Starting phenix.real_space_refine on Fri May 16 01:33:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9njr_49488/05_2025/9njr_49488.cif Found real_map, /net/cci-nas-00/data/ceres_data/9njr_49488/05_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_49488/05_2025/9njr_49488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9njr_49488/05_2025/9njr_49488.map" model { file = "/net/cci-nas-00/data/ceres_data/9njr_49488/05_2025/9njr_49488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9njr_49488/05_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-5687/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: 8.85, per 1000 atoms: 0.64 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: 3.28 Conformation dependent library (CDL) restraints added in 1.7 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: 1.89 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: 4.26 Time building geometry restraints manager: 3.84 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: 3.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 32.660 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.060 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:12.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.930 ------------------------------------------------------------------------------- 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 : 1.576 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: 1.2007 time to fit residues: 304.4853 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 : 1.470 ------------------------------------------------------------------------------- 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 = 0.4073 r_free = 0.4073 target = 0.145465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.113452 restraints weight = 25536.343| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 3.52 r_work: 0.3498 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14021 Z= 0.159 Angle : 0.608 8.599 18869 Z= 0.309 Chirality : 0.045 0.170 2172 Planarity : 0.004 0.044 2434 Dihedral : 6.175 126.378 1967 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.37 % Allowed : 9.21 % Favored : 88.42 % 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: 0.08 (0.20), residues: 1744 helix: 0.37 (0.18), residues: 837 sheet: -0.33 (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 0.004 0.000 ARG E 124 Details of bonding type rmsd hydrogen bonds : bond 0.04496 ( 675) hydrogen bonds : angle 5.00248 ( 1878) covalent geometry : bond 0.00366 (14021) covalent geometry : angle 0.60839 (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: 36 poor density : 193 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.6686 (mpt) REVERT: A 237 GLN cc_start: 0.8713 (tp-100) cc_final: 0.8493 (tp-100) REVERT: A 248 ARG cc_start: 0.8769 (tpp-160) cc_final: 0.8440 (tpp80) REVERT: B 33 GLN cc_start: 0.8920 (tp-100) cc_final: 0.8691 (pp30) REVERT: B 298 ARG cc_start: 0.8683 (mtm110) cc_final: 0.8446 (mtm110) REVERT: C 240 ASN cc_start: 0.8408 (m-40) cc_final: 0.8201 (m-40) REVERT: C 261 ASN cc_start: 0.8417 (t0) cc_final: 0.8188 (t0) REVERT: C 298 ARG cc_start: 0.7675 (pmt100) cc_final: 0.7361 (pmt100) REVERT: C 308 LYS cc_start: 0.7063 (ttpt) cc_final: 0.6429 (ttpp) REVERT: D 296 LEU cc_start: 0.8549 (tp) cc_final: 0.8321 (tp) REVERT: E 120 PHE cc_start: 0.7250 (p90) cc_final: 0.6761 (p90) REVERT: E 248 ARG cc_start: 0.8282 (ttp80) cc_final: 0.7115 (ttm-80) REVERT: F 76 ILE cc_start: 0.8623 (tt) cc_final: 0.8038 (pt) REVERT: F 124 ARG cc_start: 0.3991 (tpm170) cc_final: 0.3469 (tpm170) REVERT: F 135 CYS cc_start: 0.8102 (m) cc_final: 0.7694 (m) REVERT: F 144 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8212 (pmm) REVERT: F 190 ASN cc_start: 0.7692 (p0) cc_final: 0.7435 (p0) REVERT: F 204 GLU cc_start: 0.8045 (pm20) cc_final: 0.7708 (pm20) REVERT: F 225 ASP cc_start: 0.8169 (t70) cc_final: 0.7824 (t0) outliers start: 36 outliers final: 15 residues processed: 212 average time/residue: 1.1430 time to fit residues: 267.9626 Evaluate side-chains 194 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 1.633 ------------------------------------------------------------------------------- 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 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: 10.0000 chunk 79 optimal weight: 7.9990 chunk 165 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 174 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.4042 r_free = 0.4042 target = 0.142940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.110706 restraints weight = 25624.892| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 3.50 r_work: 0.3460 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1778 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= 0.207 Angle : 0.633 9.258 18869 Z= 0.319 Chirality : 0.046 0.181 2172 Planarity : 0.004 0.053 2434 Dihedral : 6.092 133.095 1959 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.36 % Allowed : 13.42 % Favored : 83.22 % 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: 0.39 (0.18), residues: 838 sheet: -0.44 (0.28), residues: 309 loop : -0.02 (0.27), residues: 597 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 0.011 0.000 ARG C 124 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 675) hydrogen bonds : angle 4.82379 ( 1878) covalent geometry : bond 0.00481 (14021) covalent geometry : angle 0.63260 (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: 51 poor density : 191 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ARG cc_start: 0.7293 (mmp-170) cc_final: 0.7079 (mmp-170) REVERT: A 195 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.6643 (mpt) REVERT: A 200 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.8071 (mp10) REVERT: A 237 GLN cc_start: 0.8716 (tp-100) cc_final: 0.8350 (tp-100) REVERT: A 248 ARG cc_start: 0.8800 (tpp-160) cc_final: 0.8515 (tpp80) REVERT: B 298 ARG cc_start: 0.8599 (mtm110) cc_final: 0.8308 (mtm110) REVERT: C 77 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8258 (tm-30) REVERT: C 144 MET cc_start: 0.7315 (pmm) cc_final: 0.7070 (pmm) REVERT: C 296 LEU cc_start: 0.8399 (tp) cc_final: 0.8178 (tm) REVERT: C 298 ARG cc_start: 0.7727 (pmt100) cc_final: 0.7500 (pmt100) REVERT: C 315 MET cc_start: 0.7830 (mpt) cc_final: 0.7601 (mpt) REVERT: D 70 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7898 (pm20) REVERT: D 237 GLN cc_start: 0.8661 (pp30) cc_final: 0.8313 (pp30) REVERT: D 241 GLN cc_start: 0.9099 (pt0) cc_final: 0.8581 (pt0) REVERT: D 296 LEU cc_start: 0.8615 (tp) cc_final: 0.8394 (tp) REVERT: E 120 PHE cc_start: 0.7378 (p90) cc_final: 0.7117 (p90) REVERT: E 124 ARG cc_start: 0.5266 (tpp-160) cc_final: 0.4775 (tpp-160) REVERT: E 248 ARG cc_start: 0.8289 (ttp80) cc_final: 0.7665 (ttm-80) REVERT: F 124 ARG cc_start: 0.4206 (tpm170) cc_final: 0.3551 (tpm170) REVERT: F 144 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8219 (pmm) REVERT: F 190 ASN cc_start: 0.7858 (p0) cc_final: 0.7587 (p0) REVERT: F 195 MET cc_start: 0.7825 (mtt) cc_final: 0.7187 (mtt) REVERT: F 204 GLU cc_start: 0.8064 (pm20) cc_final: 0.7705 (pm20) REVERT: F 225 ASP cc_start: 0.8354 (t70) cc_final: 0.8060 (t0) REVERT: F 296 LEU cc_start: 0.8111 (mm) cc_final: 0.7857 (mm) outliers start: 51 outliers final: 24 residues processed: 222 average time/residue: 1.1659 time to fit residues: 285.1996 Evaluate side-chains 209 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 1.479 ------------------------------------------------------------------------------- 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 219 MET 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 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 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 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: 5.9990 chunk 97 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 chunk 109 optimal weight: 0.1980 chunk 7 optimal weight: 5.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- 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** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN ** F 132 HIS ** 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 = 0.4033 r_free = 0.4033 target = 0.142276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.109993 restraints weight = 25738.486| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 3.52 r_work: 0.3450 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14021 Z= 0.210 Angle : 0.634 10.416 18869 Z= 0.320 Chirality : 0.046 0.179 2172 Planarity : 0.004 0.069 2434 Dihedral : 6.064 131.088 1959 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.95 % Allowed : 15.86 % Favored : 80.20 % 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: -0.05 (0.20), residues: 1744 helix: 0.40 (0.18), residues: 836 sheet: -0.57 (0.28), residues: 312 loop : -0.06 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 132 PHE 0.017 0.002 PHE B 120 TYR 0.019 0.002 TYR D 185 ARG 0.010 0.000 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.03810 ( 675) hydrogen bonds : angle 4.77980 ( 1878) covalent geometry : bond 0.00492 (14021) covalent geometry : angle 0.63363 (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 256 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 196 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.6691 (mpt) REVERT: A 200 GLN cc_start: 0.8424 (mp10) cc_final: 0.7937 (mp10) REVERT: A 236 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7790 (mp10) REVERT: A 237 GLN cc_start: 0.8725 (tp-100) cc_final: 0.8360 (tp-100) REVERT: A 248 ARG cc_start: 0.8809 (tpp-160) cc_final: 0.8539 (tpp80) REVERT: B 33 GLN cc_start: 0.8960 (tp-100) cc_final: 0.8644 (pp30) REVERT: B 124 ARG cc_start: 0.8774 (ttm-80) cc_final: 0.8517 (mmt180) REVERT: B 200 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8642 (mm-40) REVERT: B 298 ARG cc_start: 0.8566 (mtm110) cc_final: 0.8275 (mtm110) REVERT: C 66 GLU cc_start: 0.8621 (mp0) cc_final: 0.8360 (mp0) REVERT: C 124 ARG cc_start: 0.8081 (mmm160) cc_final: 0.7697 (mmm160) REVERT: C 130 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7586 (tpt) REVERT: C 315 MET cc_start: 0.7864 (mpt) cc_final: 0.7637 (mpt) REVERT: D 118 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7186 (tm-30) REVERT: D 237 GLN cc_start: 0.8658 (pp30) cc_final: 0.8265 (pp30) REVERT: D 241 GLN cc_start: 0.9105 (pt0) cc_final: 0.8579 (pt0) REVERT: D 296 LEU cc_start: 0.8666 (tp) cc_final: 0.8448 (tp) REVERT: E 53 HIS cc_start: 0.8132 (t70) cc_final: 0.7839 (m90) REVERT: E 120 PHE cc_start: 0.7459 (p90) cc_final: 0.7011 (p90) REVERT: E 124 ARG cc_start: 0.5194 (tpp-160) cc_final: 0.4762 (tpp-160) REVERT: E 180 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7881 (tp) REVERT: E 248 ARG cc_start: 0.8281 (ttp80) cc_final: 0.7669 (tmm-80) REVERT: F 111 ILE cc_start: 0.8876 (mm) cc_final: 0.8675 (mm) REVERT: F 124 ARG cc_start: 0.4263 (tpm170) cc_final: 0.3537 (tpm170) REVERT: F 135 CYS cc_start: 0.8272 (m) cc_final: 0.7960 (m) REVERT: F 143 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8364 (pp20) REVERT: F 144 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.7971 (pmm) REVERT: F 190 ASN cc_start: 0.7830 (p0) cc_final: 0.7548 (p0) REVERT: F 204 GLU cc_start: 0.8008 (pm20) cc_final: 0.7657 (pm20) REVERT: F 225 ASP cc_start: 0.8416 (t70) cc_final: 0.8099 (t0) REVERT: F 241 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8482 (tm-30) outliers start: 60 outliers final: 27 residues processed: 234 average time/residue: 1.1851 time to fit residues: 304.9771 Evaluate side-chains 212 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 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 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 114 MET 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 D residue 17 LEU 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 116 ILE Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 180 LEU 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: 3.9990 chunk 35 optimal weight: 0.9990 chunk 138 optimal weight: 0.6980 chunk 88 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 ASN B 167 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** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.144632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.112973 restraints weight = 25640.760| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 3.50 r_work: 0.3491 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14021 Z= 0.131 Angle : 0.586 11.520 18869 Z= 0.292 Chirality : 0.043 0.175 2172 Planarity : 0.003 0.035 2434 Dihedral : 5.731 129.558 1959 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.49 % Allowed : 17.43 % Favored : 79.08 % 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: 0.29 (0.21), residues: 1744 helix: 0.74 (0.18), residues: 824 sheet: -0.47 (0.29), residues: 310 loop : 0.05 (0.27), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 132 PHE 0.015 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 0.03216 ( 675) hydrogen bonds : angle 4.47725 ( 1878) covalent geometry : bond 0.00297 (14021) covalent geometry : angle 0.58561 (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 255 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 202 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.8099 (mtt) REVERT: A 195 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.6719 (mpt) REVERT: A 236 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7883 (mp10) REVERT: A 237 GLN cc_start: 0.8732 (tp-100) cc_final: 0.8368 (tp-100) REVERT: A 248 ARG cc_start: 0.8822 (tpp-160) cc_final: 0.8561 (tpp80) REVERT: B 200 GLN cc_start: 0.8872 (mm-40) cc_final: 0.8661 (mm-40) REVERT: B 248 ARG cc_start: 0.8313 (ttt180) cc_final: 0.7886 (ttt180) REVERT: B 298 ARG cc_start: 0.8573 (mtm110) cc_final: 0.8323 (mtm110) REVERT: C 66 GLU cc_start: 0.8639 (mp0) cc_final: 0.8360 (mp0) REVERT: C 124 ARG cc_start: 0.8025 (mmm160) cc_final: 0.7764 (mmm160) REVERT: C 130 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7566 (tpt) REVERT: C 144 MET cc_start: 0.7231 (pmm) cc_final: 0.6983 (pmm) REVERT: C 298 ARG cc_start: 0.7811 (pmt100) cc_final: 0.7604 (pmt100) REVERT: D 66 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7787 (tm-30) REVERT: D 70 GLU cc_start: 0.8327 (pm20) cc_final: 0.7895 (pm20) REVERT: D 118 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7814 (tm-30) REVERT: D 190 ASN cc_start: 0.7389 (m110) cc_final: 0.7006 (p0) REVERT: D 237 GLN cc_start: 0.8678 (pp30) cc_final: 0.8316 (pp30) REVERT: D 241 GLN cc_start: 0.9058 (pt0) cc_final: 0.8550 (pt0) REVERT: D 296 LEU cc_start: 0.8621 (tp) cc_final: 0.8402 (tp) REVERT: E 53 HIS cc_start: 0.8032 (t70) cc_final: 0.7800 (m90) REVERT: E 104 ASP cc_start: 0.8069 (m-30) cc_final: 0.7800 (m-30) REVERT: E 120 PHE cc_start: 0.7471 (p90) cc_final: 0.7040 (p90) REVERT: E 124 ARG cc_start: 0.4993 (tpp-160) cc_final: 0.0685 (tpt-90) REVERT: E 180 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7803 (tp) REVERT: E 195 MET cc_start: 0.7843 (mtt) cc_final: 0.7245 (mtt) REVERT: E 248 ARG cc_start: 0.8248 (ttp80) cc_final: 0.7659 (tmm-80) REVERT: F 124 ARG cc_start: 0.4360 (tpm170) cc_final: 0.3632 (tpm170) REVERT: F 135 CYS cc_start: 0.8153 (m) cc_final: 0.7849 (m) REVERT: F 143 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8332 (pp20) REVERT: F 190 ASN cc_start: 0.7738 (p0) cc_final: 0.7445 (p0) REVERT: F 204 GLU cc_start: 0.7955 (pm20) cc_final: 0.7610 (pm20) REVERT: F 225 ASP cc_start: 0.8469 (t70) cc_final: 0.8167 (t0) REVERT: F 296 LEU cc_start: 0.8135 (mm) cc_final: 0.7734 (mm) outliers start: 53 outliers final: 19 residues processed: 236 average time/residue: 1.1604 time to fit residues: 302.2578 Evaluate side-chains 215 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR 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 A residue 315 MET 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 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 D residue 49 THR Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 196 GLU 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 116 ILE Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 180 LEU 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: 0.9990 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 0.0970 chunk 30 optimal weight: 9.9990 chunk 162 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 115 optimal weight: 0.0070 chunk 74 optimal weight: 0.9990 overall best weight: 0.6202 ------------------------------------------------------------------------------- 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** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.145590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.114275 restraints weight = 25703.579| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 3.49 r_work: 0.3510 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14021 Z= 0.116 Angle : 0.577 11.994 18869 Z= 0.285 Chirality : 0.043 0.156 2172 Planarity : 0.003 0.059 2434 Dihedral : 5.586 129.031 1959 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.29 % Allowed : 19.01 % Favored : 77.70 % 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: 0.42 (0.21), residues: 1744 helix: 0.83 (0.18), residues: 828 sheet: -0.42 (0.29), residues: 308 loop : 0.13 (0.27), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 132 PHE 0.025 0.001 PHE B 123 TYR 0.025 0.001 TYR D 185 ARG 0.006 0.000 ARG B 124 Details of bonding type rmsd hydrogen bonds : bond 0.02989 ( 675) hydrogen bonds : angle 4.35564 ( 1878) covalent geometry : bond 0.00267 (14021) covalent geometry : angle 0.57669 (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 243 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 193 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.6612 (mpt) REVERT: A 236 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7773 (mp10) REVERT: A 237 GLN cc_start: 0.8716 (tp-100) cc_final: 0.8354 (tp-100) REVERT: A 248 ARG cc_start: 0.8811 (tpp-160) cc_final: 0.8535 (tpp80) REVERT: B 33 GLN cc_start: 0.8829 (tp40) cc_final: 0.8547 (pp30) REVERT: B 200 GLN cc_start: 0.8864 (mm-40) cc_final: 0.8620 (mm-40) REVERT: B 248 ARG cc_start: 0.8349 (ttt180) cc_final: 0.7990 (ttt180) REVERT: B 298 ARG cc_start: 0.8542 (mtm110) cc_final: 0.8302 (mtm110) REVERT: C 56 LYS cc_start: 0.7429 (mmpt) cc_final: 0.7107 (mttt) REVERT: C 66 GLU cc_start: 0.8651 (mp0) cc_final: 0.8327 (mp0) REVERT: C 124 ARG cc_start: 0.7924 (mmm160) cc_final: 0.7612 (mmm160) REVERT: C 144 MET cc_start: 0.7192 (pmm) cc_final: 0.6943 (pmm) REVERT: C 192 GLU cc_start: 0.8314 (mp0) cc_final: 0.8103 (mp0) REVERT: C 261 ASN cc_start: 0.8496 (t0) cc_final: 0.8289 (t0) REVERT: C 298 ARG cc_start: 0.7850 (pmt100) cc_final: 0.7581 (pmt100) REVERT: C 315 MET cc_start: 0.7634 (mpt) cc_final: 0.7429 (mpt) REVERT: D 66 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7669 (tm-30) REVERT: D 70 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7940 (pm20) REVERT: D 118 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7875 (tm-30) REVERT: D 234 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8069 (tm-30) REVERT: D 237 GLN cc_start: 0.8683 (pp30) cc_final: 0.8293 (pp30) REVERT: D 241 GLN cc_start: 0.9039 (pt0) cc_final: 0.8490 (pt0) REVERT: D 296 LEU cc_start: 0.8619 (tp) cc_final: 0.8394 (tp) REVERT: E 53 HIS cc_start: 0.8016 (t70) cc_final: 0.7790 (m90) REVERT: E 104 ASP cc_start: 0.8022 (m-30) cc_final: 0.7722 (m-30) REVERT: E 120 PHE cc_start: 0.7439 (p90) cc_final: 0.7015 (p90) REVERT: E 124 ARG cc_start: 0.4785 (tpp-160) cc_final: 0.0654 (tpt170) REVERT: E 199 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8413 (mp0) REVERT: E 248 ARG cc_start: 0.8210 (ttp80) cc_final: 0.7582 (tmm-80) REVERT: E 261 ASN cc_start: 0.8674 (t0) cc_final: 0.8407 (t0) REVERT: F 124 ARG cc_start: 0.4394 (tpm170) cc_final: 0.3673 (tpm170) REVERT: F 135 CYS cc_start: 0.8035 (m) cc_final: 0.7727 (m) REVERT: F 143 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8296 (pp20) REVERT: F 190 ASN cc_start: 0.7664 (p0) cc_final: 0.7396 (p0) REVERT: F 204 GLU cc_start: 0.7941 (pm20) cc_final: 0.7624 (pm20) REVERT: F 225 ASP cc_start: 0.8430 (t70) cc_final: 0.8129 (t0) REVERT: F 296 LEU cc_start: 0.8216 (mm) cc_final: 0.7848 (mm) outliers start: 50 outliers final: 21 residues processed: 227 average time/residue: 1.1648 time to fit residues: 291.1432 Evaluate side-chains 216 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 1.442 ------------------------------------------------------------------------------- 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 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 232 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 114 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 D residue 19 VAL 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 329 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 199 GLU 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: 0.9990 chunk 83 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 148 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN ** 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** ** 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** F 237 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.145397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.113881 restraints weight = 25747.505| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 3.51 r_work: 0.3506 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2474 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= 0.126 Angle : 0.584 12.028 18869 Z= 0.289 Chirality : 0.043 0.157 2172 Planarity : 0.003 0.038 2434 Dihedral : 5.549 130.117 1959 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.36 % Allowed : 19.93 % Favored : 76.71 % 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: 0.49 (0.21), residues: 1744 helix: 0.92 (0.18), residues: 824 sheet: -0.38 (0.29), residues: 310 loop : 0.13 (0.27), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 132 PHE 0.029 0.001 PHE B 123 TYR 0.007 0.001 TYR E 94 ARG 0.009 0.000 ARG B 90 Details of bonding type rmsd hydrogen bonds : bond 0.02993 ( 675) hydrogen bonds : angle 4.32577 ( 1878) covalent geometry : bond 0.00292 (14021) covalent geometry : angle 0.58363 (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 240 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 189 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLN cc_start: 0.8527 (pt0) cc_final: 0.8104 (pp30) REVERT: A 195 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.6673 (mpt) REVERT: A 236 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7831 (mp10) REVERT: A 237 GLN cc_start: 0.8737 (tp-100) cc_final: 0.8380 (tp-100) REVERT: A 248 ARG cc_start: 0.8797 (tpp-160) cc_final: 0.8541 (tpp80) REVERT: A 326 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7611 (pp20) REVERT: B 200 GLN cc_start: 0.8864 (mm-40) cc_final: 0.8629 (mm-40) REVERT: C 56 LYS cc_start: 0.7417 (mmpt) cc_final: 0.7145 (mtmm) REVERT: C 66 GLU cc_start: 0.8646 (mp0) cc_final: 0.8322 (mp0) REVERT: C 94 TYR cc_start: 0.5992 (m-10) cc_final: 0.5778 (m-10) REVERT: C 124 ARG cc_start: 0.7991 (mmm160) cc_final: 0.7627 (mmm160) REVERT: C 144 MET cc_start: 0.7267 (pmm) cc_final: 0.7024 (pmm) REVERT: C 192 GLU cc_start: 0.8344 (mp0) cc_final: 0.8101 (mp0) REVERT: C 261 ASN cc_start: 0.8512 (t0) cc_final: 0.8303 (t0) REVERT: C 298 ARG cc_start: 0.7831 (pmt100) cc_final: 0.7585 (pmt100) REVERT: D 70 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.8024 (pm20) REVERT: D 118 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7922 (tm-30) REVERT: D 234 GLU cc_start: 0.8326 (tm-30) cc_final: 0.8061 (tm-30) REVERT: D 237 GLN cc_start: 0.8695 (pp30) cc_final: 0.8293 (pp30) REVERT: D 241 GLN cc_start: 0.9037 (pt0) cc_final: 0.8540 (pt0) REVERT: D 296 LEU cc_start: 0.8655 (tp) cc_final: 0.8446 (tp) REVERT: E 53 HIS cc_start: 0.7899 (t70) cc_final: 0.7692 (m90) REVERT: E 104 ASP cc_start: 0.8021 (m-30) cc_final: 0.7738 (m-30) REVERT: E 120 PHE cc_start: 0.7459 (p90) cc_final: 0.7065 (p90) REVERT: E 124 ARG cc_start: 0.4942 (tpp-160) cc_final: 0.0776 (tpt170) REVERT: E 248 ARG cc_start: 0.8204 (ttp80) cc_final: 0.7546 (tmm-80) REVERT: E 261 ASN cc_start: 0.8672 (t0) cc_final: 0.8390 (t0) REVERT: F 124 ARG cc_start: 0.4379 (tpm170) cc_final: 0.3659 (tpm170) REVERT: F 135 CYS cc_start: 0.8022 (m) cc_final: 0.7698 (m) REVERT: F 143 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8304 (pp20) REVERT: F 190 ASN cc_start: 0.7688 (p0) cc_final: 0.7408 (p0) REVERT: F 204 GLU cc_start: 0.7945 (pm20) cc_final: 0.7636 (pm20) REVERT: F 225 ASP cc_start: 0.8422 (t70) cc_final: 0.8118 (t0) REVERT: F 296 LEU cc_start: 0.8241 (mm) cc_final: 0.7866 (mm) outliers start: 51 outliers final: 23 residues processed: 226 average time/residue: 1.1858 time to fit residues: 294.1209 Evaluate side-chains 211 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 1.435 ------------------------------------------------------------------------------- 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 195 MET Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain A residue 326 GLU 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 104 optimal weight: 1.9990 chunk 171 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 149 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN ** 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** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.145493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.114205 restraints weight = 25737.143| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 3.41 r_work: 0.3514 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14021 Z= 0.126 Angle : 0.601 12.629 18869 Z= 0.297 Chirality : 0.043 0.155 2172 Planarity : 0.003 0.035 2434 Dihedral : 5.503 129.801 1959 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.09 % Allowed : 20.79 % Favored : 76.12 % 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: 0.48 (0.21), residues: 1744 helix: 0.92 (0.18), residues: 828 sheet: -0.39 (0.29), residues: 308 loop : 0.11 (0.27), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 132 PHE 0.031 0.001 PHE B 123 TYR 0.030 0.001 TYR D 185 ARG 0.007 0.000 ARG B 90 Details of bonding type rmsd hydrogen bonds : bond 0.02971 ( 675) hydrogen bonds : angle 4.29260 ( 1878) covalent geometry : bond 0.00294 (14021) covalent geometry : angle 0.60083 (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 240 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 193 time to evaluate : 1.656 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: 0.8535 (pt0) cc_final: 0.8090 (pp30) REVERT: A 195 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.6729 (mpt) REVERT: A 236 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7852 (mp10) REVERT: A 237 GLN cc_start: 0.8731 (tp-100) cc_final: 0.8376 (tp-100) REVERT: A 248 ARG cc_start: 0.8801 (tpp-160) cc_final: 0.8582 (tpp80) REVERT: A 326 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7626 (pp20) REVERT: B 33 GLN cc_start: 0.8816 (tp40) cc_final: 0.8523 (pp30) REVERT: B 200 GLN cc_start: 0.8852 (mm-40) cc_final: 0.8607 (mm-40) REVERT: B 298 ARG cc_start: 0.8575 (mtm110) cc_final: 0.8111 (mtm110) REVERT: C 66 GLU cc_start: 0.8646 (mp0) cc_final: 0.8301 (mp0) REVERT: C 94 TYR cc_start: 0.5969 (m-10) cc_final: 0.5733 (m-10) REVERT: C 124 ARG cc_start: 0.7999 (mmm160) cc_final: 0.7618 (mmm160) REVERT: C 130 MET cc_start: 0.7694 (tpt) cc_final: 0.7104 (tpp) REVERT: C 144 MET cc_start: 0.7296 (pmm) cc_final: 0.7044 (pmm) REVERT: C 192 GLU cc_start: 0.8335 (mp0) cc_final: 0.8109 (mp0) REVERT: C 261 ASN cc_start: 0.8507 (t0) cc_final: 0.8296 (t0) REVERT: C 298 ARG cc_start: 0.7824 (pmt100) cc_final: 0.7584 (pmt100) REVERT: D 66 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7921 (tp30) REVERT: D 118 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7900 (tm-30) REVERT: D 190 ASN cc_start: 0.7282 (m-40) cc_final: 0.6912 (p0) REVERT: D 199 GLU cc_start: 0.7681 (pp20) cc_final: 0.7476 (pt0) REVERT: D 234 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7893 (tm-30) REVERT: D 237 GLN cc_start: 0.8699 (pp30) cc_final: 0.8215 (pp30) REVERT: D 241 GLN cc_start: 0.9024 (pt0) cc_final: 0.8461 (pt0) REVERT: D 296 LEU cc_start: 0.8658 (tp) cc_final: 0.8445 (tp) REVERT: E 53 HIS cc_start: 0.7904 (t70) cc_final: 0.7691 (m90) REVERT: E 104 ASP cc_start: 0.8004 (m-30) cc_final: 0.7701 (m-30) REVERT: E 120 PHE cc_start: 0.7453 (p90) cc_final: 0.7060 (p90) REVERT: E 124 ARG cc_start: 0.4939 (tpp-160) cc_final: 0.0785 (tpt170) REVERT: E 248 ARG cc_start: 0.8240 (ttp80) cc_final: 0.7775 (tmm-80) REVERT: E 261 ASN cc_start: 0.8661 (t0) cc_final: 0.8376 (t0) REVERT: F 124 ARG cc_start: 0.4497 (tpm170) cc_final: 0.3791 (tpm170) REVERT: F 135 CYS cc_start: 0.8015 (m) cc_final: 0.7685 (m) REVERT: F 143 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8271 (pp20) REVERT: F 190 ASN cc_start: 0.7640 (p0) cc_final: 0.7350 (p0) REVERT: F 204 GLU cc_start: 0.7944 (pm20) cc_final: 0.7641 (pm20) REVERT: F 225 ASP cc_start: 0.8416 (t70) cc_final: 0.8123 (t0) REVERT: F 252 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7352 (mt-10) outliers start: 47 outliers final: 27 residues processed: 227 average time/residue: 1.1448 time to fit residues: 286.1257 Evaluate side-chains 222 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 1.444 ------------------------------------------------------------------------------- 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 195 MET Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain A residue 326 GLU 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 B residue 293 THR 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 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 329 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 252 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 68 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 117 optimal weight: 7.9990 chunk 66 optimal weight: 0.5980 chunk 104 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 163 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 173 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 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** ** 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 = 0.4077 r_free = 0.4077 target = 0.145638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.114468 restraints weight = 25739.232| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 3.48 r_work: 0.3518 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14021 Z= 0.123 Angle : 0.607 13.123 18869 Z= 0.299 Chirality : 0.043 0.152 2172 Planarity : 0.003 0.035 2434 Dihedral : 5.462 129.353 1959 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.03 % Allowed : 20.66 % Favored : 76.32 % 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: 0.96 (0.19), residues: 831 sheet: -0.41 (0.29), residues: 309 loop : 0.12 (0.27), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 132 PHE 0.039 0.001 PHE B 123 TYR 0.017 0.001 TYR F 185 ARG 0.006 0.000 ARG B 90 Details of bonding type rmsd hydrogen bonds : bond 0.02914 ( 675) hydrogen bonds : angle 4.28115 ( 1878) covalent geometry : bond 0.00289 (14021) covalent geometry : angle 0.60673 (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 239 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLN cc_start: 0.8537 (pt0) cc_final: 0.8091 (pp30) REVERT: A 195 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.6792 (mpt) REVERT: A 200 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7736 (mp10) REVERT: A 237 GLN cc_start: 0.8723 (tp-100) cc_final: 0.8362 (tp-100) REVERT: A 248 ARG cc_start: 0.8785 (tpp-160) cc_final: 0.8564 (tpp80) REVERT: A 326 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7629 (pp20) REVERT: B 33 GLN cc_start: 0.8820 (tp40) cc_final: 0.8551 (pp30) REVERT: B 200 GLN cc_start: 0.8881 (mm-40) cc_final: 0.8660 (mm-40) REVERT: B 298 ARG cc_start: 0.8569 (mtm110) cc_final: 0.8157 (mtm110) REVERT: C 56 LYS cc_start: 0.7473 (mmpt) cc_final: 0.7208 (mtmt) REVERT: C 66 GLU cc_start: 0.8663 (mp0) cc_final: 0.8337 (mp0) REVERT: C 94 TYR cc_start: 0.5952 (m-10) cc_final: 0.5716 (m-10) REVERT: C 124 ARG cc_start: 0.8029 (mmm160) cc_final: 0.7595 (mmm160) REVERT: C 144 MET cc_start: 0.7296 (pmm) cc_final: 0.7084 (pmm) REVERT: C 192 GLU cc_start: 0.8368 (mp0) cc_final: 0.8160 (mp0) REVERT: C 261 ASN cc_start: 0.8511 (t0) cc_final: 0.8302 (t0) REVERT: C 298 ARG cc_start: 0.7838 (pmt100) cc_final: 0.7611 (pmt100) REVERT: D 70 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7852 (pm20) REVERT: D 118 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7875 (tm-30) REVERT: D 190 ASN cc_start: 0.7288 (m-40) cc_final: 0.7064 (p0) REVERT: D 209 ASP cc_start: 0.7561 (m-30) cc_final: 0.7227 (t70) REVERT: D 234 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7885 (tm-30) REVERT: D 237 GLN cc_start: 0.8686 (pp30) cc_final: 0.8234 (pp30) REVERT: D 241 GLN cc_start: 0.8998 (pt0) cc_final: 0.8486 (pt0) REVERT: D 296 LEU cc_start: 0.8649 (tp) cc_final: 0.8438 (tp) REVERT: E 53 HIS cc_start: 0.7904 (t70) cc_final: 0.7697 (m90) REVERT: E 104 ASP cc_start: 0.8013 (m-30) cc_final: 0.7695 (m-30) REVERT: E 120 PHE cc_start: 0.7424 (p90) cc_final: 0.7014 (p90) REVERT: E 124 ARG cc_start: 0.4946 (tpp-160) cc_final: 0.0780 (tpt170) REVERT: E 248 ARG cc_start: 0.8212 (ttp80) cc_final: 0.7761 (tmm-80) REVERT: F 124 ARG cc_start: 0.4426 (tpm170) cc_final: 0.3733 (tpm170) REVERT: F 135 CYS cc_start: 0.8033 (m) cc_final: 0.7712 (m) REVERT: F 143 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8300 (pp20) REVERT: F 190 ASN cc_start: 0.7654 (p0) cc_final: 0.7350 (p0) REVERT: F 204 GLU cc_start: 0.7980 (pm20) cc_final: 0.7675 (pm20) REVERT: F 225 ASP cc_start: 0.8488 (t70) cc_final: 0.8219 (t0) REVERT: F 296 LEU cc_start: 0.8139 (mm) cc_final: 0.7770 (mm) outliers start: 46 outliers final: 27 residues processed: 223 average time/residue: 1.2039 time to fit residues: 294.7788 Evaluate side-chains 216 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 1.456 ------------------------------------------------------------------------------- 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 195 MET Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain A residue 326 GLU 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 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 116 ILE Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 252 GLU 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: 0.7980 chunk 100 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 92 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN ** A 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 ASN ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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** F 237 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.145479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.114144 restraints weight = 25689.290| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 3.49 r_work: 0.3513 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14021 Z= 0.131 Angle : 0.620 13.418 18869 Z= 0.307 Chirality : 0.043 0.162 2172 Planarity : 0.003 0.042 2434 Dihedral : 5.469 130.357 1959 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.89 % Allowed : 20.79 % Favored : 76.32 % 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: 0.99 (0.19), residues: 826 sheet: -0.44 (0.29), residues: 314 loop : 0.09 (0.27), residues: 604 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 0.028 0.001 TYR D 185 ARG 0.006 0.000 ARG B 124 Details of bonding type rmsd hydrogen bonds : bond 0.02984 ( 675) hydrogen bonds : angle 4.30341 ( 1878) covalent geometry : bond 0.00310 (14021) covalent geometry : angle 0.62001 (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 237 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 193 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLN cc_start: 0.8537 (pt0) cc_final: 0.8091 (pp30) REVERT: A 195 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.6795 (mpt) REVERT: A 237 GLN cc_start: 0.8730 (tp-100) cc_final: 0.8369 (tp-100) REVERT: A 248 ARG cc_start: 0.8790 (tpp-160) cc_final: 0.8578 (tpp80) REVERT: A 326 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7625 (pp20) REVERT: B 200 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8641 (mm-40) REVERT: B 298 ARG cc_start: 0.8585 (mtm110) cc_final: 0.8270 (mtm110) REVERT: C 56 LYS cc_start: 0.7477 (mmpt) cc_final: 0.7200 (mtmt) REVERT: C 66 GLU cc_start: 0.8657 (mp0) cc_final: 0.8323 (mp0) REVERT: C 94 TYR cc_start: 0.5967 (m-10) cc_final: 0.5726 (m-10) REVERT: C 124 ARG cc_start: 0.7987 (mmm160) cc_final: 0.7603 (mmm160) REVERT: C 144 MET cc_start: 0.7294 (pmm) cc_final: 0.7091 (pmm) REVERT: C 192 GLU cc_start: 0.8377 (mp0) cc_final: 0.8166 (mp0) REVERT: C 261 ASN cc_start: 0.8533 (t0) cc_final: 0.8333 (t0) REVERT: C 298 ARG cc_start: 0.7819 (pmt100) cc_final: 0.7611 (pmt100) REVERT: D 66 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7737 (tm-30) REVERT: D 190 ASN cc_start: 0.7358 (m-40) cc_final: 0.7125 (p0) REVERT: D 234 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7897 (tm-30) REVERT: D 237 GLN cc_start: 0.8691 (pp30) cc_final: 0.8216 (pp30) REVERT: D 241 GLN cc_start: 0.9008 (pt0) cc_final: 0.8495 (pt0) REVERT: D 296 LEU cc_start: 0.8650 (tp) cc_final: 0.8434 (tp) REVERT: E 53 HIS cc_start: 0.7899 (t70) cc_final: 0.7688 (m90) REVERT: E 104 ASP cc_start: 0.8004 (m-30) cc_final: 0.7684 (m-30) REVERT: E 120 PHE cc_start: 0.7444 (p90) cc_final: 0.6998 (p90) REVERT: E 124 ARG cc_start: 0.4976 (tpp-160) cc_final: 0.4263 (tpp-160) REVERT: E 248 ARG cc_start: 0.8231 (ttp80) cc_final: 0.7768 (tmm-80) REVERT: E 261 ASN cc_start: 0.8492 (t0) cc_final: 0.8230 (t0) REVERT: F 124 ARG cc_start: 0.4446 (tpm170) cc_final: 0.3756 (tpm170) REVERT: F 135 CYS cc_start: 0.8029 (m) cc_final: 0.7713 (m) REVERT: F 143 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8286 (pp20) REVERT: F 190 ASN cc_start: 0.7747 (p0) cc_final: 0.7390 (p0) REVERT: F 196 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7698 (tm-30) REVERT: F 204 GLU cc_start: 0.7958 (pm20) cc_final: 0.7661 (pm20) REVERT: F 225 ASP cc_start: 0.8515 (t70) cc_final: 0.8220 (t0) REVERT: F 252 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7407 (mt-10) REVERT: F 296 LEU cc_start: 0.8162 (mm) cc_final: 0.7790 (mm) outliers start: 44 outliers final: 28 residues processed: 221 average time/residue: 1.2456 time to fit residues: 301.9484 Evaluate side-chains 212 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 1.540 ------------------------------------------------------------------------------- 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 195 MET Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain A residue 326 GLU 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 B residue 293 THR 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 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 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 252 GLU 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: 0.0970 chunk 79 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 chunk 117 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 116 optimal weight: 7.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 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** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.145292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.114094 restraints weight = 25886.946| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 3.43 r_work: 0.3514 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14021 Z= 0.136 Angle : 0.635 13.391 18869 Z= 0.316 Chirality : 0.044 0.177 2172 Planarity : 0.003 0.036 2434 Dihedral : 5.495 131.320 1959 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.50 % Allowed : 21.32 % 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: 0.47 (0.21), residues: 1744 helix: 0.93 (0.18), residues: 841 sheet: -0.44 (0.29), residues: 315 loop : 0.08 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 132 PHE 0.033 0.001 PHE B 123 TYR 0.018 0.001 TYR F 185 ARG 0.007 0.000 ARG E 298 Details of bonding type rmsd hydrogen bonds : bond 0.03034 ( 675) hydrogen bonds : angle 4.36471 ( 1878) covalent geometry : bond 0.00324 (14021) covalent geometry : angle 0.63543 (18869) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10806.22 seconds wall clock time: 187 minutes 1.20 seconds (11221.20 seconds total)