Starting phenix.real_space_refine on Tue Jul 29 19:16:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5sy1_8315/07_2025/5sy1_8315.cif Found real_map, /net/cci-nas-00/data/ceres_data/5sy1_8315/07_2025/5sy1_8315.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5sy1_8315/07_2025/5sy1_8315.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5sy1_8315/07_2025/5sy1_8315.map" model { file = "/net/cci-nas-00/data/ceres_data/5sy1_8315/07_2025/5sy1_8315.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5sy1_8315/07_2025/5sy1_8315.cif" } resolution = 3.9 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= 0.005 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 Ca 8 9.91 5 S 70 5.16 5 C 7472 2.51 5 N 1886 2.21 5 O 2026 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11462 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1154 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "A" Number of atoms: 4545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4545 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 24, 'TRANS': 557} Chain breaks: 1 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 80 Chain: "B" Number of atoms: 4545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4545 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 24, 'TRANS': 557} Chain breaks: 1 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 80 Chain: "D" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1154 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.98, per 1000 atoms: 0.61 Number of scatterers: 11462 At special positions: 0 Unit cell: (131.775, 81.575, 134.285, 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) Ca 8 19.99 S 70 16.00 O 2026 8.00 N 1886 7.00 C 7472 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: 2.65 Conformation dependent library (CDL) restraints added in 1.6 seconds 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2748 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 2 sheets defined 73.0% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'C' and resid 6 through 19 removed outlier: 3.502A pdb=" N ILE C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE C 13 " --> pdb=" O GLN C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 40 removed outlier: 3.612A pdb=" N THR C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL C 36 " --> pdb=" O GLU C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 57 removed outlier: 3.751A pdb=" N ASN C 54 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU C 55 " --> pdb=" O ASP C 51 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL C 56 " --> pdb=" O MET C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 77 removed outlier: 3.963A pdb=" N MET C 72 " --> pdb=" O GLU C 68 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET C 73 " --> pdb=" O PHE C 69 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS C 76 " --> pdb=" O MET C 72 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N MET C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 94 removed outlier: 3.588A pdb=" N ILE C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL C 92 " --> pdb=" O GLU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 113 removed outlier: 4.001A pdb=" N VAL C 109 " --> pdb=" O GLU C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 127 removed outlier: 3.705A pdb=" N ILE C 126 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG C 127 " --> pdb=" O ASP C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 148 Processing helix chain 'A' and resid 31 through 59 removed outlier: 4.582A pdb=" N LEU A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 42 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA A 45 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 107 removed outlier: 3.849A pdb=" N VAL A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N CYS A 99 " --> pdb=" O GLY A 95 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 106 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 129 removed outlier: 4.528A pdb=" N LEU A 126 " --> pdb=" O TRP A 123 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ALA A 127 " --> pdb=" O MET A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 135 through 141 removed outlier: 3.982A pdb=" N LEU A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS A 141 " --> pdb=" O PRO A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 146 through 170 removed outlier: 3.701A pdb=" N TYR A 150 " --> pdb=" O ASN A 146 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 151 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP A 170 " --> pdb=" O TRP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 186 Processing helix chain 'A' and resid 186 through 198 removed outlier: 3.637A pdb=" N LEU A 193 " --> pdb=" O GLN A 189 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 196 " --> pdb=" O CYS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 206 Processing helix chain 'A' and resid 207 through 210 Processing helix chain 'A' and resid 222 through 235 removed outlier: 3.749A pdb=" N ARG A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 229 " --> pdb=" O TYR A 225 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 232 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 262 removed outlier: 3.782A pdb=" N ALA A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 298 removed outlier: 3.657A pdb=" N SER A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 307 removed outlier: 3.706A pdb=" N ILE A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL A 304 " --> pdb=" O THR A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 319 removed outlier: 3.702A pdb=" N LEU A 315 " --> pdb=" O ASN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 377 removed outlier: 4.564A pdb=" N CYS A 340 " --> pdb=" O TYR A 336 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 354 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 365 " --> pdb=" O MET A 361 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG A 368 " --> pdb=" O MET A 364 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY A 377 " --> pdb=" O GLY A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 removed outlier: 3.618A pdb=" N HIS A 386 " --> pdb=" O VAL A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 400 removed outlier: 3.813A pdb=" N LEU A 396 " --> pdb=" O SER A 392 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 397 " --> pdb=" O ARG A 393 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS A 398 " --> pdb=" O PRO A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 430 removed outlier: 3.513A pdb=" N LEU A 410 " --> pdb=" O GLN A 406 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE A 427 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA A 428 " --> pdb=" O CYS A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 438 Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'A' and resid 453 through 472 removed outlier: 3.944A pdb=" N THR A 457 " --> pdb=" O PRO A 453 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 458 " --> pdb=" O PHE A 454 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 459 " --> pdb=" O TRP A 455 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 469 " --> pdb=" O GLN A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.725A pdb=" N LEU A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A 494 " --> pdb=" O PHE A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 522 removed outlier: 3.828A pdb=" N MET A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 515 " --> pdb=" O ARG A 511 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 518 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 525 No H-bonds generated for 'chain 'A' and resid 523 through 525' Processing helix chain 'A' and resid 532 through 538 removed outlier: 3.796A pdb=" N GLU A 536 " --> pdb=" O ARG A 533 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ALA A 537 " --> pdb=" O ASN A 534 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 538 " --> pdb=" O VAL A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 554 removed outlier: 3.542A pdb=" N ILE A 551 " --> pdb=" O HIS A 547 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 569 removed outlier: 3.957A pdb=" N GLY A 565 " --> pdb=" O LYS A 561 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 619 removed outlier: 3.530A pdb=" N TRP A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN A 618 " --> pdb=" O TYR A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 622 No H-bonds generated for 'chain 'A' and resid 620 through 622' Processing helix chain 'A' and resid 623 through 628 Processing helix chain 'B' and resid 31 through 59 removed outlier: 4.583A pdb=" N LEU B 39 " --> pdb=" O ALA B 35 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B 42 " --> pdb=" O GLY B 38 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA B 45 " --> pdb=" O HIS B 41 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 50 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET B 52 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 107 removed outlier: 3.848A pdb=" N VAL B 91 " --> pdb=" O LYS B 87 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N CYS B 99 " --> pdb=" O GLY B 95 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 129 removed outlier: 4.528A pdb=" N LEU B 126 " --> pdb=" O TRP B 123 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ALA B 127 " --> pdb=" O MET B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 135 Processing helix chain 'B' and resid 135 through 141 removed outlier: 3.981A pdb=" N LEU B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS B 141 " --> pdb=" O PRO B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 146 through 170 removed outlier: 3.701A pdb=" N TYR B 150 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 155 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP B 170 " --> pdb=" O TRP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 186 Processing helix chain 'B' and resid 186 through 198 removed outlier: 3.638A pdb=" N LEU B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 196 " --> pdb=" O CYS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 206 Processing helix chain 'B' and resid 207 through 210 Processing helix chain 'B' and resid 222 through 235 removed outlier: 3.750A pdb=" N ARG B 226 " --> pdb=" O SER B 222 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 229 " --> pdb=" O TYR B 225 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 232 " --> pdb=" O TYR B 228 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 262 removed outlier: 3.782A pdb=" N ALA B 257 " --> pdb=" O ARG B 253 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 298 removed outlier: 3.658A pdb=" N SER B 278 " --> pdb=" O LYS B 274 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL B 280 " --> pdb=" O ALA B 276 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE B 294 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 298 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 307 removed outlier: 3.706A pdb=" N ILE B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL B 304 " --> pdb=" O THR B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 319 removed outlier: 3.702A pdb=" N LEU B 315 " --> pdb=" O ASN B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 377 removed outlier: 4.563A pdb=" N CYS B 340 " --> pdb=" O TYR B 336 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 354 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET B 361 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 365 " --> pdb=" O MET B 361 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS B 367 " --> pdb=" O SER B 363 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG B 368 " --> pdb=" O MET B 364 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 377 " --> pdb=" O GLY B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 386 removed outlier: 3.616A pdb=" N HIS B 386 " --> pdb=" O VAL B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 400 removed outlier: 3.814A pdb=" N LEU B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 397 " --> pdb=" O ARG B 393 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS B 398 " --> pdb=" O PRO B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 430 removed outlier: 3.513A pdb=" N LEU B 410 " --> pdb=" O GLN B 406 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE B 423 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 426 " --> pdb=" O PHE B 422 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE B 427 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA B 428 " --> pdb=" O CYS B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 438 Processing helix chain 'B' and resid 447 through 451 Processing helix chain 'B' and resid 453 through 472 removed outlier: 3.945A pdb=" N THR B 457 " --> pdb=" O PRO B 453 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU B 458 " --> pdb=" O PHE B 454 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 459 " --> pdb=" O TRP B 455 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 480 No H-bonds generated for 'chain 'B' and resid 478 through 480' Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.724A pdb=" N LEU B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B 494 " --> pdb=" O PHE B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 522 removed outlier: 3.828A pdb=" N MET B 502 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL B 506 " --> pdb=" O MET B 502 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR B 515 " --> pdb=" O ARG B 511 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 518 " --> pdb=" O ILE B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 525 No H-bonds generated for 'chain 'B' and resid 523 through 525' Processing helix chain 'B' and resid 532 through 538 removed outlier: 3.796A pdb=" N GLU B 536 " --> pdb=" O ARG B 533 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ALA B 537 " --> pdb=" O ASN B 534 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 538 " --> pdb=" O VAL B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 554 removed outlier: 3.542A pdb=" N ILE B 551 " --> pdb=" O HIS B 547 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL B 553 " --> pdb=" O LEU B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 569 removed outlier: 3.957A pdb=" N GLY B 565 " --> pdb=" O LYS B 561 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 566 " --> pdb=" O ALA B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 619 removed outlier: 3.530A pdb=" N TRP B 610 " --> pdb=" O ALA B 606 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN B 618 " --> pdb=" O TYR B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 622 No H-bonds generated for 'chain 'B' and resid 620 through 622' Processing helix chain 'B' and resid 623 through 628 Processing helix chain 'D' and resid 6 through 19 removed outlier: 3.503A pdb=" N ILE D 10 " --> pdb=" O THR D 6 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE D 13 " --> pdb=" O GLN D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 40 removed outlier: 3.612A pdb=" N THR D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL D 36 " --> pdb=" O GLU D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 57 removed outlier: 3.752A pdb=" N ASN D 54 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU D 55 " --> pdb=" O ASP D 51 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL D 56 " --> pdb=" O MET D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 77 removed outlier: 3.964A pdb=" N MET D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET D 73 " --> pdb=" O PHE D 69 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS D 76 " --> pdb=" O MET D 72 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N MET D 77 " --> pdb=" O MET D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 94 removed outlier: 3.589A pdb=" N ILE D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG D 91 " --> pdb=" O ARG D 87 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 113 removed outlier: 4.000A pdb=" N VAL D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 127 removed outlier: 3.704A pdb=" N ILE D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG D 127 " --> pdb=" O ASP D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 148 Processing sheet with id=AA1, first strand: chain 'A' and resid 474 through 476 Processing sheet with id=AA2, first strand: chain 'B' and resid 474 through 476 575 hydrogen bonds defined for protein. 1677 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.98 Time building geometry restraints manager: 3.17 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: 3558 1.34 - 1.46: 2688 1.46 - 1.58: 5350 1.58 - 1.70: 0 1.70 - 1.82: 112 Bond restraints: 11708 Sorted by residual: bond pdb=" C TRP B 452 " pdb=" N PRO B 453 " ideal model delta sigma weight residual 1.337 1.366 -0.029 1.24e-02 6.50e+03 5.55e+00 bond pdb=" C TRP A 452 " pdb=" N PRO A 453 " ideal model delta sigma weight residual 1.337 1.366 -0.029 1.24e-02 6.50e+03 5.44e+00 bond pdb=" C THR B 264 " pdb=" N PRO B 265 " ideal model delta sigma weight residual 1.332 1.362 -0.030 1.34e-02 5.57e+03 4.90e+00 bond pdb=" C THR A 264 " pdb=" N PRO A 265 " ideal model delta sigma weight residual 1.332 1.361 -0.029 1.34e-02 5.57e+03 4.63e+00 bond pdb=" CB THR A 403 " pdb=" CG2 THR A 403 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.00e+00 ... (remaining 11703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 14955 1.94 - 3.89: 796 3.89 - 5.83: 107 5.83 - 7.78: 34 7.78 - 9.72: 18 Bond angle restraints: 15910 Sorted by residual: angle pdb=" N HIS A 109 " pdb=" CA HIS A 109 " pdb=" C HIS A 109 " ideal model delta sigma weight residual 109.81 119.53 -9.72 2.21e+00 2.05e-01 1.93e+01 angle pdb=" N HIS B 109 " pdb=" CA HIS B 109 " pdb=" C HIS B 109 " ideal model delta sigma weight residual 109.81 119.52 -9.71 2.21e+00 2.05e-01 1.93e+01 angle pdb=" N THR B 264 " pdb=" CA THR B 264 " pdb=" C THR B 264 " ideal model delta sigma weight residual 109.81 119.36 -9.55 2.21e+00 2.05e-01 1.87e+01 angle pdb=" N THR A 264 " pdb=" CA THR A 264 " pdb=" C THR A 264 " ideal model delta sigma weight residual 109.81 119.30 -9.49 2.21e+00 2.05e-01 1.84e+01 angle pdb=" C ASN B 119 " pdb=" N LYS B 120 " pdb=" CA LYS B 120 " ideal model delta sigma weight residual 121.54 129.54 -8.00 1.91e+00 2.74e-01 1.76e+01 ... (remaining 15905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.36: 6593 14.36 - 28.73: 362 28.73 - 43.09: 75 43.09 - 57.45: 16 57.45 - 71.82: 2 Dihedral angle restraints: 7048 sinusoidal: 2796 harmonic: 4252 Sorted by residual: dihedral pdb=" CA HIS B 109 " pdb=" C HIS B 109 " pdb=" N PRO B 110 " pdb=" CA PRO B 110 " ideal model delta harmonic sigma weight residual -180.00 -125.21 -54.79 0 5.00e+00 4.00e-02 1.20e+02 dihedral pdb=" CA HIS A 109 " pdb=" C HIS A 109 " pdb=" N PRO A 110 " pdb=" CA PRO A 110 " ideal model delta harmonic sigma weight residual 180.00 -125.25 -54.75 0 5.00e+00 4.00e-02 1.20e+02 dihedral pdb=" CA THR B 264 " pdb=" C THR B 264 " pdb=" N PRO B 265 " pdb=" CA PRO B 265 " ideal model delta harmonic sigma weight residual -180.00 -138.07 -41.93 0 5.00e+00 4.00e-02 7.03e+01 ... (remaining 7045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1352 0.056 - 0.112: 443 0.112 - 0.168: 63 0.168 - 0.223: 8 0.223 - 0.279: 6 Chirality restraints: 1872 Sorted by residual: chirality pdb=" C13 CLR A 701 " pdb=" C12 CLR A 701 " pdb=" C14 CLR A 701 " pdb=" C17 CLR A 701 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C13 CLR B 701 " pdb=" C12 CLR B 701 " pdb=" C14 CLR B 701 " pdb=" C17 CLR B 701 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA CYS B 171 " pdb=" N CYS B 171 " pdb=" C CYS B 171 " pdb=" CB CYS B 171 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1869 not shown) Planarity restraints: 1976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 237 " 0.052 5.00e-02 4.00e+02 7.74e-02 9.59e+00 pdb=" N PRO A 238 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 238 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 238 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 237 " -0.052 5.00e-02 4.00e+02 7.72e-02 9.54e+00 pdb=" N PRO B 238 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 238 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 238 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 532 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.57e+00 pdb=" CG ASN A 532 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN A 532 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 532 " -0.015 2.00e-02 2.50e+03 ... (remaining 1973 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.20: 10 2.20 - 2.87: 4203 2.87 - 3.55: 15687 3.55 - 4.22: 25701 4.22 - 4.90: 41675 Nonbonded interactions: 87276 Sorted by model distance: nonbonded pdb=" OD1 ASP C 57 " pdb=" OD1 ASP C 59 " model vdw 1.524 3.040 nonbonded pdb=" OD1 ASP D 57 " pdb=" OD1 ASP D 59 " model vdw 1.525 3.040 nonbonded pdb=" OD2 ASP D 21 " pdb=" OD1 ASP D 25 " model vdw 1.782 3.040 nonbonded pdb=" OD2 ASP C 21 " pdb=" OD1 ASP C 25 " model vdw 1.782 3.040 nonbonded pdb=" OD2 ASP C 23 " pdb=" OE2 GLU C 32 " model vdw 1.845 3.040 ... (remaining 87271 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.480 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: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.690 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.070 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 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 : 0.008 0.074 11708 Z= 0.354 Angle : 1.022 9.721 15910 Z= 0.540 Chirality : 0.055 0.279 1872 Planarity : 0.008 0.077 1976 Dihedral : 10.045 71.817 4300 Min Nonbonded Distance : 1.524 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.12 % Favored : 92.74 % Rotamer: Outliers : 0.08 % Allowed : 1.63 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.29 % 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: -5.23 (0.16), residues: 1446 helix: -3.96 (0.08), residues: 936 sheet: -2.76 (1.03), residues: 20 loop : -1.90 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 399 HIS 0.007 0.002 HIS B 609 PHE 0.038 0.004 PHE A 40 TYR 0.014 0.003 TYR B 94 ARG 0.010 0.001 ARG A 486 Details of bonding type rmsd hydrogen bonds : bond 0.31774 ( 575) hydrogen bonds : angle 9.72055 ( 1677) covalent geometry : bond 0.00791 (11708) covalent geometry : angle 1.02182 (15910) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 396 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 ASP cc_start: 0.7028 (m-30) cc_final: 0.6428 (t70) REVERT: C 4 GLN cc_start: 0.8855 (tt0) cc_final: 0.8605 (tt0) REVERT: C 8 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8197 (pm20) REVERT: C 15 GLU cc_start: 0.8639 (tp30) cc_final: 0.8371 (tp30) REVERT: C 38 ARG cc_start: 0.8518 (ttm110) cc_final: 0.8168 (ptp-110) REVERT: C 52 MET cc_start: 0.8763 (mtp) cc_final: 0.8066 (ttp) REVERT: C 73 MET cc_start: 0.8033 (mmm) cc_final: 0.7756 (mmp) REVERT: C 77 MET cc_start: 0.7526 (mpt) cc_final: 0.6730 (mpp) REVERT: C 85 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7907 (tm-30) REVERT: C 93 PHE cc_start: 0.7242 (m-80) cc_final: 0.6484 (m-80) REVERT: C 101 ILE cc_start: 0.6517 (mt) cc_final: 0.6267 (mp) REVERT: C 124 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7943 (tp30) REVERT: C 125 MET cc_start: 0.7466 (mtt) cc_final: 0.6561 (mmm) REVERT: A 52 MET cc_start: 0.7390 (mtp) cc_final: 0.6923 (ttt) REVERT: A 104 MET cc_start: 0.8396 (ttp) cc_final: 0.8059 (tmm) REVERT: A 109 HIS cc_start: 0.7137 (p90) cc_final: 0.6588 (t70) REVERT: A 150 TYR cc_start: 0.8249 (m-80) cc_final: 0.8022 (m-80) REVERT: A 187 LEU cc_start: 0.8634 (mt) cc_final: 0.8409 (mt) REVERT: A 215 ASN cc_start: 0.6243 (p0) cc_final: 0.5617 (m-40) REVERT: A 220 LEU cc_start: 0.8833 (tp) cc_final: 0.8534 (mt) REVERT: A 249 LYS cc_start: 0.6213 (tttt) cc_final: 0.6004 (mtmt) REVERT: A 268 VAL cc_start: 0.8414 (t) cc_final: 0.7780 (p) REVERT: A 286 LEU cc_start: 0.6102 (tp) cc_final: 0.5902 (tp) REVERT: A 532 ASN cc_start: 0.8530 (t0) cc_final: 0.8102 (t0) REVERT: A 550 LYS cc_start: 0.7850 (ttmm) cc_final: 0.7459 (mmtp) REVERT: A 602 ASN cc_start: 0.7139 (t0) cc_final: 0.6652 (t0) REVERT: A 604 LYS cc_start: 0.8333 (tptt) cc_final: 0.8083 (mtpp) REVERT: B 53 LEU cc_start: 0.7843 (mt) cc_final: 0.7418 (tt) REVERT: B 109 HIS cc_start: 0.7039 (p90) cc_final: 0.6189 (t70) REVERT: B 125 ILE cc_start: 0.7715 (mt) cc_final: 0.7458 (pt) REVERT: B 130 TYR cc_start: 0.7500 (t80) cc_final: 0.7263 (t80) REVERT: B 181 TYR cc_start: 0.8668 (t80) cc_final: 0.8468 (t80) REVERT: B 186 SER cc_start: 0.7362 (m) cc_final: 0.7123 (p) REVERT: B 220 LEU cc_start: 0.8656 (tp) cc_final: 0.8371 (mt) REVERT: B 235 LYS cc_start: 0.7346 (tttt) cc_final: 0.6555 (tmtt) REVERT: B 268 VAL cc_start: 0.8198 (t) cc_final: 0.7456 (p) REVERT: B 326 ASP cc_start: 0.6283 (t0) cc_final: 0.5855 (t0) REVERT: D 4 GLN cc_start: 0.9047 (tt0) cc_final: 0.8237 (tm-30) REVERT: D 8 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8182 (pm20) REVERT: D 15 GLU cc_start: 0.8882 (tp30) cc_final: 0.8680 (tp30) REVERT: D 17 PHE cc_start: 0.8742 (t80) cc_final: 0.8515 (t80) REVERT: D 38 ARG cc_start: 0.8606 (ttm110) cc_final: 0.8385 (ptp-110) REVERT: D 69 PHE cc_start: 0.6796 (t80) cc_final: 0.6557 (t80) REVERT: D 85 GLU cc_start: 0.8415 (mt-10) cc_final: 0.7774 (tm-30) REVERT: D 93 PHE cc_start: 0.7375 (m-80) cc_final: 0.6851 (m-80) REVERT: D 95 LYS cc_start: 0.7247 (mttt) cc_final: 0.6959 (mtmt) REVERT: D 101 ILE cc_start: 0.7001 (mt) cc_final: 0.6519 (mp) REVERT: D 124 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7740 (tp30) REVERT: D 125 MET cc_start: 0.7875 (mtt) cc_final: 0.7095 (mmm) outliers start: 1 outliers final: 0 residues processed: 397 average time/residue: 0.2662 time to fit residues: 143.2791 Evaluate side-chains 225 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 37 optimal weight: 0.0370 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 overall best weight: 1.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 HIS A 465 GLN A 466 HIS A 500 ASN B 209 GLN B 465 GLN B 519 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.136082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.098273 restraints weight = 23135.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.100771 restraints weight = 13950.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.102364 restraints weight = 10389.895| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11708 Z= 0.152 Angle : 0.711 7.969 15910 Z= 0.372 Chirality : 0.043 0.204 1872 Planarity : 0.007 0.084 1976 Dihedral : 6.474 47.442 1692 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.04 % Allowed : 10.42 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.19), residues: 1446 helix: -1.83 (0.13), residues: 996 sheet: -1.53 (1.26), residues: 20 loop : -1.92 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 158 HIS 0.006 0.001 HIS D 108 PHE 0.025 0.002 PHE C 17 TYR 0.025 0.002 TYR B 178 ARG 0.004 0.001 ARG B 255 Details of bonding type rmsd hydrogen bonds : bond 0.06485 ( 575) hydrogen bonds : angle 5.06923 ( 1677) covalent geometry : bond 0.00308 (11708) covalent geometry : angle 0.71134 (15910) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 285 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 GLN cc_start: 0.8493 (tt0) cc_final: 0.8110 (tm-30) REVERT: C 38 ARG cc_start: 0.8277 (ttm110) cc_final: 0.7814 (ttm110) REVERT: C 91 ARG cc_start: 0.7791 (mtt90) cc_final: 0.7382 (mmt90) REVERT: C 93 PHE cc_start: 0.7543 (m-80) cc_final: 0.6887 (m-80) REVERT: C 125 MET cc_start: 0.7552 (mtt) cc_final: 0.7308 (mmm) REVERT: A 52 MET cc_start: 0.7213 (mtp) cc_final: 0.6596 (ttm) REVERT: A 186 SER cc_start: 0.8615 (m) cc_final: 0.8085 (p) REVERT: A 215 ASN cc_start: 0.7113 (p0) cc_final: 0.5975 (m-40) REVERT: A 268 VAL cc_start: 0.9058 (t) cc_final: 0.8814 (p) REVERT: A 343 ILE cc_start: 0.8790 (mt) cc_final: 0.8389 (tp) REVERT: A 414 MET cc_start: 0.9065 (mmm) cc_final: 0.8708 (tpp) REVERT: A 496 LEU cc_start: 0.8460 (mt) cc_final: 0.8189 (mt) REVERT: B 53 LEU cc_start: 0.7986 (mt) cc_final: 0.7540 (tt) REVERT: B 235 LYS cc_start: 0.7753 (tttt) cc_final: 0.6842 (tmtt) REVERT: B 268 VAL cc_start: 0.8670 (t) cc_final: 0.8360 (p) REVERT: B 455 TRP cc_start: 0.8335 (m-10) cc_final: 0.8101 (m-10) REVERT: B 610 TRP cc_start: 0.7306 (m-10) cc_final: 0.7054 (m-10) REVERT: D 4 GLN cc_start: 0.8760 (tt0) cc_final: 0.8304 (tm-30) REVERT: D 91 ARG cc_start: 0.8210 (mtt90) cc_final: 0.7491 (mtt-85) REVERT: D 106 LEU cc_start: 0.8691 (tt) cc_final: 0.8414 (pp) REVERT: D 117 LEU cc_start: 0.6372 (mt) cc_final: 0.6111 (tp) REVERT: D 120 GLU cc_start: 0.7814 (pm20) cc_final: 0.7597 (pm20) REVERT: D 125 MET cc_start: 0.7382 (mtt) cc_final: 0.6992 (mmm) REVERT: D 139 TYR cc_start: 0.7183 (t80) cc_final: 0.6728 (t80) outliers start: 25 outliers final: 10 residues processed: 302 average time/residue: 0.2214 time to fit residues: 95.6635 Evaluate side-chains 207 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 197 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain D residue 53 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 42 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 58 optimal weight: 0.0670 chunk 78 optimal weight: 0.9990 chunk 114 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 54 ASN C 112 ASN B 109 HIS B 547 HIS D 54 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.132703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.097668 restraints weight = 23706.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.097390 restraints weight = 15368.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.097800 restraints weight = 12081.138| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11708 Z= 0.181 Angle : 0.704 7.857 15910 Z= 0.363 Chirality : 0.044 0.203 1872 Planarity : 0.006 0.088 1976 Dihedral : 6.033 46.007 1692 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.42 % Allowed : 12.54 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.14 % 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: -1.70 (0.21), residues: 1446 helix: -0.75 (0.15), residues: 998 sheet: -1.64 (1.19), residues: 20 loop : -1.67 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 452 HIS 0.010 0.001 HIS C 108 PHE 0.017 0.002 PHE B 427 TYR 0.032 0.002 TYR B 178 ARG 0.004 0.001 ARG B 255 Details of bonding type rmsd hydrogen bonds : bond 0.05573 ( 575) hydrogen bonds : angle 4.71690 ( 1677) covalent geometry : bond 0.00403 (11708) covalent geometry : angle 0.70359 (15910) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 215 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 GLN cc_start: 0.8700 (tt0) cc_final: 0.8215 (tm-30) REVERT: C 12 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8042 (tp30) REVERT: C 72 MET cc_start: 0.8462 (mtp) cc_final: 0.8212 (mtp) REVERT: C 81 ASP cc_start: 0.7265 (p0) cc_final: 0.7015 (p0) REVERT: C 83 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7608 (mp0) REVERT: C 93 PHE cc_start: 0.7546 (m-80) cc_final: 0.6909 (m-80) REVERT: C 125 MET cc_start: 0.7730 (mtt) cc_final: 0.7461 (mmm) REVERT: A 52 MET cc_start: 0.7287 (mtp) cc_final: 0.6690 (ttm) REVERT: A 200 TYR cc_start: 0.8274 (m-10) cc_final: 0.8066 (m-80) REVERT: A 215 ASN cc_start: 0.6695 (p0) cc_final: 0.5862 (m-40) REVERT: A 268 VAL cc_start: 0.9043 (t) cc_final: 0.8823 (p) REVERT: A 414 MET cc_start: 0.9179 (mmm) cc_final: 0.8893 (tpt) REVERT: B 53 LEU cc_start: 0.7820 (mt) cc_final: 0.7564 (tt) REVERT: B 235 LYS cc_start: 0.7741 (tttt) cc_final: 0.6740 (tmtt) REVERT: B 259 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8135 (pttm) REVERT: B 268 VAL cc_start: 0.8775 (t) cc_final: 0.8465 (p) REVERT: B 364 MET cc_start: 0.8651 (tpp) cc_final: 0.8356 (tpp) REVERT: B 455 TRP cc_start: 0.8494 (m-10) cc_final: 0.8256 (m-10) REVERT: B 568 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8414 (mm) REVERT: B 610 TRP cc_start: 0.7256 (m-10) cc_final: 0.7052 (m-10) REVERT: D 4 GLN cc_start: 0.8726 (tt0) cc_final: 0.8266 (tm-30) REVERT: D 72 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8139 (mtp) REVERT: D 91 ARG cc_start: 0.8237 (mtt90) cc_final: 0.7520 (mtt-85) REVERT: D 108 HIS cc_start: 0.7825 (t-170) cc_final: 0.7518 (t-170) REVERT: D 120 GLU cc_start: 0.7708 (pm20) cc_final: 0.7423 (pm20) REVERT: D 125 MET cc_start: 0.7472 (mtt) cc_final: 0.7103 (mmm) REVERT: D 139 TYR cc_start: 0.7259 (t80) cc_final: 0.6997 (t80) outliers start: 42 outliers final: 31 residues processed: 240 average time/residue: 0.2179 time to fit residues: 75.8193 Evaluate side-chains 221 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 455 TRP Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 72 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN A 109 HIS ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.133994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.098171 restraints weight = 23635.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.098674 restraints weight = 15178.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.098943 restraints weight = 11648.030| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11708 Z= 0.141 Angle : 0.648 9.120 15910 Z= 0.333 Chirality : 0.042 0.204 1872 Planarity : 0.005 0.085 1976 Dihedral : 5.698 46.050 1692 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.09 % Allowed : 13.36 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.77 % Twisted General : 0.14 % 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: -1.02 (0.22), residues: 1446 helix: -0.18 (0.16), residues: 998 sheet: -1.62 (1.20), residues: 20 loop : -1.57 (0.33), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 452 HIS 0.009 0.001 HIS C 108 PHE 0.038 0.002 PHE B 40 TYR 0.029 0.001 TYR B 178 ARG 0.004 0.000 ARG C 38 Details of bonding type rmsd hydrogen bonds : bond 0.04805 ( 575) hydrogen bonds : angle 4.46295 ( 1677) covalent geometry : bond 0.00307 (11708) covalent geometry : angle 0.64785 (15910) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 216 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 GLN cc_start: 0.8744 (tt0) cc_final: 0.8165 (tm-30) REVERT: C 12 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8032 (tp30) REVERT: C 72 MET cc_start: 0.8424 (mtp) cc_final: 0.8135 (mtp) REVERT: C 83 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7691 (mp0) REVERT: C 93 PHE cc_start: 0.7516 (m-80) cc_final: 0.6858 (m-80) REVERT: C 125 MET cc_start: 0.7702 (mtt) cc_final: 0.7314 (mmm) REVERT: A 52 MET cc_start: 0.7355 (mtp) cc_final: 0.6857 (ttm) REVERT: A 215 ASN cc_start: 0.6591 (p0) cc_final: 0.5760 (m-40) REVERT: A 268 VAL cc_start: 0.8997 (t) cc_final: 0.8766 (p) REVERT: A 343 ILE cc_start: 0.8842 (mt) cc_final: 0.8414 (tp) REVERT: A 509 ILE cc_start: 0.9227 (pt) cc_final: 0.8988 (mm) REVERT: B 109 HIS cc_start: 0.6857 (OUTLIER) cc_final: 0.6332 (t-90) REVERT: B 259 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8146 (pttm) REVERT: B 268 VAL cc_start: 0.8701 (t) cc_final: 0.8425 (p) REVERT: B 316 LEU cc_start: 0.6525 (mt) cc_final: 0.6068 (tp) REVERT: B 568 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8663 (mm) REVERT: D 4 GLN cc_start: 0.8742 (tt0) cc_final: 0.8273 (tm-30) REVERT: D 72 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8209 (mtp) REVERT: D 75 ARG cc_start: 0.8267 (mmm-85) cc_final: 0.8044 (mmm-85) REVERT: D 91 ARG cc_start: 0.8269 (mtt90) cc_final: 0.7674 (mtm-85) REVERT: D 120 GLU cc_start: 0.7832 (pm20) cc_final: 0.7524 (pm20) outliers start: 38 outliers final: 24 residues processed: 237 average time/residue: 0.2286 time to fit residues: 78.3736 Evaluate side-chains 215 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 455 TRP Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 72 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 32 optimal weight: 0.5980 chunk 11 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 13 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 HIS B 465 GLN B 609 HIS D 9 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.130698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.096607 restraints weight = 23801.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.095372 restraints weight = 16520.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.095838 restraints weight = 14722.332| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11708 Z= 0.219 Angle : 0.717 7.761 15910 Z= 0.368 Chirality : 0.044 0.196 1872 Planarity : 0.006 0.092 1976 Dihedral : 5.805 44.132 1692 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 4.15 % Allowed : 14.09 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.14 % 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: -0.86 (0.22), residues: 1446 helix: -0.05 (0.16), residues: 996 sheet: -1.91 (1.08), residues: 20 loop : -1.51 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 158 HIS 0.014 0.001 HIS A 109 PHE 0.046 0.002 PHE B 40 TYR 0.031 0.002 TYR B 178 ARG 0.005 0.001 ARG B 255 Details of bonding type rmsd hydrogen bonds : bond 0.05105 ( 575) hydrogen bonds : angle 4.69786 ( 1677) covalent geometry : bond 0.00502 (11708) covalent geometry : angle 0.71703 (15910) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 193 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 4 GLN cc_start: 0.8613 (tt0) cc_final: 0.8223 (tm-30) REVERT: C 81 ASP cc_start: 0.7159 (p0) cc_final: 0.6522 (p0) REVERT: C 83 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7624 (mp0) REVERT: C 93 PHE cc_start: 0.7529 (m-80) cc_final: 0.6953 (m-80) REVERT: C 125 MET cc_start: 0.7744 (mtt) cc_final: 0.7353 (mmm) REVERT: A 52 MET cc_start: 0.7428 (mtp) cc_final: 0.6895 (ttm) REVERT: A 215 ASN cc_start: 0.6718 (p0) cc_final: 0.6012 (m-40) REVERT: B 109 HIS cc_start: 0.7231 (OUTLIER) cc_final: 0.6775 (t-90) REVERT: B 259 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8232 (pttm) REVERT: B 268 VAL cc_start: 0.8829 (t) cc_final: 0.8536 (p) REVERT: B 443 MET cc_start: 0.7387 (mtt) cc_final: 0.7119 (mtt) REVERT: B 496 LEU cc_start: 0.8679 (mt) cc_final: 0.8425 (mt) REVERT: D 4 GLN cc_start: 0.8761 (tt0) cc_final: 0.8295 (tm-30) REVERT: D 72 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.7931 (mtp) REVERT: D 91 ARG cc_start: 0.8310 (mtt90) cc_final: 0.7510 (mtt-85) REVERT: D 120 GLU cc_start: 0.7897 (pm20) cc_final: 0.7617 (pm20) REVERT: D 125 MET cc_start: 0.7318 (mmm) cc_final: 0.7092 (mmm) outliers start: 51 outliers final: 36 residues processed: 224 average time/residue: 0.2054 time to fit residues: 67.3051 Evaluate side-chains 216 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 455 TRP Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 109 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 0.3980 chunk 125 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 143 optimal weight: 20.0000 chunk 49 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 HIS C 136 GLN ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.133509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.098243 restraints weight = 23683.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.099100 restraints weight = 14713.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.099413 restraints weight = 11247.819| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11708 Z= 0.132 Angle : 0.657 8.736 15910 Z= 0.332 Chirality : 0.041 0.209 1872 Planarity : 0.005 0.083 1976 Dihedral : 5.543 44.020 1692 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.77 % Allowed : 15.96 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.14 % 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: -0.39 (0.22), residues: 1446 helix: 0.33 (0.16), residues: 988 sheet: -1.71 (1.09), residues: 20 loop : -1.38 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 158 HIS 0.008 0.001 HIS A 109 PHE 0.021 0.001 PHE A 427 TYR 0.026 0.001 TYR B 178 ARG 0.003 0.000 ARG C 38 Details of bonding type rmsd hydrogen bonds : bond 0.04493 ( 575) hydrogen bonds : angle 4.36996 ( 1677) covalent geometry : bond 0.00286 (11708) covalent geometry : angle 0.65725 (15910) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 207 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 4 GLN cc_start: 0.8648 (tt0) cc_final: 0.8156 (tm-30) REVERT: C 83 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7571 (mp0) REVERT: C 93 PHE cc_start: 0.7497 (m-80) cc_final: 0.6942 (m-80) REVERT: C 125 MET cc_start: 0.7738 (mtt) cc_final: 0.7413 (mmm) REVERT: A 52 MET cc_start: 0.7396 (mtp) cc_final: 0.7172 (ttp) REVERT: A 316 LEU cc_start: 0.6361 (mt) cc_final: 0.5977 (mt) REVERT: A 509 ILE cc_start: 0.9308 (pt) cc_final: 0.9029 (mm) REVERT: B 109 HIS cc_start: 0.7407 (OUTLIER) cc_final: 0.6941 (t-90) REVERT: B 268 VAL cc_start: 0.8694 (t) cc_final: 0.8424 (p) REVERT: B 316 LEU cc_start: 0.6584 (mt) cc_final: 0.6187 (tp) REVERT: B 443 MET cc_start: 0.7449 (mtt) cc_final: 0.7167 (mtt) REVERT: D 72 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7987 (mtp) REVERT: D 91 ARG cc_start: 0.8309 (mtt90) cc_final: 0.7530 (mtt-85) REVERT: D 120 GLU cc_start: 0.7809 (pm20) cc_final: 0.7565 (pm20) REVERT: D 125 MET cc_start: 0.7393 (mmm) cc_final: 0.7153 (mmm) outliers start: 34 outliers final: 24 residues processed: 225 average time/residue: 0.2208 time to fit residues: 72.7879 Evaluate side-chains 212 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 455 TRP Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 109 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 57 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 132 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 80 optimal weight: 0.0020 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.134945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.099981 restraints weight = 23769.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.100507 restraints weight = 14812.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.100980 restraints weight = 11243.394| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11708 Z= 0.121 Angle : 0.637 8.643 15910 Z= 0.321 Chirality : 0.041 0.207 1872 Planarity : 0.005 0.081 1976 Dihedral : 5.322 42.571 1692 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.52 % Allowed : 16.21 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.77 % Twisted General : 0.14 % 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: -0.09 (0.23), residues: 1446 helix: 0.57 (0.16), residues: 988 sheet: -1.34 (1.18), residues: 20 loop : -1.30 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 452 HIS 0.010 0.001 HIS C 108 PHE 0.021 0.001 PHE A 427 TYR 0.022 0.001 TYR B 178 ARG 0.003 0.000 ARG B 255 Details of bonding type rmsd hydrogen bonds : bond 0.04098 ( 575) hydrogen bonds : angle 4.19611 ( 1677) covalent geometry : bond 0.00255 (11708) covalent geometry : angle 0.63661 (15910) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 GLN cc_start: 0.8682 (tt0) cc_final: 0.8222 (tm-30) REVERT: C 83 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7689 (mp0) REVERT: C 93 PHE cc_start: 0.7452 (m-80) cc_final: 0.6928 (m-80) REVERT: C 125 MET cc_start: 0.7732 (mtt) cc_final: 0.7301 (mmm) REVERT: A 36 ASP cc_start: 0.5943 (t0) cc_final: 0.4636 (m-30) REVERT: A 52 MET cc_start: 0.7340 (mtp) cc_final: 0.7124 (ttp) REVERT: A 316 LEU cc_start: 0.6698 (mt) cc_final: 0.6369 (mt) REVERT: A 414 MET cc_start: 0.8925 (tpt) cc_final: 0.8719 (mmm) REVERT: A 509 ILE cc_start: 0.9286 (pt) cc_final: 0.9042 (mm) REVERT: B 109 HIS cc_start: 0.7586 (OUTLIER) cc_final: 0.7173 (t-90) REVERT: B 268 VAL cc_start: 0.8602 (t) cc_final: 0.8378 (p) REVERT: B 316 LEU cc_start: 0.6533 (mt) cc_final: 0.6205 (tp) REVERT: B 443 MET cc_start: 0.7434 (mtt) cc_final: 0.7117 (mtt) REVERT: B 568 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8721 (mm) REVERT: D 4 GLN cc_start: 0.8395 (tm-30) cc_final: 0.7555 (tm-30) REVERT: D 91 ARG cc_start: 0.8293 (mtt90) cc_final: 0.7643 (mtt-85) REVERT: D 125 MET cc_start: 0.7389 (mmm) cc_final: 0.7121 (mmm) outliers start: 31 outliers final: 19 residues processed: 216 average time/residue: 0.2024 time to fit residues: 64.7733 Evaluate side-chains 209 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 455 TRP Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain D residue 109 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 18 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 114 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 117 optimal weight: 20.0000 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 HIS ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.132792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.097598 restraints weight = 23690.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.097906 restraints weight = 15829.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.098524 restraints weight = 11798.393| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11708 Z= 0.150 Angle : 0.656 9.882 15910 Z= 0.332 Chirality : 0.042 0.201 1872 Planarity : 0.005 0.081 1976 Dihedral : 5.340 43.361 1692 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.77 % Allowed : 16.45 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.14 % 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: -0.01 (0.23), residues: 1446 helix: 0.61 (0.16), residues: 994 sheet: -1.41 (1.18), residues: 20 loop : -1.24 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 158 HIS 0.009 0.001 HIS C 108 PHE 0.020 0.001 PHE A 427 TYR 0.026 0.001 TYR B 178 ARG 0.003 0.000 ARG D 75 Details of bonding type rmsd hydrogen bonds : bond 0.04327 ( 575) hydrogen bonds : angle 4.30893 ( 1677) covalent geometry : bond 0.00341 (11708) covalent geometry : angle 0.65640 (15910) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 GLN cc_start: 0.8641 (tt0) cc_final: 0.8158 (tm-30) REVERT: C 93 PHE cc_start: 0.7495 (m-80) cc_final: 0.6922 (m-80) REVERT: C 125 MET cc_start: 0.7783 (mtt) cc_final: 0.7300 (mmm) REVERT: A 52 MET cc_start: 0.7430 (mtp) cc_final: 0.7226 (ttp) REVERT: A 104 MET cc_start: 0.8521 (ttm) cc_final: 0.8309 (tmm) REVERT: A 316 LEU cc_start: 0.6703 (mt) cc_final: 0.6401 (mt) REVERT: B 109 HIS cc_start: 0.7614 (OUTLIER) cc_final: 0.7242 (t-90) REVERT: B 268 VAL cc_start: 0.8648 (t) cc_final: 0.8413 (p) REVERT: B 316 LEU cc_start: 0.6675 (mt) cc_final: 0.6264 (tp) REVERT: B 443 MET cc_start: 0.7376 (mtt) cc_final: 0.7064 (mtt) REVERT: B 568 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8936 (mm) REVERT: D 4 GLN cc_start: 0.8362 (tm130) cc_final: 0.8154 (tm-30) REVERT: D 72 MET cc_start: 0.8567 (mmm) cc_final: 0.8108 (mtp) outliers start: 34 outliers final: 24 residues processed: 206 average time/residue: 0.1970 time to fit residues: 61.3598 Evaluate side-chains 207 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 455 TRP Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain D residue 40 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 134 optimal weight: 4.9990 chunk 117 optimal weight: 20.0000 chunk 74 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 101 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 105 optimal weight: 0.8980 chunk 63 optimal weight: 0.0870 chunk 25 optimal weight: 2.9990 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 HIS C 112 ASN ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.133497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.098791 restraints weight = 23824.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.099531 restraints weight = 14513.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.099892 restraints weight = 11230.276| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11708 Z= 0.132 Angle : 0.649 12.102 15910 Z= 0.326 Chirality : 0.041 0.204 1872 Planarity : 0.005 0.079 1976 Dihedral : 5.256 42.682 1692 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.52 % Allowed : 16.86 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.77 % Twisted General : 0.14 % 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: 0.13 (0.23), residues: 1446 helix: 0.73 (0.16), residues: 990 sheet: -1.19 (1.22), residues: 20 loop : -1.22 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 452 HIS 0.010 0.001 HIS C 108 PHE 0.019 0.001 PHE A 427 TYR 0.026 0.001 TYR A 178 ARG 0.002 0.000 ARG D 75 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 575) hydrogen bonds : angle 4.23262 ( 1677) covalent geometry : bond 0.00293 (11708) covalent geometry : angle 0.64941 (15910) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 GLN cc_start: 0.8678 (tt0) cc_final: 0.8203 (tm-30) REVERT: C 93 PHE cc_start: 0.7429 (m-80) cc_final: 0.6886 (m-80) REVERT: C 125 MET cc_start: 0.7728 (mtt) cc_final: 0.7321 (mmm) REVERT: A 52 MET cc_start: 0.7407 (mtp) cc_final: 0.7200 (ttp) REVERT: A 104 MET cc_start: 0.8482 (ttm) cc_final: 0.8265 (tmm) REVERT: A 316 LEU cc_start: 0.6730 (mt) cc_final: 0.6425 (mt) REVERT: B 109 HIS cc_start: 0.7633 (OUTLIER) cc_final: 0.7203 (t-90) REVERT: B 268 VAL cc_start: 0.8593 (t) cc_final: 0.8353 (p) REVERT: B 316 LEU cc_start: 0.6912 (mt) cc_final: 0.6582 (tp) REVERT: B 443 MET cc_start: 0.7365 (mtt) cc_final: 0.7068 (mtt) REVERT: B 568 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8948 (mm) REVERT: D 72 MET cc_start: 0.8593 (mmm) cc_final: 0.8253 (mtp) REVERT: D 125 MET cc_start: 0.7558 (mmm) cc_final: 0.7125 (mmm) outliers start: 31 outliers final: 26 residues processed: 209 average time/residue: 0.1888 time to fit residues: 59.8393 Evaluate side-chains 211 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 455 TRP Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 53 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 104 optimal weight: 0.0980 chunk 6 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 101 optimal weight: 20.0000 chunk 134 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 HIS ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.132544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.097470 restraints weight = 23715.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.097909 restraints weight = 14929.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.098151 restraints weight = 11886.975| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11708 Z= 0.155 Angle : 0.677 11.911 15910 Z= 0.340 Chirality : 0.043 0.199 1872 Planarity : 0.005 0.080 1976 Dihedral : 5.295 42.188 1692 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.44 % Allowed : 17.59 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.14 % 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: 0.11 (0.23), residues: 1446 helix: 0.71 (0.16), residues: 990 sheet: -1.41 (1.19), residues: 20 loop : -1.19 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 452 HIS 0.008 0.001 HIS C 108 PHE 0.020 0.001 PHE B 427 TYR 0.030 0.001 TYR A 178 ARG 0.004 0.000 ARG D 75 Details of bonding type rmsd hydrogen bonds : bond 0.04424 ( 575) hydrogen bonds : angle 4.35900 ( 1677) covalent geometry : bond 0.00352 (11708) covalent geometry : angle 0.67739 (15910) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 GLN cc_start: 0.8609 (tt0) cc_final: 0.8212 (tm-30) REVERT: C 125 MET cc_start: 0.7778 (mtt) cc_final: 0.7366 (mmm) REVERT: A 52 MET cc_start: 0.7437 (mtp) cc_final: 0.7212 (ttp) REVERT: A 104 MET cc_start: 0.8546 (ttm) cc_final: 0.8315 (tmm) REVERT: A 316 LEU cc_start: 0.6683 (mt) cc_final: 0.6468 (mt) REVERT: B 109 HIS cc_start: 0.7685 (OUTLIER) cc_final: 0.7253 (t-90) REVERT: B 268 VAL cc_start: 0.8642 (t) cc_final: 0.8387 (p) REVERT: B 316 LEU cc_start: 0.6890 (mt) cc_final: 0.6557 (tp) REVERT: B 443 MET cc_start: 0.7352 (mtt) cc_final: 0.7009 (mtt) REVERT: B 568 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8963 (mm) outliers start: 30 outliers final: 28 residues processed: 207 average time/residue: 0.1947 time to fit residues: 60.9978 Evaluate side-chains 218 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 452 TRP Chi-restraints excluded: chain A residue 455 TRP Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 53 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 58 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.131961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.096270 restraints weight = 23715.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.097971 restraints weight = 15261.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.097916 restraints weight = 10745.332| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.5542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11708 Z= 0.161 Angle : 0.676 12.201 15910 Z= 0.341 Chirality : 0.043 0.201 1872 Planarity : 0.005 0.079 1976 Dihedral : 5.341 42.135 1692 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.61 % Allowed : 17.26 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.77 % Twisted General : 0.14 % 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: 0.10 (0.23), residues: 1446 helix: 0.70 (0.16), residues: 996 sheet: -1.30 (1.18), residues: 20 loop : -1.23 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 452 HIS 0.009 0.001 HIS C 108 PHE 0.020 0.002 PHE A 427 TYR 0.030 0.001 TYR A 178 ARG 0.003 0.000 ARG D 75 Details of bonding type rmsd hydrogen bonds : bond 0.04456 ( 575) hydrogen bonds : angle 4.39507 ( 1677) covalent geometry : bond 0.00368 (11708) covalent geometry : angle 0.67576 (15910) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3424.29 seconds wall clock time: 60 minutes 18.41 seconds (3618.41 seconds total)