Starting phenix.real_space_refine on Wed Mar 4 10:25:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7osj_13053/03_2026/7osj_13053.cif Found real_map, /net/cci-nas-00/data/ceres_data/7osj_13053/03_2026/7osj_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 { model { file = "/net/cci-nas-00/data/ceres_data/7osj_13053/03_2026/7osj_13053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7osj_13053/03_2026/7osj_13053.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7osj_13053/03_2026/7osj_13053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7osj_13053/03_2026/7osj_13053.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'GLU:plan': 3, 'GLN:plan1': 2, '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: 3.01, per 1000 atoms: 0.23 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: 0.83 Conformation dependent library (CDL) restraints added in 602.2 milliseconds 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: 0.38 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: 1.94 Time building geometry restraints manager: 1.09 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: 0.630 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.140 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.570 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.008 0.001 ARG B 177 TYR 0.025 0.002 TYR C 291 PHE 0.018 0.002 PHE B 35 TRP 0.019 0.002 TRP E 20 HIS 0.010 0.002 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00644 (13094) covalent geometry : angle 1.04678 (17767) hydrogen bonds : bond 0.29564 ( 500) hydrogen bonds : angle 10.53021 ( 1407) metal coordination : bond 0.04786 ( 3) *********************** 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 : 0.510 Fit side-chains revert: symmetry clash 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: 0.7284 (tt0) REVERT: B 86 TYR cc_start: 0.8822 (m-80) cc_final: 0.8473 (m-10) REVERT: C 47 LYS cc_start: 0.9563 (mttt) cc_final: 0.9211 (mmmm) REVERT: C 102 LYS cc_start: 0.9372 (ttmt) cc_final: 0.9162 (ttmm) REVERT: C 203 LYS cc_start: 0.9078 (mmmt) cc_final: 0.8671 (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: 0.8161 (tpp) REVERT: E 76 ASP cc_start: 0.8621 (p0) cc_final: 0.8296 (p0) REVERT: E 81 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8325 (mt-10) REVERT: E 83 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8078 (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: 0.6727 (tmm) REVERT: E 171 LYS cc_start: 0.9281 (tttt) cc_final: 0.8808 (ttmm) REVERT: H 40 HIS cc_start: 0.8557 (m-70) cc_final: 0.8178 (m90) REVERT: H 161 GLN cc_start: 0.8614 (mt0) cc_final: 0.8409 (mt0) outliers start: 12 outliers final: 4 residues processed: 151 average time/residue: 0.1428 time to fit residues: 29.5161 Evaluate side-chains 97 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 98 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 7.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 A 141 GLN A 145 ASN A 160 ASN A 174 HIS A 175 ASN A 179 ASN A 190 ASN A 212 ASN A 241 ASN A 301 ASN A 324 ASN B 11 GLN B 20 HIS ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN B 176 GLN B 261 ASN B 270 GLN ** C 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN C 194 HIS C 238 GLN D 205 ASN D 225 ASN E 225 ASN H 161 GLN H 172 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.060855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.047288 restraints weight = 58339.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.048951 restraints weight = 29162.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.049966 restraints weight = 18550.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.050751 restraints weight = 13811.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.051130 restraints weight = 11194.154| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13097 Z= 0.156 Angle : 0.623 7.738 17767 Z= 0.321 Chirality : 0.042 0.154 2038 Planarity : 0.005 0.051 2282 Dihedral : 5.387 54.535 1817 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.27 % Allowed : 13.42 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.63 (0.17), residues: 1653 helix: -2.07 (0.15), residues: 719 sheet: -2.65 (0.32), residues: 209 loop : -2.57 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 272 TYR 0.015 0.001 TYR E 93 PHE 0.014 0.001 PHE H 156 TRP 0.012 0.001 TRP E 253 HIS 0.004 0.001 HIS B 20 Details of bonding type rmsd covalent geometry : bond 0.00343 (13094) covalent geometry : angle 0.62335 (17767) hydrogen bonds : bond 0.03960 ( 500) hydrogen bonds : angle 5.13130 ( 1407) metal coordination : bond 0.00333 ( 3) *********************** 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 127 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8688 (mpp) cc_final: 0.8434 (mpp) REVERT: A 199 ILE cc_start: 0.9570 (mt) cc_final: 0.9271 (pt) REVERT: A 305 LYS cc_start: 0.8788 (mmtt) cc_final: 0.8439 (mmmt) REVERT: B 2 ASN cc_start: 0.8557 (m110) cc_final: 0.8305 (m-40) REVERT: B 295 MET cc_start: 0.9426 (mmp) cc_final: 0.9075 (mmp) REVERT: C 47 LYS cc_start: 0.9596 (mttt) cc_final: 0.9373 (mmtp) REVERT: C 203 LYS cc_start: 0.8823 (mmmt) cc_final: 0.8602 (mmtp) REVERT: D 11 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8081 (mm-30) REVERT: D 66 MET cc_start: 0.9126 (mmm) cc_final: 0.8666 (mmm) REVERT: E 76 ASP cc_start: 0.8576 (p0) cc_final: 0.8368 (p0) REVERT: E 81 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7998 (mt-10) REVERT: E 135 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8594 (tm-30) REVERT: E 138 MET cc_start: 0.7365 (tpt) cc_final: 0.6982 (tmm) REVERT: H 98 MET cc_start: 0.8314 (tpp) cc_final: 0.8029 (mmt) outliers start: 17 outliers final: 7 residues processed: 123 average time/residue: 0.1070 time to fit residues: 19.1109 Evaluate side-chains 97 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 ASN Chi-restraints excluded: chain B residue 133 MET 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 E residue 188 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 62 optimal weight: 30.0000 chunk 101 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 66 optimal weight: 0.5980 chunk 144 optimal weight: 0.1980 chunk 135 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 HIS ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 HIS C 37 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.060795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.047340 restraints weight = 58244.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.048989 restraints weight = 29114.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.050041 restraints weight = 18526.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.050798 restraints weight = 13670.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.051228 restraints weight = 11063.978| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13097 Z= 0.132 Angle : 0.579 8.215 17767 Z= 0.293 Chirality : 0.042 0.166 2038 Planarity : 0.004 0.035 2282 Dihedral : 4.773 22.682 1813 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.27 % Allowed : 15.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.20), residues: 1653 helix: -0.49 (0.19), residues: 724 sheet: -2.39 (0.32), residues: 218 loop : -2.31 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 239 TYR 0.014 0.001 TYR B 86 PHE 0.011 0.001 PHE H 156 TRP 0.010 0.001 TRP B 240 HIS 0.010 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00293 (13094) covalent geometry : angle 0.57900 (17767) hydrogen bonds : bond 0.03235 ( 500) hydrogen bonds : angle 4.47097 ( 1407) metal coordination : bond 0.00160 ( 3) *********************** 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 113 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 199 ILE cc_start: 0.9551 (mt) cc_final: 0.9291 (pt) REVERT: A 305 LYS cc_start: 0.8801 (mmtt) cc_final: 0.8450 (mmmt) REVERT: B 2 ASN cc_start: 0.8606 (m110) cc_final: 0.8243 (m-40) REVERT: B 295 MET cc_start: 0.9446 (mmp) cc_final: 0.9236 (mmm) REVERT: C 47 LYS cc_start: 0.9572 (mttt) cc_final: 0.9273 (mmmm) REVERT: D 66 MET cc_start: 0.9045 (mmm) cc_final: 0.8590 (mmm) REVERT: D 264 LEU cc_start: 0.9201 (tp) cc_final: 0.8901 (tp) REVERT: E 11 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8332 (mm-30) REVERT: E 76 ASP cc_start: 0.8615 (p0) cc_final: 0.8343 (p0) REVERT: E 81 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7967 (mt-10) REVERT: E 135 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8535 (tm-30) REVERT: E 138 MET cc_start: 0.7369 (tpt) cc_final: 0.6902 (tmm) REVERT: H 98 MET cc_start: 0.8412 (tpp) cc_final: 0.7937 (mmt) REVERT: H 160 ASP cc_start: 0.8640 (p0) cc_final: 0.8385 (p0) outliers start: 17 outliers final: 11 residues processed: 108 average time/residue: 0.1160 time to fit residues: 18.3835 Evaluate side-chains 96 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 ILE 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 D residue 265 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 113 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN B 37 HIS B 82 ASN B 135 GLN C 25 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.059011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.045681 restraints weight = 59745.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.047281 restraints weight = 29983.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.048319 restraints weight = 19206.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.049026 restraints weight = 14234.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.049435 restraints weight = 11576.642| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13097 Z= 0.200 Angle : 0.615 9.495 17767 Z= 0.309 Chirality : 0.043 0.154 2038 Planarity : 0.004 0.036 2282 Dihedral : 4.754 24.430 1813 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.46 % Allowed : 14.99 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.21), residues: 1653 helix: 0.49 (0.20), residues: 717 sheet: -2.17 (0.32), residues: 238 loop : -2.10 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 100 TYR 0.010 0.001 TYR E 93 PHE 0.015 0.001 PHE D 157 TRP 0.011 0.001 TRP E 253 HIS 0.004 0.001 HIS H 149 Details of bonding type rmsd covalent geometry : bond 0.00438 (13094) covalent geometry : angle 0.61496 (17767) hydrogen bonds : bond 0.03216 ( 500) hydrogen bonds : angle 4.33573 ( 1407) metal coordination : bond 0.00278 ( 3) *********************** 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 119 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 86 time to evaluate : 0.518 Fit side-chains REVERT: A 199 ILE cc_start: 0.9540 (mt) cc_final: 0.9292 (pt) REVERT: A 305 LYS cc_start: 0.8708 (mmtt) cc_final: 0.8466 (mmmt) REVERT: B 2 ASN cc_start: 0.8645 (m110) cc_final: 0.8416 (m-40) REVERT: B 86 TYR cc_start: 0.8808 (OUTLIER) cc_final: 0.8319 (m-80) REVERT: C 47 LYS cc_start: 0.9661 (mttt) cc_final: 0.9361 (mmmm) REVERT: D 264 LEU cc_start: 0.9287 (tp) cc_final: 0.8979 (tp) REVERT: E 11 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8321 (mm-30) REVERT: E 64 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8872 (m-80) REVERT: E 81 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7919 (mt-10) REVERT: H 98 MET cc_start: 0.8484 (tpp) cc_final: 0.7859 (mmt) outliers start: 33 outliers final: 18 residues processed: 111 average time/residue: 0.1023 time to fit residues: 17.3232 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 : 0.476 ------------------------------------------------------------------------------- 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 82 ASN Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 171 ILE 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 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 63 VAL Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 165 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 9 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 162 optimal weight: 0.9990 chunk 111 optimal weight: 0.0770 chunk 60 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 69 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 ASN H 149 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.061097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.048024 restraints weight = 60163.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.049663 restraints weight = 29851.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.050729 restraints weight = 18837.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.051356 restraints weight = 13847.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.051876 restraints weight = 11360.017| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3022 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= 0.098 Angle : 0.546 9.110 17767 Z= 0.272 Chirality : 0.041 0.155 2038 Planarity : 0.003 0.034 2282 Dihedral : 4.425 22.487 1813 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.34 % Allowed : 16.55 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.22), residues: 1653 helix: 1.03 (0.21), residues: 718 sheet: -1.91 (0.33), residues: 237 loop : -1.97 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 175 TYR 0.010 0.001 TYR B 293 PHE 0.012 0.001 PHE H 156 TRP 0.006 0.001 TRP E 253 HIS 0.006 0.001 HIS H 149 Details of bonding type rmsd covalent geometry : bond 0.00219 (13094) covalent geometry : angle 0.54578 (17767) hydrogen bonds : bond 0.02735 ( 500) hydrogen bonds : angle 3.91603 ( 1407) metal coordination : bond 0.00032 ( 3) *********************** 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 106 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.474 Fit side-chains REVERT: A 199 ILE cc_start: 0.9555 (mt) cc_final: 0.9293 (pt) REVERT: A 305 LYS cc_start: 0.8690 (mmtt) cc_final: 0.8429 (mmmt) REVERT: B 86 TYR cc_start: 0.8675 (OUTLIER) cc_final: 0.8303 (m-80) REVERT: C 47 LYS cc_start: 0.9648 (mttt) cc_final: 0.9352 (mmmm) REVERT: C 131 LYS cc_start: 0.9312 (tmtt) cc_final: 0.9061 (tmtt) REVERT: D 66 MET cc_start: 0.8980 (mmm) cc_final: 0.8693 (mmm) REVERT: D 264 LEU cc_start: 0.9212 (tp) cc_final: 0.8903 (tp) REVERT: E 11 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8353 (mm-30) REVERT: E 64 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.8810 (m-80) REVERT: H 92 LYS cc_start: 0.8306 (mtmt) cc_final: 0.8052 (mttt) REVERT: H 98 MET cc_start: 0.8352 (tpp) cc_final: 0.7600 (mmt) outliers start: 18 outliers final: 7 residues processed: 101 average time/residue: 0.0978 time to fit residues: 15.1801 Evaluate side-chains 89 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 187 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 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 110 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 134 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 127 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN B 82 ASN ** 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 = 0.3318 r_free = 0.3318 target = 0.058733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.045856 restraints weight = 59989.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.047341 restraints weight = 30961.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.048362 restraints weight = 20050.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.048980 restraints weight = 14948.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.049349 restraints weight = 12303.733| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13097 Z= 0.208 Angle : 0.624 10.284 17767 Z= 0.309 Chirality : 0.043 0.158 2038 Planarity : 0.003 0.034 2282 Dihedral : 4.573 25.154 1812 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.39 % Allowed : 16.70 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.22), residues: 1653 helix: 1.20 (0.21), residues: 719 sheet: -1.94 (0.33), residues: 229 loop : -1.85 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 100 TYR 0.010 0.001 TYR A 249 PHE 0.016 0.001 PHE D 157 TRP 0.011 0.001 TRP E 211 HIS 0.004 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00459 (13094) covalent geometry : angle 0.62409 (17767) hydrogen bonds : bond 0.03077 ( 500) hydrogen bonds : angle 4.12289 ( 1407) metal coordination : bond 0.00293 ( 3) *********************** 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 112 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 80 time to evaluate : 0.534 Fit side-chains REVERT: A 199 ILE cc_start: 0.9558 (mt) cc_final: 0.9317 (pt) REVERT: A 305 LYS cc_start: 0.8724 (mmtt) cc_final: 0.8491 (mmmt) REVERT: B 172 ASP cc_start: 0.9051 (OUTLIER) cc_final: 0.8825 (t0) REVERT: C 76 LEU cc_start: 0.9590 (OUTLIER) cc_final: 0.9343 (tt) REVERT: D 147 MET cc_start: 0.8425 (mmm) cc_final: 0.8202 (mmm) REVERT: D 264 LEU cc_start: 0.9264 (tp) cc_final: 0.8917 (tp) REVERT: E 11 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8142 (mm-30) REVERT: E 64 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8875 (m-80) REVERT: E 81 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7783 (mt-10) REVERT: H 72 CYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8336 (p) REVERT: H 92 LYS cc_start: 0.8174 (mtmt) cc_final: 0.7907 (mttt) REVERT: H 98 MET cc_start: 0.8410 (tpp) cc_final: 0.7858 (mmt) outliers start: 32 outliers final: 16 residues processed: 106 average time/residue: 0.0977 time to fit residues: 16.0094 Evaluate side-chains 95 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 407 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 82 ASN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 172 ASP 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 5 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 130 optimal weight: 8.9990 chunk 141 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 44 optimal weight: 0.0270 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN B 82 ASN ** 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 = 0.3370 r_free = 0.3370 target = 0.060776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.047716 restraints weight = 59660.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.049320 restraints weight = 29582.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.050387 restraints weight = 18666.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.051090 restraints weight = 13764.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.051537 restraints weight = 11175.470| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3312 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= 0.096 Angle : 0.553 9.418 17767 Z= 0.272 Chirality : 0.041 0.142 2038 Planarity : 0.003 0.036 2282 Dihedral : 4.330 22.767 1812 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.27 % Allowed : 18.27 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.22), residues: 1653 helix: 1.53 (0.21), residues: 716 sheet: -1.93 (0.32), residues: 249 loop : -1.81 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 175 TYR 0.010 0.001 TYR B 293 PHE 0.011 0.001 PHE H 156 TRP 0.007 0.001 TRP E 211 HIS 0.003 0.001 HIS B 20 Details of bonding type rmsd covalent geometry : bond 0.00218 (13094) covalent geometry : angle 0.55296 (17767) hydrogen bonds : bond 0.02646 ( 500) hydrogen bonds : angle 3.75189 ( 1407) metal coordination : bond 0.00023 ( 3) *********************** 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 99 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8042 (pp) REVERT: A 199 ILE cc_start: 0.9564 (mt) cc_final: 0.9303 (pt) REVERT: A 231 MET cc_start: 0.8278 (mtt) cc_final: 0.7913 (mtm) REVERT: A 305 LYS cc_start: 0.8720 (mmtt) cc_final: 0.8457 (mmmt) REVERT: B 169 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9139 (pp) REVERT: C 24 LEU cc_start: 0.9409 (tp) cc_final: 0.9143 (tt) REVERT: C 131 LYS cc_start: 0.9332 (tmtt) cc_final: 0.9022 (tmtt) REVERT: D 66 MET cc_start: 0.9090 (mmm) cc_final: 0.8751 (mmm) REVERT: D 264 LEU cc_start: 0.9256 (tp) cc_final: 0.8829 (tt) REVERT: E 11 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8015 (mm-30) REVERT: E 64 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.8780 (m-80) REVERT: E 81 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7651 (mt-10) REVERT: E 147 MET cc_start: 0.7818 (mmt) cc_final: 0.7329 (mmt) REVERT: H 92 LYS cc_start: 0.8160 (mtmt) cc_final: 0.7891 (mtmt) REVERT: H 98 MET cc_start: 0.8286 (tpp) cc_final: 0.7657 (mmt) outliers start: 17 outliers final: 11 residues processed: 96 average time/residue: 0.0982 time to fit residues: 14.3451 Evaluate side-chains 94 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 82 ASN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 187 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 64 PHE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 110 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 129 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 63 optimal weight: 30.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN ** B 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3332 r_free = 0.3332 target = 0.059311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.046458 restraints weight = 60435.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.047969 restraints weight = 31144.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.048953 restraints weight = 20180.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.049606 restraints weight = 15084.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.049972 restraints weight = 12391.528| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13097 Z= 0.179 Angle : 0.599 10.405 17767 Z= 0.294 Chirality : 0.042 0.146 2038 Planarity : 0.003 0.033 2282 Dihedral : 4.388 24.597 1812 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.09 % Allowed : 18.42 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.22), residues: 1653 helix: 1.63 (0.21), residues: 718 sheet: -1.91 (0.33), residues: 248 loop : -1.75 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 100 TYR 0.009 0.001 TYR A 249 PHE 0.015 0.001 PHE D 157 TRP 0.011 0.001 TRP E 211 HIS 0.003 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00398 (13094) covalent geometry : angle 0.59912 (17767) hydrogen bonds : bond 0.02876 ( 500) hydrogen bonds : angle 3.88869 ( 1407) metal coordination : bond 0.00246 ( 3) *********************** 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 106 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8107 (pp) REVERT: A 199 ILE cc_start: 0.9565 (mt) cc_final: 0.9334 (pt) REVERT: A 231 MET cc_start: 0.8145 (mtt) cc_final: 0.7598 (mtm) REVERT: A 305 LYS cc_start: 0.8719 (mmtt) cc_final: 0.8486 (mmmt) REVERT: D 147 MET cc_start: 0.8359 (mmm) cc_final: 0.8081 (mmm) REVERT: D 264 LEU cc_start: 0.9284 (tp) cc_final: 0.8970 (tp) REVERT: E 11 GLU cc_start: 0.8587 (mm-30) cc_final: 0.7783 (mm-30) REVERT: E 64 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8796 (m-80) REVERT: E 147 MET cc_start: 0.7844 (mmt) cc_final: 0.7208 (mmt) REVERT: H 72 CYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8292 (p) REVERT: H 92 LYS cc_start: 0.8190 (mtmt) cc_final: 0.7911 (mtmt) REVERT: H 98 MET cc_start: 0.8369 (tpp) cc_final: 0.7829 (mmt) outliers start: 28 outliers final: 15 residues processed: 103 average time/residue: 0.0871 time to fit residues: 14.1604 Evaluate side-chains 94 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU 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 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 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 63 VAL 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 65 optimal weight: 0.0470 chunk 114 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 ASN ** B 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3373 r_free = 0.3373 target = 0.060800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.047791 restraints weight = 59998.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.049374 restraints weight = 29658.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.050425 restraints weight = 18832.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.051072 restraints weight = 13854.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.051555 restraints weight = 11317.863| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3466 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= 0.099 Angle : 0.562 9.785 17767 Z= 0.272 Chirality : 0.041 0.142 2038 Planarity : 0.003 0.035 2282 Dihedral : 4.235 23.027 1812 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.34 % Allowed : 19.02 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.22), residues: 1653 helix: 1.81 (0.21), residues: 714 sheet: -1.80 (0.32), residues: 260 loop : -1.73 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 360 TYR 0.008 0.001 TYR B 293 PHE 0.012 0.001 PHE D 157 TRP 0.008 0.001 TRP A 45 HIS 0.003 0.001 HIS B 20 Details of bonding type rmsd covalent geometry : bond 0.00225 (13094) covalent geometry : angle 0.56180 (17767) hydrogen bonds : bond 0.02614 ( 500) hydrogen bonds : angle 3.66654 ( 1407) metal coordination : bond 0.00046 ( 3) *********************** 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 101 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8068 (pp) REVERT: A 231 MET cc_start: 0.7927 (mtt) cc_final: 0.7345 (mtm) REVERT: A 305 LYS cc_start: 0.8660 (mmtt) cc_final: 0.8413 (mmmt) REVERT: B 169 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9173 (pp) REVERT: C 24 LEU cc_start: 0.9405 (tp) cc_final: 0.9146 (tt) REVERT: C 131 LYS cc_start: 0.9354 (tmtt) cc_final: 0.9149 (tmtt) REVERT: D 147 MET cc_start: 0.8371 (mmm) cc_final: 0.8095 (mmm) REVERT: D 264 LEU cc_start: 0.9240 (tp) cc_final: 0.8812 (tt) REVERT: E 11 GLU cc_start: 0.8640 (mm-30) cc_final: 0.7995 (mm-30) REVERT: E 64 PHE cc_start: 0.9092 (OUTLIER) cc_final: 0.8832 (m-80) REVERT: H 72 CYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8396 (p) REVERT: H 92 LYS cc_start: 0.8271 (mtmt) cc_final: 0.8010 (mttt) REVERT: H 98 MET cc_start: 0.8324 (tpp) cc_final: 0.7753 (mmt) outliers start: 18 outliers final: 12 residues processed: 96 average time/residue: 0.1011 time to fit residues: 15.0687 Evaluate side-chains 95 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 187 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 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 129 MET 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 105 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 115 optimal weight: 0.6980 chunk 71 optimal weight: 8.9990 chunk 111 optimal weight: 0.9990 chunk 65 optimal weight: 0.1980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN ** B 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN ** 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 = 0.3331 r_free = 0.3331 target = 0.059209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.046375 restraints weight = 60852.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.047865 restraints weight = 31190.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.048852 restraints weight = 20184.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.049440 restraints weight = 15077.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.049893 restraints weight = 12485.078| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13097 Z= 0.179 Angle : 0.613 10.520 17767 Z= 0.298 Chirality : 0.042 0.142 2038 Planarity : 0.003 0.037 2282 Dihedral : 4.350 24.416 1812 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.64 % Allowed : 19.02 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.22), residues: 1653 helix: 1.80 (0.21), residues: 714 sheet: -1.75 (0.33), residues: 259 loop : -1.70 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 100 TYR 0.009 0.001 TYR B 293 PHE 0.014 0.001 PHE D 157 TRP 0.012 0.001 TRP E 211 HIS 0.003 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00397 (13094) covalent geometry : angle 0.61261 (17767) hydrogen bonds : bond 0.02836 ( 500) hydrogen bonds : angle 3.83226 ( 1407) metal coordination : bond 0.00191 ( 3) ********************** 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 97 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8000 (pp) REVERT: A 199 ILE cc_start: 0.9563 (mt) cc_final: 0.9335 (pt) REVERT: A 231 MET cc_start: 0.8077 (mtt) cc_final: 0.7494 (mtm) REVERT: D 264 LEU cc_start: 0.9266 (tp) cc_final: 0.8952 (tp) REVERT: E 11 GLU cc_start: 0.8623 (mm-30) cc_final: 0.7807 (mm-30) REVERT: E 64 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8794 (m-80) REVERT: H 72 CYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8473 (p) REVERT: H 92 LYS cc_start: 0.8117 (mtmt) cc_final: 0.7818 (mtmt) REVERT: H 98 MET cc_start: 0.8358 (tpp) cc_final: 0.7829 (mmt) outliers start: 22 outliers final: 17 residues processed: 93 average time/residue: 0.0974 time to fit residues: 14.0979 Evaluate side-chains 95 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU 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 B residue 82 ASN Chi-restraints excluded: chain B residue 187 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 4 VAL 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 63 VAL Chi-restraints excluded: chain H residue 72 CYS Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 129 MET 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 65 optimal weight: 0.4980 chunk 63 optimal weight: 8.9990 chunk 55 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 163 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 155 optimal weight: 0.2980 chunk 147 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN ** 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 = 0.3368 r_free = 0.3368 target = 0.060669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.047789 restraints weight = 59824.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.049318 restraints weight = 30344.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.050314 restraints weight = 19517.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.050996 restraints weight = 14535.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.051363 restraints weight = 11881.147| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3563 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= 0.099 Angle : 0.575 9.744 17767 Z= 0.279 Chirality : 0.041 0.153 2038 Planarity : 0.003 0.040 2282 Dihedral : 4.253 23.202 1812 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.42 % Allowed : 19.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.22), residues: 1653 helix: 1.85 (0.21), residues: 715 sheet: -1.69 (0.33), residues: 259 loop : -1.65 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 360 TYR 0.009 0.001 TYR B 293 PHE 0.010 0.001 PHE H 156 TRP 0.009 0.001 TRP A 45 HIS 0.002 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00226 (13094) covalent geometry : angle 0.57506 (17767) hydrogen bonds : bond 0.02635 ( 500) hydrogen bonds : angle 3.65845 ( 1407) metal coordination : bond 0.00096 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1776.89 seconds wall clock time: 31 minutes 29.90 seconds (1889.90 seconds total)