dihedral : 14.452 124.257 5346 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.20 % Allowed : 0.46 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: -0.15 (0.21), residues: 1744 helix: 0.09 (0.18), residues: 822 sheet: -0.37 (0.27), residues: 323 loop : 0.10 (0.28), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 242 PHE 0.015 0.001 PHE A 123 TYR 0.018 0.001 TYR D 185 ARG 0.005 0.000 ARG E 142 Details of bonding type rmsd hydrogen bonds : bond 0.17152 ( 675) hydrogen bonds : angle 6.56704 ( 1878) covalent geometry : bond 0.00384 (14021) covalent geometry : angle 0.65272 (18869) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 228 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 28 ASN cc_start: 0.8739 (p0) cc_final: 0.8477 (p0) REVERT: C 308 LYS cc_start: 0.7397 (ttpt) cc_final: 0.6888 (ttpp) REVERT: D 52 ARG cc_start: 0.7392 (ptm-80) cc_final: 0.7085 (ptt180) REVERT: E 248 ARG cc_start: 0.7866 (ttp80) cc_final: 0.7558 (ttm-80) REVERT: F 124 ARG cc_start: 0.4227 (tpm170) cc_final: 0.3936 (tpm170) REVERT: F 135 CYS cc_start: 0.7541 (m) cc_final: 0.7269 (m) REVERT: F 296 LEU cc_start: 0.8378 (mm) cc_final: 0.8000 (mm) outliers start: 3 outliers final: 4 residues processed: 231 average time/residue: 1.2196 time to fit residues: 309.2256 Evaluate side-chains 168 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 164 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 315 MET Chi-restraints excluded: chain F residue 225 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 73 optimal weight: 0.0570 chunk 45 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 137 optimal weight: 0.0470 chunk 53 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 overall best weight: 1.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN A 261 ASN ** B 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 HIS ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 ASN ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 ASN ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.145443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.113483 restraints weight = 25536.396| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 3.51 r_work: 0.3501 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14021 Z= 0.159 Angle : 0.610 8.597 18869 Z= 0.310 Chirality : 0.045 0.169 2172 Planarity : 0.004 0.078 2434 Dihedral : 6.200 130.958 1967 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.30 % Allowed : 9.14 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: 0.09 (0.20), residues: 1744 helix: 0.38 (0.18), residues: 837 sheet: -0.34 (0.28), residues: 312 loop : 0.11 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 242 PHE 0.020 0.001 PHE B 123 TYR 0.015 0.001 TYR D 185 ARG 0.007 0.000 ARG C 124 Details of bonding type rmsd hydrogen bonds : bond 0.04329 ( 675) hydrogen bonds : angle 4.97204 ( 1878) covalent geometry : bond 0.00365 (14021) covalent geometry : angle 0.61007 (18869) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.6661 (mpt) REVERT: A 237 GLN cc_start: 0.8719 (tp-100) cc_final: 0.8489 (tp-100) REVERT: A 248 ARG cc_start: 0.8776 (tpp-160) cc_final: 0.8456 (tpp80) REVERT: B 33 GLN cc_start: 0.8913 (tp-100) cc_final: 0.8687 (pp30) REVERT: B 298 ARG cc_start: 0.8692 (mtm110) cc_final: 0.8452 (mtm110) REVERT: C 144 MET cc_start: 0.7416 (pmm) cc_final: 0.7198 (pmm) REVERT: C 240 ASN cc_start: 0.8414 (m-40) cc_final: 0.8192 (m-40) REVERT: C 261 ASN cc_start: 0.8424 (t0) cc_final: 0.8217 (t0) REVERT: C 298 ARG cc_start: 0.7697 (pmt100) cc_final: 0.7381 (pmt100) REVERT: C 308 LYS cc_start: 0.7056 (ttpt) cc_final: 0.6421 (ttpp) REVERT: D 296 LEU cc_start: 0.8554 (tp) cc_final: 0.8326 (tp) REVERT: E 120 PHE cc_start: 0.7251 (p90) cc_final: 0.6759 (p90) REVERT: E 248 ARG cc_start: 0.8275 (ttp80) cc_final: 0.7145 (ttm-80) REVERT: F 76 ILE cc_start: 0.8587 (tt) cc_final: 0.7985 (pt) REVERT: F 124 ARG cc_start: 0.4019 (tpm170) cc_final: 0.3488 (tpm170) REVERT: F 135 CYS cc_start: 0.8117 (m) cc_final: 0.7710 (m) REVERT: F 144 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8212 (pmm) REVERT: F 190 ASN cc_start: 0.7716 (p0) cc_final: 0.7452 (p0) REVERT: F 204 GLU cc_start: 0.8045 (pm20) cc_final: 0.7704 (pm20) REVERT: F 225 ASP cc_start: 0.8212 (t70) cc_final: 0.7867 (t0) outliers start: 35 outliers final: 14 residues processed: 212 average time/residue: 1.1406 time to fit residues: 267.7167 Evaluate side-chains 192 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 144 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 68 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 174 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN A 261 ASN ** B 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 GLN ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.143125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.110737 restraints weight = 25663.461| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 3.52 r_work: 0.3461 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14021 Z= 0.205 Angle : 0.630 9.270 18869 Z= 0.319 Chirality : 0.046 0.180 2172 Planarity : 0.004 0.060 2434 Dihedral : 6.073 135.176 1959 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.42 % Allowed : 13.75 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: 0.01 (0.20), residues: 1744 helix: 0.40 (0.18), residues: 837 sheet: -0.46 (0.28), residues: 311 loop : -0.02 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 193 PHE 0.018 0.002 PHE B 123 TYR 0.014 0.002 TYR E 153 ARG 0.006 0.000 ARG C 124 Details of bonding type rmsd hydrogen bonds : bond 0.03981 ( 675) hydrogen bonds : angle 4.82016 ( 1878) covalent geometry : bond 0.00476 (14021) covalent geometry : angle 0.63032 (18869) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 190 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ARG cc_start: 0.7281 (mmp-170) cc_final: 0.7072 (mmp-170) REVERT: A 195 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.6645 (mpt) REVERT: A 200 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.8080 (mp10) REVERT: A 237 GLN cc_start: 0.8721 (tp-100) cc_final: 0.8355 (tp-100) REVERT: A 248 ARG cc_start: 0.8801 (tpp-160) cc_final: 0.8457 (tpp80) REVERT: B 298 ARG cc_start: 0.8613 (mtm110) cc_final: 0.8325 (mtm110) REVERT: C 77 GLN cc_start: 0.8499 (tm-30) cc_final: 0.8251 (tm-30) REVERT: C 296 LEU cc_start: 0.8408 (tp) cc_final: 0.8195 (tm) REVERT: C 298 ARG cc_start: 0.7742 (pmt100) cc_final: 0.7497 (pmt100) REVERT: C 315 MET cc_start: 0.7822 (mpt) cc_final: 0.7593 (mpt) REVERT: D 237 GLN cc_start: 0.8645 (pp30) cc_final: 0.8265 (pp30) REVERT: D 241 GLN cc_start: 0.9099 (pt0) cc_final: 0.8538 (pm20) REVERT: D 252 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7887 (pm20) REVERT: D 296 LEU cc_start: 0.8618 (tp) cc_final: 0.8396 (tp) REVERT: E 120 PHE cc_start: 0.7364 (p90) cc_final: 0.6957 (p90) REVERT: E 124 ARG cc_start: 0.5285 (tpp-160) cc_final: 0.4780 (tpp-160) REVERT: E 248 ARG cc_start: 0.8312 (ttp80) cc_final: 0.7628 (ttm-80) REVERT: F 124 ARG cc_start: 0.4210 (tpm170) cc_final: 0.3551 (tpm170) REVERT: F 144 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8218 (pmm) REVERT: F 190 ASN cc_start: 0.7876 (p0) cc_final: 0.7591 (p0) REVERT: F 204 GLU cc_start: 0.8096 (pm20) cc_final: 0.7726 (pm20) REVERT: F 225 ASP cc_start: 0.8341 (t70) cc_final: 0.8033 (t0) REVERT: F 296 LEU cc_start: 0.8129 (mm) cc_final: 0.7719 (mm) outliers start: 52 outliers final: 22 residues processed: 222 average time/residue: 1.1745 time to fit residues: 286.9191 Evaluate side-chains 203 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 183 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 51 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 172 optimal weight: 9.9990 chunk 121 optimal weight: 7.9990 chunk 109 optimal weight: 0.0000 chunk 7 optimal weight: 0.4980 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN ** B 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN E 240 ASN ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.143908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.112037 restraints weight = 25672.375| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 3.51 r_work: 0.3480 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14021 Z= 0.157 Angle : 0.593 10.409 18869 Z= 0.297 Chirality : 0.044 0.169 2172 Planarity : 0.003 0.046 2434 Dihedral : 5.888 136.235 1959 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.68 % Allowed : 15.53 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.20), residues: 1744 helix: 0.53 (0.18), residues: 838 sheet: -0.44 (0.29), residues: 311 loop : 0.04 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 132 PHE 0.015 0.001 PHE B 123 TYR 0.019 0.001 TYR D 185 ARG 0.008 0.000 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.03468 ( 675) hydrogen bonds : angle 4.60514 ( 1878) covalent geometry : bond 0.00365 (14021) covalent geometry : angle 0.59312 (18869) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 194 time to evaluate : 2.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.8023 (mtt) REVERT: A 124 ARG cc_start: 0.7256 (mmp-170) cc_final: 0.7027 (mmp-170) REVERT: A 195 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.6628 (mpt) REVERT: A 200 GLN cc_start: 0.8421 (mp10) cc_final: 0.7939 (mp10) REVERT: A 236 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7796 (mp10) REVERT: A 237 GLN cc_start: 0.8702 (tp-100) cc_final: 0.8336 (tp-100) REVERT: A 248 ARG cc_start: 0.8802 (tpp-160) cc_final: 0.8531 (tpp80) REVERT: B 33 GLN cc_start: 0.8960 (tp-100) cc_final: 0.8640 (pp30) REVERT: B 200 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8656 (mm-40) REVERT: B 298 ARG cc_start: 0.8586 (mtm110) cc_final: 0.8312 (mtm110) REVERT: B 310 GLN cc_start: 0.7721 (tm-30) cc_final: 0.7518 (tm-30) REVERT: C 66 GLU cc_start: 0.8604 (mp0) cc_final: 0.8345 (mp0) REVERT: C 144 MET cc_start: 0.7371 (pmm) cc_final: 0.7134 (pmm) REVERT: D 70 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7852 (pm20) REVERT: D 118 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: D 237 GLN cc_start: 0.8628 (pp30) cc_final: 0.8259 (pp30) REVERT: D 241 GLN cc_start: 0.9076 (pt0) cc_final: 0.8523 (pm20) REVERT: D 296 LEU cc_start: 0.8618 (tp) cc_final: 0.8400 (tp) REVERT: E 53 HIS cc_start: 0.8088 (t70) cc_final: 0.7823 (m90) REVERT: E 104 ASP cc_start: 0.8108 (m-30) cc_final: 0.7845 (m-30) REVERT: E 120 PHE cc_start: 0.7347 (p90) cc_final: 0.6925 (p90) REVERT: E 180 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7814 (tp) REVERT: E 248 ARG cc_start: 0.8248 (ttp80) cc_final: 0.7594 (ttm-80) REVERT: F 111 ILE cc_start: 0.8914 (mm) cc_final: 0.8707 (mm) REVERT: F 124 ARG cc_start: 0.4195 (tpm170) cc_final: 0.3502 (tpm170) REVERT: F 135 CYS cc_start: 0.8204 (m) cc_final: 0.7901 (m) REVERT: F 143 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8340 (pp20) REVERT: F 144 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.7922 (pmm) REVERT: F 190 ASN cc_start: 0.7727 (p0) cc_final: 0.7454 (p0) REVERT: F 204 GLU cc_start: 0.7963 (pm20) cc_final: 0.7614 (pm20) REVERT: F 225 ASP cc_start: 0.8408 (t70) cc_final: 0.8104 (t0) REVERT: F 241 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8512 (tm-30) REVERT: F 296 LEU cc_start: 0.8166 (mm) cc_final: 0.7853 (mm) outliers start: 56 outliers final: 23 residues processed: 225 average time/residue: 1.6678 time to fit residues: 414.7272 Evaluate side-chains 213 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 183 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 106 optimal weight: 4.9990 chunk 35 optimal weight: 0.1980 chunk 138 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN A 261 ASN ** B 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 ASN ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.144601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.112978 restraints weight = 25630.997| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 3.45 r_work: 0.3492 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14021 Z= 0.135 Angle : 0.582 11.509 18869 Z= 0.287 Chirality : 0.043 0.173 2172 Planarity : 0.003 0.035 2434 Dihedral : 5.750 136.631 1959 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.14 % Allowed : 16.84 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: 0.27 (0.21), residues: 1744 helix: 0.66 (0.18), residues: 840 sheet: -0.40 (0.29), residues: 310 loop : 0.06 (0.27), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 132 PHE 0.016 0.001 PHE B 120 TYR 0.009 0.001 TYR E 153 ARG 0.005 0.000 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.03228 ( 675) hydrogen bonds : angle 4.45124 ( 1878) covalent geometry : bond 0.00314 (14021) covalent geometry : angle 0.58160 (18869) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 198 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.8060 (mtt) REVERT: A 195 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.6735 (mpt) REVERT: A 236 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7881 (mp10) REVERT: A 237 GLN cc_start: 0.8721 (tp-100) cc_final: 0.8346 (tp-100) REVERT: A 248 ARG cc_start: 0.8817 (tpp-160) cc_final: 0.8553 (tpp80) REVERT: B 120 PHE cc_start: 0.8345 (p90) cc_final: 0.8141 (p90) REVERT: B 200 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8664 (mm-40) REVERT: B 298 ARG cc_start: 0.8588 (mtm110) cc_final: 0.8346 (mtm110) REVERT: B 310 GLN cc_start: 0.7734 (tm-30) cc_final: 0.7524 (tm-30) REVERT: C 66 GLU cc_start: 0.8639 (mp0) cc_final: 0.8345 (mp0) REVERT: C 252 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7908 (mp0) REVERT: C 261 ASN cc_start: 0.8489 (t0) cc_final: 0.8251 (t0) REVERT: C 298 ARG cc_start: 0.7788 (pmt100) cc_final: 0.7579 (pmt100) REVERT: C 315 MET cc_start: 0.7718 (mpt) cc_final: 0.7482 (mpt) REVERT: D 70 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7874 (pm20) REVERT: D 118 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7813 (tm-30) REVERT: D 190 ASN cc_start: 0.7379 (m110) cc_final: 0.7008 (p0) REVERT: D 237 GLN cc_start: 0.8658 (pp30) cc_final: 0.8316 (pp30) REVERT: D 241 GLN cc_start: 0.9093 (pt0) cc_final: 0.8569 (pt0) REVERT: D 296 LEU cc_start: 0.8656 (tp) cc_final: 0.8439 (tp) REVERT: D 311 ASP cc_start: 0.7838 (t0) cc_final: 0.7637 (t0) REVERT: E 53 HIS cc_start: 0.8010 (t70) cc_final: 0.7780 (m90) REVERT: E 104 ASP cc_start: 0.8012 (m-30) cc_final: 0.7727 (m-30) REVERT: E 120 PHE cc_start: 0.7408 (p90) cc_final: 0.6937 (p90) REVERT: E 124 ARG cc_start: 0.5046 (tpp-160) cc_final: 0.3517 (tpp-160) REVERT: E 180 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7833 (tp) REVERT: E 195 MET cc_start: 0.7860 (mtt) cc_final: 0.7215 (mtt) REVERT: E 248 ARG cc_start: 0.8241 (ttp80) cc_final: 0.7464 (ttm-80) REVERT: F 124 ARG cc_start: 0.4286 (tpm170) cc_final: 0.3564 (tpm170) REVERT: F 135 CYS cc_start: 0.8146 (m) cc_final: 0.7849 (m) REVERT: F 143 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8322 (pp20) REVERT: F 190 ASN cc_start: 0.7704 (p0) cc_final: 0.7422 (p0) REVERT: F 204 GLU cc_start: 0.7994 (pm20) cc_final: 0.7647 (pm20) REVERT: F 225 ASP cc_start: 0.8424 (t70) cc_final: 0.8114 (t0) outliers start: 63 outliers final: 24 residues processed: 238 average time/residue: 1.2379 time to fit residues: 324.7313 Evaluate side-chains 219 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 315 MET Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 151 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 32 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 162 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN ** B 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.144909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.113257 restraints weight = 25689.328| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 3.50 r_work: 0.3500 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14021 Z= 0.134 Angle : 0.587 11.900 18869 Z= 0.290 Chirality : 0.043 0.162 2172 Planarity : 0.003 0.035 2434 Dihedral : 5.680 136.122 1959 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.62 % Allowed : 18.09 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: 0.36 (0.21), residues: 1744 helix: 0.82 (0.18), residues: 827 sheet: -0.45 (0.29), residues: 309 loop : 0.05 (0.27), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 132 PHE 0.014 0.001 PHE F 120 TYR 0.022 0.001 TYR D 185 ARG 0.003 0.000 ARG E 124 Details of bonding type rmsd hydrogen bonds : bond 0.03114 ( 675) hydrogen bonds : angle 4.39852 ( 1878) covalent geometry : bond 0.00315 (14021) covalent geometry : angle 0.58683 (18869) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 196 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.8038 (mtt) REVERT: A 195 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.6583 (mpt) REVERT: A 236 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7794 (mp10) REVERT: A 237 GLN cc_start: 0.8711 (tp-100) cc_final: 0.8341 (tp-100) REVERT: A 248 ARG cc_start: 0.8804 (tpp-160) cc_final: 0.8541 (tpp80) REVERT: B 33 GLN cc_start: 0.8834 (tp40) cc_final: 0.8551 (pp30) REVERT: B 200 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8663 (mm-40) REVERT: B 298 ARG cc_start: 0.8546 (mtm110) cc_final: 0.8283 (mtm110) REVERT: B 310 GLN cc_start: 0.7663 (tm-30) cc_final: 0.7370 (tm-30) REVERT: C 66 GLU cc_start: 0.8633 (mp0) cc_final: 0.8347 (mp0) REVERT: C 144 MET cc_start: 0.7003 (pmm) cc_final: 0.6760 (pmm) REVERT: C 192 GLU cc_start: 0.8314 (mp0) cc_final: 0.8055 (mp0) REVERT: C 252 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7974 (mp0) REVERT: C 261 ASN cc_start: 0.8503 (t0) cc_final: 0.8279 (t0) REVERT: C 298 ARG cc_start: 0.7860 (pmt100) cc_final: 0.7565 (pmt100) REVERT: C 315 MET cc_start: 0.7725 (mpt) cc_final: 0.7475 (mpt) REVERT: D 70 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7860 (pm20) REVERT: D 118 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7789 (tm-30) REVERT: D 234 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8062 (tm-30) REVERT: D 237 GLN cc_start: 0.8688 (pp30) cc_final: 0.8300 (pp30) REVERT: D 241 GLN cc_start: 0.9049 (pt0) cc_final: 0.8486 (pt0) REVERT: D 296 LEU cc_start: 0.8643 (tp) cc_final: 0.8428 (tp) REVERT: E 53 HIS cc_start: 0.8006 (t70) cc_final: 0.7781 (m90) REVERT: E 104 ASP cc_start: 0.8053 (m-30) cc_final: 0.7766 (m-30) REVERT: E 120 PHE cc_start: 0.7359 (p90) cc_final: 0.6871 (p90) REVERT: E 124 ARG cc_start: 0.4911 (tpp-160) cc_final: 0.3447 (tpp-160) REVERT: E 180 LEU cc_start: 0.8132 (mm) cc_final: 0.7826 (tp) REVERT: E 199 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8374 (mp0) REVERT: E 248 ARG cc_start: 0.8206 (ttp80) cc_final: 0.7600 (tmm-80) REVERT: F 124 ARG cc_start: 0.4412 (tpm170) cc_final: 0.3695 (tpm170) REVERT: F 135 CYS cc_start: 0.8076 (m) cc_final: 0.7763 (m) REVERT: F 143 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8325 (pp20) REVERT: F 190 ASN cc_start: 0.7652 (p0) cc_final: 0.7360 (p0) REVERT: F 204 GLU cc_start: 0.7955 (pm20) cc_final: 0.7607 (pm20) REVERT: F 225 ASP cc_start: 0.8414 (t70) cc_final: 0.8098 (t0) REVERT: F 296 LEU cc_start: 0.8027 (mm) cc_final: 0.7659 (mm) outliers start: 55 outliers final: 26 residues processed: 232 average time/residue: 1.3269 time to fit residues: 340.2407 Evaluate side-chains 228 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 194 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 315 MET Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 183 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 118 optimal weight: 0.4980 chunk 4 optimal weight: 20.0000 chunk 148 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN ** B 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 GLN D 194 GLN E 247 ASN ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.144561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.112736 restraints weight = 25744.545| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 3.51 r_work: 0.3494 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14021 Z= 0.140 Angle : 0.588 12.005 18869 Z= 0.290 Chirality : 0.044 0.162 2172 Planarity : 0.003 0.053 2434 Dihedral : 5.717 135.820 1959 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.95 % Allowed : 18.82 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: 0.44 (0.21), residues: 1744 helix: 0.89 (0.18), residues: 823 sheet: -0.44 (0.29), residues: 310 loop : 0.09 (0.27), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 132 PHE 0.022 0.001 PHE B 123 TYR 0.009 0.001 TYR E 153 ARG 0.006 0.000 ARG B 124 Details of bonding type rmsd hydrogen bonds : bond 0.03142 ( 675) hydrogen bonds : angle 4.40766 ( 1878) covalent geometry : bond 0.00329 (14021) covalent geometry : angle 0.58755 (18869) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 194 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.6642 (mpt) REVERT: A 236 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7786 (mp10) REVERT: A 237 GLN cc_start: 0.8701 (tp-100) cc_final: 0.8336 (tp-100) REVERT: A 248 ARG cc_start: 0.8795 (tpp-160) cc_final: 0.8547 (tpp80) REVERT: B 200 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8656 (mm-40) REVERT: B 310 GLN cc_start: 0.7681 (tm-30) cc_final: 0.7382 (tm-30) REVERT: C 66 GLU cc_start: 0.8630 (mp0) cc_final: 0.8318 (mp0) REVERT: C 192 GLU cc_start: 0.8334 (mp0) cc_final: 0.8076 (mp0) REVERT: C 261 ASN cc_start: 0.8511 (t0) cc_final: 0.8296 (t0) REVERT: C 298 ARG cc_start: 0.7876 (pmt100) cc_final: 0.7582 (pmt100) REVERT: D 70 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7848 (pm20) REVERT: D 118 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7791 (tm-30) REVERT: D 234 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8103 (tm-30) REVERT: D 237 GLN cc_start: 0.8696 (pp30) cc_final: 0.8286 (pp30) REVERT: D 241 GLN cc_start: 0.9040 (pt0) cc_final: 0.8461 (pt0) REVERT: D 296 LEU cc_start: 0.8641 (tp) cc_final: 0.8412 (tp) REVERT: D 311 ASP cc_start: 0.7753 (t0) cc_final: 0.7423 (t0) REVERT: E 53 HIS cc_start: 0.7998 (t70) cc_final: 0.7776 (m90) REVERT: E 104 ASP cc_start: 0.8045 (m-30) cc_final: 0.7755 (m-30) REVERT: E 120 PHE cc_start: 0.7404 (p90) cc_final: 0.6921 (p90) REVERT: E 180 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7823 (tp) REVERT: E 248 ARG cc_start: 0.8206 (ttp80) cc_final: 0.7618 (tmm-80) REVERT: E 261 ASN cc_start: 0.8545 (t0) cc_final: 0.8306 (t0) REVERT: F 124 ARG cc_start: 0.4403 (tpm170) cc_final: 0.3674 (tpm170) REVERT: F 135 CYS cc_start: 0.8069 (m) cc_final: 0.7744 (m) REVERT: F 143 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8311 (pp20) REVERT: F 190 ASN cc_start: 0.7610 (p0) cc_final: 0.7317 (p0) REVERT: F 196 GLU cc_start: 0.8309 (tm-30) cc_final: 0.8037 (pp20) REVERT: F 204 GLU cc_start: 0.7952 (pm20) cc_final: 0.7595 (pm20) REVERT: F 225 ASP cc_start: 0.8426 (t70) cc_final: 0.8112 (t0) REVERT: F 252 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7444 (mt-10) REVERT: F 296 LEU cc_start: 0.8102 (mm) cc_final: 0.7762 (mm) outliers start: 60 outliers final: 30 residues processed: 235 average time/residue: 1.2276 time to fit residues: 317.4258 Evaluate side-chains 219 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 315 MET Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 252 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 104 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 chunk 149 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN ** B 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.144596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.112942 restraints weight = 25685.519| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 3.50 r_work: 0.3496 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14021 Z= 0.140 Angle : 0.606 12.422 18869 Z= 0.298 Chirality : 0.044 0.159 2172 Planarity : 0.003 0.039 2434 Dihedral : 5.680 134.628 1959 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.22 % Allowed : 20.33 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: 0.39 (0.21), residues: 1744 helix: 0.84 (0.18), residues: 842 sheet: -0.46 (0.29), residues: 310 loop : 0.05 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 132 PHE 0.030 0.001 PHE B 123 TYR 0.027 0.001 TYR D 185 ARG 0.008 0.000 ARG B 90 Details of bonding type rmsd hydrogen bonds : bond 0.03097 ( 675) hydrogen bonds : angle 4.38413 ( 1878) covalent geometry : bond 0.00330 (14021) covalent geometry : angle 0.60586 (18869) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 190 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.6693 (mpt) REVERT: A 236 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7772 (mp10) REVERT: A 237 GLN cc_start: 0.8705 (tp-100) cc_final: 0.8340 (tp-100) REVERT: A 248 ARG cc_start: 0.8780 (tpp-160) cc_final: 0.8566 (tpp80) REVERT: B 33 GLN cc_start: 0.8817 (tp40) cc_final: 0.8508 (pp30) REVERT: B 136 VAL cc_start: 0.7805 (t) cc_final: 0.7603 (p) REVERT: B 195 MET cc_start: 0.7035 (mtt) cc_final: 0.6775 (mtt) REVERT: B 200 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8651 (mm-40) REVERT: B 298 ARG cc_start: 0.8547 (mtm110) cc_final: 0.8080 (mtm110) REVERT: B 310 GLN cc_start: 0.7745 (tm-30) cc_final: 0.7444 (tm-30) REVERT: C 66 GLU cc_start: 0.8647 (mp0) cc_final: 0.8333 (mp0) REVERT: C 124 ARG cc_start: 0.8066 (mmm160) cc_final: 0.7579 (mmm160) REVERT: C 192 GLU cc_start: 0.8345 (mp0) cc_final: 0.8109 (mp0) REVERT: C 252 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8061 (mp0) REVERT: C 261 ASN cc_start: 0.8514 (t0) cc_final: 0.8280 (t0) REVERT: C 298 ARG cc_start: 0.7860 (pmt100) cc_final: 0.7593 (pmt100) REVERT: D 70 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7889 (pm20) REVERT: D 118 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7826 (tm-30) REVERT: D 190 ASN cc_start: 0.7231 (m-40) cc_final: 0.6906 (p0) REVERT: D 199 GLU cc_start: 0.7676 (pp20) cc_final: 0.7438 (pt0) REVERT: D 234 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7891 (tm-30) REVERT: D 237 GLN cc_start: 0.8703 (pp30) cc_final: 0.8204 (pp30) REVERT: D 241 GLN cc_start: 0.9048 (pt0) cc_final: 0.8465 (pt0) REVERT: D 296 LEU cc_start: 0.8646 (tp) cc_final: 0.8416 (tp) REVERT: E 53 HIS cc_start: 0.7966 (t70) cc_final: 0.7739 (m90) REVERT: E 104 ASP cc_start: 0.8039 (m-30) cc_final: 0.7749 (m-30) REVERT: E 120 PHE cc_start: 0.7400 (p90) cc_final: 0.6886 (p90) REVERT: E 124 ARG cc_start: 0.4857 (tpp-160) cc_final: 0.3272 (tpp-160) REVERT: E 180 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7829 (tp) REVERT: E 248 ARG cc_start: 0.8203 (ttp80) cc_final: 0.7626 (tmm-80) REVERT: E 261 ASN cc_start: 0.8566 (t0) cc_final: 0.8308 (t0) REVERT: F 124 ARG cc_start: 0.4428 (tpm170) cc_final: 0.3678 (tpm170) REVERT: F 135 CYS cc_start: 0.8051 (m) cc_final: 0.7712 (m) REVERT: F 143 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8292 (pp20) REVERT: F 190 ASN cc_start: 0.7646 (p0) cc_final: 0.7336 (p0) REVERT: F 204 GLU cc_start: 0.7943 (pm20) cc_final: 0.7626 (pm20) REVERT: F 225 ASP cc_start: 0.8431 (t70) cc_final: 0.8112 (t0) REVERT: F 296 LEU cc_start: 0.8097 (mm) cc_final: 0.7763 (mm) outliers start: 49 outliers final: 28 residues processed: 225 average time/residue: 1.1844 time to fit residues: 293.7490 Evaluate side-chains 220 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 315 MET Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 183 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 68 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 117 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 118 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 chunk 173 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN ** B 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 ASN ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.144379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.112722 restraints weight = 25605.476| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 3.50 r_work: 0.3494 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14021 Z= 0.144 Angle : 0.613 13.072 18869 Z= 0.301 Chirality : 0.044 0.159 2172 Planarity : 0.003 0.037 2434 Dihedral : 5.682 133.877 1959 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.22 % Allowed : 20.20 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: 0.41 (0.21), residues: 1744 helix: 0.87 (0.18), residues: 842 sheet: -0.47 (0.29), residues: 311 loop : 0.05 (0.27), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 132 PHE 0.042 0.002 PHE B 123 TYR 0.020 0.001 TYR A 41 ARG 0.008 0.000 ARG E 298 Details of bonding type rmsd hydrogen bonds : bond 0.03101 ( 675) hydrogen bonds : angle 4.37788 ( 1878) covalent geometry : bond 0.00338 (14021) covalent geometry : angle 0.61280 (18869) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 188 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7962 (mtt) REVERT: A 236 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7758 (mp10) REVERT: A 237 GLN cc_start: 0.8723 (tp-100) cc_final: 0.8361 (tp-100) REVERT: A 248 ARG cc_start: 0.8780 (tpp-160) cc_final: 0.8570 (tpp80) REVERT: B 33 GLN cc_start: 0.8821 (tp40) cc_final: 0.8539 (pp30) REVERT: B 195 MET cc_start: 0.7036 (mtt) cc_final: 0.6811 (mtt) REVERT: B 200 GLN cc_start: 0.8883 (mm-40) cc_final: 0.8663 (mm-40) REVERT: B 298 ARG cc_start: 0.8560 (mtm110) cc_final: 0.8123 (mtm110) REVERT: B 310 GLN cc_start: 0.7775 (tm-30) cc_final: 0.7490 (tm-30) REVERT: C 66 GLU cc_start: 0.8654 (mp0) cc_final: 0.8350 (mp0) REVERT: C 124 ARG cc_start: 0.8134 (mmm160) cc_final: 0.7624 (mmm160) REVERT: C 192 GLU cc_start: 0.8357 (mp0) cc_final: 0.8112 (mp0) REVERT: C 261 ASN cc_start: 0.8522 (t0) cc_final: 0.8292 (t0) REVERT: C 298 ARG cc_start: 0.7907 (pmt100) cc_final: 0.7659 (pmt100) REVERT: D 70 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7933 (pm20) REVERT: D 118 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7826 (tm-30) REVERT: D 209 ASP cc_start: 0.7642 (m-30) cc_final: 0.7242 (t70) REVERT: D 234 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7873 (tm-30) REVERT: D 237 GLN cc_start: 0.8706 (pp30) cc_final: 0.8215 (pp30) REVERT: D 241 GLN cc_start: 0.9047 (pt0) cc_final: 0.8466 (pt0) REVERT: D 296 LEU cc_start: 0.8653 (tp) cc_final: 0.8425 (tp) REVERT: D 311 ASP cc_start: 0.7656 (t0) cc_final: 0.7246 (t0) REVERT: E 53 HIS cc_start: 0.7970 (t70) cc_final: 0.7743 (m90) REVERT: E 104 ASP cc_start: 0.8040 (m-30) cc_final: 0.7744 (m-30) REVERT: E 120 PHE cc_start: 0.7422 (p90) cc_final: 0.6900 (p90) REVERT: E 124 ARG cc_start: 0.4966 (tpp-160) cc_final: 0.3497 (tpp-160) REVERT: E 180 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7829 (tp) REVERT: E 248 ARG cc_start: 0.8268 (ttp80) cc_final: 0.7664 (tmm-80) REVERT: E 261 ASN cc_start: 0.8571 (t0) cc_final: 0.8314 (t0) REVERT: F 124 ARG cc_start: 0.4465 (tpm170) cc_final: 0.3713 (tpm170) REVERT: F 135 CYS cc_start: 0.8043 (m) cc_final: 0.7705 (m) REVERT: F 143 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8284 (pp20) REVERT: F 190 ASN cc_start: 0.7656 (p0) cc_final: 0.7347 (p0) REVERT: F 204 GLU cc_start: 0.7938 (pm20) cc_final: 0.7620 (pm20) REVERT: F 225 ASP cc_start: 0.8425 (t70) cc_final: 0.8106 (t0) outliers start: 49 outliers final: 29 residues processed: 221 average time/residue: 1.2380 time to fit residues: 301.9027 Evaluate side-chains 221 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 186 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 315 MET Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 183 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 128 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 87 optimal weight: 0.1980 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 171 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN ** B 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.145685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.114396 restraints weight = 25684.922| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 3.44 r_work: 0.3519 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14021 Z= 0.121 Angle : 0.609 13.407 18869 Z= 0.298 Chirality : 0.043 0.149 2172 Planarity : 0.003 0.035 2434 Dihedral : 5.509 129.901 1959 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.76 % Allowed : 20.72 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: 0.52 (0.21), residues: 1744 helix: 0.97 (0.18), residues: 837 sheet: -0.38 (0.30), residues: 308 loop : 0.08 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 132 PHE 0.040 0.001 PHE B 123 TYR 0.026 0.001 TYR D 185 ARG 0.008 0.000 ARG E 305 Details of bonding type rmsd hydrogen bonds : bond 0.02944 ( 675) hydrogen bonds : angle 4.31194 ( 1878) covalent geometry : bond 0.00283 (14021) covalent geometry : angle 0.60880 (18869) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 201 time to evaluate : 2.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLN cc_start: 0.8551 (pt0) cc_final: 0.8109 (pp30) REVERT: A 236 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7825 (mp10) REVERT: A 237 GLN cc_start: 0.8724 (tp-100) cc_final: 0.8359 (tp-100) REVERT: A 248 ARG cc_start: 0.8779 (tpp-160) cc_final: 0.8572 (tpp80) REVERT: B 33 GLN cc_start: 0.8807 (tp40) cc_final: 0.8510 (pp30) REVERT: B 200 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8645 (mm-40) REVERT: B 298 ARG cc_start: 0.8588 (mtm110) cc_final: 0.8284 (mtm110) REVERT: B 310 GLN cc_start: 0.7773 (tm-30) cc_final: 0.7463 (tm-30) REVERT: C 66 GLU cc_start: 0.8636 (mp0) cc_final: 0.8326 (mp0) REVERT: C 94 TYR cc_start: 0.5926 (m-10) cc_final: 0.5678 (m-10) REVERT: C 192 GLU cc_start: 0.8355 (mp0) cc_final: 0.8148 (mp0) REVERT: C 261 ASN cc_start: 0.8552 (t0) cc_final: 0.8340 (t0) REVERT: C 298 ARG cc_start: 0.7877 (pmt100) cc_final: 0.7654 (pmt100) REVERT: D 70 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7949 (pm20) REVERT: D 118 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7827 (tm-30) REVERT: D 234 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7968 (tm-30) REVERT: D 237 GLN cc_start: 0.8694 (pp30) cc_final: 0.8230 (pp30) REVERT: D 241 GLN cc_start: 0.8992 (pt0) cc_final: 0.8467 (pt0) REVERT: D 296 LEU cc_start: 0.8623 (tp) cc_final: 0.8412 (tp) REVERT: E 53 HIS cc_start: 0.8066 (t70) cc_final: 0.7830 (m90) REVERT: E 104 ASP cc_start: 0.8001 (m-30) cc_final: 0.7701 (m-30) REVERT: E 120 PHE cc_start: 0.7369 (p90) cc_final: 0.6878 (p90) REVERT: E 124 ARG cc_start: 0.4851 (tpp-160) cc_final: 0.3530 (tpp-160) REVERT: E 180 LEU cc_start: 0.8113 (mm) cc_final: 0.7803 (tp) REVERT: E 248 ARG cc_start: 0.8267 (ttp80) cc_final: 0.7763 (tmm-80) REVERT: E 261 ASN cc_start: 0.8558 (t0) cc_final: 0.8296 (t0) REVERT: E 323 VAL cc_start: 0.8243 (p) cc_final: 0.7985 (m) REVERT: F 124 ARG cc_start: 0.4405 (tpm170) cc_final: 0.3665 (tpm170) REVERT: F 135 CYS cc_start: 0.8016 (m) cc_final: 0.7702 (m) REVERT: F 143 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8272 (pp20) REVERT: F 190 ASN cc_start: 0.7600 (p0) cc_final: 0.7305 (p0) REVERT: F 204 GLU cc_start: 0.7927 (pm20) cc_final: 0.7655 (pm20) REVERT: F 225 ASP cc_start: 0.8531 (t70) cc_final: 0.8205 (t0) REVERT: F 252 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7424 (mt-10) REVERT: F 296 LEU cc_start: 0.8139 (mm) cc_final: 0.7782 (mm) outliers start: 42 outliers final: 26 residues processed: 228 average time/residue: 1.8055 time to fit residues: 453.6788 Evaluate side-chains 213 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 2.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 315 MET Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 252 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 1 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 79 optimal weight: 0.0030 chunk 123 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 117 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 116 optimal weight: 0.0070 overall best weight: 0.5410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN A 240 ASN ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 ASN ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.146505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.116210 restraints weight = 25884.546| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 3.42 r_work: 0.3559 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14021 Z= 0.116 Angle : 0.610 13.429 18869 Z= 0.299 Chirality : 0.043 0.155 2172 Planarity : 0.003 0.045 2434 Dihedral : 5.408 128.047 1959 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.57 % Allowed : 21.25 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: 0.51 (0.21), residues: 1744 helix: 0.96 (0.18), residues: 843 sheet: -0.36 (0.30), residues: 313 loop : 0.04 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 132 PHE 0.044 0.001 PHE B 123 TYR 0.020 0.001 TYR A 41 ARG 0.010 0.000 ARG E 298 Details of bonding type rmsd hydrogen bonds : bond 0.02865 ( 675) hydrogen bonds : angle 4.26879 ( 1878) covalent geometry : bond 0.00269 (14021) covalent geometry : angle 0.61003 (18869) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12070.04 seconds wall clock time: 213 minutes 52.46 seconds (12832.46 seconds total)