Starting phenix.real_space_refine on Sun Dec 29 00:41:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tyh_26179/12_2024/7tyh_26179.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyh_26179/12_2024/7tyh_26179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tyh_26179/12_2024/7tyh_26179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyh_26179/12_2024/7tyh_26179.map" model { file = "/net/cci-nas-00/data/ceres_data/7tyh_26179/12_2024/7tyh_26179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyh_26179/12_2024/7tyh_26179.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 6015 2.51 5 N 1663 2.21 5 O 1746 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9492 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1894 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2598 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 413 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 514 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 6, 'TRANS': 90} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 317 Unresolved non-hydrogen angles: 414 Unresolved non-hydrogen dihedrals: 272 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 3, 'ASP:plan': 6, 'PHE:plan': 7, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 186 Chain: "P" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 238 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2867 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 17, 'TRANS': 351} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 260 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 122 Time building chain proxies: 5.94, per 1000 atoms: 0.63 Number of scatterers: 9492 At special positions: 0 Unit cell: (89.88, 102.72, 156.648, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 1746 8.00 N 1663 7.00 C 6015 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.01 Simple disulfide: pdb=" SG CYS E 68 " - pdb=" SG CYS E 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 131 " distance=2.03 Simple disulfide: pdb=" SG CYS P 1 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 956.2 milliseconds 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2350 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 12 sheets defined 40.4% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 4.162A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 27 " --> pdb=" O ASN A 23 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 57 removed outlier: 3.537A pdb=" N ILE A 56 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL A 57 " --> pdb=" O ASN A 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 53 through 57' Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.689A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 238 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 239' Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.729A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 301 removed outlier: 3.843A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 311 removed outlier: 3.960A pdb=" N ASP A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.248A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.639A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.518A pdb=" N ARG B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 22 removed outlier: 3.821A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 34 through 44 removed outlier: 3.588A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 77 removed outlier: 3.608A pdb=" N GLN E 66 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE E 67 " --> pdb=" O THR E 63 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN E 70 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N HIS E 71 " --> pdb=" O PHE E 67 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS E 73 " --> pdb=" O TRP E 69 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP E 77 " --> pdb=" O LYS E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 80 No H-bonds generated for 'chain 'E' and resid 78 through 80' Processing helix chain 'E' and resid 89 through 104 removed outlier: 3.551A pdb=" N TYR E 93 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU E 96 " --> pdb=" O PRO E 92 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG E 97 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP E 98 " --> pdb=" O SER E 94 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N CYS E 99 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU E 100 " --> pdb=" O LEU E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 127 removed outlier: 3.602A pdb=" N ARG E 118 " --> pdb=" O PRO E 114 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS E 124 " --> pdb=" O ILE E 120 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN E 125 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS E 127 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 156 removed outlier: 3.531A pdb=" N ALA E 152 " --> pdb=" O ALA E 148 " (cutoff:3.500A) Proline residue: E 153 - end of helix Processing helix chain 'E' and resid 157 through 166 removed outlier: 3.551A pdb=" N LEU E 163 " --> pdb=" O PHE E 159 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL E 165 " --> pdb=" O ILE E 161 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 22 removed outlier: 3.659A pdb=" N ASN P 17 " --> pdb=" O THR P 13 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE P 19 " --> pdb=" O ASP P 15 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N HIS P 20 " --> pdb=" O PHE P 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 62 removed outlier: 3.753A pdb=" N ASP R 50 " --> pdb=" O LYS R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 136 removed outlier: 3.925A pdb=" N ASN R 135 " --> pdb=" O TYR R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 162 removed outlier: 3.572A pdb=" N LYS R 143 " --> pdb=" O PRO R 139 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU R 148 " --> pdb=" O ASN R 144 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS R 156 " --> pdb=" O ALA R 152 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER R 159 " --> pdb=" O GLY R 155 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE R 160 " --> pdb=" O HIS R 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 171 removed outlier: 4.246A pdb=" N PHE R 170 " --> pdb=" O SER R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 205 removed outlier: 3.720A pdb=" N ILE R 199 " --> pdb=" O SER R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 214 removed outlier: 3.796A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 246 removed outlier: 3.991A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET R 237 " --> pdb=" O ASN R 233 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU R 238 " --> pdb=" O TYR R 234 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU R 244 " --> pdb=" O GLU R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 268 removed outlier: 3.584A pdb=" N TRP R 267 " --> pdb=" O TYR R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 284 removed outlier: 3.539A pdb=" N VAL R 283 " --> pdb=" O ILE R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 315 Proline residue: R 304 - end of helix removed outlier: 3.789A pdb=" N VAL R 310 " --> pdb=" O MET R 306 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL R 311 " --> pdb=" O ALA R 307 " (cutoff:3.500A) Processing helix chain 'R' and resid 318 through 329 Processing helix chain 'R' and resid 333 through 338 removed outlier: 3.941A pdb=" N TYR R 338 " --> pdb=" O GLU R 334 " (cutoff:3.500A) Processing helix chain 'R' and resid 338 through 344 removed outlier: 3.798A pdb=" N LYS R 343 " --> pdb=" O LEU R 339 " (cutoff:3.500A) Processing helix chain 'R' and resid 344 through 353 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 365 through 382 removed outlier: 3.797A pdb=" N GLY R 369 " --> pdb=" O ASN R 365 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ILE R 371 " --> pdb=" O MET R 367 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR R 374 " --> pdb=" O LYS R 370 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS R 377 " --> pdb=" O ASP R 373 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER R 378 " --> pdb=" O TYR R 374 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU R 379 " --> pdb=" O VAL R 375 " (cutoff:3.500A) Processing helix chain 'R' and resid 382 through 389 Processing helix chain 'R' and resid 395 through 400 Processing helix chain 'R' and resid 400 through 405 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 213 removed outlier: 3.539A pdb=" N PHE A 222 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 45 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.927A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.919A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.368A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.959A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.155A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.679A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 275 removed outlier: 3.553A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.575A pdb=" N VAL N 12 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 17 through 19 Processing sheet with id=AB3, first strand: chain 'R' and resid 75 through 76 removed outlier: 3.533A pdb=" N THR R 75 " --> pdb=" O TRP R 82 " (cutoff:3.500A) 357 hydrogen bonds defined for protein. 1038 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: 2.61 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1556 1.31 - 1.44: 2703 1.44 - 1.56: 5345 1.56 - 1.69: 0 1.69 - 1.81: 95 Bond restraints: 9699 Sorted by residual: bond pdb=" C PRO N 100 " pdb=" O PRO N 100 " ideal model delta sigma weight residual 1.237 1.189 0.049 1.26e-02 6.30e+03 1.49e+01 bond pdb=" N ARG N 98 " pdb=" CA ARG N 98 " ideal model delta sigma weight residual 1.455 1.500 -0.045 1.21e-02 6.83e+03 1.36e+01 bond pdb=" N ASP N 106 " pdb=" CA ASP N 106 " ideal model delta sigma weight residual 1.455 1.498 -0.043 1.22e-02 6.72e+03 1.24e+01 bond pdb=" N ILE A 276 " pdb=" CA ILE A 276 " ideal model delta sigma weight residual 1.460 1.497 -0.038 1.21e-02 6.83e+03 9.65e+00 bond pdb=" N CYS P 7 " pdb=" CA CYS P 7 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.18e-02 7.18e+03 9.22e+00 ... (remaining 9694 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 12985 2.36 - 4.72: 174 4.72 - 7.07: 15 7.07 - 9.43: 2 9.43 - 11.79: 1 Bond angle restraints: 13177 Sorted by residual: angle pdb=" CA PRO P 32 " pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 112.00 100.21 11.79 1.40e+00 5.10e-01 7.09e+01 angle pdb=" N PRO N 102 " pdb=" CA PRO N 102 " pdb=" C PRO N 102 " ideal model delta sigma weight residual 111.77 120.11 -8.34 1.67e+00 3.59e-01 2.49e+01 angle pdb=" CA PRO N 102 " pdb=" C PRO N 102 " pdb=" O PRO N 102 " ideal model delta sigma weight residual 122.13 116.49 5.64 1.23e+00 6.61e-01 2.10e+01 angle pdb=" CA VAL N 110 " pdb=" C VAL N 110 " pdb=" O VAL N 110 " ideal model delta sigma weight residual 120.85 116.37 4.48 1.06e+00 8.90e-01 1.78e+01 angle pdb=" CA PRO N 102 " pdb=" C PRO N 102 " pdb=" N PHE N 103 " ideal model delta sigma weight residual 114.58 119.39 -4.81 1.16e+00 7.43e-01 1.72e+01 ... (remaining 13172 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5337 17.98 - 35.97: 336 35.97 - 53.95: 58 53.95 - 71.93: 12 71.93 - 89.91: 6 Dihedral angle restraints: 5749 sinusoidal: 2117 harmonic: 3632 Sorted by residual: dihedral pdb=" CB CYS P 1 " pdb=" SG CYS P 1 " pdb=" SG CYS P 7 " pdb=" CB CYS P 7 " ideal model delta sinusoidal sigma weight residual 93.00 154.15 -61.15 1 1.00e+01 1.00e-02 4.97e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -127.86 41.86 1 1.00e+01 1.00e-02 2.45e+01 dihedral pdb=" CA ASP N 106 " pdb=" CB ASP N 106 " pdb=" CG ASP N 106 " pdb=" OD1 ASP N 106 " ideal model delta sinusoidal sigma weight residual -30.00 -87.44 57.44 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 5746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1085 0.041 - 0.081: 274 0.081 - 0.122: 104 0.122 - 0.163: 14 0.163 - 0.204: 5 Chirality restraints: 1482 Sorted by residual: chirality pdb=" CA PRO P 32 " pdb=" N PRO P 32 " pdb=" C PRO P 32 " pdb=" CB PRO P 32 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA MET P 8 " pdb=" N MET P 8 " pdb=" C MET P 8 " pdb=" CB MET P 8 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.41e-01 chirality pdb=" CA LEU P 4 " pdb=" N LEU P 4 " pdb=" C LEU P 4 " pdb=" CB LEU P 4 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.11e-01 ... (remaining 1479 not shown) Planarity restraints: 1698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA P 31 " -0.117 5.00e-02 4.00e+02 1.67e-01 4.47e+01 pdb=" N PRO P 32 " 0.289 5.00e-02 4.00e+02 pdb=" CA PRO P 32 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO P 32 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO N 100 " -0.009 2.00e-02 2.50e+03 1.98e-02 3.90e+00 pdb=" C PRO N 100 " 0.034 2.00e-02 2.50e+03 pdb=" O PRO N 100 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA N 101 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 234 " 0.018 2.00e-02 2.50e+03 1.19e-02 3.54e+00 pdb=" CG TRP A 234 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 234 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP A 234 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 234 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 234 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 234 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 234 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 234 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 234 " -0.001 2.00e-02 2.50e+03 ... (remaining 1695 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2607 2.80 - 3.32: 8568 3.32 - 3.85: 15089 3.85 - 4.37: 18611 4.37 - 4.90: 31274 Nonbonded interactions: 76149 Sorted by model distance: nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.274 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.306 3.040 nonbonded pdb=" O CYS B 204 " pdb=" OH TYR N 117 " model vdw 2.315 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.321 3.040 nonbonded pdb=" O ALA A 48 " pdb=" OG SER A 51 " model vdw 2.328 3.040 ... (remaining 76144 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 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: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 23.510 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 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 : 0.003 0.053 9699 Z= 0.208 Angle : 0.605 11.790 13177 Z= 0.407 Chirality : 0.043 0.204 1482 Planarity : 0.005 0.167 1698 Dihedral : 12.285 89.913 3375 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.05 % Allowed : 7.96 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.19), residues: 1226 helix: -3.18 (0.18), residues: 442 sheet: -3.15 (0.31), residues: 197 loop : -2.32 (0.22), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 234 HIS 0.002 0.000 HIS R 302 PHE 0.024 0.001 PHE N 108 TYR 0.021 0.001 TYR N 115 ARG 0.002 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 190 time to evaluate : 1.625 Fit side-chains revert: symmetry clash REVERT: R 230 MET cc_start: 0.7125 (ttp) cc_final: 0.6373 (ttm) REVERT: R 255 GLU cc_start: 0.3382 (mt-10) cc_final: 0.3129 (tt0) REVERT: R 340 LYS cc_start: 0.7578 (mmmm) cc_final: 0.7312 (mmtm) outliers start: 10 outliers final: 7 residues processed: 200 average time/residue: 0.2556 time to fit residues: 68.9028 Evaluate side-chains 152 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 145 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain R residue 349 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 6.9990 chunk 90 optimal weight: 0.0770 chunk 50 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 230 ASN G 18 GLN N 31 ASN E 124 HIS P 17 ASN R 93 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9699 Z= 0.239 Angle : 0.523 6.346 13177 Z= 0.280 Chirality : 0.042 0.156 1482 Planarity : 0.004 0.053 1698 Dihedral : 4.622 59.819 1356 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.72 % Allowed : 12.46 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.21), residues: 1226 helix: -1.55 (0.22), residues: 472 sheet: -2.75 (0.32), residues: 204 loop : -1.94 (0.23), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.004 0.001 HIS R 381 PHE 0.016 0.001 PHE N 108 TYR 0.018 0.001 TYR N 80 ARG 0.009 0.001 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 1.026 Fit side-chains REVERT: B 264 TYR cc_start: 0.7385 (m-80) cc_final: 0.6934 (m-80) REVERT: R 230 MET cc_start: 0.6984 (ttp) cc_final: 0.6514 (ttm) outliers start: 26 outliers final: 16 residues processed: 189 average time/residue: 0.2322 time to fit residues: 60.9690 Evaluate side-chains 150 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain R residue 375 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN R 144 ASN ** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 405 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9699 Z= 0.227 Angle : 0.513 7.425 13177 Z= 0.271 Chirality : 0.042 0.167 1482 Planarity : 0.004 0.058 1698 Dihedral : 4.655 58.841 1355 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.46 % Allowed : 14.24 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.22), residues: 1226 helix: -0.75 (0.23), residues: 474 sheet: -2.57 (0.32), residues: 204 loop : -1.72 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.019 0.001 PHE R 161 TYR 0.016 0.001 TYR P 12 ARG 0.006 0.001 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6785 (mt-10) REVERT: B 264 TYR cc_start: 0.7392 (m-80) cc_final: 0.7061 (m-80) REVERT: P 8 MET cc_start: 0.7039 (tpt) cc_final: 0.6785 (tpp) REVERT: R 230 MET cc_start: 0.7029 (ttp) cc_final: 0.6573 (ttm) outliers start: 33 outliers final: 23 residues processed: 167 average time/residue: 0.2047 time to fit residues: 48.8890 Evaluate side-chains 157 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain R residue 375 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN B 175 GLN N 31 ASN R 144 ASN R 233 ASN ** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 383 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 9699 Z= 0.312 Angle : 0.567 9.922 13177 Z= 0.298 Chirality : 0.044 0.146 1482 Planarity : 0.004 0.056 1698 Dihedral : 5.012 58.718 1355 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.08 % Allowed : 17.38 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.23), residues: 1226 helix: -0.57 (0.24), residues: 474 sheet: -2.44 (0.32), residues: 211 loop : -1.69 (0.24), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.004 0.001 HIS B 142 PHE 0.022 0.002 PHE R 161 TYR 0.016 0.002 TYR P 12 ARG 0.006 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: B 264 TYR cc_start: 0.7458 (m-80) cc_final: 0.7154 (m-80) REVERT: P 8 MET cc_start: 0.7073 (tpt) cc_final: 0.6544 (ttm) REVERT: R 204 GLU cc_start: 0.6046 (OUTLIER) cc_final: 0.5761 (tt0) REVERT: R 230 MET cc_start: 0.6935 (ttp) cc_final: 0.6570 (ttm) outliers start: 39 outliers final: 30 residues processed: 165 average time/residue: 0.2052 time to fit residues: 48.5311 Evaluate side-chains 159 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 204 GLU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain R residue 375 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 86 optimal weight: 20.0000 chunk 47 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 0 optimal weight: 0.8980 chunk 59 optimal weight: 0.1980 chunk 104 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 175 GLN R 144 ASN R 233 ASN ** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9699 Z= 0.184 Angle : 0.487 8.030 13177 Z= 0.256 Chirality : 0.041 0.146 1482 Planarity : 0.004 0.052 1698 Dihedral : 4.615 57.254 1355 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.46 % Allowed : 19.37 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.23), residues: 1226 helix: -0.02 (0.25), residues: 469 sheet: -2.36 (0.33), residues: 201 loop : -1.49 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 381 PHE 0.024 0.001 PHE R 161 TYR 0.015 0.001 TYR P 12 ARG 0.005 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 1.118 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6780 (mt-10) REVERT: B 264 TYR cc_start: 0.7315 (m-80) cc_final: 0.6984 (m-80) REVERT: N 108 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.7666 (m-80) REVERT: P 8 MET cc_start: 0.7049 (tpt) cc_final: 0.6514 (ttm) REVERT: R 230 MET cc_start: 0.6933 (ttp) cc_final: 0.6576 (ttm) outliers start: 33 outliers final: 23 residues processed: 166 average time/residue: 0.2122 time to fit residues: 50.1869 Evaluate side-chains 154 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain R residue 375 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 53 optimal weight: 0.3980 chunk 9 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN ** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9699 Z= 0.172 Angle : 0.483 8.186 13177 Z= 0.252 Chirality : 0.041 0.143 1482 Planarity : 0.003 0.049 1698 Dihedral : 4.500 57.522 1355 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.14 % Allowed : 20.21 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.24), residues: 1226 helix: 0.25 (0.25), residues: 470 sheet: -2.31 (0.33), residues: 200 loop : -1.36 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.000 HIS R 381 PHE 0.026 0.001 PHE R 161 TYR 0.015 0.001 TYR P 12 ARG 0.007 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 264 TYR cc_start: 0.7206 (m-80) cc_final: 0.6908 (m-80) REVERT: P 8 MET cc_start: 0.7003 (tpt) cc_final: 0.6491 (ttm) REVERT: R 230 MET cc_start: 0.6898 (ttp) cc_final: 0.6546 (ttm) outliers start: 30 outliers final: 26 residues processed: 164 average time/residue: 0.2071 time to fit residues: 48.8844 Evaluate side-chains 161 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain R residue 375 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 115 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN ** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9699 Z= 0.159 Angle : 0.482 9.504 13177 Z= 0.250 Chirality : 0.040 0.141 1482 Planarity : 0.003 0.049 1698 Dihedral : 4.360 56.624 1353 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.56 % Allowed : 20.00 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.24), residues: 1226 helix: 0.49 (0.25), residues: 469 sheet: -2.21 (0.33), residues: 201 loop : -1.30 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.000 HIS R 381 PHE 0.028 0.001 PHE R 161 TYR 0.015 0.001 TYR N 60 ARG 0.007 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 226 GLU cc_start: 0.6836 (mt-10) cc_final: 0.6572 (mt-10) REVERT: B 264 TYR cc_start: 0.7173 (m-80) cc_final: 0.6916 (m-80) REVERT: G 22 GLU cc_start: 0.6479 (mt-10) cc_final: 0.6171 (mt-10) REVERT: P 8 MET cc_start: 0.7002 (tpt) cc_final: 0.6497 (ttm) REVERT: R 204 GLU cc_start: 0.5960 (OUTLIER) cc_final: 0.5575 (tt0) REVERT: R 230 MET cc_start: 0.6885 (ttp) cc_final: 0.6583 (ttm) REVERT: R 306 MET cc_start: 0.8494 (mmm) cc_final: 0.8290 (tpt) outliers start: 34 outliers final: 30 residues processed: 163 average time/residue: 0.2042 time to fit residues: 48.4075 Evaluate side-chains 165 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 204 GLU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain R residue 375 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.0470 chunk 46 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 0.0060 chunk 73 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 105 optimal weight: 0.0870 overall best weight: 0.3872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN P 17 ASN R 144 ASN R 377 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9699 Z= 0.131 Angle : 0.469 8.945 13177 Z= 0.241 Chirality : 0.040 0.137 1482 Planarity : 0.003 0.047 1698 Dihedral : 4.151 54.617 1353 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.41 % Allowed : 21.47 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.24), residues: 1226 helix: 0.70 (0.25), residues: 480 sheet: -2.03 (0.34), residues: 194 loop : -1.29 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.000 HIS R 381 PHE 0.031 0.001 PHE R 161 TYR 0.013 0.001 TYR P 12 ARG 0.006 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7776 (tp40) cc_final: 0.7330 (mm-40) REVERT: B 226 GLU cc_start: 0.6758 (mt-10) cc_final: 0.6510 (mt-10) REVERT: B 264 TYR cc_start: 0.7077 (m-80) cc_final: 0.6817 (m-80) REVERT: G 22 GLU cc_start: 0.6396 (mt-10) cc_final: 0.6135 (mt-10) REVERT: N 90 ASP cc_start: 0.7904 (m-30) cc_final: 0.7674 (m-30) REVERT: N 111 THR cc_start: 0.8095 (p) cc_final: 0.7826 (p) REVERT: P 8 MET cc_start: 0.6986 (tpt) cc_final: 0.6508 (ttm) REVERT: R 230 MET cc_start: 0.6794 (ttp) cc_final: 0.6535 (ttm) REVERT: R 306 MET cc_start: 0.8334 (mmm) cc_final: 0.8075 (tpt) outliers start: 23 outliers final: 20 residues processed: 162 average time/residue: 0.2065 time to fit residues: 47.9307 Evaluate side-chains 156 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain R residue 375 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9699 Z= 0.235 Angle : 0.531 9.268 13177 Z= 0.276 Chirality : 0.043 0.356 1482 Planarity : 0.004 0.047 1698 Dihedral : 4.460 54.917 1353 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.04 % Allowed : 21.26 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.24), residues: 1226 helix: 0.65 (0.25), residues: 473 sheet: -2.09 (0.33), residues: 204 loop : -1.17 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.002 0.001 HIS B 142 PHE 0.029 0.001 PHE R 161 TYR 0.014 0.001 TYR P 12 ARG 0.007 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 1.070 Fit side-chains revert: symmetry clash REVERT: B 226 GLU cc_start: 0.6907 (mt-10) cc_final: 0.6620 (mt-10) REVERT: B 264 TYR cc_start: 0.7311 (m-80) cc_final: 0.7052 (m-80) REVERT: N 90 ASP cc_start: 0.7978 (m-30) cc_final: 0.7776 (m-30) REVERT: P 8 MET cc_start: 0.7024 (tpt) cc_final: 0.6479 (ttm) REVERT: R 204 GLU cc_start: 0.5987 (OUTLIER) cc_final: 0.5698 (tt0) REVERT: R 230 MET cc_start: 0.6797 (ttp) cc_final: 0.6441 (ttm) outliers start: 29 outliers final: 27 residues processed: 153 average time/residue: 0.2013 time to fit residues: 44.9624 Evaluate side-chains 158 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain R residue 204 GLU Chi-restraints excluded: chain R residue 246 THR Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain R residue 375 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 4.9990 chunk 79 optimal weight: 0.0870 chunk 119 optimal weight: 1.9990 chunk 110 optimal weight: 0.3980 chunk 95 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 58 optimal weight: 0.4980 chunk 75 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 29 optimal weight: 0.0070 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN R 156 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 9699 Z= 0.139 Angle : 0.489 8.819 13177 Z= 0.253 Chirality : 0.041 0.310 1482 Planarity : 0.003 0.046 1698 Dihedral : 4.197 54.234 1353 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.20 % Allowed : 22.09 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.24), residues: 1226 helix: 0.81 (0.25), residues: 481 sheet: -2.00 (0.34), residues: 198 loop : -1.17 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.000 HIS A 220 PHE 0.029 0.001 PHE R 161 TYR 0.013 0.001 TYR P 12 ARG 0.007 0.000 ARG A 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: B 226 GLU cc_start: 0.6814 (mt-10) cc_final: 0.6546 (mt-10) REVERT: B 264 TYR cc_start: 0.7116 (m-80) cc_final: 0.6835 (m-80) REVERT: G 22 GLU cc_start: 0.6402 (mt-10) cc_final: 0.6116 (mt-10) REVERT: N 111 THR cc_start: 0.8166 (p) cc_final: 0.7935 (p) REVERT: P 8 MET cc_start: 0.6927 (tpt) cc_final: 0.6653 (tpp) REVERT: R 230 MET cc_start: 0.6755 (ttp) cc_final: 0.6550 (ttm) REVERT: R 306 MET cc_start: 0.8306 (tpt) cc_final: 0.8002 (tpt) outliers start: 21 outliers final: 20 residues processed: 157 average time/residue: 0.2032 time to fit residues: 46.6396 Evaluate side-chains 154 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain R residue 375 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.0470 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN R 144 ASN R 156 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.191544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.158035 restraints weight = 10945.772| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.01 r_work: 0.3640 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9699 Z= 0.190 Angle : 0.507 8.914 13177 Z= 0.265 Chirality : 0.042 0.310 1482 Planarity : 0.003 0.049 1698 Dihedral : 4.328 54.603 1353 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.83 % Allowed : 21.78 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.24), residues: 1226 helix: 0.89 (0.25), residues: 472 sheet: -2.00 (0.34), residues: 205 loop : -1.11 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS A 220 PHE 0.029 0.001 PHE R 161 TYR 0.014 0.001 TYR P 12 ARG 0.007 0.000 ARG A 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2302.50 seconds wall clock time: 42 minutes 47.49 seconds (2567.49 seconds total)