Starting phenix.real_space_refine on Sat Dec 28 21:25:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yj1_33868/12_2024/7yj1_33868.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yj1_33868/12_2024/7yj1_33868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yj1_33868/12_2024/7yj1_33868.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yj1_33868/12_2024/7yj1_33868.map" model { file = "/net/cci-nas-00/data/ceres_data/7yj1_33868/12_2024/7yj1_33868.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yj1_33868/12_2024/7yj1_33868.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 50 5.16 5 C 5889 2.51 5 N 1545 2.21 5 O 1655 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9140 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3962 Classifications: {'peptide': 502} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 483} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1165 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 8, 'TRANS': 134} Chain: "C" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 411 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain: "A" Number of atoms: 3285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3285 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 401} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 5.58, per 1000 atoms: 0.61 Number of scatterers: 9140 At special positions: 0 Unit cell: (92.88, 83.16, 123.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 P 1 15.00 O 1655 8.00 N 1545 7.00 C 5889 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.0 seconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 10 sheets defined 48.0% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'B' and resid 67 through 95 removed outlier: 3.592A pdb=" N THR B 74 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B 76 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TRP B 94 " --> pdb=" O PHE B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 removed outlier: 4.029A pdb=" N LYS B 109 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 177 through 181 removed outlier: 4.134A pdb=" N PHE B 181 " --> pdb=" O TYR B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 195 removed outlier: 3.668A pdb=" N ALA B 191 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.769A pdb=" N GLU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 243 removed outlier: 3.942A pdb=" N ASN B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 243 " --> pdb=" O PHE B 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 238 through 243' Processing helix chain 'B' and resid 245 through 249 Processing helix chain 'B' and resid 263 through 274 removed outlier: 3.832A pdb=" N GLY B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 292 Processing helix chain 'B' and resid 326 through 337 removed outlier: 3.690A pdb=" N LYS B 336 " --> pdb=" O ALA B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 364 Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.867A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 399 removed outlier: 3.573A pdb=" N TYR B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 408 removed outlier: 3.663A pdb=" N VAL B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 427 removed outlier: 3.622A pdb=" N GLN B 418 " --> pdb=" O PRO B 414 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS B 425 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET B 427 " --> pdb=" O MET B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 455 removed outlier: 3.718A pdb=" N VAL B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG B 452 " --> pdb=" O TYR B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 489 removed outlier: 3.728A pdb=" N GLY B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG B 484 " --> pdb=" O GLY B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 536 Processing helix chain 'E' and resid 11 through 20 removed outlier: 3.949A pdb=" N GLN E 15 " --> pdb=" O VAL E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 38 removed outlier: 3.709A pdb=" N LEU E 25 " --> pdb=" O PRO E 21 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU E 27 " --> pdb=" O TYR E 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 39 removed outlier: 3.622A pdb=" N ILE D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 37 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 66 Processing helix chain 'D' and resid 88 through 93 Processing helix chain 'D' and resid 96 through 116 removed outlier: 3.664A pdb=" N THR D 103 " --> pdb=" O ARG D 99 " (cutoff:3.500A) Proline residue: D 106 - end of helix removed outlier: 3.512A pdb=" N TYR D 110 " --> pdb=" O PRO D 106 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU D 112 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 134 removed outlier: 3.598A pdb=" N SER D 133 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 143 Proline residue: D 140 - end of helix removed outlier: 3.831A pdb=" N HIS D 143 " --> pdb=" O PRO D 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.537A pdb=" N TRP C 15 " --> pdb=" O LYS C 11 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE C 16 " --> pdb=" O GLN C 12 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR C 24 " --> pdb=" O TYR C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 55 removed outlier: 3.790A pdb=" N VAL C 36 " --> pdb=" O TRP C 32 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE C 37 " --> pdb=" O GLU C 33 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE C 44 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR C 51 " --> pdb=" O MET C 47 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.632A pdb=" N GLU A 58 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TRP A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 129 removed outlier: 4.077A pdb=" N SER A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 157 removed outlier: 3.729A pdb=" N ALA A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 154 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.783A pdb=" N ALA A 172 " --> pdb=" O PHE A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 179 removed outlier: 3.712A pdb=" N TYR A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 213 through 230 removed outlier: 3.564A pdb=" N LEU A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 268 removed outlier: 4.064A pdb=" N LYS A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR A 265 " --> pdb=" O VAL A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 296 through 300 removed outlier: 3.723A pdb=" N ILE A 300 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.670A pdb=" N ASP A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 330 removed outlier: 3.564A pdb=" N LEU A 330 " --> pdb=" O HIS A 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 327 through 330' Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 359 removed outlier: 3.509A pdb=" N GLU A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 377 removed outlier: 3.684A pdb=" N VAL A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A 369 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N HIS A 374 " --> pdb=" O CYS A 370 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS A 375 " --> pdb=" O GLY A 371 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A 376 " --> pdb=" O GLN A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 420 removed outlier: 3.956A pdb=" N ASP A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 467 removed outlier: 3.641A pdb=" N LYS A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL A 467 " --> pdb=" O THR A 463 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 48 removed outlier: 3.646A pdb=" N HIS B 47 " --> pdb=" O TYR B 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 61 through 62 removed outlier: 3.617A pdb=" N ALA B 62 " --> pdb=" O GLY B 462 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.102A pdb=" N VAL B 146 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY B 169 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 148 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ASN B 165 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N GLN B 152 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR B 163 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N GLY B 492 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE B 171 " --> pdb=" O GLY B 492 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 231 through 234 removed outlier: 6.625A pdb=" N LEU B 341 " --> pdb=" O VAL B 372 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N MET B 374 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU B 343 " --> pdb=" O MET B 374 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N THR B 376 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP B 259 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N GLU B 315 " --> pdb=" O ASP B 259 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE B 256 " --> pdb=" O ARG B 278 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N PHE B 280 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N SER B 258 " --> pdb=" O PHE B 280 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 317 through 318 removed outlier: 3.567A pdb=" N SER B 323 " --> pdb=" O TYR B 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 471 through 472 removed outlier: 3.807A pdb=" N ARG B 507 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 92 through 94 removed outlier: 7.359A pdb=" N ALA A 425 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE A 101 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 160 through 164 Processing sheet with id=AA9, first strand: chain 'A' and resid 205 through 209 removed outlier: 6.146A pdb=" N VAL A 185 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N PHE A 209 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL A 187 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP A 188 " --> pdb=" O VAL A 243 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 383 through 386 removed outlier: 3.509A pdb=" N LYS A 384 " --> pdb=" O GLN A 397 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 386 " --> pdb=" O HIS A 395 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR A 427 " --> pdb=" O ARG A 445 " (cutoff:3.500A) 338 hydrogen bonds defined for protein. 948 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: 2.35 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2924 1.34 - 1.46: 1484 1.46 - 1.57: 4850 1.57 - 1.69: 1 1.69 - 1.81: 83 Bond restraints: 9342 Sorted by residual: bond pdb=" C2 PLP B 601 " pdb=" C3 PLP B 601 " ideal model delta sigma weight residual 1.390 1.484 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C4 PLP B 601 " pdb=" C5 PLP B 601 " ideal model delta sigma weight residual 1.390 1.483 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C3 PLP B 601 " pdb=" C4 PLP B 601 " ideal model delta sigma weight residual 1.390 1.480 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" CA ASN A 107 " pdb=" CB ASN A 107 " ideal model delta sigma weight residual 1.525 1.555 -0.030 1.47e-02 4.63e+03 4.12e+00 bond pdb=" C ILE D 136 " pdb=" O ILE D 136 " ideal model delta sigma weight residual 1.242 1.226 0.016 8.60e-03 1.35e+04 3.29e+00 ... (remaining 9337 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 12154 1.94 - 3.88: 433 3.88 - 5.82: 51 5.82 - 7.76: 7 7.76 - 9.70: 2 Bond angle restraints: 12647 Sorted by residual: angle pdb=" N PRO A 78 " pdb=" CA PRO A 78 " pdb=" CB PRO A 78 " ideal model delta sigma weight residual 103.33 110.23 -6.90 1.10e+00 8.26e-01 3.93e+01 angle pdb=" CA ILE D 136 " pdb=" C ILE D 136 " pdb=" N PRO D 137 " ideal model delta sigma weight residual 120.83 117.08 3.75 6.10e-01 2.69e+00 3.79e+01 angle pdb=" N ILE B 503 " pdb=" CA ILE B 503 " pdb=" C ILE B 503 " ideal model delta sigma weight residual 110.23 116.24 -6.01 1.04e+00 9.25e-01 3.34e+01 angle pdb=" N GLY B 497 " pdb=" CA GLY B 497 " pdb=" C GLY B 497 " ideal model delta sigma weight residual 112.55 119.97 -7.42 1.44e+00 4.82e-01 2.65e+01 angle pdb=" N TYR E 44 " pdb=" CA TYR E 44 " pdb=" C TYR E 44 " ideal model delta sigma weight residual 110.80 120.50 -9.70 2.13e+00 2.20e-01 2.07e+01 ... (remaining 12642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4815 17.95 - 35.89: 522 35.89 - 53.84: 173 53.84 - 71.78: 53 71.78 - 89.73: 16 Dihedral angle restraints: 5579 sinusoidal: 2237 harmonic: 3342 Sorted by residual: dihedral pdb=" CA PRO B 142 " pdb=" C PRO B 142 " pdb=" N GLY B 143 " pdb=" CA GLY B 143 " ideal model delta harmonic sigma weight residual 180.00 160.09 19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA TYR B 461 " pdb=" C TYR B 461 " pdb=" N GLY B 462 " pdb=" CA GLY B 462 " ideal model delta harmonic sigma weight residual 180.00 160.21 19.79 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA LEU B 473 " pdb=" C LEU B 473 " pdb=" N TYR B 474 " pdb=" CA TYR B 474 " ideal model delta harmonic sigma weight residual -180.00 -162.11 -17.89 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 5576 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1106 0.057 - 0.114: 260 0.114 - 0.171: 43 0.171 - 0.228: 1 0.228 - 0.285: 3 Chirality restraints: 1413 Sorted by residual: chirality pdb=" CA TYR E 44 " pdb=" N TYR E 44 " pdb=" C TYR E 44 " pdb=" CB TYR E 44 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA GLU A 400 " pdb=" N GLU A 400 " pdb=" C GLU A 400 " pdb=" CB GLU A 400 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA PRO A 78 " pdb=" N PRO A 78 " pdb=" C PRO A 78 " pdb=" CB PRO A 78 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1410 not shown) Planarity restraints: 1605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 42 " 0.012 2.00e-02 2.50e+03 1.61e-02 4.52e+00 pdb=" CG PHE D 42 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE D 42 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE D 42 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE D 42 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 42 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 42 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 135 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C PRO A 135 " 0.030 2.00e-02 2.50e+03 pdb=" O PRO A 135 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG A 136 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 501 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.91e+00 pdb=" N PRO B 502 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 502 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 502 " -0.024 5.00e-02 4.00e+02 ... (remaining 1602 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.17: 2 2.17 - 2.85: 3237 2.85 - 3.53: 11282 3.53 - 4.22: 19969 4.22 - 4.90: 36184 Nonbonded interactions: 70674 Sorted by model distance: nonbonded pdb=" OG SER A 381 " pdb=" OE1 GLN A 469 " model vdw 1.486 3.040 nonbonded pdb=" OH TYR A 128 " pdb=" OD1 ASP A 143 " model vdw 2.143 3.040 nonbonded pdb=" O ARG B 399 " pdb=" OH TYR A 82 " model vdw 2.190 3.040 nonbonded pdb=" OD2 ASP D 76 " pdb=" NH1 ARG A 181 " model vdw 2.214 3.120 nonbonded pdb=" OD1 ASN B 245 " pdb=" OG SER B 402 " model vdw 2.219 3.040 ... (remaining 70669 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=0.80 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: 1.110 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: 0.100 Process input model: 22.790 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 9342 Z= 0.368 Angle : 0.838 9.697 12647 Z= 0.547 Chirality : 0.051 0.285 1413 Planarity : 0.004 0.043 1605 Dihedral : 18.001 89.730 3441 Min Nonbonded Distance : 1.486 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.43 % Favored : 91.87 % Rotamer: Outliers : 9.53 % Allowed : 5.64 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.24), residues: 1144 helix: -1.36 (0.23), residues: 504 sheet: -1.93 (0.51), residues: 109 loop : -2.61 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 32 HIS 0.004 0.001 HIS A 327 PHE 0.037 0.002 PHE D 42 TYR 0.025 0.002 TYR B 461 ARG 0.002 0.000 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 113 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8797 (mttt) REVERT: B 109 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8048 (mtmm) REVERT: B 136 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8932 (mtt180) REVERT: B 196 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8782 (tp) REVERT: B 197 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7680 (tp30) REVERT: B 288 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8645 (tp) REVERT: B 429 GLN cc_start: 0.7285 (OUTLIER) cc_final: 0.7072 (tt0) REVERT: B 471 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8418 (tp) REVERT: B 475 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.7656 (mmt) REVERT: B 505 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7356 (mt-10) REVERT: B 538 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8864 (mttp) REVERT: E 38 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8479 (pt) REVERT: D 118 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8057 (mtpt) REVERT: D 124 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.7911 (t80) REVERT: A 58 GLU cc_start: 0.7939 (tp30) cc_final: 0.7275 (tp30) REVERT: A 77 HIS cc_start: 0.5934 (OUTLIER) cc_final: 0.4069 (t-90) REVERT: A 136 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8440 (ttt180) REVERT: A 234 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8238 (tttt) outliers start: 93 outliers final: 49 residues processed: 190 average time/residue: 0.2741 time to fit residues: 67.9620 Evaluate side-chains 165 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 99 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 134 TRP Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 293 LYS Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 440 GLN Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 538 LYS Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 467 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 ASN D 121 GLN A 428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9342 Z= 0.386 Angle : 0.668 6.699 12647 Z= 0.352 Chirality : 0.047 0.247 1413 Planarity : 0.005 0.044 1605 Dihedral : 12.254 82.443 1439 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.24 % Favored : 94.67 % Rotamer: Outliers : 4.82 % Allowed : 12.81 % Favored : 82.38 % 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: -2.23 (0.24), residues: 1144 helix: -0.58 (0.24), residues: 500 sheet: -1.59 (0.47), residues: 121 loop : -2.35 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 94 HIS 0.007 0.001 HIS B 47 PHE 0.019 0.002 PHE B 449 TYR 0.024 0.002 TYR E 44 ARG 0.003 0.000 ARG B 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 108 time to evaluate : 1.102 Fit side-chains REVERT: B 46 HIS cc_start: 0.7424 (t-90) cc_final: 0.6807 (t-90) REVERT: B 289 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.7677 (tp30) REVERT: B 292 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8239 (mp) REVERT: B 429 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.7095 (tt0) REVERT: B 505 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7396 (mt-10) REVERT: A 58 GLU cc_start: 0.7918 (tp30) cc_final: 0.7258 (tp30) REVERT: A 77 HIS cc_start: 0.5967 (OUTLIER) cc_final: 0.4121 (t-90) REVERT: A 234 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8273 (tttt) outliers start: 47 outliers final: 28 residues processed: 147 average time/residue: 0.2399 time to fit residues: 48.2618 Evaluate side-chains 136 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 467 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 HIS A 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9342 Z= 0.176 Angle : 0.536 11.546 12647 Z= 0.280 Chirality : 0.043 0.205 1413 Planarity : 0.004 0.047 1605 Dihedral : 8.910 75.093 1334 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.28 % Allowed : 15.06 % Favored : 81.66 % 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: -1.72 (0.25), residues: 1144 helix: -0.02 (0.24), residues: 506 sheet: -1.52 (0.46), residues: 125 loop : -2.19 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 94 HIS 0.005 0.001 HIS B 47 PHE 0.014 0.001 PHE D 42 TYR 0.019 0.001 TYR E 44 ARG 0.002 0.000 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 1.102 Fit side-chains REVERT: B 46 HIS cc_start: 0.7326 (t-90) cc_final: 0.6761 (t-90) REVERT: B 109 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8228 (mtmm) REVERT: B 198 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7754 (pp20) REVERT: B 289 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.7715 (tp30) REVERT: B 292 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8362 (mp) REVERT: B 345 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7949 (pt0) REVERT: B 429 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.6923 (tt0) REVERT: B 505 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7647 (mm-30) REVERT: A 58 GLU cc_start: 0.7959 (tp30) cc_final: 0.7337 (tp30) REVERT: A 77 HIS cc_start: 0.5825 (OUTLIER) cc_final: 0.3846 (t-90) REVERT: A 274 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7901 (tm-30) outliers start: 32 outliers final: 15 residues processed: 136 average time/residue: 0.2537 time to fit residues: 46.7105 Evaluate side-chains 124 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 367 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 53 optimal weight: 20.0000 chunk 11 optimal weight: 0.0270 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 109 optimal weight: 0.0050 chunk 97 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.7256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9342 Z= 0.163 Angle : 0.505 8.425 12647 Z= 0.262 Chirality : 0.042 0.187 1413 Planarity : 0.004 0.047 1605 Dihedral : 6.987 70.661 1307 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.87 % Allowed : 16.80 % Favored : 80.33 % 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: -1.13 (0.26), residues: 1144 helix: 0.55 (0.25), residues: 499 sheet: -1.31 (0.47), residues: 125 loop : -1.93 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 94 HIS 0.005 0.001 HIS E 24 PHE 0.009 0.001 PHE D 101 TYR 0.021 0.001 TYR E 44 ARG 0.002 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 1.645 Fit side-chains REVERT: B 46 HIS cc_start: 0.7243 (t-90) cc_final: 0.6721 (t-90) REVERT: B 198 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7738 (pp20) REVERT: B 289 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.7671 (tp30) REVERT: E 26 ILE cc_start: 0.8523 (mm) cc_final: 0.8320 (mm) REVERT: A 58 GLU cc_start: 0.7924 (tp30) cc_final: 0.7323 (tp30) REVERT: A 77 HIS cc_start: 0.5927 (OUTLIER) cc_final: 0.4016 (t-90) REVERT: A 274 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7952 (tm-30) outliers start: 28 outliers final: 19 residues processed: 130 average time/residue: 0.2785 time to fit residues: 49.8625 Evaluate side-chains 123 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 24 HIS Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 419 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 98 optimal weight: 0.0870 chunk 27 optimal weight: 0.2980 chunk 36 optimal weight: 0.0970 overall best weight: 1.4960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9342 Z= 0.253 Angle : 0.536 8.169 12647 Z= 0.279 Chirality : 0.044 0.188 1413 Planarity : 0.004 0.050 1605 Dihedral : 6.505 69.075 1297 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.59 % Allowed : 16.70 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.26), residues: 1144 helix: 0.61 (0.25), residues: 501 sheet: -1.20 (0.47), residues: 125 loop : -1.90 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 94 HIS 0.012 0.001 HIS E 24 PHE 0.014 0.001 PHE D 101 TYR 0.018 0.001 TYR E 44 ARG 0.002 0.000 ARG B 151 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 104 time to evaluate : 1.115 Fit side-chains REVERT: B 46 HIS cc_start: 0.7249 (t-90) cc_final: 0.6702 (t-90) REVERT: B 198 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7741 (pp20) REVERT: B 289 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.7701 (tp30) REVERT: B 472 MET cc_start: 0.9235 (mmm) cc_final: 0.8620 (mmm) REVERT: B 473 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8786 (pp) REVERT: C 40 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.7428 (mtp) REVERT: A 58 GLU cc_start: 0.7946 (tp30) cc_final: 0.7335 (tp30) REVERT: A 59 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7703 (mm-30) REVERT: A 77 HIS cc_start: 0.5971 (OUTLIER) cc_final: 0.4038 (t-90) REVERT: A 274 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7940 (tm-30) outliers start: 35 outliers final: 22 residues processed: 131 average time/residue: 0.2530 time to fit residues: 45.2142 Evaluate side-chains 129 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 367 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 105 optimal weight: 0.1980 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 HIS A 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9342 Z= 0.275 Angle : 0.556 7.498 12647 Z= 0.289 Chirality : 0.044 0.183 1413 Planarity : 0.004 0.051 1605 Dihedral : 6.472 66.386 1297 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.79 % Allowed : 16.60 % Favored : 79.61 % 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: -0.93 (0.26), residues: 1144 helix: 0.71 (0.25), residues: 501 sheet: -1.13 (0.47), residues: 125 loop : -1.84 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 94 HIS 0.005 0.001 HIS B 47 PHE 0.014 0.001 PHE D 101 TYR 0.018 0.001 TYR E 44 ARG 0.002 0.000 ARG B 151 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 100 time to evaluate : 1.169 Fit side-chains REVERT: B 46 HIS cc_start: 0.7261 (t-90) cc_final: 0.6703 (t-90) REVERT: B 198 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7789 (pp20) REVERT: B 289 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.7702 (tp30) REVERT: B 472 MET cc_start: 0.9221 (mmm) cc_final: 0.8650 (mmm) REVERT: C 40 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7380 (mtp) REVERT: A 58 GLU cc_start: 0.7962 (tp30) cc_final: 0.7342 (tp30) REVERT: A 59 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7742 (mm-30) REVERT: A 77 HIS cc_start: 0.5951 (OUTLIER) cc_final: 0.3856 (t-90) REVERT: A 274 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7932 (tm-30) outliers start: 37 outliers final: 24 residues processed: 128 average time/residue: 0.3044 time to fit residues: 52.3258 Evaluate side-chains 126 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 419 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 79 optimal weight: 0.0030 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 0.2980 chunk 108 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9342 Z= 0.157 Angle : 0.510 11.110 12647 Z= 0.265 Chirality : 0.042 0.184 1413 Planarity : 0.004 0.048 1605 Dihedral : 6.100 62.199 1297 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.97 % Allowed : 17.73 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.26), residues: 1144 helix: 0.90 (0.25), residues: 508 sheet: -1.06 (0.47), residues: 125 loop : -1.65 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 94 HIS 0.004 0.000 HIS B 47 PHE 0.009 0.001 PHE A 209 TYR 0.019 0.001 TYR E 44 ARG 0.002 0.000 ARG D 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 1.114 Fit side-chains REVERT: B 46 HIS cc_start: 0.7249 (t-90) cc_final: 0.6604 (t-90) REVERT: B 92 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.6399 (ptm160) REVERT: B 198 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7789 (pp20) REVERT: B 472 MET cc_start: 0.9177 (mmm) cc_final: 0.8554 (mmm) REVERT: A 58 GLU cc_start: 0.7966 (tp30) cc_final: 0.7441 (tp30) REVERT: A 77 HIS cc_start: 0.5944 (OUTLIER) cc_final: 0.3852 (t-90) outliers start: 29 outliers final: 22 residues processed: 127 average time/residue: 0.2424 time to fit residues: 42.1849 Evaluate side-chains 125 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 419 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.4980 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 74 optimal weight: 0.0870 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 0.0050 chunk 95 optimal weight: 3.9990 overall best weight: 0.4774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9342 Z= 0.143 Angle : 0.498 9.478 12647 Z= 0.259 Chirality : 0.042 0.200 1413 Planarity : 0.004 0.048 1605 Dihedral : 5.619 55.889 1294 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.77 % Allowed : 18.03 % Favored : 79.20 % 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: -0.30 (0.26), residues: 1144 helix: 1.25 (0.25), residues: 507 sheet: -0.92 (0.48), residues: 123 loop : -1.52 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 94 HIS 0.003 0.000 HIS B 47 PHE 0.008 0.001 PHE A 317 TYR 0.019 0.001 TYR E 44 ARG 0.003 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 1.186 Fit side-chains REVERT: B 46 HIS cc_start: 0.7213 (t-90) cc_final: 0.6547 (t-90) REVERT: B 198 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7789 (pp20) REVERT: B 472 MET cc_start: 0.9137 (mmm) cc_final: 0.8523 (mmm) REVERT: A 58 GLU cc_start: 0.7875 (tp30) cc_final: 0.7382 (tp30) REVERT: A 77 HIS cc_start: 0.5922 (OUTLIER) cc_final: 0.3842 (t-90) outliers start: 27 outliers final: 19 residues processed: 127 average time/residue: 0.2427 time to fit residues: 42.6714 Evaluate side-chains 118 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 419 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 3.9990 chunk 104 optimal weight: 0.0980 chunk 61 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9342 Z= 0.213 Angle : 0.530 9.206 12647 Z= 0.277 Chirality : 0.044 0.238 1413 Planarity : 0.004 0.050 1605 Dihedral : 5.295 53.199 1282 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.56 % Allowed : 18.44 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.26), residues: 1144 helix: 1.34 (0.25), residues: 501 sheet: -0.90 (0.48), residues: 123 loop : -1.54 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 94 HIS 0.004 0.001 HIS B 47 PHE 0.042 0.002 PHE D 42 TYR 0.021 0.001 TYR E 44 ARG 0.003 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 1.133 Fit side-chains REVERT: B 46 HIS cc_start: 0.7225 (t-90) cc_final: 0.6529 (t-90) REVERT: B 198 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7800 (pp20) REVERT: B 472 MET cc_start: 0.9171 (mmm) cc_final: 0.8574 (mmm) REVERT: A 58 GLU cc_start: 0.7914 (tp30) cc_final: 0.7378 (tp30) REVERT: A 77 HIS cc_start: 0.6026 (OUTLIER) cc_final: 0.3991 (t-90) REVERT: A 274 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7875 (tp30) outliers start: 25 outliers final: 19 residues processed: 122 average time/residue: 0.2286 time to fit residues: 38.8012 Evaluate side-chains 124 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 419 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 103 optimal weight: 0.0980 chunk 89 optimal weight: 2.9990 chunk 9 optimal weight: 0.0470 chunk 69 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 27 optimal weight: 0.0370 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 9342 Z= 0.142 Angle : 0.493 9.187 12647 Z= 0.256 Chirality : 0.042 0.196 1413 Planarity : 0.004 0.046 1605 Dihedral : 4.634 50.703 1279 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.95 % Allowed : 18.75 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.26), residues: 1144 helix: 1.57 (0.25), residues: 503 sheet: -0.82 (0.48), residues: 123 loop : -1.33 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 94 HIS 0.003 0.000 HIS B 47 PHE 0.009 0.001 PHE D 95 TYR 0.017 0.001 TYR E 44 ARG 0.003 0.000 ARG A 236 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 1.053 Fit side-chains REVERT: B 46 HIS cc_start: 0.7158 (t-90) cc_final: 0.6479 (t-90) REVERT: B 198 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7807 (pp20) REVERT: B 472 MET cc_start: 0.9108 (mmm) cc_final: 0.8444 (mmm) REVERT: C 50 TYR cc_start: 0.7937 (t80) cc_final: 0.7632 (t80) REVERT: A 58 GLU cc_start: 0.7836 (tp30) cc_final: 0.7260 (tp30) REVERT: A 77 HIS cc_start: 0.6086 (OUTLIER) cc_final: 0.4035 (t-90) REVERT: A 274 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7926 (tp30) outliers start: 19 outliers final: 15 residues processed: 123 average time/residue: 0.2165 time to fit residues: 37.3313 Evaluate side-chains 123 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 92 optimal weight: 0.4980 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.113459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.092075 restraints weight = 12960.421| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 1.92 r_work: 0.2784 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9342 Z= 0.227 Angle : 0.547 8.618 12647 Z= 0.283 Chirality : 0.044 0.231 1413 Planarity : 0.004 0.051 1605 Dihedral : 4.502 50.769 1275 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.25 % Allowed : 18.55 % Favored : 79.20 % 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: -0.02 (0.26), residues: 1144 helix: 1.53 (0.24), residues: 501 sheet: -0.82 (0.48), residues: 123 loop : -1.39 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 94 HIS 0.004 0.001 HIS B 47 PHE 0.040 0.002 PHE D 42 TYR 0.018 0.001 TYR E 44 ARG 0.003 0.000 ARG A 236 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2169.73 seconds wall clock time: 40 minutes 34.79 seconds (2434.79 seconds total)