Starting phenix.real_space_refine on Fri Jul 3 18:22:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7fcv_31532/07_2026/7fcv_31532.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fcv_31532/07_2026/7fcv_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 { model { file = "/net/cci-nas-00/data/ceres_data/7fcv_31532/07_2026/7fcv_31532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fcv_31532/07_2026/7fcv_31532.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fcv_31532/07_2026/7fcv_31532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fcv_31532/07_2026/7fcv_31532.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7fcv_31532/07_2026/7fcv_31532.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7fcv_31532/07_2026/7fcv_31532.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 3.51, per 1000 atoms: 0.23 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: 1.31 Conformation dependent library (CDL) restraints added in 685.9 milliseconds 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: 0.45 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: 2.61 Time building geometry restraints manager: 1.78 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: 9047 30.37 - 60.73: 122 60.73 - 91.10: 8 91.10 - 121.46: 4 121.46 - 151.83: 4 Dihedral angle restraints: 9185 sinusoidal: 3713 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 9182 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 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 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: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 15.060 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 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= 0.374 Angle : 1.035 10.952 21023 Z= 0.571 Chirality : 0.060 0.459 2380 Planarity : 0.007 0.061 2623 Dihedral : 11.936 151.830 5641 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.014 0.001 ARG D 464 TYR 0.032 0.003 TYR B 209 PHE 0.038 0.003 PHE C 109 TRP 0.034 0.005 TRP A 135 HIS 0.016 0.004 HIS C 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00847 / 0.37 (15500) covalent geometry : angle 1.03511 / 0.57 (21023) hydrogen bonds : bond 0.18144 / 11.83 ( 860) hydrogen bonds : angle 6.26867 / 4.46 ( 2502) *********************** 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 : 0.572 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: 0.6070 (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: 0.5272 time to fit residues: 121.3439 Evaluate side-chains 119 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 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 461 GLN B 486 ASN C 294 HIS C 311 ASN C 378 ASN C 486 ASN C 502 ASN C 509 ASN D 97 ASN D 311 ASN D 343 GLN D 378 ASN D 486 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.097251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.073986 restraints weight = 48141.063| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.05 r_work: 0.3249 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1781 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= 0.139 Angle : 0.670 9.679 21023 Z= 0.351 Chirality : 0.042 0.175 2380 Planarity : 0.006 0.067 2623 Dihedral : 10.535 156.753 2160 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 1.72 % Allowed : 8.67 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.19), residues: 1840 helix: -0.16 (0.15), residues: 1156 sheet: -2.14 (0.45), residues: 88 loop : -2.33 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 315 TYR 0.017 0.002 TYR A 131 PHE 0.051 0.001 PHE D 99 TRP 0.021 0.002 TRP D 73 HIS 0.005 0.001 HIS D 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (15500) covalent geometry : angle 0.66956 / 0.35 (21023) hydrogen bonds : bond 0.05236 / 3.37 ( 860) hydrogen bonds : angle 4.46420 / 3.18 ( 2502) *********************** 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 169 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7961 (tmt) REVERT: A 163 LEU cc_start: 0.9458 (tp) cc_final: 0.9233 (mt) REVERT: A 326 MET cc_start: 0.9073 (mtm) cc_final: 0.8792 (mtp) REVERT: A 388 MET cc_start: 0.8867 (mmm) cc_final: 0.8540 (mmm) REVERT: B 106 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.8027 (tmt) REVERT: B 388 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8485 (mmm) REVERT: C 129 PHE cc_start: 0.6835 (m-10) cc_final: 0.6624 (m-80) REVERT: C 388 MET cc_start: 0.9040 (mmm) cc_final: 0.8596 (mmm) REVERT: D 133 ARG cc_start: 0.4002 (mmt180) cc_final: 0.3633 (tmt-80) REVERT: D 188 TRP cc_start: 0.7133 (m100) cc_final: 0.5289 (t60) REVERT: D 388 MET cc_start: 0.9066 (mmm) cc_final: 0.8852 (mmm) REVERT: D 485 MET cc_start: 0.7233 (pp-130) cc_final: 0.6787 (ptt) REVERT: D 510 MET cc_start: 0.5475 (mtm) cc_final: 0.4988 (mtt) outliers start: 28 outliers final: 7 residues processed: 155 average time/residue: 0.4879 time to fit residues: 84.6462 Evaluate side-chains 120 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 B residue 388 MET Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 290 ASN 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 111 optimal weight: 0.6980 chunk 171 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 178 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 49 optimal weight: 0.0470 chunk 26 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 ASN B 290 ASN B 461 GLN D 97 ASN D 294 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.097157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.073809 restraints weight = 48612.627| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.06 r_work: 0.3240 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15500 Z= 0.144 Angle : 0.644 12.337 21023 Z= 0.331 Chirality : 0.042 0.166 2380 Planarity : 0.005 0.111 2623 Dihedral : 10.145 165.415 2160 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.20), residues: 1840 helix: 0.80 (0.16), residues: 1124 sheet: -1.92 (0.45), residues: 88 loop : -2.25 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 335 TYR 0.013 0.002 TYR B 283 PHE 0.025 0.001 PHE D 136 TRP 0.016 0.002 TRP D 73 HIS 0.005 0.001 HIS D 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (15500) covalent geometry : angle 0.64390 / 0.33 (21023) hydrogen bonds : bond 0.04598 / 2.95 ( 860) hydrogen bonds : angle 4.10836 / 2.94 ( 2502) *********************** 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 157 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 106 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.8026 (tmt) REVERT: A 163 LEU cc_start: 0.9449 (tp) cc_final: 0.9217 (mt) REVERT: A 326 MET cc_start: 0.9085 (mtm) cc_final: 0.8803 (mtp) REVERT: A 388 MET cc_start: 0.8695 (mmm) cc_final: 0.8374 (mmm) REVERT: A 504 LEU cc_start: 0.9572 (tm) cc_final: 0.9228 (mm) REVERT: B 288 MET cc_start: 0.9284 (tpp) cc_final: 0.9069 (mmm) REVERT: B 388 MET cc_start: 0.9175 (mmm) cc_final: 0.8332 (mmm) REVERT: B 485 MET cc_start: 0.7736 (pp-130) cc_final: 0.7475 (ptt) REVERT: B 495 MET cc_start: 0.7055 (pmm) cc_final: 0.6550 (pmm) REVERT: C 106 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7450 (tmm) REVERT: C 388 MET cc_start: 0.8994 (mmm) cc_final: 0.8535 (mmm) REVERT: D 133 ARG cc_start: 0.3732 (mmt180) cc_final: 0.3225 (tmt170) REVERT: D 188 TRP cc_start: 0.7169 (m100) cc_final: 0.5206 (t60) REVERT: D 485 MET cc_start: 0.7270 (pp-130) cc_final: 0.6841 (ptt) REVERT: D 510 MET cc_start: 0.5568 (mtm) cc_final: 0.5025 (mtt) outliers start: 33 outliers final: 9 residues processed: 145 average time/residue: 0.4403 time to fit residues: 72.7818 Evaluate side-chains 122 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 326 MET 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 59 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 172 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 39 optimal weight: 0.0570 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 ASN C 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.098148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.074891 restraints weight = 48484.302| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 3.07 r_work: 0.3268 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2648 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= 0.119 Angle : 0.622 15.764 21023 Z= 0.314 Chirality : 0.041 0.161 2380 Planarity : 0.004 0.052 2623 Dihedral : 9.529 165.074 2160 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.91 % Allowed : 11.00 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.20), residues: 1840 helix: 1.01 (0.16), residues: 1152 sheet: -1.69 (0.45), residues: 88 loop : -2.13 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 355 TYR 0.012 0.001 TYR D 131 PHE 0.019 0.001 PHE C 129 TRP 0.011 0.002 TRP D 73 HIS 0.003 0.001 HIS C 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (15500) covalent geometry : angle 0.62167 / 0.31 (21023) hydrogen bonds : bond 0.04050 / 2.59 ( 860) hydrogen bonds : angle 3.89039 / 2.78 ( 2502) *********************** 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 164 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 326 MET cc_start: 0.9024 (mtm) cc_final: 0.8751 (mtp) REVERT: A 388 MET cc_start: 0.8624 (mmm) cc_final: 0.8247 (mmm) REVERT: A 471 LEU cc_start: 0.9066 (mm) cc_final: 0.8766 (mm) REVERT: B 288 MET cc_start: 0.9295 (tpp) cc_final: 0.9070 (mmm) REVERT: B 388 MET cc_start: 0.9151 (mmm) cc_final: 0.8327 (mmm) REVERT: B 485 MET cc_start: 0.7821 (pp-130) cc_final: 0.7599 (ptt) REVERT: B 500 MET cc_start: 0.7554 (pmm) cc_final: 0.7344 (pmm) REVERT: C 106 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7455 (tmm) REVERT: C 388 MET cc_start: 0.8915 (mmm) cc_final: 0.8547 (mmm) REVERT: D 106 MET cc_start: 0.3893 (tmt) cc_final: 0.3587 (mtt) REVERT: D 133 ARG cc_start: 0.3627 (mmt180) cc_final: 0.3209 (tmt-80) REVERT: D 188 TRP cc_start: 0.7176 (m100) cc_final: 0.5220 (t60) REVERT: D 485 MET cc_start: 0.7258 (pp-130) cc_final: 0.6920 (ptt) REVERT: D 510 MET cc_start: 0.5602 (mtm) cc_final: 0.5095 (mtt) outliers start: 31 outliers final: 11 residues processed: 155 average time/residue: 0.4294 time to fit residues: 75.8631 Evaluate side-chains 127 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 93 ASP Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 163 LEU 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 D residue 64 LEU 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 27 optimal weight: 0.9990 chunk 76 optimal weight: 0.0070 chunk 154 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 80 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.098428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.075205 restraints weight = 48758.960| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.09 r_work: 0.3278 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15500 Z= 0.115 Angle : 0.613 11.004 21023 Z= 0.308 Chirality : 0.041 0.177 2380 Planarity : 0.004 0.050 2623 Dihedral : 9.016 158.008 2160 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 1.66 % Allowed : 12.17 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.20), residues: 1840 helix: 1.27 (0.16), residues: 1128 sheet: -1.55 (0.45), residues: 88 loop : -1.92 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 355 TYR 0.024 0.001 TYR D 283 PHE 0.027 0.001 PHE C 129 TRP 0.010 0.001 TRP A 73 HIS 0.003 0.000 HIS B 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (15500) covalent geometry : angle 0.61327 / 0.31 (21023) hydrogen bonds : bond 0.03893 / 2.49 ( 860) hydrogen bonds : angle 3.78482 / 2.71 ( 2502) *********************** 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 147 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 326 MET cc_start: 0.9021 (mtm) cc_final: 0.8717 (mtp) REVERT: A 388 MET cc_start: 0.8635 (mmm) cc_final: 0.8262 (mmm) REVERT: A 504 LEU cc_start: 0.9553 (tm) cc_final: 0.9231 (mt) REVERT: B 388 MET cc_start: 0.9136 (mmm) cc_final: 0.8279 (mmm) REVERT: C 106 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7467 (tmm) REVERT: C 388 MET cc_start: 0.8866 (mmm) cc_final: 0.8514 (mmm) REVERT: C 485 MET cc_start: 0.7801 (pp-130) cc_final: 0.7430 (ptt) REVERT: D 106 MET cc_start: 0.3805 (tmt) cc_final: 0.3569 (mtt) REVERT: D 132 LEU cc_start: 0.7852 (pp) cc_final: 0.7498 (pt) REVERT: D 133 ARG cc_start: 0.3266 (mmt180) cc_final: 0.2886 (tmt-80) REVERT: D 188 TRP cc_start: 0.7090 (m100) cc_final: 0.5178 (t60) REVERT: D 485 MET cc_start: 0.7130 (pp-130) cc_final: 0.6819 (ptt) REVERT: D 510 MET cc_start: 0.5549 (mtm) cc_final: 0.5092 (mtt) outliers start: 27 outliers final: 11 residues processed: 137 average time/residue: 0.4577 time to fit residues: 71.3765 Evaluate side-chains 126 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 93 ASP Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 447 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 32 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.096428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.072986 restraints weight = 48266.631| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.04 r_work: 0.3230 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15500 Z= 0.168 Angle : 0.651 11.381 21023 Z= 0.326 Chirality : 0.043 0.153 2380 Planarity : 0.004 0.050 2623 Dihedral : 8.917 146.742 2160 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 1.78 % Allowed : 13.15 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.20), residues: 1840 helix: 1.55 (0.16), residues: 1080 sheet: -1.36 (0.46), residues: 88 loop : -1.88 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 355 TYR 0.024 0.001 TYR D 283 PHE 0.021 0.002 PHE C 129 TRP 0.010 0.002 TRP D 73 HIS 0.003 0.001 HIS C 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (15500) covalent geometry : angle 0.65062 / 0.33 (21023) hydrogen bonds : bond 0.04349 / 2.79 ( 860) hydrogen bonds : angle 3.85118 / 2.77 ( 2502) *********************** 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 145 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 326 MET cc_start: 0.9069 (mtm) cc_final: 0.8731 (mtp) REVERT: A 504 LEU cc_start: 0.9559 (tm) cc_final: 0.9231 (mt) REVERT: B 388 MET cc_start: 0.9183 (mmm) cc_final: 0.8222 (mmm) REVERT: C 106 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7500 (tmm) REVERT: C 388 MET cc_start: 0.8916 (mmm) cc_final: 0.8476 (mmm) REVERT: D 106 MET cc_start: 0.3893 (tmt) cc_final: 0.3592 (mtt) REVERT: D 132 LEU cc_start: 0.8086 (pp) cc_final: 0.7791 (pt) REVERT: D 133 ARG cc_start: 0.3663 (mmt180) cc_final: 0.3271 (tmt-80) REVERT: D 188 TRP cc_start: 0.7064 (m100) cc_final: 0.5246 (t60) REVERT: D 485 MET cc_start: 0.7357 (pp-130) cc_final: 0.6994 (ptt) REVERT: D 510 MET cc_start: 0.5848 (mtm) cc_final: 0.5325 (mtt) outliers start: 29 outliers final: 13 residues processed: 136 average time/residue: 0.4695 time to fit residues: 72.7274 Evaluate side-chains 125 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 93 ASP Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 106 MET 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 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 168 optimal weight: 0.9980 chunk 147 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 181 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 161 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.097521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.074240 restraints weight = 47713.283| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 3.03 r_work: 0.3256 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15500 Z= 0.122 Angle : 0.630 11.887 21023 Z= 0.314 Chirality : 0.042 0.235 2380 Planarity : 0.004 0.050 2623 Dihedral : 8.821 146.166 2160 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 1.60 % Allowed : 13.83 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.20), residues: 1840 helix: 1.55 (0.16), residues: 1096 sheet: -1.22 (0.47), residues: 88 loop : -1.86 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 355 TYR 0.025 0.001 TYR D 283 PHE 0.015 0.001 PHE D 100 TRP 0.009 0.001 TRP D 135 HIS 0.002 0.001 HIS C 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (15500) covalent geometry : angle 0.62972 / 0.31 (21023) hydrogen bonds : bond 0.04024 / 2.58 ( 860) hydrogen bonds : angle 3.82232 / 2.74 ( 2502) *********************** 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 147 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: A 326 MET cc_start: 0.9034 (mtm) cc_final: 0.8685 (mtp) REVERT: A 388 MET cc_start: 0.8704 (mmm) cc_final: 0.8417 (mmm) REVERT: A 504 LEU cc_start: 0.9546 (tm) cc_final: 0.9218 (mt) REVERT: B 388 MET cc_start: 0.9134 (mmm) cc_final: 0.8210 (mmm) REVERT: C 388 MET cc_start: 0.8876 (mmm) cc_final: 0.8513 (mmm) REVERT: C 485 MET cc_start: 0.7923 (pp-130) cc_final: 0.7606 (ptt) REVERT: D 106 MET cc_start: 0.3898 (tmt) cc_final: 0.3599 (mtt) REVERT: D 132 LEU cc_start: 0.8136 (pp) cc_final: 0.7870 (pt) REVERT: D 133 ARG cc_start: 0.3653 (mmt180) cc_final: 0.3242 (tmt-80) REVERT: D 188 TRP cc_start: 0.7063 (m100) cc_final: 0.5271 (t60) REVERT: D 485 MET cc_start: 0.7210 (pp-130) cc_final: 0.6790 (ptt) REVERT: D 510 MET cc_start: 0.5858 (mtm) cc_final: 0.5326 (mtt) outliers start: 26 outliers final: 12 residues processed: 138 average time/residue: 0.4762 time to fit residues: 74.5635 Evaluate side-chains 123 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 93 ASP Chi-restraints excluded: chain B residue 146 SER 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 326 MET Chi-restraints excluded: chain C residue 368 ASP 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 66 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 175 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 171 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.094229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.070717 restraints weight = 48753.182| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.02 r_work: 0.3173 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 15500 Z= 0.261 Angle : 0.733 12.261 21023 Z= 0.366 Chirality : 0.046 0.202 2380 Planarity : 0.005 0.046 2623 Dihedral : 9.159 145.064 2160 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 1.66 % Allowed : 14.26 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.20), residues: 1840 helix: 1.41 (0.16), residues: 1104 sheet: -1.14 (0.50), residues: 88 loop : -1.85 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 355 TYR 0.030 0.002 TYR D 283 PHE 0.019 0.002 PHE D 100 TRP 0.014 0.002 TRP D 135 HIS 0.005 0.001 HIS D 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.26 (15500) covalent geometry : angle 0.73263 / 0.37 (21023) hydrogen bonds : bond 0.04902 / 3.15 ( 860) hydrogen bonds : angle 4.04435 / 2.91 ( 2502) *********************** 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 137 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: A 326 MET cc_start: 0.9101 (mtm) cc_final: 0.8786 (mtp) REVERT: A 388 MET cc_start: 0.8720 (mmm) cc_final: 0.8476 (mmm) REVERT: A 504 LEU cc_start: 0.9541 (tm) cc_final: 0.9232 (mt) REVERT: B 388 MET cc_start: 0.9164 (mmm) cc_final: 0.8153 (mmm) REVERT: B 485 MET cc_start: 0.7941 (pp-130) cc_final: 0.7692 (ptt) REVERT: C 238 MET cc_start: 0.8516 (ttp) cc_final: 0.8135 (tmm) REVERT: C 248 ILE cc_start: 0.9394 (mm) cc_final: 0.9182 (tp) REVERT: C 388 MET cc_start: 0.8921 (mmm) cc_final: 0.8471 (mmm) REVERT: C 485 MET cc_start: 0.8051 (pp-130) cc_final: 0.7665 (ptt) REVERT: D 188 TRP cc_start: 0.7030 (m100) cc_final: 0.5223 (t60) REVERT: D 495 MET cc_start: 0.7700 (mpp) cc_final: 0.7237 (ptp) REVERT: D 510 MET cc_start: 0.5584 (mtm) cc_final: 0.5203 (mtt) outliers start: 27 outliers final: 16 residues processed: 128 average time/residue: 0.4697 time to fit residues: 68.3571 Evaluate side-chains 122 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 501 THR Chi-restraints excluded: chain B residue 505 LEU 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 290 ASN Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 143 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 33 optimal weight: 0.9980 chunk 182 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 161 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 73 optimal weight: 0.1980 chunk 183 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.095977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.072694 restraints weight = 48330.596| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.04 r_work: 0.3214 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 15500 Z= 0.138 Angle : 0.679 17.305 21023 Z= 0.333 Chirality : 0.043 0.194 2380 Planarity : 0.004 0.049 2623 Dihedral : 8.990 146.084 2160 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.04 % Allowed : 14.81 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.20), residues: 1840 helix: 1.59 (0.16), residues: 1104 sheet: -1.05 (0.49), residues: 88 loop : -1.85 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 355 TYR 0.024 0.001 TYR D 283 PHE 0.015 0.001 PHE D 100 TRP 0.010 0.001 TRP B 246 HIS 0.002 0.001 HIS C 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (15500) covalent geometry : angle 0.67904 / 0.33 (21023) hydrogen bonds : bond 0.04289 / 2.75 ( 860) hydrogen bonds : angle 3.91292 / 2.80 ( 2502) *********************** 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 130 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 326 MET cc_start: 0.9067 (mtm) cc_final: 0.8770 (mtp) REVERT: A 388 MET cc_start: 0.8703 (mmm) cc_final: 0.8235 (mmm) REVERT: A 504 LEU cc_start: 0.9533 (tm) cc_final: 0.9235 (mt) REVERT: B 238 MET cc_start: 0.8357 (ttp) cc_final: 0.7811 (tmm) REVERT: B 388 MET cc_start: 0.9122 (mmm) cc_final: 0.8258 (mmm) REVERT: B 485 MET cc_start: 0.7861 (pp-130) cc_final: 0.7659 (ptt) REVERT: C 238 MET cc_start: 0.8437 (ttp) cc_final: 0.8058 (tmm) REVERT: C 388 MET cc_start: 0.8887 (mmm) cc_final: 0.8487 (mmm) REVERT: C 485 MET cc_start: 0.7963 (pp-130) cc_final: 0.7590 (ptt) REVERT: D 188 TRP cc_start: 0.7013 (m100) cc_final: 0.5238 (t60) REVERT: D 485 MET cc_start: 0.7408 (pp-130) cc_final: 0.7035 (ptt) REVERT: D 495 MET cc_start: 0.7792 (mpp) cc_final: 0.7380 (ptp) REVERT: D 510 MET cc_start: 0.5804 (mtm) cc_final: 0.5352 (mtt) outliers start: 17 outliers final: 13 residues processed: 124 average time/residue: 0.4689 time to fit residues: 65.7587 Evaluate side-chains 120 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 93 ASP Chi-restraints excluded: chain B residue 146 SER 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 D residue 64 LEU Chi-restraints excluded: chain D residue 143 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 15 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 121 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 ASN B 290 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.096173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.072831 restraints weight = 48481.590| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.06 r_work: 0.3226 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15500 Z= 0.140 Angle : 0.680 15.089 21023 Z= 0.334 Chirality : 0.042 0.204 2380 Planarity : 0.005 0.175 2623 Dihedral : 8.890 145.326 2160 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.98 % Allowed : 15.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.20), residues: 1840 helix: 1.72 (0.16), residues: 1092 sheet: -0.93 (0.48), residues: 88 loop : -1.94 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.000 ARG C 355 TYR 0.028 0.001 TYR D 283 PHE 0.014 0.001 PHE D 100 TRP 0.010 0.002 TRP B 246 HIS 0.003 0.001 HIS C 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (15500) covalent geometry : angle 0.68021 / 0.33 (21023) hydrogen bonds : bond 0.04195 / 2.68 ( 860) hydrogen bonds : angle 3.88347 / 2.79 ( 2502) ********************** 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 130 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 326 MET cc_start: 0.9065 (mtm) cc_final: 0.8769 (mtp) REVERT: A 388 MET cc_start: 0.8728 (mmm) cc_final: 0.8495 (mmm) REVERT: A 504 LEU cc_start: 0.9521 (tm) cc_final: 0.9240 (mt) REVERT: B 238 MET cc_start: 0.8392 (ttp) cc_final: 0.7873 (tmm) REVERT: B 388 MET cc_start: 0.9140 (mmm) cc_final: 0.8274 (mmm) REVERT: B 485 MET cc_start: 0.7871 (pp-130) cc_final: 0.7640 (ptt) REVERT: C 238 MET cc_start: 0.8478 (ttp) cc_final: 0.8124 (tmm) REVERT: C 388 MET cc_start: 0.8879 (mmm) cc_final: 0.8537 (mmm) REVERT: C 485 MET cc_start: 0.7993 (pp-130) cc_final: 0.7628 (ptt) REVERT: D 188 TRP cc_start: 0.7076 (m100) cc_final: 0.5333 (t60) REVERT: D 485 MET cc_start: 0.7461 (pp-130) cc_final: 0.7064 (ptt) REVERT: D 510 MET cc_start: 0.5539 (mtm) cc_final: 0.5152 (mtt) outliers start: 16 outliers final: 11 residues processed: 125 average time/residue: 0.4795 time to fit residues: 67.8537 Evaluate side-chains 119 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 93 ASP Chi-restraints excluded: chain B residue 146 SER 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 368 ASP Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 143 THR 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 68 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.093666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.070268 restraints weight = 48601.987| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.01 r_work: 0.3162 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 15500 Z= 0.267 Angle : 0.768 15.302 21023 Z= 0.381 Chirality : 0.046 0.194 2380 Planarity : 0.005 0.127 2623 Dihedral : 9.336 145.677 2160 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 1.11 % Allowed : 15.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.20), residues: 1840 helix: 1.45 (0.16), residues: 1104 sheet: -0.81 (0.51), residues: 88 loop : -1.89 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 355 TYR 0.033 0.002 TYR D 283 PHE 0.018 0.002 PHE D 100 TRP 0.019 0.002 TRP D 188 HIS 0.006 0.001 HIS D 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00613 / 0.27 (15500) covalent geometry : angle 0.76757 / 0.38 (21023) hydrogen bonds : bond 0.04979 / 3.20 ( 860) hydrogen bonds : angle 4.11609 / 2.96 ( 2502) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4656.52 seconds wall clock time: 80 minutes 7.64 seconds (4807.64 seconds total)