Starting phenix.real_space_refine on Thu Jul 31 00:19:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7osj_13053/07_2025/7osj_13053.cif Found real_map, /net/cci-nas-00/data/ceres_data/7osj_13053/07_2025/7osj_13053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7osj_13053/07_2025/7osj_13053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7osj_13053/07_2025/7osj_13053.map" model { file = "/net/cci-nas-00/data/ceres_data/7osj_13053/07_2025/7osj_13053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7osj_13053/07_2025/7osj_13053.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 Cu 1 5.60 5 Mg 1 5.21 5 S 45 5.16 5 C 8217 2.51 5 N 2252 2.21 5 O 2336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12853 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3077 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 16, 'TRANS': 375} Chain breaks: 1 Chain: "B" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2375 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 12, 'TRANS': 295} Chain: "C" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2367 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 12, 'TRANS': 294} Chain: "D" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2015 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 8, 'TRANS': 258} Chain breaks: 1 Chain: "E" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1896 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 8, 'TRANS': 239} Chain breaks: 2 Chain: "H" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1119 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 145} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11876 SG CYS H 45 45.635 42.945 48.071 1.00134.07 S ATOM 11899 SG CYS H 48 43.473 44.057 45.660 1.00133.90 S ATOM 12070 SG CYS H 72 46.294 44.996 44.126 1.00133.41 S Time building chain proxies: 8.20, per 1000 atoms: 0.64 Number of scatterers: 12853 At special positions: 0 Unit cell: (80.352, 92.016, 190.512, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Cu 1 28.99 S 45 16.00 Mg 1 11.99 O 2336 8.00 N 2252 7.00 C 8217 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: 3.88 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 72 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 48 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 45 " 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3010 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 13 sheets defined 45.7% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.713A pdb=" N LEU A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TRP A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'A' and resid 392 through 405 removed outlier: 3.696A pdb=" N TRP A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 50 Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 90 through 103 removed outlier: 3.565A pdb=" N LEU B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 107 No H-bonds generated for 'chain 'B' and resid 105 through 107' Processing helix chain 'B' and resid 108 through 116 Processing helix chain 'B' and resid 130 through 141 Processing helix chain 'B' and resid 160 through 178 removed outlier: 3.982A pdb=" N GLN B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG B 177 " --> pdb=" O ARG B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 192 removed outlier: 3.939A pdb=" N VAL B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 219 Processing helix chain 'B' and resid 232 through 238 removed outlier: 4.140A pdb=" N GLN B 238 " --> pdb=" O ASP B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 243 removed outlier: 4.019A pdb=" N ASP B 242 " --> pdb=" O GLN B 238 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 238 through 243' Processing helix chain 'B' and resid 263 through 275 removed outlier: 3.716A pdb=" N LEU B 267 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ARG B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN B 270 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 removed outlier: 3.501A pdb=" N ALA B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.607A pdb=" N MET C 46 " --> pdb=" O LYS C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 74 Processing helix chain 'C' and resid 90 through 102 Processing helix chain 'C' and resid 105 through 109 removed outlier: 3.622A pdb=" N VAL C 109 " --> pdb=" O LEU C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 129 Processing helix chain 'C' and resid 130 through 141 Processing helix chain 'C' and resid 160 through 177 removed outlier: 3.768A pdb=" N GLN C 176 " --> pdb=" O ASP C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 218 removed outlier: 3.504A pdb=" N ALA C 217 " --> pdb=" O SER C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 Processing helix chain 'C' and resid 240 through 244 removed outlier: 3.727A pdb=" N ALA C 243 " --> pdb=" O TRP C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 274 removed outlier: 3.909A pdb=" N LEU C 268 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU C 274 " --> pdb=" O GLN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 removed outlier: 3.536A pdb=" N TYR C 293 " --> pdb=" O ASP C 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 16 removed outlier: 3.578A pdb=" N ILE D 7 " --> pdb=" O GLN D 3 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU D 11 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 42 removed outlier: 3.552A pdb=" N ILE D 24 " --> pdb=" O TRP D 20 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE D 28 " --> pdb=" O ILE D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 75 removed outlier: 3.532A pdb=" N ILE D 55 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA D 56 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE D 64 " --> pdb=" O SER D 60 " (cutoff:3.500A) Proline residue: D 67 - end of helix removed outlier: 3.543A pdb=" N TYR D 75 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 83 Processing helix chain 'D' and resid 85 through 91 removed outlier: 3.737A pdb=" N LEU D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 129 removed outlier: 4.066A pdb=" N LYS D 104 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU D 112 " --> pdb=" O HIS D 108 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 168 removed outlier: 3.580A pdb=" N SER D 149 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR D 151 " --> pdb=" O MET D 147 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL D 168 " --> pdb=" O LEU D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 188 removed outlier: 3.696A pdb=" N GLY D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 200 removed outlier: 3.538A pdb=" N LEU D 194 " --> pdb=" O ASP D 190 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER D 200 " --> pdb=" O LEU D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 215 Processing helix chain 'D' and resid 216 through 226 removed outlier: 3.538A pdb=" N ASN D 225 " --> pdb=" O TYR D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 244 removed outlier: 3.522A pdb=" N SER D 240 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU D 241 " --> pdb=" O VAL D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 273 removed outlier: 3.576A pdb=" N LEU D 252 " --> pdb=" O PRO D 248 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER D 263 " --> pdb=" O TRP D 259 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 7 Processing helix chain 'E' and resid 7 through 16 removed outlier: 3.722A pdb=" N GLU E 11 " --> pdb=" O ILE E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 38 removed outlier: 3.537A pdb=" N ILE E 24 " --> pdb=" O TRP E 20 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA E 36 " --> pdb=" O ALA E 32 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 75 removed outlier: 3.507A pdb=" N ALA E 56 " --> pdb=" O PRO E 52 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET E 66 " --> pdb=" O ALA E 62 " (cutoff:3.500A) Proline residue: E 67 - end of helix removed outlier: 3.573A pdb=" N TYR E 75 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 84 Processing helix chain 'E' and resid 85 through 91 removed outlier: 3.588A pdb=" N LEU E 89 " --> pdb=" O GLY E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 120 removed outlier: 3.706A pdb=" N ILE E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU E 112 " --> pdb=" O HIS E 108 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 129 removed outlier: 3.567A pdb=" N ALA E 126 " --> pdb=" O CYS E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 143 removed outlier: 3.814A pdb=" N LEU E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TRP E 141 " --> pdb=" O GLY E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 168 removed outlier: 3.562A pdb=" N SER E 149 " --> pdb=" O ARG E 145 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE E 157 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL E 168 " --> pdb=" O LEU E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 188 removed outlier: 3.550A pdb=" N GLY E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL E 186 " --> pdb=" O TRP E 182 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 199 Processing helix chain 'E' and resid 208 through 213 Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.578A pdb=" N ILE E 224 " --> pdb=" O ILE E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 272 removed outlier: 4.058A pdb=" N LEU E 252 " --> pdb=" O PRO E 248 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER E 263 " --> pdb=" O TRP E 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 34 removed outlier: 3.787A pdb=" N GLN H 32 " --> pdb=" O GLU H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 55 removed outlier: 3.749A pdb=" N ASP H 54 " --> pdb=" O ILE H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 82 Processing helix chain 'H' and resid 139 through 150 removed outlier: 3.503A pdb=" N GLY H 147 " --> pdb=" O LYS H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 172 removed outlier: 3.678A pdb=" N GLN H 165 " --> pdb=" O GLN H 161 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU H 166 " --> pdb=" O ALA H 162 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47 Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.277A pdb=" N PHE A 56 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLY A 131 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A 135 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE A 162 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ASP A 187 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU A 164 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE A 184 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N MET A 209 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE A 186 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TYR A 204 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ALA A 229 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N VAL A 206 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N MET A 231 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N TYR A 208 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU A 252 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR A 228 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ASN A 254 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU A 230 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N MET A 253 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL A 333 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N HIS A 311 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 73 removed outlier: 5.944A pdb=" N MET A 125 " --> pdb=" O ASP A 148 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE A 147 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL A 177 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N THR A 221 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N SER A 243 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL A 266 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.590A pdb=" N VAL A 90 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL A 142 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 215 through 217 removed outlier: 6.335A pdb=" N LEU A 216 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N SER A 322 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE A 298 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 19 through 25 removed outlier: 5.893A pdb=" N VAL B 9 " --> pdb=" O ASP B 21 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ASN B 23 " --> pdb=" O GLN B 7 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN B 7 " --> pdb=" O ASN B 23 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN B 25 " --> pdb=" O GLU B 5 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLU B 5 " --> pdb=" O ASN B 25 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLN B 59 " --> pdb=" O GLN B 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 79 removed outlier: 7.545A pdb=" N GLY B 77 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ASP B 153 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU B 79 " --> pdb=" O ASP B 153 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU B 150 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N CYS B 184 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 152 " --> pdb=" O CYS B 184 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LEU B 32 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLY B 33 " --> pdb=" O ALA B 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 246 through 248 removed outlier: 3.579A pdb=" N ARG B 248 " --> pdb=" O GLU B 256 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU B 256 " --> pdb=" O ARG B 248 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79 removed outlier: 6.245A pdb=" N GLY C 77 " --> pdb=" O LEU C 151 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ASP C 153 " --> pdb=" O GLY C 77 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU C 79 " --> pdb=" O ASP C 153 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU C 32 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL C 31 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ALA C 199 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLY C 33 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU C 201 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE C 35 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA C 202 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU C 206 " --> pdb=" O ALA C 202 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 246 through 249 removed outlier: 3.807A pdb=" N SER C 246 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 258 " --> pdb=" O SER C 246 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ARG C 248 " --> pdb=" O GLU C 256 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE C 255 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA C 227 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER C 228 " --> pdb=" O ASP C 279 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP C 279 " --> pdb=" O SER C 228 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 69 through 70 Processing sheet with id=AB4, first strand: chain 'H' and resid 119 through 120 500 hydrogen bonds defined for protein. 1407 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: 4.00 Time building geometry restraints manager: 3.74 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: 4065 1.34 - 1.46: 2313 1.46 - 1.58: 6637 1.58 - 1.69: 2 1.69 - 1.81: 77 Bond restraints: 13094 Sorted by residual: bond pdb=" CA ILE E 51 " pdb=" C ILE E 51 " ideal model delta sigma weight residual 1.525 1.587 -0.062 2.10e-02 2.27e+03 8.68e+00 bond pdb=" CA ILE E 51 " pdb=" CB ILE E 51 " ideal model delta sigma weight residual 1.540 1.595 -0.055 2.70e-02 1.37e+03 4.21e+00 bond pdb=" CB VAL A 336 " pdb=" CG1 VAL A 336 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.56e+00 bond pdb=" CB VAL A 202 " pdb=" CG1 VAL A 202 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.28e+00 bond pdb=" CG1 ILE B 181 " pdb=" CD1 ILE B 181 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.27e+00 ... (remaining 13089 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 17449 3.38 - 6.77: 279 6.77 - 10.15: 33 10.15 - 13.53: 5 13.53 - 16.92: 1 Bond angle restraints: 17767 Sorted by residual: angle pdb=" C GLU B 81 " pdb=" N ASN B 82 " pdb=" CA ASN B 82 " ideal model delta sigma weight residual 122.08 129.88 -7.80 1.47e+00 4.63e-01 2.82e+01 angle pdb=" C GLU H 138 " pdb=" N GLU H 139 " pdb=" CA GLU H 139 " ideal model delta sigma weight residual 121.54 130.81 -9.27 1.91e+00 2.74e-01 2.35e+01 angle pdb=" CA LEU A 35 " pdb=" CB LEU A 35 " pdb=" CG LEU A 35 " ideal model delta sigma weight residual 116.30 133.22 -16.92 3.50e+00 8.16e-02 2.34e+01 angle pdb=" C GLN A 247 " pdb=" N ASN A 248 " pdb=" CA ASN A 248 " ideal model delta sigma weight residual 121.54 130.22 -8.68 1.91e+00 2.74e-01 2.07e+01 angle pdb=" N LEU C 188 " pdb=" CA LEU C 188 " pdb=" C LEU C 188 " ideal model delta sigma weight residual 109.81 119.58 -9.77 2.21e+00 2.05e-01 1.95e+01 ... (remaining 17762 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 6876 17.70 - 35.40: 695 35.40 - 53.10: 144 53.10 - 70.79: 29 70.79 - 88.49: 3 Dihedral angle restraints: 7747 sinusoidal: 3030 harmonic: 4717 Sorted by residual: dihedral pdb=" CA GLY B 299 " pdb=" C GLY B 299 " pdb=" N ASP B 300 " pdb=" CA ASP B 300 " ideal model delta harmonic sigma weight residual 180.00 146.95 33.05 0 5.00e+00 4.00e-02 4.37e+01 dihedral pdb=" CA GLU B 305 " pdb=" C GLU B 305 " pdb=" N GLY B 306 " pdb=" CA GLY B 306 " ideal model delta harmonic sigma weight residual 180.00 148.51 31.49 0 5.00e+00 4.00e-02 3.97e+01 dihedral pdb=" CA LEU D 73 " pdb=" C LEU D 73 " pdb=" N ALA D 74 " pdb=" CA ALA D 74 " ideal model delta harmonic sigma weight residual -180.00 -156.90 -23.10 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 7744 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1785 0.089 - 0.177: 221 0.177 - 0.265: 26 0.265 - 0.354: 3 0.354 - 0.442: 3 Chirality restraints: 2038 Sorted by residual: chirality pdb=" CB VAL A 202 " pdb=" CA VAL A 202 " pdb=" CG1 VAL A 202 " pdb=" CG2 VAL A 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.89e+00 chirality pdb=" CB VAL A 413 " pdb=" CA VAL A 413 " pdb=" CG1 VAL A 413 " pdb=" CG2 VAL A 413 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.84e+00 chirality pdb=" CB VAL C 187 " pdb=" CA VAL C 187 " pdb=" CG1 VAL C 187 " pdb=" CG2 VAL C 187 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 2035 not shown) Planarity restraints: 2282 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 35 " 0.076 5.00e-02 4.00e+02 1.18e-01 2.22e+01 pdb=" N PRO H 36 " -0.204 5.00e-02 4.00e+02 pdb=" CA PRO H 36 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO H 36 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 66 " 0.051 5.00e-02 4.00e+02 7.68e-02 9.44e+00 pdb=" N PRO D 67 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 307 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.02e+00 pdb=" C ARG B 307 " 0.052 2.00e-02 2.50e+03 pdb=" O ARG B 307 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU B 308 " -0.018 2.00e-02 2.50e+03 ... (remaining 2279 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 115 2.56 - 3.14: 9116 3.14 - 3.73: 20070 3.73 - 4.31: 28227 4.31 - 4.90: 46395 Nonbonded interactions: 103923 Sorted by model distance: nonbonded pdb=" OE1 GLU H 76 " pdb="ZN ZN H 201 " model vdw 1.972 2.230 nonbonded pdb=" NE2 HIS A 207 " pdb="CU CU A 502 " model vdw 2.003 2.320 nonbonded pdb=" OD2 ASP A 367 " pdb="MG MG A 501 " model vdw 2.113 2.170 nonbonded pdb=" O TRP A 358 " pdb="MG MG A 501 " model vdw 2.118 2.170 nonbonded pdb=" SD MET A 231 " pdb="CU CU A 502 " model vdw 2.187 2.600 ... (remaining 103918 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 'B' and resid 2 through 308) selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 42 or resid 51 through 227 or resid 245 through \ 274)) selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.400 Find NCS groups from input model: 0.390 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:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 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 : 0.006 0.091 13097 Z= 0.293 Angle : 1.047 16.917 17767 Z= 0.556 Chirality : 0.063 0.442 2038 Planarity : 0.007 0.118 2282 Dihedral : 14.561 88.492 4737 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.35 % Favored : 93.59 % Rotamer: Outliers : 0.89 % Allowed : 9.02 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -5.62 (0.14), residues: 1653 helix: -4.46 (0.08), residues: 708 sheet: -3.07 (0.30), residues: 208 loop : -2.98 (0.18), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 20 HIS 0.010 0.002 HIS A 207 PHE 0.018 0.002 PHE B 35 TYR 0.025 0.002 TYR C 291 ARG 0.008 0.001 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.29564 ( 500) hydrogen bonds : angle 10.53021 ( 1407) metal coordination : bond 0.04786 ( 3) covalent geometry : bond 0.00644 (13094) covalent geometry : angle 1.04678 (17767) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ILE cc_start: 0.9581 (mt) cc_final: 0.9130 (pt) REVERT: A 235 LYS cc_start: 0.9320 (mmtt) cc_final: 0.9109 (mmmm) REVERT: A 305 LYS cc_start: 0.8998 (mmtt) cc_final: 0.8594 (mmmt) REVERT: B 57 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7283 (tt0) REVERT: B 86 TYR cc_start: 0.8822 (m-80) cc_final: 0.8470 (m-10) REVERT: C 47 LYS cc_start: 0.9563 (mttt) cc_final: 0.9287 (mmtp) REVERT: C 102 LYS cc_start: 0.9372 (ttmt) cc_final: 0.9161 (ttmm) REVERT: C 203 LYS cc_start: 0.9078 (mmmt) cc_final: 0.8672 (mmmm) REVERT: D 14 ASP cc_start: 0.8999 (t0) cc_final: 0.8761 (t0) REVERT: D 66 MET cc_start: 0.9191 (mmm) cc_final: 0.8749 (mmm) REVERT: D 88 MET cc_start: 0.8512 (tpp) cc_final: 0.8181 (tpp) REVERT: E 76 ASP cc_start: 0.8621 (p0) cc_final: 0.8297 (p0) REVERT: E 81 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8325 (mt-10) REVERT: E 83 GLU cc_start: 0.8292 (mt-10) cc_final: 0.8079 (mt-10) REVERT: E 135 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8492 (tm-30) REVERT: E 138 MET cc_start: 0.7043 (tpt) cc_final: 0.6726 (tmm) REVERT: E 171 LYS cc_start: 0.9281 (tttt) cc_final: 0.8809 (ttmm) REVERT: H 40 HIS cc_start: 0.8557 (m-70) cc_final: 0.8178 (m90) REVERT: H 161 GLN cc_start: 0.8615 (mt0) cc_final: 0.8409 (mt0) outliers start: 12 outliers final: 4 residues processed: 151 average time/residue: 0.3042 time to fit residues: 62.4196 Evaluate side-chains 95 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 84 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 77 GLN ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN A 174 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 ASN A 190 ASN A 212 ASN A 301 ASN A 324 ASN A 417 HIS B 11 GLN B 20 HIS ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 270 GLN C 25 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN D 205 ASN D 225 ASN E 108 HIS E 225 ASN H 161 GLN H 172 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.060005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.046531 restraints weight = 58504.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.048155 restraints weight = 29936.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.049138 restraints weight = 19261.282| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13097 Z= 0.203 Angle : 0.657 7.249 17767 Z= 0.337 Chirality : 0.043 0.152 2038 Planarity : 0.005 0.050 2282 Dihedral : 5.432 56.075 1817 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.12 % Allowed : 13.50 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.17), residues: 1653 helix: -1.98 (0.16), residues: 720 sheet: -2.65 (0.32), residues: 209 loop : -2.59 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 253 HIS 0.005 0.001 HIS B 20 PHE 0.015 0.001 PHE H 71 TYR 0.016 0.001 TYR E 93 ARG 0.003 0.000 ARG H 100 Details of bonding type rmsd hydrogen bonds : bond 0.03816 ( 500) hydrogen bonds : angle 5.11335 ( 1407) metal coordination : bond 0.00458 ( 3) covalent geometry : bond 0.00438 (13094) covalent geometry : angle 0.65692 (17767) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ILE cc_start: 0.9578 (mt) cc_final: 0.9309 (pt) REVERT: A 305 LYS cc_start: 0.8793 (mmtt) cc_final: 0.8439 (mmmt) REVERT: B 184 CYS cc_start: 0.8196 (m) cc_final: 0.7963 (m) REVERT: B 264 LYS cc_start: 0.4267 (pttp) cc_final: 0.4043 (tttt) REVERT: B 295 MET cc_start: 0.9468 (mmp) cc_final: 0.9115 (mmp) REVERT: C 47 LYS cc_start: 0.9601 (mttt) cc_final: 0.9275 (mmmm) REVERT: D 11 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8095 (mm-30) REVERT: D 66 MET cc_start: 0.9159 (mmm) cc_final: 0.8651 (mmm) REVERT: E 81 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7975 (mt-10) REVERT: E 135 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8553 (tm-30) REVERT: E 138 MET cc_start: 0.7319 (tpt) cc_final: 0.6934 (tmm) REVERT: H 98 MET cc_start: 0.8449 (tpp) cc_final: 0.8115 (mmt) outliers start: 15 outliers final: 7 residues processed: 117 average time/residue: 0.2630 time to fit residues: 44.5056 Evaluate side-chains 91 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain E residue 188 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 70 optimal weight: 7.9990 chunk 119 optimal weight: 0.4980 chunk 107 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.058568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.045316 restraints weight = 59176.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.046852 restraints weight = 30353.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.047877 restraints weight = 19584.687| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13097 Z= 0.239 Angle : 0.669 9.366 17767 Z= 0.336 Chirality : 0.044 0.165 2038 Planarity : 0.004 0.037 2282 Dihedral : 5.018 25.100 1814 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.72 % Allowed : 15.44 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.20), residues: 1653 helix: -0.30 (0.19), residues: 719 sheet: -2.25 (0.32), residues: 228 loop : -2.44 (0.21), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 253 HIS 0.011 0.001 HIS B 194 PHE 0.016 0.002 PHE D 157 TYR 0.014 0.002 TYR B 86 ARG 0.004 0.000 ARG H 100 Details of bonding type rmsd hydrogen bonds : bond 0.03574 ( 500) hydrogen bonds : angle 4.71237 ( 1407) metal coordination : bond 0.00253 ( 3) covalent geometry : bond 0.00520 (13094) covalent geometry : angle 0.66860 (17767) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 1.350 Fit side-chains revert: symmetry clash REVERT: A 199 ILE cc_start: 0.9543 (mt) cc_final: 0.9269 (pt) REVERT: A 305 LYS cc_start: 0.8760 (mmtt) cc_final: 0.8456 (mmmt) REVERT: B 184 CYS cc_start: 0.8336 (m) cc_final: 0.8090 (m) REVERT: B 264 LYS cc_start: 0.4999 (pttp) cc_final: 0.4726 (tttt) REVERT: B 295 MET cc_start: 0.9455 (mmp) cc_final: 0.9115 (mmp) REVERT: C 47 LYS cc_start: 0.9633 (mttt) cc_final: 0.9339 (mmmm) REVERT: D 264 LEU cc_start: 0.9264 (tp) cc_final: 0.9010 (tp) REVERT: E 11 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8380 (mm-30) REVERT: E 81 GLU cc_start: 0.8272 (mt-10) cc_final: 0.8024 (mt-10) REVERT: H 98 MET cc_start: 0.8585 (tpp) cc_final: 0.8225 (mmt) outliers start: 23 outliers final: 15 residues processed: 104 average time/residue: 0.2358 time to fit residues: 37.0611 Evaluate side-chains 93 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 110 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 126 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 80 optimal weight: 0.0870 chunk 127 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 146 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 HIS C 97 HIS ** C 115 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 = 0.3338 r_free = 0.3338 target = 0.060022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.046785 restraints weight = 58419.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.048382 restraints weight = 29898.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.049398 restraints weight = 19254.134| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13097 Z= 0.127 Angle : 0.561 8.827 17767 Z= 0.282 Chirality : 0.042 0.147 2038 Planarity : 0.003 0.032 2282 Dihedral : 4.655 22.873 1814 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.86 % Allowed : 15.36 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.21), residues: 1653 helix: 0.53 (0.20), residues: 713 sheet: -2.20 (0.32), residues: 237 loop : -2.17 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 253 HIS 0.011 0.001 HIS B 194 PHE 0.012 0.001 PHE D 157 TYR 0.011 0.001 TYR B 293 ARG 0.002 0.000 ARG D 272 Details of bonding type rmsd hydrogen bonds : bond 0.02947 ( 500) hydrogen bonds : angle 4.20181 ( 1407) metal coordination : bond 0.00201 ( 3) covalent geometry : bond 0.00283 (13094) covalent geometry : angle 0.56061 (17767) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 ILE cc_start: 0.9556 (mt) cc_final: 0.9297 (pt) REVERT: A 305 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8458 (mmmt) REVERT: B 2 ASN cc_start: 0.8662 (m110) cc_final: 0.8443 (m-40) REVERT: B 264 LYS cc_start: 0.4330 (pttp) cc_final: 0.4057 (tttp) REVERT: C 24 LEU cc_start: 0.9479 (tp) cc_final: 0.9243 (tt) REVERT: C 47 LYS cc_start: 0.9635 (mttt) cc_final: 0.9336 (mmmm) REVERT: C 131 LYS cc_start: 0.9246 (tmtt) cc_final: 0.9024 (tmtt) REVERT: D 66 MET cc_start: 0.9079 (mmm) cc_final: 0.8728 (mmm) REVERT: D 264 LEU cc_start: 0.9251 (tp) cc_final: 0.8806 (tt) REVERT: E 11 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8300 (mm-30) REVERT: E 64 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.8824 (m-80) REVERT: H 59 LYS cc_start: 0.8838 (mptt) cc_final: 0.8627 (mptt) REVERT: H 98 MET cc_start: 0.8369 (tpp) cc_final: 0.7725 (mmt) outliers start: 25 outliers final: 13 residues processed: 108 average time/residue: 0.2580 time to fit residues: 41.1207 Evaluate side-chains 97 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 110 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 160 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 ASN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 GLN H 149 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.057680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.044623 restraints weight = 59506.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.046119 restraints weight = 30793.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.047115 restraints weight = 20043.370| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 13097 Z= 0.272 Angle : 0.687 10.206 17767 Z= 0.340 Chirality : 0.045 0.168 2038 Planarity : 0.004 0.035 2282 Dihedral : 4.905 26.093 1813 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.68 % Allowed : 17.15 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.21), residues: 1653 helix: 0.82 (0.21), residues: 713 sheet: -2.37 (0.31), residues: 244 loop : -2.04 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 253 HIS 0.007 0.001 HIS H 149 PHE 0.018 0.002 PHE D 157 TYR 0.013 0.002 TYR B 86 ARG 0.004 0.000 ARG H 100 Details of bonding type rmsd hydrogen bonds : bond 0.03342 ( 500) hydrogen bonds : angle 4.45699 ( 1407) metal coordination : bond 0.00451 ( 3) covalent geometry : bond 0.00593 (13094) covalent geometry : angle 0.68667 (17767) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 79 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 ILE cc_start: 0.9546 (mt) cc_final: 0.9289 (pt) REVERT: A 305 LYS cc_start: 0.8768 (mmtt) cc_final: 0.8515 (mmmt) REVERT: C 76 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9351 (tt) REVERT: D 264 LEU cc_start: 0.9274 (tp) cc_final: 0.8957 (tp) REVERT: E 11 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8382 (mm-30) REVERT: E 64 PHE cc_start: 0.9163 (OUTLIER) cc_final: 0.8896 (m-80) REVERT: H 50 MET cc_start: 0.8144 (ptt) cc_final: 0.7907 (ptt) REVERT: H 72 CYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8424 (p) outliers start: 36 outliers final: 19 residues processed: 111 average time/residue: 0.2329 time to fit residues: 39.4554 Evaluate side-chains 97 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 72 CYS Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 165 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 14 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 ASN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.058408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.045152 restraints weight = 60353.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.046733 restraints weight = 30386.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.047769 restraints weight = 19402.122| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13097 Z= 0.198 Angle : 0.622 10.084 17767 Z= 0.309 Chirality : 0.043 0.154 2038 Planarity : 0.003 0.031 2282 Dihedral : 4.770 24.548 1813 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.16 % Allowed : 18.57 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.22), residues: 1653 helix: 1.08 (0.21), residues: 714 sheet: -2.26 (0.32), residues: 246 loop : -1.93 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 253 HIS 0.005 0.001 HIS C 37 PHE 0.015 0.001 PHE D 157 TYR 0.013 0.001 TYR B 86 ARG 0.003 0.000 ARG H 100 Details of bonding type rmsd hydrogen bonds : bond 0.03068 ( 500) hydrogen bonds : angle 4.25523 ( 1407) metal coordination : bond 0.00302 ( 3) covalent geometry : bond 0.00438 (13094) covalent geometry : angle 0.62151 (17767) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 80 time to evaluate : 1.357 Fit side-chains REVERT: A 199 ILE cc_start: 0.9553 (mt) cc_final: 0.9287 (pt) REVERT: A 305 LYS cc_start: 0.8781 (mmtt) cc_final: 0.8525 (mmmt) REVERT: B 264 LYS cc_start: 0.5054 (pttp) cc_final: 0.4671 (tttp) REVERT: C 24 LEU cc_start: 0.9452 (tp) cc_final: 0.9233 (tt) REVERT: C 76 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9358 (tt) REVERT: C 131 LYS cc_start: 0.9313 (tmtt) cc_final: 0.9059 (tmtt) REVERT: C 133 MET cc_start: 0.8638 (mtp) cc_final: 0.8317 (mtt) REVERT: D 147 MET cc_start: 0.8533 (mmm) cc_final: 0.8217 (mmm) REVERT: D 264 LEU cc_start: 0.9312 (tp) cc_final: 0.8920 (tt) REVERT: E 11 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8172 (mm-30) REVERT: E 64 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8819 (m-80) outliers start: 29 outliers final: 20 residues processed: 105 average time/residue: 0.2422 time to fit residues: 38.4102 Evaluate side-chains 101 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 165 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 122 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 163 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 103 optimal weight: 0.0070 overall best weight: 1.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 ASN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.059765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.046804 restraints weight = 59903.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.048368 restraints weight = 30772.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.049352 restraints weight = 19876.632| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13097 Z= 0.121 Angle : 0.563 9.600 17767 Z= 0.280 Chirality : 0.042 0.147 2038 Planarity : 0.003 0.034 2282 Dihedral : 4.513 23.644 1813 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.39 % Allowed : 18.64 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.22), residues: 1653 helix: 1.40 (0.21), residues: 714 sheet: -2.10 (0.33), residues: 246 loop : -1.85 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 253 HIS 0.007 0.001 HIS C 37 PHE 0.012 0.001 PHE D 157 TYR 0.011 0.001 TYR B 86 ARG 0.003 0.000 ARG B 175 Details of bonding type rmsd hydrogen bonds : bond 0.02776 ( 500) hydrogen bonds : angle 3.96163 ( 1407) metal coordination : bond 0.00230 ( 3) covalent geometry : bond 0.00273 (13094) covalent geometry : angle 0.56289 (17767) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 81 time to evaluate : 1.448 Fit side-chains revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8022 (pp) REVERT: A 199 ILE cc_start: 0.9545 (mt) cc_final: 0.9303 (pt) REVERT: B 264 LYS cc_start: 0.5298 (pttp) cc_final: 0.4947 (tttp) REVERT: C 24 LEU cc_start: 0.9358 (tp) cc_final: 0.9156 (tt) REVERT: D 264 LEU cc_start: 0.9288 (tp) cc_final: 0.8896 (tt) REVERT: E 11 GLU cc_start: 0.8594 (mm-30) cc_final: 0.7914 (mm-30) REVERT: E 64 PHE cc_start: 0.9092 (OUTLIER) cc_final: 0.8805 (m-80) REVERT: H 98 MET cc_start: 0.8358 (tpp) cc_final: 0.7795 (mmt) outliers start: 32 outliers final: 18 residues processed: 108 average time/residue: 0.2283 time to fit residues: 37.5618 Evaluate side-chains 98 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 165 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 77 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 111 optimal weight: 0.0870 chunk 24 optimal weight: 9.9990 chunk 160 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 chunk 159 optimal weight: 9.9990 chunk 139 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 overall best weight: 1.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 ASN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.059847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.046894 restraints weight = 59963.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.048443 restraints weight = 30724.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.049453 restraints weight = 19860.126| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13097 Z= 0.124 Angle : 0.583 9.975 17767 Z= 0.284 Chirality : 0.042 0.146 2038 Planarity : 0.003 0.032 2282 Dihedral : 4.400 23.949 1812 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.46 % Allowed : 19.39 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.22), residues: 1653 helix: 1.54 (0.21), residues: 716 sheet: -1.93 (0.34), residues: 246 loop : -1.76 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 253 HIS 0.006 0.001 HIS C 37 PHE 0.012 0.001 PHE D 157 TYR 0.010 0.001 TYR B 86 ARG 0.002 0.000 ARG B 175 Details of bonding type rmsd hydrogen bonds : bond 0.02730 ( 500) hydrogen bonds : angle 3.85116 ( 1407) metal coordination : bond 0.00149 ( 3) covalent geometry : bond 0.00283 (13094) covalent geometry : angle 0.58270 (17767) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 80 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 ILE cc_start: 0.9537 (mt) cc_final: 0.9306 (pt) REVERT: B 86 TYR cc_start: 0.8494 (m-80) cc_final: 0.8025 (m-80) REVERT: B 264 LYS cc_start: 0.5374 (pttp) cc_final: 0.5017 (tttp) REVERT: C 133 MET cc_start: 0.8502 (mtp) cc_final: 0.8253 (mtt) REVERT: D 147 MET cc_start: 0.8416 (mmm) cc_final: 0.8212 (mmm) REVERT: D 264 LEU cc_start: 0.9281 (tp) cc_final: 0.8869 (tt) REVERT: E 11 GLU cc_start: 0.8603 (mm-30) cc_final: 0.7960 (mm-30) REVERT: E 64 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8786 (m-80) REVERT: E 81 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7583 (mt-10) REVERT: H 72 CYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8490 (p) REVERT: H 98 MET cc_start: 0.8368 (tpp) cc_final: 0.7797 (mmt) outliers start: 33 outliers final: 23 residues processed: 109 average time/residue: 0.2324 time to fit residues: 39.2293 Evaluate side-chains 100 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 72 CYS Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 165 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 22 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 70 optimal weight: 0.0470 chunk 106 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.058626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.045827 restraints weight = 60596.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.047331 restraints weight = 31075.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.048327 restraints weight = 20136.881| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13097 Z= 0.191 Angle : 0.624 10.440 17767 Z= 0.305 Chirality : 0.043 0.150 2038 Planarity : 0.003 0.032 2282 Dihedral : 4.492 24.486 1812 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.46 % Allowed : 19.46 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.22), residues: 1653 helix: 1.60 (0.21), residues: 715 sheet: -1.94 (0.34), residues: 248 loop : -1.72 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 211 HIS 0.005 0.001 HIS C 37 PHE 0.016 0.001 PHE D 157 TYR 0.011 0.001 TYR B 86 ARG 0.004 0.000 ARG D 272 Details of bonding type rmsd hydrogen bonds : bond 0.02932 ( 500) hydrogen bonds : angle 3.99482 ( 1407) metal coordination : bond 0.00267 ( 3) covalent geometry : bond 0.00424 (13094) covalent geometry : angle 0.62378 (17767) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 81 time to evaluate : 1.369 Fit side-chains REVERT: A 199 ILE cc_start: 0.9540 (mt) cc_final: 0.9313 (pt) REVERT: B 264 LYS cc_start: 0.5421 (pttp) cc_final: 0.4954 (tttp) REVERT: C 292 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8185 (ttm-80) REVERT: D 264 LEU cc_start: 0.9198 (tp) cc_final: 0.8997 (tp) REVERT: E 11 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8004 (mm-30) REVERT: E 64 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8815 (m-80) REVERT: H 72 CYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8523 (p) REVERT: H 98 MET cc_start: 0.8425 (tpp) cc_final: 0.8035 (mmt) outliers start: 33 outliers final: 23 residues processed: 109 average time/residue: 0.2073 time to fit residues: 35.3027 Evaluate side-chains 104 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 72 CYS Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 165 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 34 optimal weight: 0.9980 chunk 94 optimal weight: 0.0970 chunk 136 optimal weight: 20.0000 chunk 113 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 161 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 108 optimal weight: 0.6980 overall best weight: 1.1180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 59 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.060265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.047402 restraints weight = 59684.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.048935 restraints weight = 30495.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.049941 restraints weight = 19631.281| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13097 Z= 0.106 Angle : 0.586 9.967 17767 Z= 0.283 Chirality : 0.042 0.146 2038 Planarity : 0.003 0.042 2282 Dihedral : 4.325 23.288 1812 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.79 % Allowed : 20.06 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.22), residues: 1653 helix: 1.80 (0.21), residues: 715 sheet: -1.95 (0.33), residues: 267 loop : -1.71 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 45 HIS 0.005 0.001 HIS C 37 PHE 0.012 0.001 PHE D 157 TYR 0.010 0.001 TYR B 86 ARG 0.004 0.000 ARG D 272 Details of bonding type rmsd hydrogen bonds : bond 0.02655 ( 500) hydrogen bonds : angle 3.75906 ( 1407) metal coordination : bond 0.00096 ( 3) covalent geometry : bond 0.00244 (13094) covalent geometry : angle 0.58610 (17767) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 1.331 Fit side-chains revert: symmetry clash REVERT: B 86 TYR cc_start: 0.8501 (m-80) cc_final: 0.8050 (m-80) REVERT: B 264 LYS cc_start: 0.5508 (pttp) cc_final: 0.5184 (tttp) REVERT: C 292 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8214 (ttm-80) REVERT: D 147 MET cc_start: 0.8395 (mmm) cc_final: 0.7696 (mmt) REVERT: E 11 GLU cc_start: 0.8608 (mm-30) cc_final: 0.7990 (mm-30) REVERT: E 64 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8764 (m-80) REVERT: H 72 CYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8539 (p) REVERT: H 98 MET cc_start: 0.8323 (tpp) cc_final: 0.7744 (mmt) outliers start: 24 outliers final: 19 residues processed: 101 average time/residue: 0.2183 time to fit residues: 34.5311 Evaluate side-chains 97 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 72 CYS Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 165 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 40 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 125 optimal weight: 0.0170 chunk 156 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 161 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 overall best weight: 1.9624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.059728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.046868 restraints weight = 59595.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.048399 restraints weight = 30586.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.049406 restraints weight = 19750.876| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13097 Z= 0.135 Angle : 0.595 10.250 17767 Z= 0.287 Chirality : 0.042 0.178 2038 Planarity : 0.003 0.044 2282 Dihedral : 4.316 24.216 1812 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 1.94 % Allowed : 20.36 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.22), residues: 1653 helix: 1.83 (0.21), residues: 716 sheet: -1.93 (0.32), residues: 272 loop : -1.64 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 211 HIS 0.006 0.001 HIS C 37 PHE 0.012 0.001 PHE D 157 TYR 0.011 0.001 TYR B 86 ARG 0.004 0.000 ARG D 272 Details of bonding type rmsd hydrogen bonds : bond 0.02719 ( 500) hydrogen bonds : angle 3.79481 ( 1407) metal coordination : bond 0.00201 ( 3) covalent geometry : bond 0.00308 (13094) covalent geometry : angle 0.59501 (17767) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3458.46 seconds wall clock time: 61 minutes 5.36 seconds (3665.36 seconds total)