Starting phenix.real_space_refine on Tue Dec 31 11:15:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fcv_31532/12_2024/7fcv_31532.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fcv_31532/12_2024/7fcv_31532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fcv_31532/12_2024/7fcv_31532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fcv_31532/12_2024/7fcv_31532.map" model { file = "/net/cci-nas-00/data/ceres_data/7fcv_31532/12_2024/7fcv_31532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fcv_31532/12_2024/7fcv_31532.cif" } resolution = 2.9 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= 0.002 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: 6 Type Number sf(0) Gaussians K 3 8.98 5 P 4 5.49 5 S 92 5.16 5 C 9862 2.51 5 N 2526 2.21 5 O 2656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15143 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3747 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 16, 'TRANS': 445} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 3739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3739 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 445} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 3743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3743 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 445} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 3739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3739 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 445} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 46 Unusual residues: {' K': 3, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 9.95, per 1000 atoms: 0.66 Number of scatterers: 15143 At special positions: 0 Unit cell: (127.735, 136.395, 123.405, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 3 19.00 S 92 16.00 P 4 15.00 O 2656 8.00 N 2526 7.00 C 9862 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: 3.82 Conformation dependent library (CDL) restraints added in 2.0 seconds 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3544 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 12 sheets defined 64.1% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 54 through 82 removed outlier: 3.983A pdb=" N ILE A 59 " --> pdb=" O HIS A 55 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TRP A 60 " --> pdb=" O LYS A 56 " (cutoff:3.500A) Proline residue: A 76 - end of helix Processing helix chain 'A' and resid 86 through 107 removed outlier: 5.212A pdb=" N THR A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 135 removed outlier: 3.507A pdb=" N TRP A 135 " --> pdb=" O TYR A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 142 removed outlier: 3.515A pdb=" N ASP A 139 " --> pdb=" O TRP A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 153 removed outlier: 3.847A pdb=" N ALA A 149 " --> pdb=" O PRO A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 162 Processing helix chain 'A' and resid 163 through 167 removed outlier: 3.557A pdb=" N TRP A 166 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 181 Processing helix chain 'A' and resid 185 through 215 Processing helix chain 'A' and resid 223 through 228 removed outlier: 4.501A pdb=" N ASN A 227 " --> pdb=" O TRP A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 252 Processing helix chain 'A' and resid 263 through 296 removed outlier: 3.534A pdb=" N GLY A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 316 removed outlier: 3.564A pdb=" N ARG A 315 " --> pdb=" O ASN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 336 removed outlier: 3.931A pdb=" N TYR A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 347 Processing helix chain 'A' and resid 354 through 363 Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 378 through 387 removed outlier: 3.514A pdb=" N PHE A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A 387 " --> pdb=" O GLN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 476 removed outlier: 4.193A pdb=" N ALA A 476 " --> pdb=" O ASN A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 493 removed outlier: 3.689A pdb=" N HIS A 491 " --> pdb=" O ASN A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 510 removed outlier: 3.540A pdb=" N VAL A 503 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 507 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 82 removed outlier: 4.047A pdb=" N ILE B 59 " --> pdb=" O HIS B 55 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TRP B 60 " --> pdb=" O LYS B 56 " (cutoff:3.500A) Proline residue: B 76 - end of helix removed outlier: 3.508A pdb=" N LEU B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 107 removed outlier: 4.964A pdb=" N THR B 92 " --> pdb=" O PRO B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 135 removed outlier: 3.558A pdb=" N TRP B 135 " --> pdb=" O TYR B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 142 Processing helix chain 'B' and resid 145 through 153 removed outlier: 3.846A pdb=" N ALA B 149 " --> pdb=" O PRO B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 162 Processing helix chain 'B' and resid 163 through 167 removed outlier: 3.519A pdb=" N TRP B 166 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 181 Processing helix chain 'B' and resid 185 through 215 Processing helix chain 'B' and resid 235 through 252 Processing helix chain 'B' and resid 263 through 296 Processing helix chain 'B' and resid 297 through 316 Processing helix chain 'B' and resid 319 through 336 removed outlier: 3.803A pdb=" N TYR B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 347 removed outlier: 3.684A pdb=" N GLN B 344 " --> pdb=" O GLY B 340 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU B 345 " --> pdb=" O LEU B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 350 No H-bonds generated for 'chain 'B' and resid 348 through 350' Processing helix chain 'B' and resid 354 through 363 Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.542A pdb=" N ASP B 368 " --> pdb=" O TYR B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 387 removed outlier: 3.566A pdb=" N GLU B 387 " --> pdb=" O GLN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 476 removed outlier: 3.536A pdb=" N ILE B 473 " --> pdb=" O THR B 469 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA B 476 " --> pdb=" O ASN B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 493 removed outlier: 3.955A pdb=" N ILE B 483 " --> pdb=" O GLY B 479 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS B 491 " --> pdb=" O ASN B 487 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS B 493 " --> pdb=" O LEU B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 510 removed outlier: 3.809A pdb=" N GLU B 506 " --> pdb=" O ASN B 502 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU B 508 " --> pdb=" O LEU B 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 82 removed outlier: 3.925A pdb=" N ILE C 59 " --> pdb=" O HIS C 55 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TRP C 60 " --> pdb=" O LYS C 56 " (cutoff:3.500A) Proline residue: C 76 - end of helix Processing helix chain 'C' and resid 86 through 107 removed outlier: 5.186A pdb=" N THR C 92 " --> pdb=" O PRO C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 135 removed outlier: 3.708A pdb=" N TRP C 135 " --> pdb=" O TYR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 142 Processing helix chain 'C' and resid 145 through 153 removed outlier: 3.959A pdb=" N ALA C 149 " --> pdb=" O PRO C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 162 Processing helix chain 'C' and resid 163 through 167 removed outlier: 3.617A pdb=" N TRP C 166 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG C 167 " --> pdb=" O ARG C 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 163 through 167' Processing helix chain 'C' and resid 168 through 181 Processing helix chain 'C' and resid 185 through 215 Processing helix chain 'C' and resid 223 through 228 removed outlier: 4.551A pdb=" N ASN C 227 " --> pdb=" O TRP C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 252 Processing helix chain 'C' and resid 263 through 296 Processing helix chain 'C' and resid 297 through 316 Processing helix chain 'C' and resid 319 through 336 removed outlier: 4.053A pdb=" N TYR C 334 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR C 336 " --> pdb=" O LEU C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 347 removed outlier: 3.831A pdb=" N GLN C 344 " --> pdb=" O GLY C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 350 No H-bonds generated for 'chain 'C' and resid 348 through 350' Processing helix chain 'C' and resid 354 through 363 Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.620A pdb=" N ASP C 368 " --> pdb=" O TYR C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 387 removed outlier: 3.727A pdb=" N PHE C 382 " --> pdb=" O ASN C 378 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU C 387 " --> pdb=" O GLN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 475 Processing helix chain 'C' and resid 479 through 495 removed outlier: 4.018A pdb=" N ILE C 483 " --> pdb=" O GLY C 479 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS C 491 " --> pdb=" O ASN C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 510 removed outlier: 3.747A pdb=" N GLU C 508 " --> pdb=" O LEU C 504 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN C 509 " --> pdb=" O LEU C 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 82 removed outlier: 3.976A pdb=" N TRP D 60 " --> pdb=" O LYS D 56 " (cutoff:3.500A) Proline residue: D 76 - end of helix removed outlier: 3.528A pdb=" N LEU D 82 " --> pdb=" O GLU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 107 removed outlier: 5.074A pdb=" N THR D 92 " --> pdb=" O PRO D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 135 removed outlier: 4.300A pdb=" N SER D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N TRP D 135 " --> pdb=" O TYR D 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 130 through 135' Processing helix chain 'D' and resid 135 through 142 Processing helix chain 'D' and resid 145 through 153 Processing helix chain 'D' and resid 156 through 162 Processing helix chain 'D' and resid 163 through 167 removed outlier: 3.946A pdb=" N TRP D 166 " --> pdb=" O LEU D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 181 Processing helix chain 'D' and resid 185 through 215 Processing helix chain 'D' and resid 235 through 252 removed outlier: 3.612A pdb=" N ARG D 239 " --> pdb=" O SER D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 296 Processing helix chain 'D' and resid 297 through 316 Processing helix chain 'D' and resid 319 through 336 removed outlier: 3.875A pdb=" N TYR D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR D 336 " --> pdb=" O LEU D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 347 removed outlier: 4.160A pdb=" N GLN D 344 " --> pdb=" O GLY D 340 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU D 345 " --> pdb=" O LEU D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 350 No H-bonds generated for 'chain 'D' and resid 348 through 350' Processing helix chain 'D' and resid 354 through 363 Processing helix chain 'D' and resid 365 through 369 Processing helix chain 'D' and resid 378 through 387 removed outlier: 3.569A pdb=" N PHE D 382 " --> pdb=" O ASN D 378 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU D 387 " --> pdb=" O GLN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 476 removed outlier: 3.958A pdb=" N ALA D 476 " --> pdb=" O ASN D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 493 removed outlier: 3.886A pdb=" N HIS D 491 " --> pdb=" O ASN D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 510 removed outlier: 3.712A pdb=" N GLU D 506 " --> pdb=" O ASN D 502 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE D 507 " --> pdb=" O VAL D 503 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N MET D 510 " --> pdb=" O GLU D 506 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 113 Processing sheet with id=AA2, first strand: chain 'A' and resid 389 through 393 Processing sheet with id=AA3, first strand: chain 'A' and resid 397 through 400 removed outlier: 3.523A pdb=" N GLU A 397 " --> pdb=" O THR A 456 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A 454 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA A 417 " --> pdb=" O GLU A 432 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLU A 432 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU A 419 " --> pdb=" O VAL A 430 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 428 " --> pdb=" O ASP A 421 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 113 Processing sheet with id=AA5, first strand: chain 'B' and resid 389 through 393 Processing sheet with id=AA6, first strand: chain 'B' and resid 397 through 400 removed outlier: 6.569A pdb=" N VAL B 454 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA B 417 " --> pdb=" O GLU B 432 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLU B 432 " --> pdb=" O ALA B 417 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU B 419 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 112 through 113 Processing sheet with id=AA8, first strand: chain 'C' and resid 389 through 393 removed outlier: 3.570A pdb=" N ILE C 411 " --> pdb=" O LEU C 463 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 398 through 400 removed outlier: 6.592A pdb=" N VAL C 454 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG C 431 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ASP C 421 " --> pdb=" O ILE C 429 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE C 429 " --> pdb=" O ASP C 421 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 112 through 113 Processing sheet with id=AB2, first strand: chain 'D' and resid 389 through 393 removed outlier: 6.722A pdb=" N GLN D 461 " --> pdb=" O VAL D 413 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 397 through 400 removed outlier: 6.629A pdb=" N VAL D 454 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA D 417 " --> pdb=" O GLU D 432 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU D 432 " --> pdb=" O ALA D 417 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU D 419 " --> pdb=" O VAL D 430 " (cutoff:3.500A) 860 hydrogen bonds defined for protein. 2502 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: 5.15 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2593 1.32 - 1.45: 4174 1.45 - 1.57: 8567 1.57 - 1.69: 10 1.69 - 1.81: 156 Bond restraints: 15500 Sorted by residual: bond pdb=" C ALA B 349 " pdb=" N LEU B 350 " ideal model delta sigma weight residual 1.331 1.246 0.085 2.83e-02 1.25e+03 9.12e+00 bond pdb=" CA PHE B 109 " pdb=" CB PHE B 109 " ideal model delta sigma weight residual 1.531 1.611 -0.080 3.12e-02 1.03e+03 6.58e+00 bond pdb=" C PRO D 406 " pdb=" N THR D 407 " ideal model delta sigma weight residual 1.332 1.298 0.034 1.40e-02 5.10e+03 5.91e+00 bond pdb=" CA ASP D 122 " pdb=" CB ASP D 122 " ideal model delta sigma weight residual 1.532 1.570 -0.038 1.62e-02 3.81e+03 5.45e+00 bond pdb=" O14 PTY D 901 " pdb=" P1 PTY D 901 " ideal model delta sigma weight residual 1.646 1.602 0.044 2.00e-02 2.50e+03 4.77e+00 ... (remaining 15495 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 20008 2.19 - 4.38: 886 4.38 - 6.57: 93 6.57 - 8.76: 21 8.76 - 10.95: 15 Bond angle restraints: 21023 Sorted by residual: angle pdb=" N PRO B 87 " pdb=" CA PRO B 87 " pdb=" C PRO B 87 " ideal model delta sigma weight residual 110.70 117.76 -7.06 1.22e+00 6.72e-01 3.35e+01 angle pdb=" N VAL D 413 " pdb=" CA VAL D 413 " pdb=" C VAL D 413 " ideal model delta sigma weight residual 111.62 107.12 4.50 7.90e-01 1.60e+00 3.25e+01 angle pdb=" C TYR A 256 " pdb=" N GLY A 257 " pdb=" CA GLY A 257 " ideal model delta sigma weight residual 123.30 117.56 5.74 1.06e+00 8.90e-01 2.94e+01 angle pdb=" N PRO C 87 " pdb=" CA PRO C 87 " pdb=" C PRO C 87 " ideal model delta sigma weight residual 110.70 117.19 -6.49 1.22e+00 6.72e-01 2.83e+01 angle pdb=" N PRO A 87 " pdb=" CA PRO A 87 " pdb=" C PRO A 87 " ideal model delta sigma weight residual 110.70 117.11 -6.41 1.22e+00 6.72e-01 2.76e+01 ... (remaining 21018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.37: 9063 30.37 - 60.73: 128 60.73 - 91.10: 10 91.10 - 121.46: 4 121.46 - 151.83: 4 Dihedral angle restraints: 9209 sinusoidal: 3737 harmonic: 5472 Sorted by residual: dihedral pdb=" CA ASP C 497 " pdb=" C ASP C 497 " pdb=" N PRO C 498 " pdb=" CA PRO C 498 " ideal model delta harmonic sigma weight residual 180.00 -128.24 -51.76 0 5.00e+00 4.00e-02 1.07e+02 dihedral pdb=" CA ASN C 496 " pdb=" C ASN C 496 " pdb=" N ASP C 497 " pdb=" CA ASP C 497 " ideal model delta harmonic sigma weight residual 180.00 150.41 29.59 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA MET D 106 " pdb=" C MET D 106 " pdb=" N THR D 107 " pdb=" CA THR D 107 " ideal model delta harmonic sigma weight residual 180.00 -152.44 -27.56 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 9206 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2143 0.092 - 0.184: 220 0.184 - 0.275: 13 0.275 - 0.367: 0 0.367 - 0.459: 4 Chirality restraints: 2380 Sorted by residual: chirality pdb=" C6 PTY A 901 " pdb=" C1 PTY A 901 " pdb=" C5 PTY A 901 " pdb=" O7 PTY A 901 " both_signs ideal model delta sigma weight residual False 2.49 2.03 0.46 2.00e-01 2.50e+01 5.27e+00 chirality pdb=" C6 PTY B 901 " pdb=" C1 PTY B 901 " pdb=" C5 PTY B 901 " pdb=" O7 PTY B 901 " both_signs ideal model delta sigma weight residual False 2.49 2.06 0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" C6 PTY D 901 " pdb=" C1 PTY D 901 " pdb=" C5 PTY D 901 " pdb=" O7 PTY D 901 " both_signs ideal model delta sigma weight residual False 2.49 2.07 0.42 2.00e-01 2.50e+01 4.33e+00 ... (remaining 2377 not shown) Planarity restraints: 2623 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 246 " -0.027 2.00e-02 2.50e+03 1.56e-02 6.07e+00 pdb=" CG TRP B 246 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP B 246 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP B 246 " 0.016 2.00e-02 2.50e+03 pdb=" NE1 TRP B 246 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 246 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP B 246 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 246 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 246 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP B 246 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 260 " -0.041 5.00e-02 4.00e+02 6.13e-02 6.01e+00 pdb=" N PRO B 261 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 87 " -0.041 5.00e-02 4.00e+02 6.11e-02 5.98e+00 pdb=" N PRO D 88 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO D 88 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 88 " -0.035 5.00e-02 4.00e+02 ... (remaining 2620 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.85: 4995 2.85 - 3.42: 16713 3.42 - 3.99: 28090 3.99 - 4.57: 38867 4.57 - 5.14: 56796 Nonbonded interactions: 145461 Sorted by model distance: nonbonded pdb=" OG SER D 359 " pdb=" O VAL D 385 " model vdw 2.271 3.040 nonbonded pdb=" OG SER A 359 " pdb=" O VAL A 385 " model vdw 2.276 3.040 nonbonded pdb=" OH TYR D 371 " pdb=" OE2 GLU D 441 " model vdw 2.282 3.040 nonbonded pdb=" OG SER C 359 " pdb=" O VAL C 385 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR C 371 " pdb=" OE2 GLU C 441 " model vdw 2.292 3.040 ... (remaining 145456 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 49 through 343 or (resid 344 through 345 and (name N or na \ me CA or name C or name O or name CB )) or resid 346 through 510 or resid 901)) selection = chain 'B' selection = (chain 'C' and (resid 49 through 343 or (resid 344 through 345 and (name N or na \ me CA or name C or name O or name CB )) or resid 346 through 510 or resid 901)) 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 36.010 Find NCS groups from input model: 1.030 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:14.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 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 0.085 15500 Z= 0.534 Angle : 1.035 10.952 21023 Z= 0.571 Chirality : 0.060 0.459 2380 Planarity : 0.007 0.061 2623 Dihedral : 12.123 151.830 5665 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.16), residues: 1840 helix: -1.78 (0.12), residues: 1056 sheet: -2.57 (0.49), residues: 84 loop : -2.59 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.005 TRP A 135 HIS 0.016 0.004 HIS C 294 PHE 0.038 0.003 PHE C 109 TYR 0.032 0.003 TYR B 209 ARG 0.014 0.001 ARG D 464 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 ASN cc_start: 0.8919 (t0) cc_final: 0.8610 (t0) REVERT: B 368 ASP cc_start: 0.8229 (m-30) cc_final: 0.7796 (m-30) REVERT: B 466 ASN cc_start: 0.8954 (t0) cc_final: 0.8737 (t0) REVERT: C 368 ASP cc_start: 0.8475 (m-30) cc_final: 0.8173 (p0) REVERT: C 388 MET cc_start: 0.8742 (mmm) cc_final: 0.8197 (mmm) REVERT: D 96 VAL cc_start: 0.6645 (t) cc_final: 0.6110 (p) REVERT: D 133 ARG cc_start: 0.4106 (mmt180) cc_final: 0.3856 (tmt-80) REVERT: D 510 MET cc_start: 0.5140 (mtm) cc_final: 0.4890 (mtt) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 1.1862 time to fit residues: 272.8807 Evaluate side-chains 120 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 167 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN A 378 ASN A 486 ASN A 502 ASN A 509 ASN B 290 ASN B 294 HIS B 311 ASN B 343 GLN B 378 ASN B 486 ASN C 294 HIS C 311 ASN C 378 ASN C 486 ASN C 502 ASN C 509 ASN D 311 ASN D 343 GLN D 378 ASN D 486 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15500 Z= 0.187 Angle : 0.671 8.383 21023 Z= 0.351 Chirality : 0.042 0.175 2380 Planarity : 0.006 0.069 2623 Dihedral : 10.739 156.653 2184 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 1.60 % Allowed : 8.73 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.06 % 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: -1.48 (0.19), residues: 1840 helix: -0.14 (0.15), residues: 1156 sheet: -2.17 (0.45), residues: 88 loop : -2.37 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 73 HIS 0.005 0.001 HIS D 294 PHE 0.050 0.001 PHE D 99 TYR 0.018 0.002 TYR A 131 ARG 0.008 0.001 ARG B 315 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7906 (tmt) REVERT: A 326 MET cc_start: 0.8854 (mtm) cc_final: 0.8534 (mtp) REVERT: A 388 MET cc_start: 0.8463 (mmm) cc_final: 0.7801 (mmm) REVERT: A 504 LEU cc_start: 0.9382 (tm) cc_final: 0.9092 (mm) REVERT: B 106 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7928 (tmt) REVERT: B 388 MET cc_start: 0.8764 (mmm) cc_final: 0.7998 (mmm) REVERT: C 388 MET cc_start: 0.8731 (mmm) cc_final: 0.8263 (mmm) REVERT: D 133 ARG cc_start: 0.3755 (mmt180) cc_final: 0.3406 (tpt170) REVERT: D 188 TRP cc_start: 0.6822 (m100) cc_final: 0.5382 (t60) REVERT: D 388 MET cc_start: 0.8740 (mmm) cc_final: 0.8535 (mmm) REVERT: D 485 MET cc_start: 0.7043 (pp-130) cc_final: 0.6838 (ptt) REVERT: D 510 MET cc_start: 0.5323 (mtm) cc_final: 0.4812 (mtt) outliers start: 26 outliers final: 8 residues processed: 155 average time/residue: 1.1690 time to fit residues: 203.2527 Evaluate side-chains 124 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 143 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 167 optimal weight: 8.9990 chunk 180 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 134 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 ASN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN D 97 ASN D 294 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15500 Z= 0.280 Angle : 0.669 13.521 21023 Z= 0.346 Chirality : 0.043 0.166 2380 Planarity : 0.005 0.050 2623 Dihedral : 10.380 164.554 2184 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.03 % Allowed : 10.14 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.06 % 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: -0.53 (0.20), residues: 1840 helix: 0.78 (0.16), residues: 1112 sheet: -1.93 (0.45), residues: 88 loop : -2.14 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 73 HIS 0.005 0.001 HIS D 294 PHE 0.023 0.002 PHE D 136 TYR 0.022 0.002 TYR D 283 ARG 0.006 0.001 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7960 (tmt) REVERT: A 326 MET cc_start: 0.8929 (mtm) cc_final: 0.8557 (mtp) REVERT: A 388 MET cc_start: 0.8508 (mmm) cc_final: 0.7437 (mmm) REVERT: B 388 MET cc_start: 0.8884 (mmm) cc_final: 0.7900 (mmm) REVERT: B 495 MET cc_start: 0.6570 (pmm) cc_final: 0.6267 (pmm) REVERT: B 496 ASN cc_start: 0.8061 (m-40) cc_final: 0.7664 (m-40) REVERT: C 106 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7575 (tmm) REVERT: C 388 MET cc_start: 0.8776 (mmm) cc_final: 0.8170 (mmm) REVERT: D 133 ARG cc_start: 0.3725 (mmt180) cc_final: 0.3482 (tmt-80) REVERT: D 188 TRP cc_start: 0.6870 (m100) cc_final: 0.5380 (t60) REVERT: D 244 MET cc_start: 0.8756 (mmp) cc_final: 0.8409 (mmp) REVERT: D 510 MET cc_start: 0.5537 (mtm) cc_final: 0.4968 (mtt) outliers start: 33 outliers final: 12 residues processed: 143 average time/residue: 1.0055 time to fit residues: 164.1657 Evaluate side-chains 126 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 447 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 7.9990 chunk 125 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 177 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15500 Z= 0.213 Angle : 0.632 12.351 21023 Z= 0.325 Chirality : 0.042 0.164 2380 Planarity : 0.004 0.053 2623 Dihedral : 9.892 162.916 2184 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.09 % Allowed : 10.57 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.06 % 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 (0.20), residues: 1840 helix: 1.12 (0.16), residues: 1112 sheet: -1.81 (0.45), residues: 88 loop : -2.03 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 73 HIS 0.005 0.001 HIS D 491 PHE 0.032 0.001 PHE C 129 TYR 0.012 0.001 TYR B 283 ARG 0.004 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7960 (tmt) REVERT: A 326 MET cc_start: 0.8877 (mtm) cc_final: 0.8523 (mtp) REVERT: B 288 MET cc_start: 0.8850 (tpp) cc_final: 0.8610 (mmm) REVERT: B 388 MET cc_start: 0.8826 (mmm) cc_final: 0.7903 (mmm) REVERT: B 495 MET cc_start: 0.6483 (pmm) cc_final: 0.6257 (pmm) REVERT: B 496 ASN cc_start: 0.8055 (m-40) cc_final: 0.7685 (m-40) REVERT: C 188 TRP cc_start: 0.8300 (m100) cc_final: 0.7479 (m-10) REVERT: C 384 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9249 (mp) REVERT: C 388 MET cc_start: 0.8690 (mmm) cc_final: 0.8118 (mmm) REVERT: D 188 TRP cc_start: 0.6861 (m100) cc_final: 0.5394 (t60) REVERT: D 510 MET cc_start: 0.5558 (mtm) cc_final: 0.5033 (mtt) outliers start: 34 outliers final: 14 residues processed: 149 average time/residue: 1.0003 time to fit residues: 170.1074 Evaluate side-chains 124 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 447 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.0970 chunk 100 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 73 optimal weight: 0.0000 chunk 151 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 0.1980 chunk 159 optimal weight: 0.1980 chunk 44 optimal weight: 0.7980 overall best weight: 0.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15500 Z= 0.149 Angle : 0.615 10.795 21023 Z= 0.309 Chirality : 0.040 0.184 2380 Planarity : 0.004 0.053 2623 Dihedral : 9.124 150.341 2184 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 1.72 % Allowed : 12.23 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.06 % 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: 0.07 (0.20), residues: 1840 helix: 1.19 (0.16), residues: 1156 sheet: -1.57 (0.45), residues: 88 loop : -1.99 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 135 HIS 0.003 0.001 HIS B 294 PHE 0.024 0.001 PHE D 136 TYR 0.020 0.001 TYR C 131 ARG 0.003 0.000 ARG C 335 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 1.700 Fit side-chains revert: symmetry clash REVERT: A 326 MET cc_start: 0.8847 (mtm) cc_final: 0.8535 (mtp) REVERT: A 388 MET cc_start: 0.8291 (mmm) cc_final: 0.7431 (mmm) REVERT: B 288 MET cc_start: 0.8912 (tpp) cc_final: 0.8562 (mmm) REVERT: B 388 MET cc_start: 0.8810 (mmm) cc_final: 0.7948 (mmm) REVERT: B 496 ASN cc_start: 0.7979 (m-40) cc_final: 0.7561 (m-40) REVERT: C 106 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7953 (tmt) REVERT: C 388 MET cc_start: 0.8603 (mmm) cc_final: 0.8208 (mmm) REVERT: D 188 TRP cc_start: 0.6750 (m100) cc_final: 0.5375 (t60) REVERT: D 510 MET cc_start: 0.5532 (mtm) cc_final: 0.4968 (mtt) outliers start: 28 outliers final: 10 residues processed: 143 average time/residue: 0.9535 time to fit residues: 156.5913 Evaluate side-chains 125 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 447 TYR Chi-restraints excluded: chain D residue 471 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 178 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15500 Z= 0.277 Angle : 0.656 11.235 21023 Z= 0.330 Chirality : 0.043 0.168 2380 Planarity : 0.004 0.048 2623 Dihedral : 9.117 144.574 2184 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 1.84 % Allowed : 13.40 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.06 % 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: 0.32 (0.20), residues: 1840 helix: 1.52 (0.16), residues: 1084 sheet: -1.35 (0.48), residues: 88 loop : -1.82 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 246 HIS 0.003 0.001 HIS C 329 PHE 0.016 0.002 PHE D 269 TYR 0.026 0.002 TYR D 283 ARG 0.006 0.000 ARG D 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 2.002 Fit side-chains revert: symmetry clash REVERT: A 326 MET cc_start: 0.8876 (mtm) cc_final: 0.8498 (mtp) REVERT: A 388 MET cc_start: 0.8397 (mmm) cc_final: 0.7950 (mmm) REVERT: A 504 LEU cc_start: 0.9406 (tm) cc_final: 0.9107 (mt) REVERT: B 288 MET cc_start: 0.8883 (tpp) cc_final: 0.8642 (mmm) REVERT: B 388 MET cc_start: 0.8846 (mmm) cc_final: 0.7965 (mmm) REVERT: B 496 ASN cc_start: 0.8134 (m-40) cc_final: 0.7705 (m-40) REVERT: C 106 MET cc_start: 0.8353 (tmm) cc_final: 0.7934 (tmt) REVERT: C 384 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9297 (mp) REVERT: C 388 MET cc_start: 0.8634 (mmm) cc_final: 0.8106 (mmm) REVERT: C 485 MET cc_start: 0.7607 (pp-130) cc_final: 0.7396 (ptt) REVERT: D 188 TRP cc_start: 0.6777 (m100) cc_final: 0.5393 (t60) REVERT: D 510 MET cc_start: 0.5604 (mtm) cc_final: 0.5105 (mtt) outliers start: 30 outliers final: 18 residues processed: 136 average time/residue: 1.0232 time to fit residues: 161.5244 Evaluate side-chains 128 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 447 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 130 optimal weight: 20.0000 chunk 100 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 81 optimal weight: 0.4980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15500 Z= 0.257 Angle : 0.648 11.373 21023 Z= 0.327 Chirality : 0.043 0.176 2380 Planarity : 0.004 0.052 2623 Dihedral : 9.168 146.220 2184 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 1.78 % Allowed : 13.71 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.06 % 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: 0.34 (0.20), residues: 1840 helix: 1.45 (0.16), residues: 1116 sheet: -1.21 (0.49), residues: 88 loop : -1.81 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 246 HIS 0.003 0.001 HIS B 203 PHE 0.013 0.001 PHE D 269 TYR 0.028 0.001 TYR D 283 ARG 0.004 0.000 ARG C 170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 MET cc_start: 0.8890 (mtm) cc_final: 0.8556 (mtp) REVERT: A 388 MET cc_start: 0.8410 (mmm) cc_final: 0.7956 (mmm) REVERT: A 504 LEU cc_start: 0.9416 (tm) cc_final: 0.9118 (mt) REVERT: B 388 MET cc_start: 0.8863 (mmm) cc_final: 0.7940 (mmm) REVERT: C 188 TRP cc_start: 0.8179 (m100) cc_final: 0.7311 (m-10) REVERT: C 388 MET cc_start: 0.8628 (mmm) cc_final: 0.8155 (mmm) REVERT: D 188 TRP cc_start: 0.6790 (m100) cc_final: 0.5380 (t60) REVERT: D 510 MET cc_start: 0.5349 (mtm) cc_final: 0.4959 (mtt) outliers start: 29 outliers final: 18 residues processed: 136 average time/residue: 1.0622 time to fit residues: 163.1920 Evaluate side-chains 126 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 447 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 0.0570 chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 87 optimal weight: 0.0030 chunk 16 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 161 optimal weight: 0.6980 overall best weight: 0.7512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15500 Z= 0.169 Angle : 0.641 13.352 21023 Z= 0.318 Chirality : 0.041 0.182 2380 Planarity : 0.005 0.150 2623 Dihedral : 8.960 144.927 2184 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.48 % Allowed : 14.51 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.06 % 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: 0.46 (0.20), residues: 1840 helix: 1.65 (0.16), residues: 1100 sheet: -1.02 (0.48), residues: 88 loop : -1.93 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 246 HIS 0.002 0.001 HIS B 294 PHE 0.012 0.001 PHE B 409 TYR 0.025 0.001 TYR D 283 ARG 0.020 0.000 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 MET cc_start: 0.8855 (mtm) cc_final: 0.8514 (mtp) REVERT: A 388 MET cc_start: 0.8412 (mmm) cc_final: 0.7502 (mmm) REVERT: A 504 LEU cc_start: 0.9404 (tm) cc_final: 0.9060 (mp) REVERT: B 288 MET cc_start: 0.8897 (tpp) cc_final: 0.8634 (mmt) REVERT: B 388 MET cc_start: 0.8838 (mmm) cc_final: 0.7908 (mmm) REVERT: C 188 TRP cc_start: 0.8157 (m100) cc_final: 0.7281 (m-10) REVERT: C 388 MET cc_start: 0.8557 (mmm) cc_final: 0.8179 (mmm) REVERT: D 106 MET cc_start: 0.4495 (tmt) cc_final: 0.4004 (ptp) REVERT: D 188 TRP cc_start: 0.6745 (m100) cc_final: 0.5369 (t60) REVERT: D 510 MET cc_start: 0.5296 (mtm) cc_final: 0.4897 (mtt) outliers start: 24 outliers final: 18 residues processed: 131 average time/residue: 1.0504 time to fit residues: 156.5092 Evaluate side-chains 126 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 447 TYR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 447 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 165 optimal weight: 0.1980 chunk 99 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 164 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15500 Z= 0.172 Angle : 0.634 12.133 21023 Z= 0.314 Chirality : 0.041 0.210 2380 Planarity : 0.005 0.121 2623 Dihedral : 8.816 143.741 2184 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.48 % Allowed : 14.69 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.06 % 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: 0.51 (0.20), residues: 1840 helix: 1.71 (0.16), residues: 1100 sheet: -0.87 (0.49), residues: 88 loop : -1.98 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 246 HIS 0.002 0.001 HIS B 294 PHE 0.011 0.001 PHE B 409 TYR 0.026 0.001 TYR D 283 ARG 0.008 0.000 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 MET cc_start: 0.8858 (mtm) cc_final: 0.8528 (mtp) REVERT: A 504 LEU cc_start: 0.9363 (tm) cc_final: 0.9080 (mp) REVERT: B 288 MET cc_start: 0.8921 (tpp) cc_final: 0.8663 (mmt) REVERT: B 388 MET cc_start: 0.8811 (mmm) cc_final: 0.7933 (mmm) REVERT: C 188 TRP cc_start: 0.8146 (m100) cc_final: 0.7282 (m-10) REVERT: C 248 ILE cc_start: 0.9316 (mm) cc_final: 0.9093 (tp) REVERT: C 388 MET cc_start: 0.8785 (mmm) cc_final: 0.8184 (mmm) REVERT: D 188 TRP cc_start: 0.6670 (m100) cc_final: 0.5376 (t60) REVERT: D 495 MET cc_start: 0.7545 (mpp) cc_final: 0.7225 (ptp) REVERT: D 510 MET cc_start: 0.5390 (mtm) cc_final: 0.5003 (mtt) outliers start: 24 outliers final: 17 residues processed: 130 average time/residue: 1.0415 time to fit residues: 153.6035 Evaluate side-chains 127 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 447 TYR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 447 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 183 optimal weight: 0.0870 chunk 168 optimal weight: 0.0570 chunk 145 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15500 Z= 0.195 Angle : 0.654 12.168 21023 Z= 0.321 Chirality : 0.042 0.198 2380 Planarity : 0.004 0.089 2623 Dihedral : 8.767 143.082 2184 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 1.17 % Allowed : 15.06 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.21), residues: 1840 helix: 1.76 (0.16), residues: 1096 sheet: -0.82 (0.50), residues: 88 loop : -1.99 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 246 HIS 0.002 0.001 HIS C 329 PHE 0.012 0.001 PHE D 269 TYR 0.027 0.001 TYR D 283 ARG 0.002 0.000 ARG A 467 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 MET cc_start: 0.8870 (mtm) cc_final: 0.8497 (mtp) REVERT: A 504 LEU cc_start: 0.9345 (tm) cc_final: 0.9085 (mp) REVERT: B 238 MET cc_start: 0.7750 (ttp) cc_final: 0.7388 (tmm) REVERT: B 288 MET cc_start: 0.8915 (tpp) cc_final: 0.8651 (mmt) REVERT: B 388 MET cc_start: 0.8811 (mmm) cc_final: 0.7925 (mmm) REVERT: B 500 MET cc_start: 0.6656 (mpp) cc_final: 0.6442 (mpp) REVERT: D 188 TRP cc_start: 0.6750 (m100) cc_final: 0.5416 (t60) REVERT: D 495 MET cc_start: 0.7602 (mpp) cc_final: 0.7267 (ptp) REVERT: D 510 MET cc_start: 0.5333 (mtm) cc_final: 0.4956 (mtt) outliers start: 19 outliers final: 15 residues processed: 125 average time/residue: 1.0859 time to fit residues: 153.5606 Evaluate side-chains 123 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 447 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.0770 chunk 44 optimal weight: 0.0070 chunk 134 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 chunk 40 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 150 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.097985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.074914 restraints weight = 48123.435| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 3.04 r_work: 0.3272 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15500 Z= 0.154 Angle : 0.632 12.664 21023 Z= 0.309 Chirality : 0.041 0.189 2380 Planarity : 0.004 0.054 2623 Dihedral : 8.581 142.654 2184 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.98 % Allowed : 15.30 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.21), residues: 1840 helix: 1.80 (0.16), residues: 1100 sheet: -0.74 (0.50), residues: 88 loop : -1.97 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 188 HIS 0.002 0.000 HIS B 294 PHE 0.013 0.001 PHE B 409 TYR 0.025 0.001 TYR D 283 ARG 0.003 0.000 ARG C 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4048.46 seconds wall clock time: 74 minutes 17.62 seconds (4457.62 seconds total)