Starting phenix.real_space_refine on Wed Jul 30 14:57:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rw8_24710/07_2025/7rw8_24710.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rw8_24710/07_2025/7rw8_24710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rw8_24710/07_2025/7rw8_24710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rw8_24710/07_2025/7rw8_24710.map" model { file = "/net/cci-nas-00/data/ceres_data/7rw8_24710/07_2025/7rw8_24710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rw8_24710/07_2025/7rw8_24710.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 8136 2.51 5 N 2113 2.21 5 O 2263 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12572 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4389 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 22, 'TRANS': 575} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 329 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 266 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 17, 'ARG:plan': 15, 'ASN:plan1': 5, 'ASP:plan': 18} Unresolved non-hydrogen planarities: 232 Chain: "B" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4086 Classifications: {'peptide': 579} Incomplete info: {'truncation_to_alanine': 144} Link IDs: {'PTRANS': 26, 'TRANS': 552} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 515 Unresolved non-hydrogen angles: 618 Unresolved non-hydrogen dihedrals: 422 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 12, 'ASP:plan': 20, 'GLU:plan': 25, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 305 Chain: "M" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2969 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 17, 'TRANS': 376} Chain breaks: 3 Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 10, 'ARG:plan': 8, 'ASN:plan1': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 133 Chain: "S" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1128 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 140} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 38 Time building chain proxies: 7.70, per 1000 atoms: 0.61 Number of scatterers: 12572 At special positions: 0 Unit cell: (97.9, 110.36, 129.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 2263 8.00 N 2113 7.00 C 8136 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 1.6 seconds 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3308 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 7 sheets defined 63.1% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.597A pdb=" N SER A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 46 Processing helix chain 'A' and resid 51 through 69 removed outlier: 3.587A pdb=" N GLY A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 83 removed outlier: 3.735A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 105 through 122 Processing helix chain 'A' and resid 124 through 139 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 161 through 179 Processing helix chain 'A' and resid 180 through 183 removed outlier: 3.760A pdb=" N VAL A 183 " --> pdb=" O PRO A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 183' Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 200 through 216 Processing helix chain 'A' and resid 218 through 223 removed outlier: 4.070A pdb=" N PHE A 222 " --> pdb=" O ASN A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 238 Processing helix chain 'A' and resid 254 through 267 removed outlier: 3.646A pdb=" N CYS A 267 " --> pdb=" O ARG A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 293 Processing helix chain 'A' and resid 299 through 321 removed outlier: 3.864A pdb=" N SER A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 Processing helix chain 'A' and resid 342 through 357 removed outlier: 3.596A pdb=" N ARG A 346 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 369 removed outlier: 3.975A pdb=" N HIS A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 382 through 396 Processing helix chain 'A' and resid 401 through 416 removed outlier: 3.901A pdb=" N GLU A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 435 removed outlier: 4.218A pdb=" N GLU A 422 " --> pdb=" O TYR A 418 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N GLU A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 454 Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 460 through 472 removed outlier: 3.734A pdb=" N ILE A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 509 through 511 No H-bonds generated for 'chain 'A' and resid 509 through 511' Processing helix chain 'A' and resid 514 through 517 Processing helix chain 'A' and resid 518 through 531 removed outlier: 4.017A pdb=" N HIS A 531 " --> pdb=" O HIS A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 552 removed outlier: 3.504A pdb=" N ASN A 550 " --> pdb=" O ILE A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 564 removed outlier: 3.890A pdb=" N VAL A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 removed outlier: 3.534A pdb=" N LYS A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 589 Processing helix chain 'A' and resid 591 through 599 removed outlier: 3.537A pdb=" N THR A 597 " --> pdb=" O ASP A 593 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 598 " --> pdb=" O ILE A 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 23 removed outlier: 3.659A pdb=" N ASN B 23 " --> pdb=" O LYS B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 43 removed outlier: 3.960A pdb=" N GLU B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 58 Processing helix chain 'B' and resid 62 through 80 removed outlier: 3.563A pdb=" N LYS B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS B 78 " --> pdb=" O MET B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 86 removed outlier: 3.527A pdb=" N ALA B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 92 removed outlier: 3.563A pdb=" N PHE B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 95 No H-bonds generated for 'chain 'B' and resid 93 through 95' Processing helix chain 'B' and resid 99 through 112 removed outlier: 4.028A pdb=" N ARG B 103 " --> pdb=" O ASN B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 removed outlier: 3.903A pdb=" N THR B 119 " --> pdb=" O ASP B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 128 removed outlier: 3.589A pdb=" N LEU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG B 127 " --> pdb=" O CYS B 123 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS B 128 " --> pdb=" O GLU B 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 122 through 128' Processing helix chain 'B' and resid 134 through 151 removed outlier: 3.994A pdb=" N ARG B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS B 147 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 170 removed outlier: 4.263A pdb=" N ALA B 170 " --> pdb=" O ARG B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 189 removed outlier: 5.346A pdb=" N ALA B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 removed outlier: 4.388A pdb=" N ASN B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 228 removed outlier: 3.802A pdb=" N ILE B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 253 through 266 Processing helix chain 'B' and resid 276 through 284 Processing helix chain 'B' and resid 284 through 292 removed outlier: 3.930A pdb=" N LEU B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 313 removed outlier: 3.756A pdb=" N LEU B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 325 removed outlier: 3.616A pdb=" N VAL B 323 " --> pdb=" O GLU B 320 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE B 325 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 345 removed outlier: 3.948A pdb=" N GLU B 337 " --> pdb=" O TYR B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 362 removed outlier: 3.729A pdb=" N ALA B 356 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU B 360 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 384 removed outlier: 3.590A pdb=" N ALA B 381 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 382 " --> pdb=" O GLY B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 401 Processing helix chain 'B' and resid 403 through 421 removed outlier: 3.559A pdb=" N GLU B 409 " --> pdb=" O TYR B 405 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 428 through 435 removed outlier: 3.556A pdb=" N GLU B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASN B 435 " --> pdb=" O THR B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 454 Processing helix chain 'B' and resid 461 through 471 removed outlier: 3.808A pdb=" N GLU B 471 " --> pdb=" O GLU B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 495 Processing helix chain 'B' and resid 499 through 512 Processing helix chain 'B' and resid 516 through 531 Processing helix chain 'B' and resid 533 through 542 removed outlier: 3.559A pdb=" N ALA B 537 " --> pdb=" O ASP B 533 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS B 538 " --> pdb=" O PRO B 534 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU B 539 " --> pdb=" O VAL B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 566 Processing helix chain 'B' and resid 570 through 575 Processing helix chain 'B' and resid 577 through 581 removed outlier: 3.595A pdb=" N PHE B 581 " --> pdb=" O PRO B 578 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 36 removed outlier: 3.776A pdb=" N VAL M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 94 removed outlier: 3.534A pdb=" N VAL M 78 " --> pdb=" O ASN M 74 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE M 79 " --> pdb=" O ALA M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 104 Processing helix chain 'M' and resid 104 through 115 Processing helix chain 'M' and resid 128 through 133 removed outlier: 4.160A pdb=" N PHE M 132 " --> pdb=" O ALA M 128 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 42 removed outlier: 3.512A pdb=" N VAL S 41 " --> pdb=" O ALA S 37 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 96 Processing helix chain 'S' and resid 99 through 106 Processing helix chain 'S' and resid 106 through 117 Processing helix chain 'S' and resid 127 through 141 Processing sheet with id=AA1, first strand: chain 'M' and resid 14 through 19 Processing sheet with id=AA2, first strand: chain 'M' and resid 116 through 117 removed outlier: 3.530A pdb=" N ASP M 117 " --> pdb=" O TYR M 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 245 through 248 removed outlier: 5.917A pdb=" N GLU M 271 " --> pdb=" O SER M 204 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N SER M 204 " --> pdb=" O GLU M 271 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLU M 273 " --> pdb=" O MET M 202 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N MET M 202 " --> pdb=" O GLU M 273 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET M 275 " --> pdb=" O VAL M 200 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU M 173 " --> pdb=" O TRP M 421 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N ARG M 423 " --> pdb=" O LEU M 173 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU M 175 " --> pdb=" O ARG M 423 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE M 425 " --> pdb=" O LEU M 175 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL M 177 " --> pdb=" O ILE M 425 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ARG M 427 " --> pdb=" O VAL M 177 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU M 179 " --> pdb=" O ARG M 427 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLY M 429 " --> pdb=" O GLU M 179 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL M 181 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N TYR M 431 " --> pdb=" O VAL M 181 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU M 183 " --> pdb=" O TYR M 431 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N THR M 433 " --> pdb=" O LEU M 183 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N MET M 185 " --> pdb=" O THR M 433 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ARG M 427 " --> pdb=" O VAL M 392 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL M 392 " --> pdb=" O ARG M 427 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY M 429 " --> pdb=" O PHE M 390 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N PHE M 390 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR M 431 " --> pdb=" O MET M 388 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLU M 391 " --> pdb=" O LYS M 319 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LYS M 319 " --> pdb=" O GLU M 391 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU M 316 " --> pdb=" O ALA M 359 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA M 359 " --> pdb=" O LEU M 316 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLN M 318 " --> pdb=" O ARG M 357 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ARG M 357 " --> pdb=" O GLN M 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 253 through 254 Processing sheet with id=AA5, first strand: chain 'M' and resid 287 through 294 removed outlier: 3.524A pdb=" N GLY M 332 " --> pdb=" O GLU M 371 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 14 through 19 removed outlier: 6.531A pdb=" N THR S 14 " --> pdb=" O ASN S 9 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN S 9 " --> pdb=" O THR S 14 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N CYS S 70 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE S 5 " --> pdb=" O CYS S 68 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N CYS S 68 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE S 7 " --> pdb=" O TYR S 66 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TYR S 66 " --> pdb=" O ILE S 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 118 through 119 794 hydrogen bonds defined for protein. 2325 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: 4.20 Time building geometry restraints manager: 3.48 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: 4064 1.34 - 1.46: 1943 1.46 - 1.57: 6713 1.57 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 12808 Sorted by residual: bond pdb=" CG1 ILE A 17 " pdb=" CD1 ILE A 17 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.57e+00 bond pdb=" CB CYS A 171 " pdb=" SG CYS A 171 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.40e+00 bond pdb=" CB VAL A 483 " pdb=" CG1 VAL A 483 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.24e+00 bond pdb=" CB VAL B 298 " pdb=" CG1 VAL B 298 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.05e+00 bond pdb=" CB MET S 117 " pdb=" CG MET S 117 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.81e-01 ... (remaining 12803 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 17038 1.48 - 2.96: 388 2.96 - 4.44: 57 4.44 - 5.92: 17 5.92 - 7.40: 9 Bond angle restraints: 17509 Sorted by residual: angle pdb=" N ASN B 179 " pdb=" CA ASN B 179 " pdb=" C ASN B 179 " ideal model delta sigma weight residual 113.18 105.78 7.40 1.33e+00 5.65e-01 3.10e+01 angle pdb=" CA GLU A 601 " pdb=" C GLU A 601 " pdb=" O GLU A 601 " ideal model delta sigma weight residual 120.51 113.88 6.63 1.43e+00 4.89e-01 2.15e+01 angle pdb=" CA GLU A 601 " pdb=" C GLU A 601 " pdb=" N MET A 602 " ideal model delta sigma weight residual 116.84 123.58 -6.74 1.71e+00 3.42e-01 1.56e+01 angle pdb=" N HIS A 493 " pdb=" CA HIS A 493 " pdb=" C HIS A 493 " ideal model delta sigma weight residual 108.34 113.09 -4.75 1.31e+00 5.83e-01 1.32e+01 angle pdb=" C GLU A 600 " pdb=" N GLU A 601 " pdb=" CA GLU A 601 " ideal model delta sigma weight residual 121.54 127.75 -6.21 1.91e+00 2.74e-01 1.06e+01 ... (remaining 17504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 7048 18.00 - 35.99: 513 35.99 - 53.99: 83 53.99 - 71.99: 15 71.99 - 89.98: 10 Dihedral angle restraints: 7669 sinusoidal: 2595 harmonic: 5074 Sorted by residual: dihedral pdb=" CA HIS A 493 " pdb=" C HIS A 493 " pdb=" N GLU A 494 " pdb=" CA GLU A 494 " ideal model delta harmonic sigma weight residual 180.00 -154.97 -25.03 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA TRP A 462 " pdb=" C TRP A 462 " pdb=" N TYR A 463 " pdb=" CA TYR A 463 " ideal model delta harmonic sigma weight residual 180.00 159.45 20.55 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA LEU B 248 " pdb=" C LEU B 248 " pdb=" N SER B 249 " pdb=" CA SER B 249 " ideal model delta harmonic sigma weight residual -180.00 -161.34 -18.66 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 7666 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1400 0.034 - 0.069: 577 0.069 - 0.103: 140 0.103 - 0.137: 45 0.137 - 0.172: 8 Chirality restraints: 2170 Sorted by residual: chirality pdb=" CG LEU B 68 " pdb=" CB LEU B 68 " pdb=" CD1 LEU B 68 " pdb=" CD2 LEU B 68 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.36e-01 chirality pdb=" CA ILE S 58 " pdb=" N ILE S 58 " pdb=" C ILE S 58 " pdb=" CB ILE S 58 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.02e-01 chirality pdb=" CA THR B 245 " pdb=" N THR B 245 " pdb=" C THR B 245 " pdb=" CB THR B 245 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 2167 not shown) Planarity restraints: 2207 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 179 " -0.037 5.00e-02 4.00e+02 5.53e-02 4.90e+00 pdb=" N PRO A 180 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 180 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 180 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 64 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.63e+00 pdb=" C GLU B 64 " -0.037 2.00e-02 2.50e+03 pdb=" O GLU B 64 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU B 65 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 97 " 0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO B 98 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 98 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 98 " 0.029 5.00e-02 4.00e+02 ... (remaining 2204 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 75 2.63 - 3.20: 11575 3.20 - 3.77: 18770 3.77 - 4.33: 24370 4.33 - 4.90: 41725 Nonbonded interactions: 96515 Sorted by model distance: nonbonded pdb=" O ILE A 511 " pdb=" OG SER A 517 " model vdw 2.069 3.040 nonbonded pdb=" OE1 GLU B 297 " pdb=" OH TYR M 83 " model vdw 2.095 3.040 nonbonded pdb=" OD2 ASP A 444 " pdb=" OH TYR A 478 " model vdw 2.199 3.040 nonbonded pdb=" O VAL A 300 " pdb=" OG SER A 303 " model vdw 2.233 3.040 nonbonded pdb=" O LEU A 244 " pdb=" OG1 THR A 248 " model vdw 2.233 3.040 ... (remaining 96510 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 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: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 30.340 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 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 : 0.004 0.049 12808 Z= 0.166 Angle : 0.581 7.401 17509 Z= 0.321 Chirality : 0.041 0.172 2170 Planarity : 0.004 0.055 2207 Dihedral : 13.413 89.982 4361 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.20), residues: 1696 helix: 1.59 (0.17), residues: 981 sheet: 1.03 (0.37), residues: 183 loop : -1.26 (0.24), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 462 HIS 0.004 0.001 HIS A 70 PHE 0.019 0.002 PHE S 49 TYR 0.028 0.002 TYR B 70 ARG 0.003 0.000 ARG B 419 Details of bonding type rmsd hydrogen bonds : bond 0.14062 ( 794) hydrogen bonds : angle 5.14739 ( 2325) covalent geometry : bond 0.00391 (12808) covalent geometry : angle 0.58058 (17509) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.533 Fit side-chains REVERT: S 29 GLN cc_start: 0.6340 (mm-40) cc_final: 0.5580 (mm-40) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.2312 time to fit residues: 39.5721 Evaluate side-chains 74 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 307 ASN M 49 ASN M 195 HIS M 334 GLN M 412 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.063827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.046599 restraints weight = 56291.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.048306 restraints weight = 30825.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.049452 restraints weight = 21255.022| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12808 Z= 0.202 Angle : 0.571 11.207 17509 Z= 0.298 Chirality : 0.041 0.151 2170 Planarity : 0.004 0.044 2207 Dihedral : 4.045 25.230 1823 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.81 % Allowed : 5.61 % Favored : 93.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.20), residues: 1696 helix: 1.76 (0.17), residues: 993 sheet: 1.03 (0.39), residues: 183 loop : -1.17 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 462 HIS 0.008 0.001 HIS A 200 PHE 0.015 0.002 PHE M 32 TYR 0.029 0.002 TYR A 247 ARG 0.004 0.000 ARG A 341 Details of bonding type rmsd hydrogen bonds : bond 0.04148 ( 794) hydrogen bonds : angle 4.38416 ( 2325) covalent geometry : bond 0.00465 (12808) covalent geometry : angle 0.57137 (17509) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 1.367 Fit side-chains REVERT: A 409 MET cc_start: 0.8969 (mtp) cc_final: 0.8758 (mtp) REVERT: M 77 MET cc_start: 0.8735 (ttm) cc_final: 0.8490 (tpp) REVERT: S 33 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8603 (mm-30) outliers start: 10 outliers final: 5 residues processed: 86 average time/residue: 0.1841 time to fit residues: 26.3827 Evaluate side-chains 79 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 MET Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 22 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 130 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 77 optimal weight: 0.0020 chunk 15 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 93 optimal weight: 0.0870 chunk 153 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 overall best weight: 0.5166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 305 ASN M 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.065602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.048428 restraints weight = 55818.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.050232 restraints weight = 30038.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.051469 restraints weight = 20437.648| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12808 Z= 0.098 Angle : 0.480 11.629 17509 Z= 0.249 Chirality : 0.039 0.143 2170 Planarity : 0.003 0.035 2207 Dihedral : 3.807 23.708 1823 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.90 % Allowed : 7.65 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.21), residues: 1696 helix: 2.05 (0.17), residues: 989 sheet: 1.13 (0.38), residues: 181 loop : -1.01 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 462 HIS 0.005 0.001 HIS A 200 PHE 0.014 0.001 PHE M 105 TYR 0.016 0.001 TYR B 70 ARG 0.003 0.000 ARG A 341 Details of bonding type rmsd hydrogen bonds : bond 0.03254 ( 794) hydrogen bonds : angle 3.99442 ( 2325) covalent geometry : bond 0.00211 (12808) covalent geometry : angle 0.48027 (17509) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 1.414 Fit side-chains REVERT: S 29 GLN cc_start: 0.9162 (mm-40) cc_final: 0.8573 (mm-40) REVERT: S 33 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8520 (mm-30) outliers start: 11 outliers final: 5 residues processed: 90 average time/residue: 0.1822 time to fit residues: 26.9999 Evaluate side-chains 81 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 68 CYS Chi-restraints excluded: chain S residue 115 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 105 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 14 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 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 = 0.3379 r_free = 0.3379 target = 0.065245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.048108 restraints weight = 55078.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.049885 restraints weight = 29798.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.051081 restraints weight = 20342.640| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12808 Z= 0.105 Angle : 0.471 11.631 17509 Z= 0.243 Chirality : 0.038 0.139 2170 Planarity : 0.003 0.033 2207 Dihedral : 3.681 22.696 1823 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.46 % Allowed : 8.62 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.21), residues: 1696 helix: 2.14 (0.17), residues: 994 sheet: 1.11 (0.38), residues: 181 loop : -0.99 (0.25), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 462 HIS 0.004 0.001 HIS A 200 PHE 0.011 0.001 PHE B 221 TYR 0.021 0.001 TYR M 277 ARG 0.002 0.000 ARG A 341 Details of bonding type rmsd hydrogen bonds : bond 0.03013 ( 794) hydrogen bonds : angle 3.87014 ( 2325) covalent geometry : bond 0.00238 (12808) covalent geometry : angle 0.47095 (17509) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 1.345 Fit side-chains REVERT: A 391 ASP cc_start: 0.8945 (m-30) cc_final: 0.8734 (m-30) REVERT: A 418 TYR cc_start: 0.8437 (m-10) cc_final: 0.7972 (m-10) REVERT: S 33 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8607 (mm-30) REVERT: S 53 ARG cc_start: 0.8975 (mtp85) cc_final: 0.8587 (mmt90) outliers start: 18 outliers final: 10 residues processed: 93 average time/residue: 0.1895 time to fit residues: 28.9251 Evaluate side-chains 84 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 68 CYS Chi-restraints excluded: chain S residue 75 ASP Chi-restraints excluded: chain S residue 115 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 30 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.063393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.046319 restraints weight = 55926.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.048040 restraints weight = 30372.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.049206 restraints weight = 20778.603| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12808 Z= 0.164 Angle : 0.508 13.727 17509 Z= 0.261 Chirality : 0.039 0.145 2170 Planarity : 0.003 0.038 2207 Dihedral : 3.735 23.113 1823 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.22 % Allowed : 9.93 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.21), residues: 1696 helix: 2.24 (0.17), residues: 996 sheet: 0.96 (0.38), residues: 187 loop : -0.94 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 462 HIS 0.003 0.001 HIS S 85 PHE 0.011 0.001 PHE M 56 TYR 0.012 0.001 TYR M 8 ARG 0.002 0.000 ARG M 278 Details of bonding type rmsd hydrogen bonds : bond 0.03316 ( 794) hydrogen bonds : angle 3.96433 ( 2325) covalent geometry : bond 0.00379 (12808) covalent geometry : angle 0.50821 (17509) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 1.472 Fit side-chains REVERT: M 218 ASP cc_start: 0.8491 (t0) cc_final: 0.8248 (t0) REVERT: S 33 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8634 (mm-30) outliers start: 15 outliers final: 10 residues processed: 88 average time/residue: 0.1848 time to fit residues: 27.0778 Evaluate side-chains 83 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 75 ASP Chi-restraints excluded: chain S residue 115 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 152 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.063259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.046221 restraints weight = 56250.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.047926 restraints weight = 30369.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.049094 restraints weight = 20750.288| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12808 Z= 0.142 Angle : 0.487 12.453 17509 Z= 0.250 Chirality : 0.039 0.147 2170 Planarity : 0.003 0.037 2207 Dihedral : 3.730 23.202 1823 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.98 % Allowed : 10.66 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.21), residues: 1696 helix: 2.32 (0.17), residues: 996 sheet: 1.00 (0.38), residues: 187 loop : -0.91 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 462 HIS 0.003 0.001 HIS A 200 PHE 0.009 0.001 PHE M 32 TYR 0.010 0.001 TYR M 8 ARG 0.004 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.03133 ( 794) hydrogen bonds : angle 3.89254 ( 2325) covalent geometry : bond 0.00328 (12808) covalent geometry : angle 0.48727 (17509) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 1.564 Fit side-chains REVERT: M 218 ASP cc_start: 0.8654 (t0) cc_final: 0.8340 (t0) REVERT: S 33 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8654 (mm-30) outliers start: 12 outliers final: 11 residues processed: 84 average time/residue: 0.2062 time to fit residues: 28.6137 Evaluate side-chains 88 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 75 ASP Chi-restraints excluded: chain S residue 115 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 32 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3320 r_free = 0.3320 target = 0.062374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.045358 restraints weight = 56676.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.047018 restraints weight = 30837.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.048163 restraints weight = 21158.615| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12808 Z= 0.180 Angle : 0.520 12.291 17509 Z= 0.267 Chirality : 0.039 0.145 2170 Planarity : 0.003 0.040 2207 Dihedral : 3.809 23.898 1823 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.46 % Allowed : 10.66 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.21), residues: 1696 helix: 2.31 (0.17), residues: 998 sheet: 0.96 (0.38), residues: 187 loop : -0.91 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 462 HIS 0.004 0.001 HIS A 70 PHE 0.011 0.001 PHE A 64 TYR 0.012 0.001 TYR M 8 ARG 0.002 0.000 ARG M 278 Details of bonding type rmsd hydrogen bonds : bond 0.03459 ( 794) hydrogen bonds : angle 4.02187 ( 2325) covalent geometry : bond 0.00418 (12808) covalent geometry : angle 0.52015 (17509) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 1.486 Fit side-chains REVERT: M 218 ASP cc_start: 0.8615 (t0) cc_final: 0.8311 (t0) REVERT: S 33 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8705 (mm-30) REVERT: S 53 ARG cc_start: 0.9005 (mtp85) cc_final: 0.8688 (mmt90) outliers start: 18 outliers final: 14 residues processed: 88 average time/residue: 0.2004 time to fit residues: 28.8032 Evaluate side-chains 89 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 MET Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 75 ASP Chi-restraints excluded: chain S residue 115 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 64 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 0.0670 chunk 116 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 412 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.063492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.046524 restraints weight = 55810.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.048227 restraints weight = 30138.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.049385 restraints weight = 20620.775| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12808 Z= 0.109 Angle : 0.471 12.558 17509 Z= 0.244 Chirality : 0.038 0.153 2170 Planarity : 0.003 0.036 2207 Dihedral : 3.706 23.646 1823 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.06 % Allowed : 10.98 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.21), residues: 1696 helix: 2.42 (0.17), residues: 1000 sheet: 1.16 (0.38), residues: 179 loop : -0.85 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 462 HIS 0.003 0.001 HIS A 527 PHE 0.009 0.001 PHE M 32 TYR 0.008 0.001 TYR M 8 ARG 0.002 0.000 ARG M 278 Details of bonding type rmsd hydrogen bonds : bond 0.02984 ( 794) hydrogen bonds : angle 3.82072 ( 2325) covalent geometry : bond 0.00248 (12808) covalent geometry : angle 0.47112 (17509) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 1.359 Fit side-chains REVERT: A 161 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7942 (tpt) REVERT: B 253 SER cc_start: 0.8346 (p) cc_final: 0.8089 (p) REVERT: M 218 ASP cc_start: 0.8539 (t0) cc_final: 0.8198 (t0) REVERT: M 421 TRP cc_start: 0.8717 (OUTLIER) cc_final: 0.7425 (m-10) REVERT: S 29 GLN cc_start: 0.9222 (mm-40) cc_final: 0.8464 (mm-40) REVERT: S 33 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8662 (mm-30) REVERT: S 53 ARG cc_start: 0.8989 (mtp85) cc_final: 0.8676 (mmt90) outliers start: 13 outliers final: 9 residues processed: 87 average time/residue: 0.1887 time to fit residues: 27.0414 Evaluate side-chains 88 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 421 TRP Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 75 ASP Chi-restraints excluded: chain S residue 115 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 136 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 157 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 305 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.063638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.046706 restraints weight = 55775.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.048421 restraints weight = 30105.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.049595 restraints weight = 20538.203| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12808 Z= 0.105 Angle : 0.472 14.015 17509 Z= 0.243 Chirality : 0.038 0.141 2170 Planarity : 0.003 0.036 2207 Dihedral : 3.615 22.372 1823 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.81 % Allowed : 11.47 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.21), residues: 1696 helix: 2.47 (0.17), residues: 1001 sheet: 1.05 (0.38), residues: 187 loop : -0.75 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 462 HIS 0.003 0.001 HIS A 70 PHE 0.013 0.001 PHE A 16 TYR 0.009 0.001 TYR M 8 ARG 0.001 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.02901 ( 794) hydrogen bonds : angle 3.78036 ( 2325) covalent geometry : bond 0.00239 (12808) covalent geometry : angle 0.47191 (17509) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 1.371 Fit side-chains REVERT: B 253 SER cc_start: 0.8300 (p) cc_final: 0.8072 (p) REVERT: M 218 ASP cc_start: 0.8532 (t0) cc_final: 0.8184 (t0) REVERT: M 421 TRP cc_start: 0.8699 (OUTLIER) cc_final: 0.7347 (m-10) REVERT: S 29 GLN cc_start: 0.9207 (mm-40) cc_final: 0.8333 (mm-40) REVERT: S 33 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8650 (mm-30) outliers start: 10 outliers final: 9 residues processed: 87 average time/residue: 0.1919 time to fit residues: 27.5543 Evaluate side-chains 86 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 421 TRP Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 75 ASP Chi-restraints excluded: chain S residue 115 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 75 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 305 ASN M 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.063150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.046264 restraints weight = 55509.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.047956 restraints weight = 30053.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.049099 restraints weight = 20565.950| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12808 Z= 0.131 Angle : 0.489 14.120 17509 Z= 0.250 Chirality : 0.038 0.147 2170 Planarity : 0.003 0.037 2207 Dihedral : 3.645 23.048 1823 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.90 % Allowed : 11.55 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.21), residues: 1696 helix: 2.49 (0.17), residues: 1001 sheet: 1.21 (0.39), residues: 176 loop : -0.76 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 462 HIS 0.003 0.001 HIS A 70 PHE 0.010 0.001 PHE M 32 TYR 0.010 0.001 TYR M 8 ARG 0.003 0.000 ARG S 53 Details of bonding type rmsd hydrogen bonds : bond 0.03015 ( 794) hydrogen bonds : angle 3.83501 ( 2325) covalent geometry : bond 0.00304 (12808) covalent geometry : angle 0.48930 (17509) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 1.459 Fit side-chains REVERT: A 161 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7946 (tpt) REVERT: B 253 SER cc_start: 0.8394 (p) cc_final: 0.8170 (p) REVERT: M 218 ASP cc_start: 0.8498 (t0) cc_final: 0.8141 (t0) REVERT: M 421 TRP cc_start: 0.8700 (OUTLIER) cc_final: 0.7356 (m-10) REVERT: S 29 GLN cc_start: 0.9208 (mm-40) cc_final: 0.8315 (mm-40) REVERT: S 33 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8641 (mm-30) REVERT: S 53 ARG cc_start: 0.9051 (mtp85) cc_final: 0.8703 (mmt-90) outliers start: 11 outliers final: 9 residues processed: 83 average time/residue: 0.1952 time to fit residues: 26.7638 Evaluate side-chains 86 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 421 TRP Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 75 ASP Chi-restraints excluded: chain S residue 115 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 157 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 168 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 305 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.063567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.046659 restraints weight = 55877.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.048377 restraints weight = 30026.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.049546 restraints weight = 20461.960| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12808 Z= 0.106 Angle : 0.474 14.067 17509 Z= 0.243 Chirality : 0.038 0.141 2170 Planarity : 0.003 0.037 2207 Dihedral : 3.593 22.419 1823 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.98 % Allowed : 11.55 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.21), residues: 1696 helix: 2.53 (0.17), residues: 1001 sheet: 1.23 (0.39), residues: 176 loop : -0.72 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 462 HIS 0.003 0.001 HIS A 70 PHE 0.009 0.001 PHE M 32 TYR 0.009 0.001 TYR M 8 ARG 0.003 0.000 ARG S 53 Details of bonding type rmsd hydrogen bonds : bond 0.02862 ( 794) hydrogen bonds : angle 3.76632 ( 2325) covalent geometry : bond 0.00245 (12808) covalent geometry : angle 0.47367 (17509) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3607.55 seconds wall clock time: 63 minutes 35.14 seconds (3815.14 seconds total)