Starting phenix.real_space_refine on Sat Aug 23 02:29:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yj1_33868/08_2025/7yj1_33868.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yj1_33868/08_2025/7yj1_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_33868/08_2025/7yj1_33868.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yj1_33868/08_2025/7yj1_33868.map" model { file = "/net/cci-nas-00/data/ceres_data/7yj1_33868/08_2025/7yj1_33868.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yj1_33868/08_2025/7yj1_33868.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ARG:plan': 1, 'GLU: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: {'GLU:plan': 1, 'GLN:plan1': 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: 1.85, per 1000 atoms: 0.20 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: 0.75 Conformation dependent library (CDL) restraints added in 267.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.21 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: 1.06 Time building geometry restraints manager: 0.93 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.650 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.010 ------------------------------------------------------------------------------- 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 0.106 9343 Z= 0.304 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG B 509 TYR 0.025 0.002 TYR B 461 PHE 0.037 0.002 PHE D 42 TRP 0.011 0.001 TRP C 32 HIS 0.004 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00558 ( 9342) covalent geometry : angle 0.83823 (12647) hydrogen bonds : bond 0.25912 ( 338) hydrogen bonds : angle 7.44691 ( 948) Misc. bond : bond 0.10551 ( 1) *********************** 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 : 0.281 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: 0.0931 time to fit residues: 23.2243 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 : 0.218 ------------------------------------------------------------------------------- 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 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.0970 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.107636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.085782 restraints weight = 13225.902| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.98 r_work: 0.2762 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 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 = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9343 Z= 0.124 Angle : 0.570 6.200 12647 Z= 0.302 Chirality : 0.043 0.226 1413 Planarity : 0.004 0.037 1605 Dihedral : 11.806 78.515 1439 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.00 % Allowed : 12.60 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.08 (0.25), residues: 1144 helix: -0.48 (0.24), residues: 512 sheet: -1.56 (0.48), residues: 121 loop : -2.25 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 422 TYR 0.021 0.001 TYR E 44 PHE 0.013 0.001 PHE D 42 TRP 0.025 0.002 TRP B 94 HIS 0.005 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9342) covalent geometry : angle 0.56974 (12647) hydrogen bonds : bond 0.04873 ( 338) hydrogen bonds : angle 4.88658 ( 948) Misc. bond : bond 0.00015 ( 1) *********************** 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 145 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 106 time to evaluate : 0.209 Fit side-chains REVERT: B 46 HIS cc_start: 0.7332 (t-90) cc_final: 0.6469 (t-90) REVERT: B 128 MET cc_start: 0.8846 (tpp) cc_final: 0.8644 (tpp) REVERT: B 149 MET cc_start: 0.8868 (mtp) cc_final: 0.8600 (mtp) REVERT: B 289 GLU cc_start: 0.9291 (OUTLIER) cc_final: 0.8133 (tp30) REVERT: B 292 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8329 (mp) REVERT: B 374 MET cc_start: 0.8849 (ttt) cc_final: 0.8582 (ttt) REVERT: B 427 MET cc_start: 0.9031 (mtm) cc_final: 0.8813 (mtp) REVERT: B 429 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6657 (tt0) REVERT: A 58 GLU cc_start: 0.8441 (tp30) cc_final: 0.7681 (tp30) REVERT: A 77 HIS cc_start: 0.5543 (OUTLIER) cc_final: 0.3651 (t-90) REVERT: A 406 GLU cc_start: 0.7399 (tt0) cc_final: 0.7105 (tt0) outliers start: 39 outliers final: 21 residues processed: 140 average time/residue: 0.0845 time to fit residues: 16.1397 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 : 0.225 ------------------------------------------------------------------------------- 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 289 GLU Chi-restraints excluded: chain B residue 292 LEU 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 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 A residue 77 HIS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 214 MET 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 467 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 88 optimal weight: 0.1980 chunk 67 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 chunk 34 optimal weight: 0.6980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.105677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.083627 restraints weight = 13391.571| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 1.99 r_work: 0.2723 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9343 Z= 0.165 Angle : 0.562 6.105 12647 Z= 0.296 Chirality : 0.044 0.215 1413 Planarity : 0.004 0.047 1605 Dihedral : 8.561 75.656 1325 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.48 % Allowed : 14.55 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.66 (0.25), residues: 1144 helix: 0.01 (0.24), residues: 506 sheet: -1.46 (0.47), residues: 123 loop : -2.16 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 92 TYR 0.019 0.002 TYR E 44 PHE 0.016 0.002 PHE D 101 TRP 0.021 0.001 TRP B 94 HIS 0.005 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 9342) covalent geometry : angle 0.56189 (12647) hydrogen bonds : bond 0.04942 ( 338) hydrogen bonds : angle 4.53352 ( 948) Misc. bond : bond 0.00054 ( 1) *********************** 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: 34 poor density : 108 time to evaluate : 0.287 Fit side-chains REVERT: B 46 HIS cc_start: 0.7260 (t-90) cc_final: 0.6446 (t-90) REVERT: B 149 MET cc_start: 0.8885 (mtp) cc_final: 0.8656 (mtp) REVERT: B 198 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8120 (pp20) REVERT: B 289 GLU cc_start: 0.9255 (OUTLIER) cc_final: 0.8056 (tp30) REVERT: B 292 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8469 (mp) REVERT: B 429 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.6619 (mt0) REVERT: B 473 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8863 (pp) REVERT: B 530 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8046 (mt-10) REVERT: A 58 GLU cc_start: 0.8509 (tp30) cc_final: 0.7763 (tp30) REVERT: A 59 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8214 (mm-30) REVERT: A 77 HIS cc_start: 0.5353 (OUTLIER) cc_final: 0.3522 (t-90) REVERT: A 234 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8115 (tttt) outliers start: 34 outliers final: 18 residues processed: 132 average time/residue: 0.0870 time to fit residues: 15.7831 Evaluate side-chains 125 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 292 LEU 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 473 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 530 GLU 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 132 MET Chi-restraints excluded: chain D residue 145 VAL 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 80 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 0.0870 chunk 66 optimal weight: 0.4980 chunk 79 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- 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 = 0.3322 r_free = 0.3322 target = 0.115205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.094034 restraints weight = 13087.577| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.91 r_work: 0.2775 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9343 Z= 0.112 Angle : 0.512 8.097 12647 Z= 0.267 Chirality : 0.042 0.190 1413 Planarity : 0.004 0.046 1605 Dihedral : 7.434 72.634 1313 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.77 % Allowed : 16.19 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.26), residues: 1144 helix: 0.39 (0.25), residues: 506 sheet: -1.40 (0.46), residues: 125 loop : -2.00 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 136 TYR 0.019 0.001 TYR E 44 PHE 0.010 0.001 PHE D 101 TRP 0.013 0.001 TRP B 94 HIS 0.005 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9342) covalent geometry : angle 0.51193 (12647) hydrogen bonds : bond 0.03902 ( 338) hydrogen bonds : angle 4.28526 ( 948) Misc. bond : bond 0.00028 ( 1) *********************** 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 130 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.262 Fit side-chains REVERT: B 46 HIS cc_start: 0.7234 (t-90) cc_final: 0.6512 (t-90) REVERT: B 198 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8169 (pp20) REVERT: B 289 GLU cc_start: 0.9195 (OUTLIER) cc_final: 0.8071 (tp30) REVERT: B 374 MET cc_start: 0.9277 (tmt) cc_final: 0.8220 (tmt) REVERT: B 505 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8116 (mt-10) REVERT: B 530 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8155 (mt-10) REVERT: E 36 ILE cc_start: 0.8504 (mm) cc_final: 0.8280 (tp) REVERT: A 58 GLU cc_start: 0.8510 (tp30) cc_final: 0.7794 (tp30) REVERT: A 59 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8247 (mm-30) REVERT: A 77 HIS cc_start: 0.5576 (OUTLIER) cc_final: 0.3650 (t-90) REVERT: A 274 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8390 (tm-30) outliers start: 27 outliers final: 17 residues processed: 125 average time/residue: 0.0845 time to fit residues: 14.5713 Evaluate side-chains 119 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 434 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 530 GLU 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 344 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 408 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 8 optimal weight: 3.9990 chunk 55 optimal weight: 0.0570 chunk 70 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 HIS A 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.103672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.081609 restraints weight = 13478.615| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.00 r_work: 0.2695 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 9343 Z= 0.234 Angle : 0.619 10.529 12647 Z= 0.320 Chirality : 0.047 0.197 1413 Planarity : 0.004 0.049 1605 Dihedral : 6.943 71.347 1299 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.30 % Allowed : 15.57 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.25), residues: 1144 helix: 0.38 (0.24), residues: 500 sheet: -1.38 (0.46), residues: 123 loop : -1.98 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 183 TYR 0.020 0.002 TYR E 44 PHE 0.018 0.002 PHE D 101 TRP 0.015 0.001 TRP B 94 HIS 0.006 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00585 ( 9342) covalent geometry : angle 0.61913 (12647) hydrogen bonds : bond 0.05316 ( 338) hydrogen bonds : angle 4.42209 ( 948) Misc. bond : bond 0.00070 ( 1) *********************** 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 143 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 101 time to evaluate : 0.267 Fit side-chains REVERT: B 46 HIS cc_start: 0.7256 (t-90) cc_final: 0.6475 (t-90) REVERT: B 198 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8163 (pp20) REVERT: B 289 GLU cc_start: 0.9260 (OUTLIER) cc_final: 0.8072 (tp30) REVERT: B 292 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8518 (mp) REVERT: B 505 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7850 (mt-10) REVERT: B 530 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8019 (mt-10) REVERT: E 36 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8206 (tp) REVERT: C 40 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8241 (mtp) REVERT: A 58 GLU cc_start: 0.8524 (tp30) cc_final: 0.7752 (tp30) REVERT: A 77 HIS cc_start: 0.5461 (OUTLIER) cc_final: 0.3487 (t-90) outliers start: 42 outliers final: 23 residues processed: 133 average time/residue: 0.0739 time to fit residues: 13.5800 Evaluate side-chains 131 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 134 TRP 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 423 MET 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 517 THR Chi-restraints excluded: chain B residue 530 GLU 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 Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 419 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 43 optimal weight: 0.4980 chunk 74 optimal weight: 0.0870 chunk 50 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 HIS A 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.115986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.094961 restraints weight = 13031.065| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.90 r_work: 0.2797 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 9343 Z= 0.096 Angle : 0.494 8.511 12647 Z= 0.256 Chirality : 0.042 0.175 1413 Planarity : 0.004 0.046 1605 Dihedral : 6.330 67.008 1297 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.18 % Allowed : 16.91 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.26), residues: 1144 helix: 0.69 (0.25), residues: 515 sheet: -1.11 (0.47), residues: 125 loop : -1.75 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 136 TYR 0.019 0.001 TYR E 44 PHE 0.010 0.001 PHE A 317 TRP 0.014 0.001 TRP B 94 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 9342) covalent geometry : angle 0.49418 (12647) hydrogen bonds : bond 0.03334 ( 338) hydrogen bonds : angle 4.11658 ( 948) Misc. bond : bond 0.00012 ( 1) *********************** 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 142 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.342 Fit side-chains REVERT: B 46 HIS cc_start: 0.7198 (t-90) cc_final: 0.6321 (t-90) REVERT: B 198 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8172 (pp20) REVERT: B 289 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.8157 (tp30) REVERT: B 505 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8163 (mt-10) REVERT: B 530 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.8027 (mt-10) REVERT: E 36 ILE cc_start: 0.8451 (mm) cc_final: 0.8237 (tp) REVERT: A 58 GLU cc_start: 0.8503 (tp30) cc_final: 0.7813 (tp30) REVERT: A 77 HIS cc_start: 0.5586 (OUTLIER) cc_final: 0.3566 (t-90) REVERT: A 274 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8461 (tm-30) outliers start: 31 outliers final: 20 residues processed: 134 average time/residue: 0.0944 time to fit residues: 17.0515 Evaluate side-chains 126 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 289 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 494 VAL Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 530 GLU 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 C residue 13 MET 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 301 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 18 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 HIS ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.115309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.094209 restraints weight = 13035.871| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.91 r_work: 0.2784 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9343 Z= 0.112 Angle : 0.507 7.449 12647 Z= 0.265 Chirality : 0.042 0.186 1413 Planarity : 0.004 0.048 1605 Dihedral : 6.098 63.758 1297 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.66 % Allowed : 17.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.26), residues: 1144 helix: 0.95 (0.25), residues: 508 sheet: -1.03 (0.47), residues: 125 loop : -1.62 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 236 TYR 0.020 0.001 TYR E 44 PHE 0.009 0.001 PHE D 101 TRP 0.017 0.001 TRP B 94 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9342) covalent geometry : angle 0.50725 (12647) hydrogen bonds : bond 0.03551 ( 338) hydrogen bonds : angle 4.05093 ( 948) Misc. bond : bond 0.00023 ( 1) *********************** 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 129 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.363 Fit side-chains REVERT: B 46 HIS cc_start: 0.7206 (t-90) cc_final: 0.6309 (t-90) REVERT: B 92 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.6376 (ptm160) REVERT: B 198 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8191 (pp20) REVERT: B 289 GLU cc_start: 0.9214 (OUTLIER) cc_final: 0.8099 (tp30) REVERT: B 374 MET cc_start: 0.9283 (tmt) cc_final: 0.8414 (tmt) REVERT: B 472 MET cc_start: 0.9435 (mmm) cc_final: 0.8823 (mmm) REVERT: B 505 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8192 (mt-10) REVERT: B 530 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8032 (mt-10) REVERT: E 36 ILE cc_start: 0.8466 (mm) cc_final: 0.8249 (tp) REVERT: A 58 GLU cc_start: 0.8507 (tp30) cc_final: 0.7834 (tp30) REVERT: A 77 HIS cc_start: 0.5559 (OUTLIER) cc_final: 0.3506 (t-90) REVERT: A 274 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8409 (tm-30) outliers start: 26 outliers final: 20 residues processed: 124 average time/residue: 0.0936 time to fit residues: 15.8542 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 : 0.248 ------------------------------------------------------------------------------- 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 423 MET Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 530 GLU 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 C residue 13 MET 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 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 64 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.114666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.093504 restraints weight = 13000.480| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.91 r_work: 0.2796 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9343 Z= 0.129 Angle : 0.521 6.706 12647 Z= 0.272 Chirality : 0.043 0.218 1413 Planarity : 0.004 0.049 1605 Dihedral : 5.976 60.357 1295 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.97 % Allowed : 17.93 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.26), residues: 1144 helix: 1.09 (0.25), residues: 502 sheet: -1.01 (0.47), residues: 125 loop : -1.65 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 236 TYR 0.019 0.001 TYR E 44 PHE 0.012 0.001 PHE D 101 TRP 0.015 0.001 TRP B 94 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9342) covalent geometry : angle 0.52051 (12647) hydrogen bonds : bond 0.03824 ( 338) hydrogen bonds : angle 4.04550 ( 948) Misc. bond : bond 0.00032 ( 1) *********************** 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 131 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.611 Fit side-chains REVERT: B 46 HIS cc_start: 0.7277 (t-90) cc_final: 0.6425 (t-90) REVERT: B 92 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.6437 (ptm160) REVERT: B 198 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8274 (pp20) REVERT: B 472 MET cc_start: 0.9386 (mmm) cc_final: 0.8811 (mmm) REVERT: E 36 ILE cc_start: 0.8630 (mm) cc_final: 0.8397 (tp) REVERT: A 58 GLU cc_start: 0.8557 (tp30) cc_final: 0.7917 (tp30) REVERT: A 77 HIS cc_start: 0.5705 (OUTLIER) cc_final: 0.3556 (t-90) REVERT: A 274 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8405 (tm-30) outliers start: 29 outliers final: 24 residues processed: 123 average time/residue: 0.0802 time to fit residues: 13.4470 Evaluate side-chains 128 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 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 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 114 SER 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 367 LYS 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 34 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 20 optimal weight: 0.0980 chunk 93 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.107078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.085153 restraints weight = 13252.891| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 1.99 r_work: 0.2748 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9343 Z= 0.121 Angle : 0.512 7.829 12647 Z= 0.266 Chirality : 0.043 0.192 1413 Planarity : 0.004 0.048 1605 Dihedral : 5.702 56.257 1290 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.28 % Allowed : 17.32 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.26), residues: 1144 helix: 1.20 (0.25), residues: 502 sheet: -0.99 (0.47), residues: 125 loop : -1.58 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 136 TYR 0.019 0.001 TYR E 44 PHE 0.010 0.001 PHE D 101 TRP 0.018 0.001 TRP B 94 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9342) covalent geometry : angle 0.51164 (12647) hydrogen bonds : bond 0.03693 ( 338) hydrogen bonds : angle 4.00214 ( 948) Misc. bond : bond 0.00032 ( 1) *********************** 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 137 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.256 Fit side-chains REVERT: B 46 HIS cc_start: 0.7104 (t-90) cc_final: 0.6173 (t-90) REVERT: B 92 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.6292 (ptm160) REVERT: B 198 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8195 (pp20) REVERT: B 292 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8438 (mp) REVERT: B 472 MET cc_start: 0.9445 (mmm) cc_final: 0.8836 (mmm) REVERT: E 36 ILE cc_start: 0.8414 (mm) cc_final: 0.8183 (tp) REVERT: A 58 GLU cc_start: 0.8481 (tp30) cc_final: 0.7780 (tp30) REVERT: A 77 HIS cc_start: 0.5465 (OUTLIER) cc_final: 0.3435 (t-90) REVERT: A 274 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8386 (tp30) outliers start: 32 outliers final: 25 residues processed: 130 average time/residue: 0.0797 time to fit residues: 14.3357 Evaluate side-chains 131 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 292 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 490 ASN 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 114 SER 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 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 390 LEU 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 87 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.107121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.085258 restraints weight = 13281.835| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.98 r_work: 0.2750 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9343 Z= 0.120 Angle : 0.518 7.984 12647 Z= 0.270 Chirality : 0.043 0.243 1413 Planarity : 0.004 0.048 1605 Dihedral : 5.641 53.091 1290 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.07 % Allowed : 17.73 % Favored : 79.20 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.26), residues: 1144 helix: 1.26 (0.25), residues: 504 sheet: -0.94 (0.47), residues: 125 loop : -1.52 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 20 TYR 0.018 0.001 TYR E 44 PHE 0.039 0.001 PHE D 42 TRP 0.018 0.001 TRP B 94 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9342) covalent geometry : angle 0.51830 (12647) hydrogen bonds : bond 0.03658 ( 338) hydrogen bonds : angle 3.99014 ( 948) Misc. bond : bond 0.00030 ( 1) ********************** 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 130 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.293 Fit side-chains REVERT: B 46 HIS cc_start: 0.7121 (t-90) cc_final: 0.6158 (t-90) REVERT: B 92 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.6307 (ptm160) REVERT: B 198 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8204 (pp20) REVERT: B 292 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8457 (mp) REVERT: B 472 MET cc_start: 0.9443 (mmm) cc_final: 0.8839 (mmm) REVERT: E 36 ILE cc_start: 0.8438 (mm) cc_final: 0.8201 (tp) REVERT: A 58 GLU cc_start: 0.8479 (tp30) cc_final: 0.7757 (tp30) REVERT: A 77 HIS cc_start: 0.5496 (OUTLIER) cc_final: 0.3438 (t-90) REVERT: A 274 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8418 (tm-30) outliers start: 30 outliers final: 24 residues processed: 124 average time/residue: 0.0792 time to fit residues: 13.4538 Evaluate side-chains 128 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 292 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 542 HIS 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 114 SER 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 107 ASN 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 390 LEU 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 32 optimal weight: 0.0270 chunk 110 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN C 38 ASN A 107 ASN A 428 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.110228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.088798 restraints weight = 13068.644| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 1.92 r_work: 0.2707 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2578 r_free = 0.2578 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2578 r_free = 0.2578 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9343 Z= 0.234 Angle : 0.620 8.959 12647 Z= 0.322 Chirality : 0.047 0.201 1413 Planarity : 0.005 0.051 1605 Dihedral : 5.375 51.265 1285 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.07 % Allowed : 17.42 % Favored : 79.51 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.26), residues: 1144 helix: 1.03 (0.24), residues: 495 sheet: -1.02 (0.47), residues: 123 loop : -1.63 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 422 TYR 0.019 0.002 TYR D 26 PHE 0.017 0.002 PHE D 101 TRP 0.015 0.001 TRP B 94 HIS 0.006 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00586 ( 9342) covalent geometry : angle 0.61976 (12647) hydrogen bonds : bond 0.05035 ( 338) hydrogen bonds : angle 4.21571 ( 948) Misc. bond : bond 0.00075 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1900.66 seconds wall clock time: 33 minutes 11.47 seconds (1991.47 seconds total)