Starting phenix.real_space_refine on Sun Jun 8 09:16:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tyh_26179/06_2025/7tyh_26179.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyh_26179/06_2025/7tyh_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_26179/06_2025/7tyh_26179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyh_26179/06_2025/7tyh_26179.map" model { file = "/net/cci-nas-00/data/ceres_data/7tyh_26179/06_2025/7tyh_26179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyh_26179/06_2025/7tyh_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 6.29, per 1000 atoms: 0.66 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: 2.57 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.07 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: 2.67 Time building geometry restraints manager: 3.02 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: 1.850 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.590 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.170 ------------------------------------------------------------------------------- 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 0.107 9708 Z= 0.247 Angle : 0.607 11.790 13193 Z= 0.408 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 Details of bonding type rmsd hydrogen bonds : bond 0.30188 ( 357) hydrogen bonds : angle 10.11470 ( 1038) SS BOND : bond 0.00581 ( 8) SS BOND : angle 1.35222 ( 16) covalent geometry : bond 0.00316 ( 9699) covalent geometry : angle 0.60539 (13177) Misc. bond : bond 0.10690 ( 1) *********************** 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 : 1.033 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: 0.2468 time to fit residues: 66.7750 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 : 1.044 ------------------------------------------------------------------------------- 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: 0.9990 chunk 70 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.187721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.155257 restraints weight = 11134.054| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 1.99 r_work: 0.3684 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9708 Z= 0.144 Angle : 0.516 6.172 13193 Z= 0.275 Chirality : 0.042 0.190 1482 Planarity : 0.004 0.055 1698 Dihedral : 4.598 59.896 1356 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.72 % Allowed : 12.15 % Favored : 85.13 % 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: -2.99 (0.21), residues: 1226 helix: -1.56 (0.22), residues: 472 sheet: -2.73 (0.32), residues: 204 loop : -1.93 (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 0.016 0.001 TYR N 80 ARG 0.009 0.001 ARG N 19 Details of bonding type rmsd hydrogen bonds : bond 0.04214 ( 357) hydrogen bonds : angle 5.36505 ( 1038) SS BOND : bond 0.00335 ( 8) SS BOND : angle 1.08141 ( 16) covalent geometry : bond 0.00338 ( 9699) covalent geometry : angle 0.51496 (13177) Misc. bond : bond 0.00014 ( 1) *********************** 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 : 0.975 Fit side-chains REVERT: A 53 LYS cc_start: 0.6603 (ptmt) cc_final: 0.6388 (tttt) REVERT: A 280 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7612 (ptmt) REVERT: B 215 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7786 (pm20) REVERT: B 264 TYR cc_start: 0.7654 (m-80) cc_final: 0.7123 (m-80) REVERT: R 213 ARG cc_start: 0.6612 (mtp85) cc_final: 0.6377 (mtp180) REVERT: R 230 MET cc_start: 0.7145 (ttp) cc_final: 0.6614 (ttm) outliers start: 26 outliers final: 17 residues processed: 189 average time/residue: 0.2139 time to fit residues: 55.9816 Evaluate side-chains 156 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 280 LYS 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 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 70 ILE 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 101 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN G 18 GLN R 144 ASN ** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.183084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.150491 restraints weight = 11390.020| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.05 r_work: 0.3637 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9708 Z= 0.183 Angle : 0.549 7.202 13193 Z= 0.291 Chirality : 0.043 0.167 1482 Planarity : 0.004 0.058 1698 Dihedral : 4.864 59.454 1355 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.66 % Allowed : 14.24 % Favored : 82.09 % 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: -2.43 (0.22), residues: 1226 helix: -0.87 (0.23), residues: 474 sheet: -2.62 (0.32), residues: 204 loop : -1.75 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 234 HIS 0.004 0.001 HIS B 225 PHE 0.018 0.002 PHE R 161 TYR 0.015 0.001 TYR P 12 ARG 0.007 0.001 ARG N 19 Details of bonding type rmsd hydrogen bonds : bond 0.03856 ( 357) hydrogen bonds : angle 4.99669 ( 1038) SS BOND : bond 0.00307 ( 8) SS BOND : angle 1.30778 ( 16) covalent geometry : bond 0.00434 ( 9699) covalent geometry : angle 0.54729 (13177) Misc. bond : bond 0.00019 ( 1) *********************** 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 178 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: A 53 LYS cc_start: 0.6696 (ptmt) cc_final: 0.6478 (tttt) REVERT: A 209 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7682 (mt-10) REVERT: A 280 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7704 (ptmt) REVERT: B 215 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: B 264 TYR cc_start: 0.7785 (m-80) cc_final: 0.7292 (m-80) REVERT: P 8 MET cc_start: 0.7193 (tpt) cc_final: 0.6912 (tpp) REVERT: R 213 ARG cc_start: 0.6784 (mtp85) cc_final: 0.6431 (mtp180) REVERT: R 230 MET cc_start: 0.7236 (ttp) cc_final: 0.6758 (ttm) outliers start: 35 outliers final: 23 residues processed: 165 average time/residue: 0.2197 time to fit residues: 50.7602 Evaluate side-chains 157 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 280 LYS 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 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 B residue 275 SER Chi-restraints excluded: chain N residue 52 SER 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 106 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 86 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 89 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 71 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN N 31 ASN R 144 ASN R 377 HIS R 383 GLN R 405 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.184998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.152156 restraints weight = 11069.821| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 1.97 r_work: 0.3633 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9708 Z= 0.101 Angle : 0.469 7.858 13193 Z= 0.246 Chirality : 0.040 0.144 1482 Planarity : 0.003 0.053 1698 Dihedral : 4.450 56.421 1355 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.14 % Allowed : 16.75 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.85 (0.23), residues: 1226 helix: -0.22 (0.24), residues: 474 sheet: -2.43 (0.32), residues: 205 loop : -1.53 (0.24), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.000 HIS B 225 PHE 0.020 0.001 PHE R 161 TYR 0.016 0.001 TYR P 12 ARG 0.005 0.000 ARG R 174 Details of bonding type rmsd hydrogen bonds : bond 0.03017 ( 357) hydrogen bonds : angle 4.46509 ( 1038) SS BOND : bond 0.00159 ( 8) SS BOND : angle 0.86189 ( 16) covalent geometry : bond 0.00235 ( 9699) covalent geometry : angle 0.46787 (13177) Misc. bond : bond 0.00003 ( 1) *********************** 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 182 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7551 (mt-10) REVERT: B 59 TYR cc_start: 0.8845 (OUTLIER) cc_final: 0.8600 (m-80) REVERT: B 215 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7684 (pm20) REVERT: B 264 TYR cc_start: 0.7536 (m-80) cc_final: 0.6949 (m-80) REVERT: P 8 MET cc_start: 0.6869 (tpt) cc_final: 0.6266 (ttm) REVERT: R 213 ARG cc_start: 0.6588 (mtp85) cc_final: 0.6361 (mtp180) REVERT: R 230 MET cc_start: 0.6945 (ttp) cc_final: 0.6532 (ttm) REVERT: R 376 MET cc_start: 0.8026 (mmm) cc_final: 0.7645 (tpp) outliers start: 30 outliers final: 21 residues processed: 175 average time/residue: 0.2161 time to fit residues: 53.6172 Evaluate side-chains 163 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 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 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER 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 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 252 VAL 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 109 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 4 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN N 31 ASN R 144 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.182860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.149510 restraints weight = 11055.641| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.89 r_work: 0.3625 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9708 Z= 0.146 Angle : 0.515 11.822 13193 Z= 0.268 Chirality : 0.042 0.147 1482 Planarity : 0.004 0.053 1698 Dihedral : 4.626 58.092 1355 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.50 % Allowed : 17.49 % Favored : 78.01 % 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: -1.60 (0.23), residues: 1226 helix: 0.04 (0.25), residues: 469 sheet: -2.29 (0.33), residues: 200 loop : -1.46 (0.24), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS B 142 PHE 0.023 0.001 PHE R 161 TYR 0.014 0.001 TYR P 12 ARG 0.006 0.001 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03183 ( 357) hydrogen bonds : angle 4.53376 ( 1038) SS BOND : bond 0.00188 ( 8) SS BOND : angle 0.87521 ( 16) covalent geometry : bond 0.00349 ( 9699) covalent geometry : angle 0.51450 (13177) Misc. bond : bond 0.00009 ( 1) *********************** 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 181 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 138 time to evaluate : 1.204 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7626 (mt-10) REVERT: B 161 SER cc_start: 0.9392 (m) cc_final: 0.9191 (t) REVERT: B 264 TYR cc_start: 0.7609 (m-80) cc_final: 0.7129 (m-80) REVERT: N 108 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7463 (m-80) REVERT: P 8 MET cc_start: 0.6840 (tpt) cc_final: 0.6238 (ttm) REVERT: R 213 ARG cc_start: 0.6560 (mtp85) cc_final: 0.6348 (mtp180) REVERT: R 230 MET cc_start: 0.6991 (ttp) cc_final: 0.6594 (ttm) REVERT: R 376 MET cc_start: 0.8154 (mmm) cc_final: 0.7827 (tpp) outliers start: 43 outliers final: 33 residues processed: 168 average time/residue: 0.2842 time to fit residues: 67.7039 Evaluate side-chains 165 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 1.266 ------------------------------------------------------------------------------- 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 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER 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 275 SER 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 108 PHE 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 176 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 45 optimal weight: 0.5980 chunk 90 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN N 123 GLN R 144 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.185726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.153253 restraints weight = 11111.240| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.95 r_work: 0.3637 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9708 Z= 0.102 Angle : 0.475 10.400 13193 Z= 0.247 Chirality : 0.040 0.145 1482 Planarity : 0.003 0.048 1698 Dihedral : 4.417 56.798 1355 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.66 % Allowed : 18.32 % Favored : 78.01 % 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: -1.30 (0.24), residues: 1226 helix: 0.39 (0.25), residues: 470 sheet: -2.26 (0.33), residues: 202 loop : -1.33 (0.25), residues: 554 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 0.006 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.02835 ( 357) hydrogen bonds : angle 4.32889 ( 1038) SS BOND : bond 0.00123 ( 8) SS BOND : angle 0.67330 ( 16) covalent geometry : bond 0.00240 ( 9699) covalent geometry : angle 0.47438 (13177) Misc. bond : bond 0.00010 ( 1) *********************** 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 179 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7608 (mt-10) REVERT: A 390 GLN cc_start: 0.7505 (mm-40) cc_final: 0.7277 (mm-40) REVERT: B 59 TYR cc_start: 0.8861 (OUTLIER) cc_final: 0.8580 (m-80) REVERT: B 215 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7611 (pm20) REVERT: B 264 TYR cc_start: 0.7498 (m-80) cc_final: 0.6936 (m-80) REVERT: P 8 MET cc_start: 0.6818 (tpt) cc_final: 0.6248 (ttm) REVERT: R 230 MET cc_start: 0.6966 (ttp) cc_final: 0.6645 (ttm) REVERT: R 255 GLU cc_start: 0.2768 (mt-10) cc_final: 0.2462 (tt0) REVERT: R 376 MET cc_start: 0.8157 (mmm) cc_final: 0.7853 (tpp) outliers start: 35 outliers final: 25 residues processed: 169 average time/residue: 0.2579 time to fit residues: 62.3590 Evaluate side-chains 162 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 1.704 ------------------------------------------------------------------------------- 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 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 215 GLU 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 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 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 8 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 76 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 96 optimal weight: 0.7980 chunk 64 optimal weight: 0.0470 chunk 83 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 111 optimal weight: 0.0770 overall best weight: 0.4036 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.188396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.157096 restraints weight = 11087.471| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.91 r_work: 0.3667 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9708 Z= 0.087 Angle : 0.461 10.149 13193 Z= 0.239 Chirality : 0.040 0.148 1482 Planarity : 0.003 0.048 1698 Dihedral : 4.197 55.114 1353 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.04 % Allowed : 19.58 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.24), residues: 1226 helix: 0.68 (0.25), residues: 474 sheet: -2.14 (0.33), residues: 202 loop : -1.20 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.000 HIS R 381 PHE 0.028 0.001 PHE R 161 TYR 0.014 0.001 TYR N 60 ARG 0.007 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.02648 ( 357) hydrogen bonds : angle 4.14837 ( 1038) SS BOND : bond 0.00095 ( 8) SS BOND : angle 0.57071 ( 16) covalent geometry : bond 0.00201 ( 9699) covalent geometry : angle 0.46127 (13177) Misc. bond : bond 0.00005 ( 1) *********************** 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 172 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7501 (mt-10) REVERT: B 215 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7685 (pm20) REVERT: B 264 TYR cc_start: 0.7447 (m-80) cc_final: 0.6936 (m-80) REVERT: N 74 ASN cc_start: 0.6234 (m-40) cc_final: 0.5736 (t0) REVERT: P 8 MET cc_start: 0.6884 (tpt) cc_final: 0.6370 (ttm) REVERT: R 230 MET cc_start: 0.7007 (ttp) cc_final: 0.6700 (ttm) REVERT: R 255 GLU cc_start: 0.2695 (mt-10) cc_final: 0.2459 (tt0) REVERT: R 306 MET cc_start: 0.8524 (mmm) cc_final: 0.8208 (tpt) outliers start: 29 outliers final: 23 residues processed: 165 average time/residue: 0.1970 time to fit residues: 47.1530 Evaluate side-chains 159 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 73 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 0.0970 chunk 74 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.186768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.155326 restraints weight = 11296.132| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 1.92 r_work: 0.3670 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9708 Z= 0.107 Angle : 0.482 9.734 13193 Z= 0.251 Chirality : 0.041 0.176 1482 Planarity : 0.003 0.048 1698 Dihedral : 3.983 54.952 1351 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % 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: -0.90 (0.24), residues: 1226 helix: 0.77 (0.25), residues: 474 sheet: -2.07 (0.34), residues: 204 loop : -1.16 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS R 381 PHE 0.026 0.001 PHE R 161 TYR 0.013 0.001 TYR P 12 ARG 0.007 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.02759 ( 357) hydrogen bonds : angle 4.18482 ( 1038) SS BOND : bond 0.00105 ( 8) SS BOND : angle 0.63576 ( 16) covalent geometry : bond 0.00254 ( 9699) covalent geometry : angle 0.48222 (13177) Misc. bond : bond 0.00003 ( 1) *********************** 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 171 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 215 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7624 (pm20) REVERT: B 264 TYR cc_start: 0.7533 (m-80) cc_final: 0.7007 (m-80) REVERT: N 90 ASP cc_start: 0.7922 (m-30) cc_final: 0.7650 (m-30) REVERT: P 8 MET cc_start: 0.6666 (tpt) cc_final: 0.6196 (ttm) REVERT: R 230 MET cc_start: 0.6874 (ttp) cc_final: 0.6583 (ttm) REVERT: R 255 GLU cc_start: 0.2707 (mt-10) cc_final: 0.2461 (tt0) REVERT: R 306 MET cc_start: 0.8401 (mmm) cc_final: 0.8056 (tpt) outliers start: 33 outliers final: 31 residues processed: 161 average time/residue: 0.1945 time to fit residues: 45.4513 Evaluate side-chains 165 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 14 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL 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 184 THR Chi-restraints excluded: chain B residue 215 GLU 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 61 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 71 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.186466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.154183 restraints weight = 11055.433| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 1.98 r_work: 0.3669 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9708 Z= 0.110 Angle : 0.486 9.658 13193 Z= 0.255 Chirality : 0.041 0.329 1482 Planarity : 0.003 0.047 1698 Dihedral : 4.012 54.117 1351 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.66 % Allowed : 19.27 % Favored : 77.07 % 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: -0.91 (0.24), residues: 1226 helix: 0.73 (0.25), residues: 481 sheet: -2.01 (0.33), residues: 203 loop : -1.18 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.000 HIS R 381 PHE 0.024 0.001 PHE R 161 TYR 0.013 0.001 TYR P 12 ARG 0.007 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.02825 ( 357) hydrogen bonds : angle 4.26804 ( 1038) SS BOND : bond 0.00101 ( 8) SS BOND : angle 0.64078 ( 16) covalent geometry : bond 0.00266 ( 9699) covalent geometry : angle 0.48621 (13177) Misc. bond : bond 0.00013 ( 1) *********************** 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 170 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 215 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7651 (pm20) REVERT: B 226 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7306 (mt-10) REVERT: B 264 TYR cc_start: 0.7458 (m-80) cc_final: 0.6947 (m-80) REVERT: N 74 ASN cc_start: 0.6239 (m-40) cc_final: 0.5667 (t0) REVERT: N 90 ASP cc_start: 0.7940 (m-30) cc_final: 0.7688 (m-30) REVERT: P 8 MET cc_start: 0.6799 (tpt) cc_final: 0.6324 (ttm) REVERT: R 230 MET cc_start: 0.6998 (ttp) cc_final: 0.6699 (ttm) REVERT: R 255 GLU cc_start: 0.2708 (mt-10) cc_final: 0.2437 (tt0) REVERT: R 306 MET cc_start: 0.8406 (mmm) cc_final: 0.8091 (tpt) outliers start: 35 outliers final: 29 residues processed: 162 average time/residue: 0.2056 time to fit residues: 48.2984 Evaluate side-chains 162 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 1.581 ------------------------------------------------------------------------------- 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 14 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN 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 B residue 275 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 58 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 109 optimal weight: 0.0970 chunk 3 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.187190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.154946 restraints weight = 11170.754| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.93 r_work: 0.3674 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9708 Z= 0.105 Angle : 0.492 9.432 13193 Z= 0.256 Chirality : 0.041 0.300 1482 Planarity : 0.003 0.048 1698 Dihedral : 3.985 53.551 1351 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.14 % Allowed : 20.31 % Favored : 76.54 % 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: -0.81 (0.24), residues: 1226 helix: 0.84 (0.25), residues: 481 sheet: -1.98 (0.33), residues: 207 loop : -1.14 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.000 HIS R 381 PHE 0.025 0.001 PHE R 161 TYR 0.013 0.001 TYR P 12 ARG 0.007 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.02782 ( 357) hydrogen bonds : angle 4.25688 ( 1038) SS BOND : bond 0.00094 ( 8) SS BOND : angle 0.61514 ( 16) covalent geometry : bond 0.00252 ( 9699) covalent geometry : angle 0.49196 (13177) Misc. bond : bond 0.00003 ( 1) ********************** 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 166 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 215 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7627 (pm20) REVERT: B 226 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7268 (mt-10) REVERT: B 264 TYR cc_start: 0.7453 (m-80) cc_final: 0.6894 (m-80) REVERT: N 74 ASN cc_start: 0.6282 (m-40) cc_final: 0.5669 (t0) REVERT: N 90 ASP cc_start: 0.7883 (m-30) cc_final: 0.7645 (m-30) REVERT: P 8 MET cc_start: 0.6646 (tpt) cc_final: 0.6190 (ttm) REVERT: R 230 MET cc_start: 0.6892 (ttp) cc_final: 0.6600 (ttm) REVERT: R 255 GLU cc_start: 0.2664 (mt-10) cc_final: 0.2445 (tt0) REVERT: R 306 MET cc_start: 0.8277 (mmm) cc_final: 0.7969 (tpt) outliers start: 30 outliers final: 28 residues processed: 160 average time/residue: 0.1970 time to fit residues: 45.8137 Evaluate side-chains 160 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 14 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN 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 B residue 275 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 50 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 0.0040 chunk 86 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 67 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 115 optimal weight: 0.5980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN R 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.187895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.155581 restraints weight = 11093.868| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 1.93 r_work: 0.3683 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 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 : 0.002 0.057 9708 Z= 0.099 Angle : 0.487 9.295 13193 Z= 0.254 Chirality : 0.041 0.275 1482 Planarity : 0.003 0.048 1698 Dihedral : 3.939 53.560 1351 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.93 % Allowed : 20.73 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.75 (0.24), residues: 1226 helix: 0.92 (0.25), residues: 481 sheet: -1.95 (0.33), residues: 207 loop : -1.13 (0.25), residues: 538 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 0.024 0.001 PHE R 161 TYR 0.013 0.001 TYR P 12 ARG 0.007 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.02751 ( 357) hydrogen bonds : angle 4.22817 ( 1038) SS BOND : bond 0.00089 ( 8) SS BOND : angle 0.58973 ( 16) covalent geometry : bond 0.00237 ( 9699) covalent geometry : angle 0.48713 (13177) Misc. bond : bond 0.00001 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6041.57 seconds wall clock time: 106 minutes 5.89 seconds (6365.89 seconds total)