Starting phenix.real_space_refine on Thu Jun 19 18:49:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eva_19996/06_2025/9eva_19996.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eva_19996/06_2025/9eva_19996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eva_19996/06_2025/9eva_19996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eva_19996/06_2025/9eva_19996.map" model { file = "/net/cci-nas-00/data/ceres_data/9eva_19996/06_2025/9eva_19996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eva_19996/06_2025/9eva_19996.cif" } resolution = 2.34 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= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 10 9.91 5 S 55 5.16 5 C 14797 2.51 5 N 3739 2.21 5 O 4327 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22928 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4633 Classifications: {'peptide': 587} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 559} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 4624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4624 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 560} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 4515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4515 Classifications: {'peptide': 573} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 545} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 4534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4534 Classifications: {'peptide': 579} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 551} Chain breaks: 3 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 4612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4612 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 558} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.52, per 1000 atoms: 0.63 Number of scatterers: 22928 At special positions: 0 Unit cell: (142.195, 143.888, 154.045, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 10 19.99 S 55 16.00 O 4327 8.00 N 3739 7.00 C 14797 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: 5.11 Conformation dependent library (CDL) restraints added in 2.6 seconds 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5378 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 29 sheets defined 29.5% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.75 Creating SS restraints... Processing helix chain 'A' and resid 88 through 100 removed outlier: 3.816A pdb=" N GLN A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 118 removed outlier: 3.709A pdb=" N THR A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 196 through 199 Processing helix chain 'A' and resid 362 through 365 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 382 through 391 Processing helix chain 'A' and resid 514 through 536 removed outlier: 3.959A pdb=" N TYR A 518 " --> pdb=" O ASN A 514 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Proline residue: A 525 - end of helix removed outlier: 3.682A pdb=" N ILE A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 539 No H-bonds generated for 'chain 'A' and resid 537 through 539' Processing helix chain 'A' and resid 541 through 564 removed outlier: 3.501A pdb=" N LEU A 554 " --> pdb=" O SER A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 567 No H-bonds generated for 'chain 'A' and resid 565 through 567' Processing helix chain 'A' and resid 574 through 604 removed outlier: 3.522A pdb=" N VAL A 591 " --> pdb=" O THR A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 636 Proline residue: A 621 - end of helix Processing helix chain 'B' and resid 88 through 100 removed outlier: 3.816A pdb=" N GLN B 94 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL B 95 " --> pdb=" O SER B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 118 removed outlier: 3.709A pdb=" N THR B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 182 Processing helix chain 'B' and resid 196 through 199 Processing helix chain 'B' and resid 362 through 365 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 382 through 391 Processing helix chain 'B' and resid 514 through 536 removed outlier: 3.834A pdb=" N TYR B 518 " --> pdb=" O ASN B 514 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N VAL B 524 " --> pdb=" O LEU B 520 " (cutoff:3.500A) Proline residue: B 525 - end of helix removed outlier: 3.702A pdb=" N ILE B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 539 No H-bonds generated for 'chain 'B' and resid 537 through 539' Processing helix chain 'B' and resid 541 through 563 Processing helix chain 'B' and resid 564 through 567 Processing helix chain 'B' and resid 574 through 604 removed outlier: 3.525A pdb=" N VAL B 591 " --> pdb=" O THR B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 637 Proline residue: B 621 - end of helix removed outlier: 3.808A pdb=" N THR B 637 " --> pdb=" O LEU B 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 100 removed outlier: 3.816A pdb=" N GLN C 94 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 118 removed outlier: 3.709A pdb=" N THR C 111 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG C 116 " --> pdb=" O ALA C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 182 Processing helix chain 'C' and resid 196 through 199 Processing helix chain 'C' and resid 308 through 314 removed outlier: 3.748A pdb=" N LEU C 311 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ARG C 312 " --> pdb=" O PRO C 309 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER C 314 " --> pdb=" O LEU C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 365 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 382 through 391 Processing helix chain 'C' and resid 514 through 536 removed outlier: 3.839A pdb=" N TYR C 518 " --> pdb=" O ASN C 514 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL C 524 " --> pdb=" O LEU C 520 " (cutoff:3.500A) Proline residue: C 525 - end of helix removed outlier: 3.689A pdb=" N ILE C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 539 No H-bonds generated for 'chain 'C' and resid 537 through 539' Processing helix chain 'C' and resid 541 through 563 removed outlier: 3.515A pdb=" N LEU C 554 " --> pdb=" O SER C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 567 Processing helix chain 'C' and resid 574 through 604 removed outlier: 3.579A pdb=" N VAL C 591 " --> pdb=" O THR C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 637 Proline residue: C 621 - end of helix removed outlier: 3.793A pdb=" N THR C 637 " --> pdb=" O LEU C 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 99 removed outlier: 3.815A pdb=" N GLN D 94 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 118 removed outlier: 3.709A pdb=" N THR D 111 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 362 through 365 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'D' and resid 382 through 391 Processing helix chain 'D' and resid 514 through 536 removed outlier: 3.909A pdb=" N TYR D 518 " --> pdb=" O ASN D 514 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N VAL D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Proline residue: D 525 - end of helix removed outlier: 3.693A pdb=" N ILE D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 539 No H-bonds generated for 'chain 'D' and resid 537 through 539' Processing helix chain 'D' and resid 541 through 563 Processing helix chain 'D' and resid 564 through 567 Processing helix chain 'D' and resid 574 through 604 removed outlier: 3.510A pdb=" N VAL D 591 " --> pdb=" O THR D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 636 Proline residue: D 621 - end of helix Processing helix chain 'E' and resid 88 through 100 removed outlier: 3.816A pdb=" N GLN E 94 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL E 95 " --> pdb=" O SER E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 118 removed outlier: 3.709A pdb=" N THR E 111 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 182 Processing helix chain 'E' and resid 196 through 199 Processing helix chain 'E' and resid 362 through 365 Processing helix chain 'E' and resid 367 through 371 Processing helix chain 'E' and resid 382 through 391 Processing helix chain 'E' and resid 514 through 536 removed outlier: 3.929A pdb=" N TYR E 518 " --> pdb=" O ASN E 514 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) Proline residue: E 525 - end of helix removed outlier: 3.621A pdb=" N ILE E 536 " --> pdb=" O VAL E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 539 No H-bonds generated for 'chain 'E' and resid 537 through 539' Processing helix chain 'E' and resid 541 through 563 Processing helix chain 'E' and resid 564 through 567 Processing helix chain 'E' and resid 574 through 604 removed outlier: 3.520A pdb=" N VAL E 591 " --> pdb=" O THR E 587 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 636 Proline residue: E 621 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 45 removed outlier: 5.995A pdb=" N SER A 167 " --> pdb=" O THR A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.686A pdb=" N GLY A 120 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 79 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY A 141 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP A 57 " --> pdb=" O GLY A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 204 through 212 removed outlier: 4.232A pdb=" N ALA A 298 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 218 through 222 removed outlier: 7.503A pdb=" N LEU A 247 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N PHE A 259 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU A 249 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 376 through 379 removed outlier: 4.353A pdb=" N GLN A 411 " --> pdb=" O PHE A 424 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE A 424 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE A 413 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER A 422 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL A 415 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG A 420 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 341 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL A 352 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE A 339 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N THR A 354 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASP A 337 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N LYS A 356 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ALA A 335 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N SER A 358 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N GLY A 333 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N HIS A 360 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 9.339A pdb=" N THR A 331 " --> pdb=" O HIS A 360 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASP A 328 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN A 464 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL A 330 " --> pdb=" O ASN A 464 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE A 466 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL A 332 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 397 through 399 removed outlier: 5.066A pdb=" N SER A 503 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN A 502 " --> pdb=" O GLU A 493 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLU A 493 " --> pdb=" O ASN A 502 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ARG A 504 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE A 491 " --> pdb=" O ARG A 504 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR A 506 " --> pdb=" O GLN A 489 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLN A 489 " --> pdb=" O THR A 506 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR A 508 " --> pdb=" O TYR A 487 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR A 487 " --> pdb=" O THR A 508 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU A 510 " --> pdb=" O THR A 485 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 38 through 45 removed outlier: 5.995A pdb=" N SER B 167 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.686A pdb=" N GLY B 120 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 79 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY B 141 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP B 57 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 204 through 212 removed outlier: 4.315A pdb=" N ALA B 298 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 218 through 222 removed outlier: 7.330A pdb=" N LEU B 247 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N PHE B 259 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU B 249 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 376 through 379 removed outlier: 4.362A pdb=" N GLN B 411 " --> pdb=" O PHE B 424 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE B 424 " --> pdb=" O GLN B 411 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE B 413 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N SER B 422 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL B 415 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG B 420 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY B 341 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL B 352 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ILE B 339 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N THR B 354 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ASP B 337 " --> pdb=" O THR B 354 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N LYS B 356 " --> pdb=" O ALA B 335 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ALA B 335 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N SER B 358 " --> pdb=" O GLY B 333 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N GLY B 333 " --> pdb=" O SER B 358 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N HIS B 360 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 9.401A pdb=" N THR B 331 " --> pdb=" O HIS B 360 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASP B 328 " --> pdb=" O ILE B 462 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASN B 464 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL B 330 " --> pdb=" O ASN B 464 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE B 466 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL B 332 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 397 through 399 removed outlier: 4.981A pdb=" N SER B 503 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN B 502 " --> pdb=" O GLU B 493 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU B 493 " --> pdb=" O ASN B 502 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ARG B 504 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE B 491 " --> pdb=" O ARG B 504 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR B 506 " --> pdb=" O GLN B 489 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN B 489 " --> pdb=" O THR B 506 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR B 508 " --> pdb=" O TYR B 487 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TYR B 487 " --> pdb=" O THR B 508 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU B 510 " --> pdb=" O THR B 485 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 38 through 45 removed outlier: 5.995A pdb=" N SER C 167 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.686A pdb=" N GLY C 120 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 79 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY C 141 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP C 57 " --> pdb=" O GLY C 141 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 204 through 208 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 204 through 208 current: chain 'C' and resid 256 through 259 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 256 through 259 current: chain 'C' and resid 269 through 274 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 376 through 379 removed outlier: 4.328A pdb=" N GLN C 411 " --> pdb=" O PHE C 424 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N PHE C 424 " --> pdb=" O GLN C 411 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE C 413 " --> pdb=" O SER C 422 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N SER C 422 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL C 415 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ARG C 420 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ASN C 348 " --> pdb=" O GLY C 341 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N GLY C 341 " --> pdb=" O ASN C 348 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N SER C 350 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ILE C 339 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL C 352 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N HIS C 360 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N LEU C 329 " --> pdb=" O HIS C 360 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASP C 328 " --> pdb=" O ILE C 462 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASN C 464 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL C 330 " --> pdb=" O ASN C 464 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE C 466 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL C 332 " --> pdb=" O ILE C 466 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 397 through 399 removed outlier: 5.001A pdb=" N SER C 503 " --> pdb=" O LEU C 454 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN C 502 " --> pdb=" O GLU C 493 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLU C 493 " --> pdb=" O ASN C 502 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG C 504 " --> pdb=" O ILE C 491 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE C 491 " --> pdb=" O ARG C 504 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR C 506 " --> pdb=" O GLN C 489 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLN C 489 " --> pdb=" O THR C 506 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR C 508 " --> pdb=" O TYR C 487 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR C 487 " --> pdb=" O THR C 508 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU C 510 " --> pdb=" O THR C 485 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 38 through 45 removed outlier: 5.996A pdb=" N SER D 167 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 120 through 122 removed outlier: 3.685A pdb=" N GLY D 120 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 79 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY D 141 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP D 57 " --> pdb=" O GLY D 141 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 204 through 212 removed outlier: 4.252A pdb=" N ALA D 298 " --> pdb=" O LEU D 212 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA D 234 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 218 through 222 removed outlier: 7.340A pdb=" N LEU D 247 " --> pdb=" O PHE D 259 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N PHE D 259 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU D 249 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 376 through 379 removed outlier: 4.330A pdb=" N GLN D 411 " --> pdb=" O PHE D 424 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N PHE D 424 " --> pdb=" O GLN D 411 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE D 413 " --> pdb=" O SER D 422 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER D 422 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL D 415 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ARG D 420 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY D 341 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL D 352 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE D 339 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N THR D 354 " --> pdb=" O ASP D 337 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ASP D 337 " --> pdb=" O THR D 354 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N LYS D 356 " --> pdb=" O ALA D 335 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ALA D 335 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N SER D 358 " --> pdb=" O GLY D 333 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N GLY D 333 " --> pdb=" O SER D 358 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N HIS D 360 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 9.406A pdb=" N THR D 331 " --> pdb=" O HIS D 360 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ASP D 328 " --> pdb=" O ILE D 462 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN D 464 " --> pdb=" O ASP D 328 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL D 330 " --> pdb=" O ASN D 464 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE D 466 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL D 332 " --> pdb=" O ILE D 466 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 397 through 399 removed outlier: 5.062A pdb=" N SER D 503 " --> pdb=" O LEU D 454 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN D 502 " --> pdb=" O GLU D 493 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLU D 493 " --> pdb=" O ASN D 502 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ARG D 504 " --> pdb=" O ILE D 491 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE D 491 " --> pdb=" O ARG D 504 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR D 506 " --> pdb=" O GLN D 489 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLN D 489 " --> pdb=" O THR D 506 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR D 508 " --> pdb=" O TYR D 487 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR D 487 " --> pdb=" O THR D 508 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU D 510 " --> pdb=" O THR D 485 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 38 through 45 removed outlier: 5.996A pdb=" N SER E 167 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 120 through 122 removed outlier: 3.686A pdb=" N GLY E 120 " --> pdb=" O ILE E 81 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL E 79 " --> pdb=" O ASP E 122 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY E 141 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP E 57 " --> pdb=" O GLY E 141 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 204 through 212 removed outlier: 4.124A pdb=" N ALA E 298 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 218 through 222 removed outlier: 7.412A pdb=" N LEU E 247 " --> pdb=" O PHE E 259 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N PHE E 259 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU E 249 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 376 through 379 removed outlier: 4.293A pdb=" N GLN E 411 " --> pdb=" O PHE E 424 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N PHE E 424 " --> pdb=" O GLN E 411 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE E 413 " --> pdb=" O SER E 422 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N SER E 422 " --> pdb=" O ILE E 413 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N VAL E 415 " --> pdb=" O ARG E 420 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG E 420 " --> pdb=" O VAL E 415 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY E 341 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL E 352 " --> pdb=" O ILE E 339 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ILE E 339 " --> pdb=" O VAL E 352 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N THR E 354 " --> pdb=" O ASP E 337 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ASP E 337 " --> pdb=" O THR E 354 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N LYS E 356 " --> pdb=" O ALA E 335 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ALA E 335 " --> pdb=" O LYS E 356 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N SER E 358 " --> pdb=" O GLY E 333 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N GLY E 333 " --> pdb=" O SER E 358 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N HIS E 360 " --> pdb=" O THR E 331 " (cutoff:3.500A) removed outlier: 9.295A pdb=" N THR E 331 " --> pdb=" O HIS E 360 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ASP E 328 " --> pdb=" O ILE E 462 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASN E 464 " --> pdb=" O ASP E 328 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL E 330 " --> pdb=" O ASN E 464 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE E 466 " --> pdb=" O VAL E 330 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL E 332 " --> pdb=" O ILE E 466 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 397 through 399 removed outlier: 5.043A pdb=" N SER E 503 " --> pdb=" O LEU E 454 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASN E 502 " --> pdb=" O GLU E 493 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLU E 493 " --> pdb=" O ASN E 502 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ARG E 504 " --> pdb=" O ILE E 491 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE E 491 " --> pdb=" O ARG E 504 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR E 506 " --> pdb=" O GLN E 489 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLN E 489 " --> pdb=" O THR E 506 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR E 508 " --> pdb=" O TYR E 487 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TYR E 487 " --> pdb=" O THR E 508 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU E 510 " --> pdb=" O THR E 485 " (cutoff:3.500A) 1059 hydrogen bonds defined for protein. 2919 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: 7.96 Time building geometry restraints manager: 6.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4918 1.33 - 1.45: 5432 1.45 - 1.57: 13008 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 23438 Sorted by residual: bond pdb=" CA GLU E 103 " pdb=" C GLU E 103 " ideal model delta sigma weight residual 1.526 1.489 0.037 9.20e-03 1.18e+04 1.63e+01 bond pdb=" CA ALA B 99 " pdb=" C ALA B 99 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.29e-02 6.01e+03 1.60e+01 bond pdb=" CA ALA E 99 " pdb=" C ALA E 99 " ideal model delta sigma weight residual 1.524 1.472 0.051 1.29e-02 6.01e+03 1.58e+01 bond pdb=" CA GLU A 103 " pdb=" C GLU A 103 " ideal model delta sigma weight residual 1.526 1.489 0.037 9.20e-03 1.18e+04 1.58e+01 bond pdb=" CA ALA A 99 " pdb=" C ALA A 99 " ideal model delta sigma weight residual 1.524 1.472 0.051 1.29e-02 6.01e+03 1.57e+01 ... (remaining 23433 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 31409 1.97 - 3.94: 422 3.94 - 5.91: 47 5.91 - 7.89: 12 7.89 - 9.86: 6 Bond angle restraints: 31896 Sorted by residual: angle pdb=" N ILE C 199 " pdb=" CA ILE C 199 " pdb=" C ILE C 199 " ideal model delta sigma weight residual 109.34 119.20 -9.86 2.08e+00 2.31e-01 2.25e+01 angle pdb=" C LYS C 200 " pdb=" N PRO C 201 " pdb=" CA PRO C 201 " ideal model delta sigma weight residual 119.84 125.53 -5.69 1.25e+00 6.40e-01 2.08e+01 angle pdb=" N GLU E 103 " pdb=" CA GLU E 103 " pdb=" C GLU E 103 " ideal model delta sigma weight residual 110.56 101.82 8.74 1.94e+00 2.66e-01 2.03e+01 angle pdb=" N GLU A 103 " pdb=" CA GLU A 103 " pdb=" C GLU A 103 " ideal model delta sigma weight residual 110.56 101.83 8.73 1.94e+00 2.66e-01 2.03e+01 angle pdb=" N TYR E 620 " pdb=" CA TYR E 620 " pdb=" C TYR E 620 " ideal model delta sigma weight residual 113.25 119.06 -5.81 1.30e+00 5.92e-01 2.00e+01 ... (remaining 31891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.50: 13208 16.50 - 32.99: 430 32.99 - 49.49: 90 49.49 - 65.99: 25 65.99 - 82.48: 7 Dihedral angle restraints: 13760 sinusoidal: 5384 harmonic: 8376 Sorted by residual: dihedral pdb=" CA ILE D 522 " pdb=" C ILE D 522 " pdb=" N PHE D 523 " pdb=" CA PHE D 523 " ideal model delta harmonic sigma weight residual -180.00 -158.91 -21.09 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA ILE B 522 " pdb=" C ILE B 522 " pdb=" N PHE B 523 " pdb=" CA PHE B 523 " ideal model delta harmonic sigma weight residual -180.00 -159.67 -20.33 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA PRO A 265 " pdb=" C PRO A 265 " pdb=" N GLY A 266 " pdb=" CA GLY A 266 " ideal model delta harmonic sigma weight residual -180.00 -159.69 -20.31 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 13757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3011 0.054 - 0.108: 513 0.108 - 0.162: 106 0.162 - 0.217: 1 0.217 - 0.271: 8 Chirality restraints: 3639 Sorted by residual: chirality pdb=" CA TYR E 620 " pdb=" N TYR E 620 " pdb=" C TYR E 620 " pdb=" CB TYR E 620 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA ASN E 104 " pdb=" N ASN E 104 " pdb=" C ASN E 104 " pdb=" CB ASN E 104 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA ASN A 104 " pdb=" N ASN A 104 " pdb=" C ASN A 104 " pdb=" CB ASN A 104 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 3636 not shown) Planarity restraints: 4125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 198 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.12e+00 pdb=" C GLU C 198 " -0.049 2.00e-02 2.50e+03 pdb=" O GLU C 198 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE C 199 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 619 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C ILE E 619 " -0.041 2.00e-02 2.50e+03 pdb=" O ILE E 619 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR E 620 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 200 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.52e+00 pdb=" N PRO C 201 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 201 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 201 " 0.028 5.00e-02 4.00e+02 ... (remaining 4122 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4611 2.78 - 3.31: 19923 3.31 - 3.84: 35568 3.84 - 4.37: 41196 4.37 - 4.90: 73905 Nonbonded interactions: 175203 Sorted by model distance: nonbonded pdb=" OG SER B 367 " pdb=" OD1 ASP B 369 " model vdw 2.252 3.040 nonbonded pdb=" OG SER C 367 " pdb=" OD1 ASP C 369 " model vdw 2.252 3.040 nonbonded pdb=" O TYR E 129 " pdb="CA CA E 702 " model vdw 2.273 2.510 nonbonded pdb=" OG SER B 533 " pdb=" OD1 ASN B 552 " model vdw 2.275 3.040 nonbonded pdb=" OG SER E 533 " pdb=" OD1 ASN E 552 " model vdw 2.308 3.040 ... (remaining 175198 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 37 through 95 or (resid 96 through 99 and (name N or name \ CA or name C or name O or name CB )) or resid 100 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB )) or resid 108 or (resid 109 and (name N \ or name CA or name C or name O or name CB )) or resid 110 through 138 or (resid \ 139 and (name N or name CA or name C or name O or name CB )) or resid 140 throug \ h 198 or (resid 199 through 200 and (name N or name CA or name C or name O or na \ me CB )) or resid 201 or (resid 202 through 203 and (name N or name CA or name C \ or name O or name CB )) or resid 204 through 209 or resid 217 through 238 or re \ sid 245 through 287 or resid 301 through 310 or resid 322 through 368 or (resid \ 369 through 370 and (name N or name CA or name C or name O or name CB )) or resi \ d 371 through 637 or resid 701 through 702)) selection = (chain 'B' and (resid 37 through 95 or (resid 96 through 99 and (name N or name \ CA or name C or name O or name CB )) or resid 100 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB )) or resid 108 or (resid 109 and (name N \ or name CA or name C or name O or name CB )) or resid 110 through 198 or (resid \ 199 through 200 and (name N or name CA or name C or name O or name CB )) or resi \ d 201 through 209 or resid 217 through 238 or resid 245 or (resid 246 and (name \ N or name CA or name C or name O or name CB )) or resid 247 through 287 or resid \ 301 through 310 or resid 321 or resid 323 through 368 or (resid 369 through 370 \ and (name N or name CA or name C or name O or name CB )) or resid 371 through 6 \ 37 or resid 701 through 702)) selection = (chain 'C' and (resid 37 through 95 or (resid 96 through 99 and (name N or name \ CA or name C or name O or name CB )) or resid 100 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB )) or resid 108 or (resid 109 and (name N \ or name CA or name C or name O or name CB )) or resid 110 through 138 or (resid \ 139 and (name N or name CA or name C or name O or name CB )) or resid 140 throug \ h 201 or (resid 202 through 203 and (name N or name CA or name C or name O or na \ me CB )) or resid 204 through 245 or (resid 246 and (name N or name CA or name C \ or name O or name CB )) or resid 247 through 310 or resid 314 or resid 323 thro \ ugh 368 or (resid 369 through 370 and (name N or name CA or name C or name O or \ name CB )) or resid 371 through 637 or resid 701 through 702)) selection = (chain 'D' and (resid 37 through 198 or (resid 199 through 200 and (name N or na \ me CA or name C or name O or name CB )) or resid 201 through 209 or resid 217 th \ rough 238 or resid 245 or (resid 246 and (name N or name CA or name C or name O \ or name CB )) or resid 247 through 287 or resid 301 through 310 or resid 322 thr \ ough 369 or (resid 370 and (name N or name CA or name C or name O or name CB )) \ or resid 371 through 637 or resid 701 through 702)) selection = (chain 'E' and (resid 37 through 95 or (resid 96 through 99 and (name N or name \ CA or name C or name O or name CB )) or resid 100 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB )) or resid 108 or (resid 109 and (name N \ or name CA or name C or name O or name CB )) or resid 110 through 198 or (resid \ 199 through 200 and (name N or name CA or name C or name O or name CB )) or resi \ d 201 through 209 or resid 217 through 238 or resid 245 or (resid 246 and (name \ N or name CA or name C or name O or name CB )) or resid 247 through 287 or resid \ 301 through 310 or resid 322 through 368 or (resid 369 through 370 and (name N \ or name CA or name C or name O or name CB )) or resid 371 through 637 or resid 7 \ 01 through 702)) } 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: 2.430 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: 1.060 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 50.980 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.100 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:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 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 : 0.003 0.053 23438 Z= 0.222 Angle : 0.590 9.857 31896 Z= 0.341 Chirality : 0.045 0.271 3639 Planarity : 0.004 0.053 4125 Dihedral : 9.401 82.484 8382 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.54 % Favored : 97.36 % Rotamer: Outliers : 0.68 % Allowed : 3.27 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.16), residues: 2875 helix: 1.66 (0.21), residues: 702 sheet: 1.04 (0.16), residues: 977 loop : -0.34 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 630 HIS 0.003 0.001 HIS A 285 PHE 0.011 0.001 PHE B 561 TYR 0.014 0.001 TYR C 517 ARG 0.004 0.000 ARG D 578 Details of bonding type rmsd hydrogen bonds : bond 0.19100 ( 1059) hydrogen bonds : angle 6.35638 ( 2919) covalent geometry : bond 0.00340 (23438) covalent geometry : angle 0.59030 (31896) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 695 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7475 (mm-30) REVERT: A 425 GLU cc_start: 0.7823 (tt0) cc_final: 0.7462 (tt0) REVERT: A 480 GLU cc_start: 0.7964 (mp0) cc_final: 0.7456 (mp0) REVERT: A 481 GLU cc_start: 0.7762 (tt0) cc_final: 0.7474 (tt0) REVERT: B 58 MET cc_start: 0.6081 (mmp) cc_final: 0.5629 (mmm) REVERT: B 236 VAL cc_start: 0.8639 (p) cc_final: 0.8390 (m) REVERT: B 345 ARG cc_start: 0.7927 (mtp85) cc_final: 0.7666 (mtp85) REVERT: C 270 GLU cc_start: 0.6769 (pt0) cc_final: 0.6541 (pt0) REVERT: C 286 VAL cc_start: 0.4468 (OUTLIER) cc_final: 0.4157 (t) REVERT: C 437 ASP cc_start: 0.8123 (t0) cc_final: 0.7889 (t70) REVERT: D 58 MET cc_start: 0.0630 (mmp) cc_final: 0.0421 (mtt) REVERT: D 347 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7569 (mt-10) REVERT: D 364 LEU cc_start: 0.8401 (mp) cc_final: 0.8149 (mp) REVERT: E 207 GLU cc_start: 0.6817 (tt0) cc_final: 0.6607 (tt0) REVERT: E 425 GLU cc_start: 0.7614 (tt0) cc_final: 0.7287 (tt0) REVERT: E 480 GLU cc_start: 0.7755 (mp0) cc_final: 0.7336 (mp0) outliers start: 17 outliers final: 5 residues processed: 706 average time/residue: 1.4656 time to fit residues: 1176.4410 Evaluate side-chains 584 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 578 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 620 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 0.9980 chunk 218 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 225 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 chunk 168 optimal weight: 0.6980 chunk 261 optimal weight: 0.8980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 338 GLN A 344 GLN A 405 ASN A 409 GLN B 154 GLN B 360 HIS B 432 GLN B 476 GLN B 611 GLN C 409 GLN C 432 GLN C 611 GLN D 233 HIS D 338 GLN D 560 ASN D 611 GLN ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 432 GLN E 514 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.158883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.138125 restraints weight = 30457.255| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.83 r_work: 0.3728 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23438 Z= 0.198 Angle : 0.625 9.920 31896 Z= 0.337 Chirality : 0.047 0.162 3639 Planarity : 0.004 0.041 4125 Dihedral : 5.373 59.100 3146 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.95 % Allowed : 10.30 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.16), residues: 2875 helix: 1.65 (0.20), residues: 736 sheet: 1.12 (0.16), residues: 913 loop : -0.39 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 121 HIS 0.006 0.001 HIS B 204 PHE 0.027 0.002 PHE E 135 TYR 0.040 0.002 TYR C 53 ARG 0.009 0.001 ARG D 521 Details of bonding type rmsd hydrogen bonds : bond 0.07237 ( 1059) hydrogen bonds : angle 4.85708 ( 2919) covalent geometry : bond 0.00454 (23438) covalent geometry : angle 0.62507 (31896) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 601 time to evaluate : 2.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LEU cc_start: 0.8537 (tt) cc_final: 0.8319 (tp) REVERT: A 347 GLU cc_start: 0.8519 (mt-10) cc_final: 0.7633 (mt-10) REVERT: A 425 GLU cc_start: 0.8160 (tt0) cc_final: 0.7947 (tt0) REVERT: A 480 GLU cc_start: 0.8406 (mp0) cc_final: 0.7765 (mp0) REVERT: A 481 GLU cc_start: 0.8234 (tt0) cc_final: 0.7998 (tt0) REVERT: A 521 ARG cc_start: 0.8218 (mmm-85) cc_final: 0.7997 (mtp-110) REVERT: C 286 VAL cc_start: 0.4994 (OUTLIER) cc_final: 0.4624 (t) REVERT: C 347 GLU cc_start: 0.8562 (mt-10) cc_final: 0.7582 (mt-10) REVERT: C 425 GLU cc_start: 0.8032 (tt0) cc_final: 0.7747 (tt0) REVERT: C 468 ARG cc_start: 0.7849 (mtt180) cc_final: 0.7602 (mtt180) REVERT: C 480 GLU cc_start: 0.8263 (mp0) cc_final: 0.7837 (mp0) REVERT: C 620 TYR cc_start: 0.7554 (OUTLIER) cc_final: 0.7176 (t80) REVERT: D 58 MET cc_start: -0.0895 (mmp) cc_final: -0.1875 (mtt) REVERT: D 347 GLU cc_start: 0.8448 (mt-10) cc_final: 0.7987 (mt-10) REVERT: D 370 GLN cc_start: 0.7589 (mp10) cc_final: 0.7297 (mp10) REVERT: E 109 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7505 (mp0) REVERT: E 347 GLU cc_start: 0.8571 (mt-10) cc_final: 0.7399 (tt0) REVERT: E 480 GLU cc_start: 0.8263 (mp0) cc_final: 0.8061 (mp0) REVERT: E 481 GLU cc_start: 0.8277 (tt0) cc_final: 0.8064 (tt0) outliers start: 74 outliers final: 35 residues processed: 632 average time/residue: 1.6095 time to fit residues: 1138.5286 Evaluate side-chains 625 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 588 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 550 SER Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 200 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 201 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 189 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 560 ASN B 154 GLN B 360 HIS B 432 GLN B 459 ASN B 476 GLN C 405 ASN C 432 GLN D 221 GLN D 432 GLN D 560 ASN E 70 ASN E 432 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.160073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.139521 restraints weight = 30374.366| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.85 r_work: 0.3748 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23438 Z= 0.137 Angle : 0.545 6.892 31896 Z= 0.292 Chirality : 0.044 0.161 3639 Planarity : 0.004 0.049 4125 Dihedral : 4.880 51.564 3138 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.31 % Allowed : 12.37 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.16), residues: 2875 helix: 1.95 (0.20), residues: 734 sheet: 1.20 (0.16), residues: 944 loop : -0.37 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 359 HIS 0.004 0.001 HIS B 285 PHE 0.023 0.002 PHE C 168 TYR 0.021 0.002 TYR C 53 ARG 0.011 0.000 ARG E 521 Details of bonding type rmsd hydrogen bonds : bond 0.05927 ( 1059) hydrogen bonds : angle 4.50496 ( 2919) covalent geometry : bond 0.00297 (23438) covalent geometry : angle 0.54484 (31896) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 583 time to evaluate : 2.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LEU cc_start: 0.8538 (tt) cc_final: 0.8323 (tp) REVERT: A 347 GLU cc_start: 0.8511 (mt-10) cc_final: 0.7615 (mt-10) REVERT: A 425 GLU cc_start: 0.8166 (tt0) cc_final: 0.7929 (tt0) REVERT: A 480 GLU cc_start: 0.8375 (mp0) cc_final: 0.7750 (mp0) REVERT: A 481 GLU cc_start: 0.8292 (tt0) cc_final: 0.8086 (tt0) REVERT: C 286 VAL cc_start: 0.4971 (OUTLIER) cc_final: 0.4593 (t) REVERT: C 347 GLU cc_start: 0.8575 (mt-10) cc_final: 0.7702 (mt-10) REVERT: C 425 GLU cc_start: 0.8024 (tt0) cc_final: 0.7792 (tt0) REVERT: C 480 GLU cc_start: 0.8249 (mp0) cc_final: 0.7868 (mp0) REVERT: C 620 TYR cc_start: 0.7543 (OUTLIER) cc_final: 0.7189 (t80) REVERT: D 58 MET cc_start: -0.0945 (mmp) cc_final: -0.2101 (mtm) REVERT: D 269 VAL cc_start: 0.7744 (t) cc_final: 0.7461 (m) REVERT: D 347 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8233 (mt-10) REVERT: D 370 GLN cc_start: 0.7629 (mp10) cc_final: 0.7320 (mp10) REVERT: E 347 GLU cc_start: 0.8558 (mt-10) cc_final: 0.7386 (tt0) REVERT: E 480 GLU cc_start: 0.8312 (mp0) cc_final: 0.8095 (mp0) REVERT: E 481 GLU cc_start: 0.8329 (tt0) cc_final: 0.8117 (tt0) REVERT: E 620 TYR cc_start: 0.7781 (OUTLIER) cc_final: 0.6827 (t80) outliers start: 83 outliers final: 42 residues processed: 614 average time/residue: 1.6862 time to fit residues: 1163.2686 Evaluate side-chains 627 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 582 time to evaluate : 2.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 270 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 373 CYS Chi-restraints excluded: chain E residue 500 SER Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 606 GLN Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 83 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 259 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 271 optimal weight: 2.9990 chunk 149 optimal weight: 0.0570 chunk 263 optimal weight: 0.7980 overall best weight: 1.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN A 405 ASN A 409 GLN A 410 ASN A 432 GLN A 502 ASN B 344 GLN B 360 HIS B 432 GLN B 476 GLN C 144 HIS C 169 GLN C 432 GLN C 560 ASN D 221 GLN D 432 GLN E 70 ASN E 344 GLN E 432 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.157651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.137300 restraints weight = 30482.022| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 1.87 r_work: 0.3723 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 23438 Z= 0.178 Angle : 0.590 8.440 31896 Z= 0.317 Chirality : 0.045 0.181 3639 Planarity : 0.004 0.041 4125 Dihedral : 5.018 51.178 3138 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.79 % Allowed : 13.13 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.16), residues: 2875 helix: 1.83 (0.20), residues: 738 sheet: 1.05 (0.16), residues: 928 loop : -0.45 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 121 HIS 0.006 0.001 HIS B 204 PHE 0.031 0.002 PHE E 414 TYR 0.030 0.002 TYR C 53 ARG 0.011 0.000 ARG C 521 Details of bonding type rmsd hydrogen bonds : bond 0.06926 ( 1059) hydrogen bonds : angle 4.60245 ( 2919) covalent geometry : bond 0.00410 (23438) covalent geometry : angle 0.58985 (31896) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 580 time to evaluate : 2.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 GLU cc_start: 0.8545 (mt-10) cc_final: 0.7681 (mt-10) REVERT: A 425 GLU cc_start: 0.8200 (tt0) cc_final: 0.7942 (tt0) REVERT: A 480 GLU cc_start: 0.8397 (mp0) cc_final: 0.7759 (mp0) REVERT: A 481 GLU cc_start: 0.8351 (tt0) cc_final: 0.8103 (tt0) REVERT: A 515 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8593 (mp) REVERT: B 560 ASN cc_start: 0.8203 (t0) cc_final: 0.8000 (t0) REVERT: C 58 MET cc_start: 0.5236 (OUTLIER) cc_final: 0.4856 (mtt) REVERT: C 177 PRO cc_start: 0.7293 (Cg_endo) cc_final: 0.7089 (Cg_exo) REVERT: C 235 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7846 (pt) REVERT: C 286 VAL cc_start: 0.5161 (OUTLIER) cc_final: 0.4777 (t) REVERT: C 347 GLU cc_start: 0.8642 (mt-10) cc_final: 0.7787 (mt-10) REVERT: C 425 GLU cc_start: 0.8027 (tt0) cc_final: 0.7773 (tt0) REVERT: C 480 GLU cc_start: 0.8248 (mp0) cc_final: 0.7852 (mp0) REVERT: C 498 ARG cc_start: 0.6077 (OUTLIER) cc_final: 0.5795 (tpp-160) REVERT: C 620 TYR cc_start: 0.7612 (OUTLIER) cc_final: 0.7266 (t80) REVERT: D 58 MET cc_start: -0.0932 (mmp) cc_final: -0.2053 (mtm) REVERT: D 269 VAL cc_start: 0.7786 (t) cc_final: 0.7498 (m) REVERT: D 520 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8597 (mp) REVERT: E 347 GLU cc_start: 0.8612 (mt-10) cc_final: 0.7810 (mt-10) REVERT: E 468 ARG cc_start: 0.8270 (mtt180) cc_final: 0.8054 (mtt180) REVERT: E 480 GLU cc_start: 0.8362 (mp0) cc_final: 0.7986 (mp0) REVERT: E 566 ASP cc_start: 0.7465 (m-30) cc_final: 0.6761 (m-30) REVERT: E 620 TYR cc_start: 0.7874 (OUTLIER) cc_final: 0.6891 (t80) outliers start: 95 outliers final: 47 residues processed: 624 average time/residue: 1.5339 time to fit residues: 1076.9358 Evaluate side-chains 627 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 572 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 270 GLU Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 373 CYS Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 564 SER Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 46 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 182 optimal weight: 0.9980 chunk 245 optimal weight: 3.9990 chunk 227 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN A 409 GLN A 410 ASN B 360 HIS B 432 GLN B 476 GLN C 60 GLN C 169 GLN C 432 GLN C 560 ASN D 221 GLN D 432 GLN E 70 ASN E 432 GLN E 560 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.154609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.134739 restraints weight = 30204.655| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.85 r_work: 0.3679 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 23438 Z= 0.264 Angle : 0.680 8.625 31896 Z= 0.368 Chirality : 0.049 0.239 3639 Planarity : 0.005 0.046 4125 Dihedral : 5.373 52.016 3138 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.11 % Allowed : 14.29 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.16), residues: 2875 helix: 1.57 (0.20), residues: 737 sheet: 0.98 (0.17), residues: 889 loop : -0.65 (0.17), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 121 HIS 0.011 0.002 HIS B 204 PHE 0.036 0.003 PHE E 414 TYR 0.044 0.003 TYR C 53 ARG 0.013 0.001 ARG E 521 Details of bonding type rmsd hydrogen bonds : bond 0.08331 ( 1059) hydrogen bonds : angle 4.91045 ( 2919) covalent geometry : bond 0.00635 (23438) covalent geometry : angle 0.67974 (31896) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 591 time to evaluate : 2.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: A 116 ARG cc_start: 0.7165 (ttp80) cc_final: 0.6919 (ptt180) REVERT: A 235 LEU cc_start: 0.8541 (tt) cc_final: 0.8309 (tp) REVERT: A 248 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7840 (ptp-170) REVERT: A 347 GLU cc_start: 0.8544 (mt-10) cc_final: 0.7637 (mt-10) REVERT: A 425 GLU cc_start: 0.8194 (tt0) cc_final: 0.7960 (tt0) REVERT: A 480 GLU cc_start: 0.8420 (mp0) cc_final: 0.7771 (mp0) REVERT: A 481 GLU cc_start: 0.8359 (tt0) cc_final: 0.8126 (tt0) REVERT: C 58 MET cc_start: 0.6376 (OUTLIER) cc_final: 0.5876 (mtt) REVERT: C 110 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8098 (tm) REVERT: C 177 PRO cc_start: 0.7305 (Cg_endo) cc_final: 0.7078 (Cg_exo) REVERT: C 235 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7999 (pt) REVERT: C 286 VAL cc_start: 0.5308 (OUTLIER) cc_final: 0.4902 (t) REVERT: C 347 GLU cc_start: 0.8642 (mt-10) cc_final: 0.7781 (mt-10) REVERT: C 425 GLU cc_start: 0.8055 (tt0) cc_final: 0.7828 (tt0) REVERT: C 480 GLU cc_start: 0.8226 (mp0) cc_final: 0.7966 (mp0) REVERT: C 498 ARG cc_start: 0.6117 (OUTLIER) cc_final: 0.5841 (tpp-160) REVERT: C 620 TYR cc_start: 0.7738 (OUTLIER) cc_final: 0.7341 (t80) REVERT: D 58 MET cc_start: -0.0807 (mmp) cc_final: -0.1877 (mtm) REVERT: D 82 MET cc_start: 0.5720 (ptp) cc_final: 0.5416 (ptm) REVERT: D 269 VAL cc_start: 0.7884 (t) cc_final: 0.7626 (m) REVERT: D 370 GLN cc_start: 0.7927 (mp10) cc_final: 0.7530 (mp10) REVERT: D 520 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8641 (mp) REVERT: E 277 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7920 (mp10) REVERT: E 347 GLU cc_start: 0.8623 (mt-10) cc_final: 0.7521 (tt0) REVERT: E 468 ARG cc_start: 0.8211 (mtt180) cc_final: 0.8010 (mtt180) REVERT: E 480 GLU cc_start: 0.8341 (mp0) cc_final: 0.8131 (mp0) REVERT: E 620 TYR cc_start: 0.7918 (OUTLIER) cc_final: 0.7061 (t80) outliers start: 103 outliers final: 58 residues processed: 635 average time/residue: 1.4996 time to fit residues: 1068.9487 Evaluate side-chains 658 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 589 time to evaluate : 2.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 363 LYS Chi-restraints excluded: chain E residue 373 CYS Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 564 SER Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 62 optimal weight: 1.9990 chunk 204 optimal weight: 6.9990 chunk 100 optimal weight: 0.0870 chunk 16 optimal weight: 0.7980 chunk 275 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 201 optimal weight: 0.9990 chunk 273 optimal weight: 0.6980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 277 GLN A 344 GLN A 405 ASN A 409 GLN A 410 ASN B 360 HIS B 410 ASN B 432 GLN B 476 GLN C 169 GLN C 432 GLN C 560 ASN D 611 GLN E 70 ASN E 432 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.157439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.137805 restraints weight = 30525.102| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 1.81 r_work: 0.3728 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23438 Z= 0.124 Angle : 0.549 7.212 31896 Z= 0.293 Chirality : 0.043 0.181 3639 Planarity : 0.004 0.041 4125 Dihedral : 4.887 51.468 3136 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.99 % Allowed : 16.32 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.16), residues: 2875 helix: 2.01 (0.20), residues: 728 sheet: 0.93 (0.16), residues: 943 loop : -0.50 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 615 HIS 0.004 0.001 HIS B 285 PHE 0.023 0.001 PHE C 168 TYR 0.020 0.002 TYR E 300 ARG 0.013 0.000 ARG C 521 Details of bonding type rmsd hydrogen bonds : bond 0.05619 ( 1059) hydrogen bonds : angle 4.44640 ( 2919) covalent geometry : bond 0.00262 (23438) covalent geometry : angle 0.54855 (31896) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 577 time to evaluate : 2.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LEU cc_start: 0.8524 (tt) cc_final: 0.8305 (tp) REVERT: A 347 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7508 (tt0) REVERT: A 425 GLU cc_start: 0.8160 (tt0) cc_final: 0.7924 (tt0) REVERT: A 480 GLU cc_start: 0.8332 (mp0) cc_final: 0.7700 (mm-30) REVERT: A 481 GLU cc_start: 0.8344 (tt0) cc_final: 0.8108 (tt0) REVERT: C 58 MET cc_start: 0.6337 (OUTLIER) cc_final: 0.5922 (mtt) REVERT: C 177 PRO cc_start: 0.7313 (Cg_endo) cc_final: 0.7107 (Cg_exo) REVERT: C 235 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8001 (pt) REVERT: C 286 VAL cc_start: 0.5201 (OUTLIER) cc_final: 0.4848 (t) REVERT: C 347 GLU cc_start: 0.8564 (mt-10) cc_final: 0.7752 (mt-10) REVERT: C 425 GLU cc_start: 0.7999 (tt0) cc_final: 0.7758 (tt0) REVERT: C 480 GLU cc_start: 0.8221 (mp0) cc_final: 0.7971 (mp0) REVERT: C 498 ARG cc_start: 0.5974 (OUTLIER) cc_final: 0.5709 (tpp-160) REVERT: D 58 MET cc_start: -0.0717 (mmp) cc_final: -0.2001 (mtm) REVERT: D 269 VAL cc_start: 0.7781 (t) cc_final: 0.7510 (m) REVERT: E 245 PRO cc_start: 0.8279 (Cg_endo) cc_final: 0.8021 (Cg_exo) REVERT: E 347 GLU cc_start: 0.8556 (mt-10) cc_final: 0.7329 (tt0) REVERT: E 468 ARG cc_start: 0.8331 (mtt180) cc_final: 0.8082 (mtt180) REVERT: E 620 TYR cc_start: 0.7799 (OUTLIER) cc_final: 0.6850 (t80) outliers start: 75 outliers final: 36 residues processed: 610 average time/residue: 1.5773 time to fit residues: 1085.7056 Evaluate side-chains 612 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 571 time to evaluate : 2.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 363 LYS Chi-restraints excluded: chain E residue 373 CYS Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 606 GLN Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 238 optimal weight: 3.9990 chunk 281 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 105 optimal weight: 0.4980 chunk 272 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 241 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN A 405 ASN A 410 ASN A 502 ASN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS B 432 GLN B 476 GLN C 169 GLN C 206 GLN D 221 GLN D 432 GLN E 70 ASN E 432 GLN E 560 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.154045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.134640 restraints weight = 30395.756| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.81 r_work: 0.3690 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 23438 Z= 0.235 Angle : 0.654 9.859 31896 Z= 0.353 Chirality : 0.048 0.189 3639 Planarity : 0.005 0.050 4125 Dihedral : 5.186 51.209 3136 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.92 % Favored : 97.04 % Rotamer: Outliers : 3.27 % Allowed : 16.24 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.16), residues: 2875 helix: 1.66 (0.20), residues: 738 sheet: 0.87 (0.16), residues: 913 loop : -0.66 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 615 HIS 0.008 0.002 HIS B 204 PHE 0.027 0.002 PHE B 561 TYR 0.038 0.003 TYR C 53 ARG 0.010 0.001 ARG C 521 Details of bonding type rmsd hydrogen bonds : bond 0.07700 ( 1059) hydrogen bonds : angle 4.75760 ( 2919) covalent geometry : bond 0.00563 (23438) covalent geometry : angle 0.65366 (31896) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 574 time to evaluate : 2.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6730 (mmt180) REVERT: A 347 GLU cc_start: 0.8513 (mt-10) cc_final: 0.7631 (mt-10) REVERT: A 425 GLU cc_start: 0.8187 (tt0) cc_final: 0.7952 (tt0) REVERT: A 480 GLU cc_start: 0.8327 (mp0) cc_final: 0.7711 (mp0) REVERT: A 481 GLU cc_start: 0.8341 (tt0) cc_final: 0.8104 (tt0) REVERT: A 633 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8437 (mp) REVERT: C 58 MET cc_start: 0.6665 (OUTLIER) cc_final: 0.6272 (mtt) REVERT: C 177 PRO cc_start: 0.7304 (Cg_endo) cc_final: 0.7092 (Cg_exo) REVERT: C 235 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8047 (pt) REVERT: C 286 VAL cc_start: 0.5419 (OUTLIER) cc_final: 0.5062 (t) REVERT: C 347 GLU cc_start: 0.8630 (mt-10) cc_final: 0.7865 (mt-10) REVERT: C 480 GLU cc_start: 0.8228 (mp0) cc_final: 0.8028 (mp0) REVERT: C 498 ARG cc_start: 0.6092 (OUTLIER) cc_final: 0.5806 (tpp-160) REVERT: C 620 TYR cc_start: 0.7670 (OUTLIER) cc_final: 0.7219 (t80) REVERT: D 58 MET cc_start: -0.0660 (mmp) cc_final: -0.1844 (mtm) REVERT: D 86 ILE cc_start: 0.0487 (OUTLIER) cc_final: 0.0238 (pp) REVERT: D 269 VAL cc_start: 0.7916 (t) cc_final: 0.7667 (m) REVERT: D 370 GLN cc_start: 0.7900 (mp10) cc_final: 0.7538 (mp10) REVERT: E 347 GLU cc_start: 0.8606 (mt-10) cc_final: 0.7433 (mt-10) REVERT: E 620 TYR cc_start: 0.7919 (OUTLIER) cc_final: 0.6924 (t80) outliers start: 82 outliers final: 53 residues processed: 612 average time/residue: 1.4940 time to fit residues: 1028.1100 Evaluate side-chains 633 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 571 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 521 ARG Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 373 CYS Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 564 SER Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 148 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 232 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 228 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 193 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN A 405 ASN A 410 ASN B 360 HIS B 476 GLN C 60 GLN C 169 GLN C 432 GLN D 221 GLN D 432 GLN E 70 ASN E 432 GLN E 459 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.156818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.137577 restraints weight = 30377.283| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 1.80 r_work: 0.3736 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23438 Z= 0.127 Angle : 0.560 8.789 31896 Z= 0.296 Chirality : 0.043 0.180 3639 Planarity : 0.004 0.043 4125 Dihedral : 4.867 51.049 3136 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.47 % Allowed : 17.28 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.16), residues: 2875 helix: 1.97 (0.20), residues: 735 sheet: 0.85 (0.16), residues: 948 loop : -0.55 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 615 HIS 0.004 0.001 HIS B 285 PHE 0.025 0.001 PHE C 168 TYR 0.023 0.002 TYR E 300 ARG 0.008 0.000 ARG C 521 Details of bonding type rmsd hydrogen bonds : bond 0.05606 ( 1059) hydrogen bonds : angle 4.41221 ( 2919) covalent geometry : bond 0.00277 (23438) covalent geometry : angle 0.55968 (31896) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 571 time to evaluate : 2.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 GLU cc_start: 0.8483 (mt-10) cc_final: 0.7550 (tt0) REVERT: A 425 GLU cc_start: 0.8163 (tt0) cc_final: 0.7921 (tt0) REVERT: A 480 GLU cc_start: 0.8334 (mp0) cc_final: 0.7692 (mm-30) REVERT: A 481 GLU cc_start: 0.8334 (tt0) cc_final: 0.8096 (tt0) REVERT: C 58 MET cc_start: 0.6623 (OUTLIER) cc_final: 0.6226 (mtt) REVERT: C 235 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7990 (pt) REVERT: C 286 VAL cc_start: 0.5351 (OUTLIER) cc_final: 0.4985 (t) REVERT: C 347 GLU cc_start: 0.8578 (mt-10) cc_final: 0.7784 (mt-10) REVERT: C 480 GLU cc_start: 0.8238 (mp0) cc_final: 0.7994 (mp0) REVERT: C 498 ARG cc_start: 0.6017 (OUTLIER) cc_final: 0.5735 (tpp-160) REVERT: C 620 TYR cc_start: 0.7565 (OUTLIER) cc_final: 0.7170 (t80) REVERT: D 58 MET cc_start: -0.0710 (mmp) cc_final: -0.1956 (mtm) REVERT: D 86 ILE cc_start: 0.0470 (OUTLIER) cc_final: 0.0197 (pp) REVERT: D 370 GLN cc_start: 0.7872 (mp10) cc_final: 0.7494 (mp10) REVERT: E 245 PRO cc_start: 0.8265 (Cg_endo) cc_final: 0.8040 (Cg_exo) REVERT: E 347 GLU cc_start: 0.8544 (mt-10) cc_final: 0.7383 (tt0) REVERT: E 620 TYR cc_start: 0.7805 (OUTLIER) cc_final: 0.6868 (t80) REVERT: E 635 PHE cc_start: 0.8248 (m-80) cc_final: 0.8045 (m-80) outliers start: 62 outliers final: 35 residues processed: 600 average time/residue: 1.5173 time to fit residues: 1022.3524 Evaluate side-chains 608 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 566 time to evaluate : 2.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 373 CYS Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 606 GLN Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 232 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 257 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 chunk 196 optimal weight: 0.2980 chunk 114 optimal weight: 2.9990 chunk 186 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 173 optimal weight: 8.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 169 GLN A 344 GLN A 405 ASN A 410 ASN A 432 GLN A 502 ASN B 360 HIS B 476 GLN C 169 GLN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 GLN D 432 GLN E 70 ASN E 432 GLN E 560 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.153954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.134716 restraints weight = 30371.133| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.81 r_work: 0.3696 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3556 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23438 Z= 0.207 Angle : 0.633 9.612 31896 Z= 0.341 Chirality : 0.047 0.201 3639 Planarity : 0.005 0.043 4125 Dihedral : 5.087 50.966 3136 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.47 % Allowed : 17.52 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.16), residues: 2875 helix: 1.72 (0.20), residues: 738 sheet: 0.83 (0.16), residues: 934 loop : -0.66 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 615 HIS 0.006 0.001 HIS B 204 PHE 0.028 0.002 PHE C 168 TYR 0.031 0.002 TYR C 53 ARG 0.008 0.000 ARG C 521 Details of bonding type rmsd hydrogen bonds : bond 0.07289 ( 1059) hydrogen bonds : angle 4.67341 ( 2919) covalent geometry : bond 0.00488 (23438) covalent geometry : angle 0.63316 (31896) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 559 time to evaluate : 3.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 GLU cc_start: 0.8527 (mt-10) cc_final: 0.7641 (mt-10) REVERT: A 425 GLU cc_start: 0.8200 (tt0) cc_final: 0.7962 (tt0) REVERT: A 480 GLU cc_start: 0.8347 (mp0) cc_final: 0.7721 (mm-30) REVERT: A 481 GLU cc_start: 0.8358 (tt0) cc_final: 0.8113 (tt0) REVERT: C 58 MET cc_start: 0.6791 (OUTLIER) cc_final: 0.6375 (mtt) REVERT: C 235 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8030 (pt) REVERT: C 286 VAL cc_start: 0.5435 (OUTLIER) cc_final: 0.5057 (t) REVERT: C 347 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8300 (mt-10) REVERT: C 498 ARG cc_start: 0.6114 (OUTLIER) cc_final: 0.5815 (tpp-160) REVERT: C 620 TYR cc_start: 0.7676 (OUTLIER) cc_final: 0.7247 (t80) REVERT: D 58 MET cc_start: -0.0622 (mmp) cc_final: -0.1794 (mtm) REVERT: D 86 ILE cc_start: 0.0350 (OUTLIER) cc_final: 0.0027 (pp) REVERT: D 370 GLN cc_start: 0.7890 (mp10) cc_final: 0.7483 (mp10) REVERT: E 245 PRO cc_start: 0.8281 (Cg_endo) cc_final: 0.8058 (Cg_exo) REVERT: E 347 GLU cc_start: 0.8597 (mt-10) cc_final: 0.7433 (mt-10) REVERT: E 479 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7682 (mm-30) REVERT: E 620 TYR cc_start: 0.7909 (OUTLIER) cc_final: 0.6937 (t80) outliers start: 62 outliers final: 39 residues processed: 586 average time/residue: 1.9455 time to fit residues: 1291.6933 Evaluate side-chains 612 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 566 time to evaluate : 2.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 363 LYS Chi-restraints excluded: chain E residue 373 CYS Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 26 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 232 optimal weight: 3.9990 chunk 276 optimal weight: 0.7980 chunk 223 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN A 410 ASN B 360 HIS B 476 GLN C 169 GLN C 432 GLN D 154 GLN D 221 GLN D 432 GLN E 70 ASN E 432 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.154612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.135536 restraints weight = 30513.037| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.80 r_work: 0.3709 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23438 Z= 0.175 Angle : 0.605 9.201 31896 Z= 0.325 Chirality : 0.045 0.201 3639 Planarity : 0.004 0.043 4125 Dihedral : 5.033 51.152 3136 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.15 % Allowed : 18.32 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.16), residues: 2875 helix: 1.85 (0.20), residues: 729 sheet: 0.84 (0.16), residues: 933 loop : -0.66 (0.18), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 615 HIS 0.005 0.001 HIS B 285 PHE 0.026 0.002 PHE C 168 TYR 0.027 0.002 TYR C 53 ARG 0.007 0.000 ARG C 521 Details of bonding type rmsd hydrogen bonds : bond 0.06587 ( 1059) hydrogen bonds : angle 4.56641 ( 2919) covalent geometry : bond 0.00408 (23438) covalent geometry : angle 0.60510 (31896) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 568 time to evaluate : 2.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7392 (tm-30) cc_final: 0.7188 (tm-30) REVERT: A 347 GLU cc_start: 0.8493 (mt-10) cc_final: 0.7554 (tt0) REVERT: A 425 GLU cc_start: 0.8161 (tt0) cc_final: 0.7927 (tt0) REVERT: A 480 GLU cc_start: 0.8328 (mp0) cc_final: 0.7691 (mm-30) REVERT: A 481 GLU cc_start: 0.8354 (tt0) cc_final: 0.8109 (tt0) REVERT: C 58 MET cc_start: 0.6804 (mtt) cc_final: 0.6285 (mtm) REVERT: C 59 LYS cc_start: 0.7151 (mmtt) cc_final: 0.6921 (mmtt) REVERT: C 235 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8029 (pt) REVERT: C 286 VAL cc_start: 0.5433 (OUTLIER) cc_final: 0.5070 (t) REVERT: C 347 GLU cc_start: 0.8611 (mt-10) cc_final: 0.7806 (mt-10) REVERT: C 498 ARG cc_start: 0.6023 (OUTLIER) cc_final: 0.5753 (tpp-160) REVERT: C 620 TYR cc_start: 0.7637 (OUTLIER) cc_final: 0.7239 (t80) REVERT: D 58 MET cc_start: -0.0526 (mmp) cc_final: -0.1822 (mtm) REVERT: D 86 ILE cc_start: 0.0340 (OUTLIER) cc_final: 0.0014 (pp) REVERT: D 370 GLN cc_start: 0.7955 (mp10) cc_final: 0.7493 (mp10) REVERT: E 245 PRO cc_start: 0.8252 (Cg_endo) cc_final: 0.8044 (Cg_exo) REVERT: E 347 GLU cc_start: 0.8559 (mt-10) cc_final: 0.7397 (tt0) REVERT: E 479 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7719 (mm-30) REVERT: E 620 TYR cc_start: 0.7876 (OUTLIER) cc_final: 0.6888 (t80) outliers start: 54 outliers final: 38 residues processed: 592 average time/residue: 1.5330 time to fit residues: 1015.9874 Evaluate side-chains 612 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 568 time to evaluate : 2.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 521 ARG Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 363 LYS Chi-restraints excluded: chain E residue 373 CYS Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 27 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 180 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 282 optimal weight: 1.9990 chunk 254 optimal weight: 4.9990 chunk 242 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 276 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 344 GLN A 405 ASN A 410 ASN A 432 GLN B 360 HIS B 476 GLN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 GLN C 432 GLN D 154 GLN D 221 GLN D 432 GLN E 70 ASN E 432 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.155329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.136355 restraints weight = 30397.469| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 1.79 r_work: 0.3721 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23438 Z= 0.152 Angle : 0.583 9.214 31896 Z= 0.312 Chirality : 0.044 0.195 3639 Planarity : 0.004 0.044 4125 Dihedral : 4.911 50.779 3136 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.11 % Allowed : 18.44 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.16), residues: 2875 helix: 1.94 (0.20), residues: 728 sheet: 0.82 (0.16), residues: 941 loop : -0.62 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 615 HIS 0.004 0.001 HIS B 285 PHE 0.033 0.002 PHE C 168 TYR 0.023 0.002 TYR E 300 ARG 0.007 0.000 ARG C 521 Details of bonding type rmsd hydrogen bonds : bond 0.06073 ( 1059) hydrogen bonds : angle 4.47243 ( 2919) covalent geometry : bond 0.00344 (23438) covalent geometry : angle 0.58266 (31896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27680.14 seconds wall clock time: 474 minutes 59.44 seconds (28499.44 seconds total)