Starting phenix.real_space_refine on Tue Jun 17 12:10:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ekm_28207/06_2025/8ekm_28207.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ekm_28207/06_2025/8ekm_28207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ekm_28207/06_2025/8ekm_28207.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ekm_28207/06_2025/8ekm_28207.map" model { file = "/net/cci-nas-00/data/ceres_data/8ekm_28207/06_2025/8ekm_28207.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ekm_28207/06_2025/8ekm_28207.cif" } resolution = 3.56 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= 0.001 sd= 0.069 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 14 9.91 5 S 35 5.16 5 C 12275 2.51 5 N 3276 2.21 5 O 4172 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19772 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2820 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 14, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 2821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2821 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 14, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2819 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 14, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "D" Number of atoms: 2821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2821 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 14, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "E" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2827 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 14, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 22 Chain: "F" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2823 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 14, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "G" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2827 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 14, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 22 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} Chain: "F" 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: "G" 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: 12.25, per 1000 atoms: 0.62 Number of scatterers: 19772 At special positions: 0 Unit cell: (139.573, 139.573, 144.018, 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 14 19.99 S 35 16.00 O 4172 8.00 N 3276 7.00 C 12275 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: 4.19 Conformation dependent library (CDL) restraints added in 2.3 seconds 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4844 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 52 sheets defined 19.7% alpha, 35.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.44 Creating SS restraints... Processing helix chain 'A' and resid 229 through 234 Processing helix chain 'A' and resid 249 through 253 removed outlier: 3.991A pdb=" N GLY A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 463 through 473 removed outlier: 3.621A pdb=" N GLY A 473 " --> pdb=" O LYS A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 513 removed outlier: 4.860A pdb=" N SER A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLN A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 555 Processing helix chain 'A' and resid 581 through 594 removed outlier: 3.708A pdb=" N THR A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 234 Processing helix chain 'B' and resid 246 through 253 removed outlier: 3.897A pdb=" N GLU B 251 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 252 " --> pdb=" O PHE B 249 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY B 253 " --> pdb=" O ALA B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 463 through 473 removed outlier: 3.649A pdb=" N GLY B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 513 removed outlier: 4.761A pdb=" N SER B 508 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N GLN B 509 " --> pdb=" O ASP B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 581 through 594 removed outlier: 3.737A pdb=" N THR B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 603 Processing helix chain 'C' and resid 229 through 234 Processing helix chain 'C' and resid 247 through 253 removed outlier: 4.164A pdb=" N GLU C 251 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY C 253 " --> pdb=" O ALA C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 279 Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 463 through 473 removed outlier: 3.641A pdb=" N GLY C 473 " --> pdb=" O LYS C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 513 removed outlier: 4.821A pdb=" N SER C 508 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N GLN C 509 " --> pdb=" O ASP C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 555 Processing helix chain 'C' and resid 581 through 591 Processing helix chain 'D' and resid 229 through 234 Processing helix chain 'D' and resid 249 through 253 removed outlier: 4.149A pdb=" N GLY D 253 " --> pdb=" O ALA D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 279 Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 463 through 473 removed outlier: 3.678A pdb=" N GLY D 473 " --> pdb=" O LYS D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 513 removed outlier: 4.816A pdb=" N SER D 508 " --> pdb=" O SER D 504 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLN D 509 " --> pdb=" O ASP D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 555 Processing helix chain 'D' and resid 581 through 593 Processing helix chain 'D' and resid 599 through 603 Processing helix chain 'E' and resid 227 through 234 Processing helix chain 'E' and resid 246 through 253 removed outlier: 3.905A pdb=" N GLU E 251 " --> pdb=" O SER E 248 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN E 252 " --> pdb=" O PHE E 249 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY E 253 " --> pdb=" O ALA E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 279 Processing helix chain 'E' and resid 286 through 290 Processing helix chain 'E' and resid 463 through 473 removed outlier: 3.692A pdb=" N GLY E 473 " --> pdb=" O LYS E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'E' and resid 506 through 513 Processing helix chain 'E' and resid 546 through 555 Processing helix chain 'E' and resid 581 through 594 removed outlier: 3.773A pdb=" N THR E 594 " --> pdb=" O ASP E 590 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 234 Processing helix chain 'F' and resid 249 through 253 removed outlier: 4.131A pdb=" N GLY F 253 " --> pdb=" O ALA F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 279 Processing helix chain 'F' and resid 286 through 290 Processing helix chain 'F' and resid 463 through 473 removed outlier: 3.634A pdb=" N GLY F 473 " --> pdb=" O LYS F 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 502 through 505 Processing helix chain 'F' and resid 506 through 513 Processing helix chain 'F' and resid 546 through 555 Processing helix chain 'F' and resid 581 through 591 Processing helix chain 'G' and resid 227 through 234 Processing helix chain 'G' and resid 249 through 253 removed outlier: 4.155A pdb=" N GLY G 253 " --> pdb=" O ALA G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 279 Processing helix chain 'G' and resid 286 through 290 Processing helix chain 'G' and resid 463 through 473 removed outlier: 3.637A pdb=" N GLY G 473 " --> pdb=" O LYS G 469 " (cutoff:3.500A) Processing helix chain 'G' and resid 503 through 513 removed outlier: 4.783A pdb=" N SER G 508 " --> pdb=" O SER G 504 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLN G 509 " --> pdb=" O ASP G 505 " (cutoff:3.500A) Processing helix chain 'G' and resid 546 through 555 Processing helix chain 'G' and resid 581 through 593 Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 238 Processing sheet with id=AA2, first strand: chain 'A' and resid 301 through 311 removed outlier: 6.673A pdb=" N ASN A 392 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU A 307 " --> pdb=" O ASN A 390 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASN A 390 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ILE A 309 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N TYR A 388 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 314 through 331 Processing sheet with id=AA4, first strand: chain 'A' and resid 418 through 423 removed outlier: 6.835A pdb=" N TYR A 404 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN A 432 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 418 through 423 removed outlier: 7.059A pdb=" N LYS A 405 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY A 485 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR A 407 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N VAL A 483 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR A 409 " --> pdb=" O THR A 481 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AA7, first strand: chain 'A' and resid 526 through 531 removed outlier: 9.658A pdb=" N ILE A 611 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N SER A 516 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE A 613 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE A 518 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 558 through 559 removed outlier: 3.704A pdb=" N LEU A 564 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 235 through 238 Processing sheet with id=AB1, first strand: chain 'B' and resid 301 through 311 removed outlier: 6.657A pdb=" N ASN B 392 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU B 307 " --> pdb=" O ASN B 390 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN B 390 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ILE B 309 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N TYR B 388 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 418 through 423 removed outlier: 6.560A pdb=" N LEU B 412 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR B 421 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR B 410 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS B 423 " --> pdb=" O PRO B 408 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TYR B 404 " --> pdb=" O ASN B 432 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASN B 432 " --> pdb=" O TYR B 404 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 418 through 423 removed outlier: 6.560A pdb=" N LEU B 412 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR B 421 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR B 410 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS B 423 " --> pdb=" O PRO B 408 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LYS B 405 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLY B 485 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR B 407 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N VAL B 483 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR B 409 " --> pdb=" O THR B 481 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB5, first strand: chain 'B' and resid 526 through 531 removed outlier: 9.680A pdb=" N ILE B 611 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER B 516 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ILE B 613 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE B 518 " --> pdb=" O ILE B 613 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 558 through 559 removed outlier: 3.914A pdb=" N LEU B 564 " --> pdb=" O ILE B 571 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 235 through 238 Processing sheet with id=AB8, first strand: chain 'C' and resid 301 through 311 removed outlier: 6.612A pdb=" N ASN C 392 " --> pdb=" O GLU C 305 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU C 307 " --> pdb=" O ASN C 390 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN C 390 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ILE C 309 " --> pdb=" O TYR C 388 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N TYR C 388 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 418 through 423 removed outlier: 6.780A pdb=" N TYR C 404 " --> pdb=" O ASN C 432 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN C 432 " --> pdb=" O TYR C 404 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 418 through 423 removed outlier: 6.935A pdb=" N LYS C 405 " --> pdb=" O GLY C 485 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY C 485 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR C 407 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N VAL C 483 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N THR C 409 " --> pdb=" O THR C 481 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 489 through 490 Processing sheet with id=AC3, first strand: chain 'C' and resid 526 through 531 removed outlier: 9.636A pdb=" N ILE C 611 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER C 516 " --> pdb=" O ILE C 611 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ILE C 613 " --> pdb=" O SER C 516 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE C 518 " --> pdb=" O ILE C 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 558 through 559 removed outlier: 4.024A pdb=" N LEU C 564 " --> pdb=" O ILE C 571 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 235 through 238 Processing sheet with id=AC6, first strand: chain 'D' and resid 301 through 311 removed outlier: 6.683A pdb=" N ASN D 392 " --> pdb=" O GLU D 305 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU D 307 " --> pdb=" O ASN D 390 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN D 390 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE D 309 " --> pdb=" O TYR D 388 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR D 388 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 301 through 311 removed outlier: 6.683A pdb=" N ASN D 392 " --> pdb=" O GLU D 305 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU D 307 " --> pdb=" O ASN D 390 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN D 390 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE D 309 " --> pdb=" O TYR D 388 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR D 388 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ILE D 460 " --> pdb=" O ILE D 389 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 418 through 423 removed outlier: 6.830A pdb=" N TYR D 404 " --> pdb=" O ASN D 432 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASN D 432 " --> pdb=" O TYR D 404 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 418 through 423 removed outlier: 7.009A pdb=" N LYS D 405 " --> pdb=" O GLY D 485 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLY D 485 " --> pdb=" O LYS D 405 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR D 407 " --> pdb=" O VAL D 483 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL D 483 " --> pdb=" O THR D 407 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR D 409 " --> pdb=" O THR D 481 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AD2, first strand: chain 'D' and resid 526 through 531 removed outlier: 9.648A pdb=" N ILE D 611 " --> pdb=" O SER D 514 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N SER D 516 " --> pdb=" O ILE D 611 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ILE D 613 " --> pdb=" O SER D 516 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE D 518 " --> pdb=" O ILE D 613 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 558 through 559 removed outlier: 4.032A pdb=" N LEU D 564 " --> pdb=" O ILE D 571 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 235 through 238 Processing sheet with id=AD5, first strand: chain 'E' and resid 301 through 311 removed outlier: 5.231A pdb=" N VAL E 302 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYR E 396 " --> pdb=" O VAL E 302 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N MET E 304 " --> pdb=" O ARG E 394 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG E 394 " --> pdb=" O MET E 304 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 301 through 311 removed outlier: 5.231A pdb=" N VAL E 302 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYR E 396 " --> pdb=" O VAL E 302 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N MET E 304 " --> pdb=" O ARG E 394 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG E 394 " --> pdb=" O MET E 304 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE E 460 " --> pdb=" O ILE E 389 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 418 through 423 removed outlier: 6.776A pdb=" N TYR E 404 " --> pdb=" O ASN E 432 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ASN E 432 " --> pdb=" O TYR E 404 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 418 through 423 removed outlier: 6.891A pdb=" N LYS E 405 " --> pdb=" O GLY E 485 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLY E 485 " --> pdb=" O LYS E 405 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR E 407 " --> pdb=" O VAL E 483 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL E 483 " --> pdb=" O THR E 407 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR E 409 " --> pdb=" O THR E 481 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 489 through 490 Processing sheet with id=AE1, first strand: chain 'E' and resid 526 through 531 removed outlier: 9.670A pdb=" N ILE E 611 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N SER E 516 " --> pdb=" O ILE E 611 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ILE E 613 " --> pdb=" O SER E 516 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE E 518 " --> pdb=" O ILE E 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 558 through 559 removed outlier: 4.233A pdb=" N LEU E 564 " --> pdb=" O ILE E 571 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 235 through 238 Processing sheet with id=AE4, first strand: chain 'F' and resid 301 through 311 removed outlier: 6.661A pdb=" N ASN F 392 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU F 307 " --> pdb=" O ASN F 390 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASN F 390 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ILE F 309 " --> pdb=" O TYR F 388 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N TYR F 388 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 418 through 423 removed outlier: 6.822A pdb=" N TYR F 404 " --> pdb=" O ASN F 432 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASN F 432 " --> pdb=" O TYR F 404 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 418 through 423 removed outlier: 7.064A pdb=" N LYS F 405 " --> pdb=" O GLY F 485 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLY F 485 " --> pdb=" O LYS F 405 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR F 407 " --> pdb=" O VAL F 483 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL F 483 " --> pdb=" O THR F 407 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR F 409 " --> pdb=" O THR F 481 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 489 through 490 Processing sheet with id=AE8, first strand: chain 'F' and resid 526 through 531 removed outlier: 9.584A pdb=" N ILE F 611 " --> pdb=" O SER F 514 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N SER F 516 " --> pdb=" O ILE F 611 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ILE F 613 " --> pdb=" O SER F 516 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE F 518 " --> pdb=" O ILE F 613 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 558 through 559 removed outlier: 3.918A pdb=" N LEU F 564 " --> pdb=" O ILE F 571 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 235 through 238 Processing sheet with id=AF2, first strand: chain 'G' and resid 301 through 311 removed outlier: 6.662A pdb=" N ASN G 392 " --> pdb=" O GLU G 305 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU G 307 " --> pdb=" O ASN G 390 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASN G 390 " --> pdb=" O LEU G 307 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE G 309 " --> pdb=" O TYR G 388 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N TYR G 388 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 418 through 423 removed outlier: 6.787A pdb=" N TYR G 404 " --> pdb=" O ASN G 432 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASN G 432 " --> pdb=" O TYR G 404 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 418 through 423 removed outlier: 6.994A pdb=" N LYS G 405 " --> pdb=" O GLY G 485 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLY G 485 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR G 407 " --> pdb=" O VAL G 483 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N VAL G 483 " --> pdb=" O THR G 407 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR G 409 " --> pdb=" O THR G 481 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 489 through 490 Processing sheet with id=AF6, first strand: chain 'G' and resid 526 through 531 removed outlier: 9.678A pdb=" N ILE G 611 " --> pdb=" O SER G 514 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N SER G 516 " --> pdb=" O ILE G 611 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ILE G 613 " --> pdb=" O SER G 516 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE G 518 " --> pdb=" O ILE G 613 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 558 through 559 removed outlier: 3.726A pdb=" N LEU G 564 " --> pdb=" O ILE G 571 " (cutoff:3.500A) 820 hydrogen bonds defined for protein. 2133 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: 6.35 Time building geometry restraints manager: 5.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6625 1.34 - 1.46: 3857 1.46 - 1.58: 9513 1.58 - 1.69: 1 1.69 - 1.81: 63 Bond restraints: 20059 Sorted by residual: bond pdb=" CB PRO C 538 " pdb=" CG PRO C 538 " ideal model delta sigma weight residual 1.492 1.601 -0.109 5.00e-02 4.00e+02 4.72e+00 bond pdb=" CB ASP A 239 " pdb=" CG ASP A 239 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.55e+00 bond pdb=" CA ASN B 225 " pdb=" CB ASN B 225 " ideal model delta sigma weight residual 1.527 1.543 -0.016 1.36e-02 5.41e+03 1.44e+00 bond pdb=" CB ASP B 239 " pdb=" CG ASP B 239 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.43e+00 bond pdb=" CA ASP A 239 " pdb=" CB ASP A 239 " ideal model delta sigma weight residual 1.529 1.547 -0.018 1.58e-02 4.01e+03 1.29e+00 ... (remaining 20054 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 26484 1.44 - 2.89: 573 2.89 - 4.33: 162 4.33 - 5.77: 25 5.77 - 7.22: 9 Bond angle restraints: 27253 Sorted by residual: angle pdb=" N GLU D 539 " pdb=" CA GLU D 539 " pdb=" C GLU D 539 " ideal model delta sigma weight residual 114.62 107.55 7.07 1.14e+00 7.69e-01 3.84e+01 angle pdb=" N ASN B 225 " pdb=" CA ASN B 225 " pdb=" C ASN B 225 " ideal model delta sigma weight residual 111.30 104.74 6.56 1.43e+00 4.89e-01 2.11e+01 angle pdb=" CA PRO C 538 " pdb=" N PRO C 538 " pdb=" CD PRO C 538 " ideal model delta sigma weight residual 112.00 106.28 5.72 1.40e+00 5.10e-01 1.67e+01 angle pdb=" CA GLU D 539 " pdb=" C GLU D 539 " pdb=" N ASP D 540 " ideal model delta sigma weight residual 119.71 115.60 4.11 1.17e+00 7.31e-01 1.23e+01 angle pdb=" N ASP A 239 " pdb=" CA ASP A 239 " pdb=" C ASP A 239 " ideal model delta sigma weight residual 111.39 107.10 4.29 1.38e+00 5.25e-01 9.65e+00 ... (remaining 27248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 10245 17.93 - 35.86: 1524 35.86 - 53.79: 382 53.79 - 71.73: 45 71.73 - 89.66: 25 Dihedral angle restraints: 12221 sinusoidal: 4675 harmonic: 7546 Sorted by residual: dihedral pdb=" CA PRO F 538 " pdb=" C PRO F 538 " pdb=" N GLU F 539 " pdb=" CA GLU F 539 " ideal model delta harmonic sigma weight residual 180.00 155.67 24.33 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA PRO E 538 " pdb=" C PRO E 538 " pdb=" N GLU E 539 " pdb=" CA GLU E 539 " ideal model delta harmonic sigma weight residual 180.00 156.53 23.47 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA ASP C 228 " pdb=" C ASP C 228 " pdb=" N SER C 229 " pdb=" CA SER C 229 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 12218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2041 0.035 - 0.070: 716 0.070 - 0.105: 261 0.105 - 0.140: 135 0.140 - 0.176: 4 Chirality restraints: 3157 Sorted by residual: chirality pdb=" CB THR A 480 " pdb=" CA THR A 480 " pdb=" OG1 THR A 480 " pdb=" CG2 THR A 480 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CA ASP A 247 " pdb=" N ASP A 247 " pdb=" C ASP A 247 " pdb=" CB ASP A 247 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.63e-01 chirality pdb=" CB ILE F 299 " pdb=" CA ILE F 299 " pdb=" CG1 ILE F 299 " pdb=" CG2 ILE F 299 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 3154 not shown) Planarity restraints: 3568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 388 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C TYR B 388 " -0.057 2.00e-02 2.50e+03 pdb=" O TYR B 388 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE B 389 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 388 " 0.016 2.00e-02 2.50e+03 3.26e-02 1.07e+01 pdb=" C TYR A 388 " -0.056 2.00e-02 2.50e+03 pdb=" O TYR A 388 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE A 389 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR G 388 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.05e+01 pdb=" C TYR G 388 " -0.056 2.00e-02 2.50e+03 pdb=" O TYR G 388 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE G 389 " 0.019 2.00e-02 2.50e+03 ... (remaining 3565 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1764 2.74 - 3.28: 18561 3.28 - 3.82: 30132 3.82 - 4.36: 34954 4.36 - 4.90: 64783 Nonbonded interactions: 150194 Sorted by model distance: nonbonded pdb=" OD1 ASP B 222 " pdb="CA CA B 901 " model vdw 2.199 2.510 nonbonded pdb=" OD2 ASP F 282 " pdb=" OH TYR F 404 " model vdw 2.206 3.040 nonbonded pdb=" OD1 ASP E 222 " pdb="CA CA E 901 " model vdw 2.207 2.510 nonbonded pdb=" NE2 GLN C 425 " pdb=" OG1 THR C 451 " model vdw 2.214 3.120 nonbonded pdb=" OD1 ASP A 222 " pdb="CA CA A 902 " model vdw 2.215 2.510 ... (remaining 150189 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 217 or (resid 218 and (name N or name CA or name C or name \ O or name CB )) or resid 219 through 329 or (resid 330 and (name N or name CA o \ r name C or name O or name CB )) or resid 331 through 363 or (resid 364 and (nam \ e N or name CA or name C or name O or name CB )) or resid 365 through 416 or (re \ sid 417 and (name N or name CA or name C or name O or name CB )) or resid 418 th \ rough 617 or resid 901 through 902)) selection = (chain 'B' and (resid 217 through 227 or (resid 228 and (name N or name CA or na \ me C or name O or name CB )) or resid 229 through 329 or (resid 330 and (name N \ or name CA or name C or name O or name CB )) or resid 331 through 363 or (resid \ 364 and (name N or name CA or name C or name O or name CB )) or resid 365 throug \ h 384 or (resid 385 and (name N or name CA or name C or name O or name CB )) or \ resid 386 through 617 or resid 901 through 902)) selection = (chain 'C' and (resid 217 through 384 or (resid 385 and (name N or name CA or na \ me C or name O or name CB )) or resid 386 through 416 or (resid 417 and (name N \ or name CA or name C or name O or name CB )) or resid 418 through 617 or resid 9 \ 01 through 902)) selection = (chain 'D' and (resid 217 through 329 or (resid 330 and (name N or name CA or na \ me C or name O or name CB )) or resid 331 through 363 or (resid 364 and (name N \ or name CA or name C or name O or name CB )) or resid 365 through 384 or (resid \ 385 and (name N or name CA or name C or name O or name CB )) or resid 386 throug \ h 416 or (resid 417 and (name N or name CA or name C or name O or name CB )) or \ resid 418 through 617 or resid 901 through 902)) selection = (chain 'E' and (resid 217 or (resid 218 and (name N or name CA or name C or name \ O or name CB )) or resid 219 through 227 or (resid 228 and (name N or name CA o \ r name C or name O or name CB )) or resid 229 through 329 or (resid 330 and (nam \ e N or name CA or name C or name O or name CB )) or resid 331 through 363 or (re \ sid 364 and (name N or name CA or name C or name O or name CB )) or resid 365 th \ rough 384 or (resid 385 and (name N or name CA or name C or name O or name CB )) \ or resid 386 through 416 or (resid 417 and (name N or name CA or name C or name \ O or name CB )) or resid 418 through 617 or resid 901 through 902)) selection = (chain 'F' and (resid 217 or (resid 218 and (name N or name CA or name C or name \ O or name CB )) or resid 219 through 329 or (resid 330 and (name N or name CA o \ r name C or name O or name CB )) or resid 331 through 384 or (resid 385 and (nam \ e N or name CA or name C or name O or name CB )) or resid 386 through 416 or (re \ sid 417 and (name N or name CA or name C or name O or name CB )) or resid 418 th \ rough 617 or resid 901 through 902)) selection = (chain 'G' and (resid 217 or (resid 218 and (name N or name CA or name C or name \ O or name CB )) or resid 219 through 227 or (resid 228 and (name N or name CA o \ r name C or name O or name CB )) or resid 229 through 329 or (resid 330 and (nam \ e N or name CA or name C or name O or name CB )) or resid 331 through 363 or (re \ sid 364 and (name N or name CA or name C or name O or name CB )) or resid 365 th \ rough 384 or (resid 385 and (name N or name CA or name C or name O or name CB )) \ or resid 386 through 416 or (resid 417 and (name N or name CA or name C or name \ O or name CB )) or resid 418 through 617 or resid 901 through 902)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 4.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 43.310 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 : 0.002 0.109 20059 Z= 0.113 Angle : 0.587 7.217 27253 Z= 0.322 Chirality : 0.044 0.176 3157 Planarity : 0.004 0.081 3568 Dihedral : 17.683 89.657 7377 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 0.37 % Allowed : 39.05 % Favored : 60.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.15), residues: 2562 helix: -0.62 (0.24), residues: 448 sheet: -0.55 (0.19), residues: 686 loop : -2.13 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 245 HIS 0.001 0.000 HIS G 314 PHE 0.009 0.001 PHE A 281 TYR 0.013 0.001 TYR B 257 ARG 0.004 0.000 ARG F 290 Details of bonding type rmsd hydrogen bonds : bond 0.08070 ( 784) hydrogen bonds : angle 5.99780 ( 2133) covalent geometry : bond 0.00246 (20059) covalent geometry : angle 0.58736 (27253) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 270 time to evaluate : 2.075 Fit side-chains REVERT: B 466 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7928 (mt0) REVERT: B 511 ASP cc_start: 0.7727 (m-30) cc_final: 0.7300 (m-30) REVERT: F 498 THR cc_start: 0.9343 (p) cc_final: 0.9133 (p) outliers start: 8 outliers final: 4 residues processed: 277 average time/residue: 0.2627 time to fit residues: 119.2441 Evaluate side-chains 253 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 248 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain C residue 427 ASN Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain F residue 385 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 0.7980 chunk 196 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 104 optimal weight: 0.0570 chunk 203 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 151 optimal weight: 0.8980 chunk 235 optimal weight: 6.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN A 427 ASN B 265 ASN B 371 ASN B 382 ASN C 265 ASN ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN D 314 HIS D 431 ASN E 260 ASN F 314 HIS F 432 ASN F 586 ASN G 428 GLN G 583 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.133740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.105643 restraints weight = 29311.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.109099 restraints weight = 14821.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.111316 restraints weight = 9753.149| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20059 Z= 0.145 Angle : 0.562 6.476 27253 Z= 0.301 Chirality : 0.045 0.168 3157 Planarity : 0.003 0.039 3568 Dihedral : 5.139 54.601 2769 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 3.26 % Allowed : 36.30 % Favored : 60.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.16), residues: 2562 helix: -0.50 (0.24), residues: 448 sheet: -0.54 (0.19), residues: 686 loop : -1.99 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 245 HIS 0.002 0.001 HIS G 314 PHE 0.017 0.002 PHE F 281 TYR 0.011 0.001 TYR A 230 ARG 0.002 0.000 ARG E 394 Details of bonding type rmsd hydrogen bonds : bond 0.03205 ( 784) hydrogen bonds : angle 4.89272 ( 2133) covalent geometry : bond 0.00344 (20059) covalent geometry : angle 0.56206 (27253) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 270 time to evaluate : 2.068 Fit side-chains REVERT: A 239 ASP cc_start: 0.7883 (t0) cc_final: 0.7593 (t0) REVERT: A 304 MET cc_start: 0.8791 (tpp) cc_final: 0.8570 (tmm) REVERT: A 388 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.7761 (m-10) REVERT: B 225 ASN cc_start: 0.7668 (t0) cc_final: 0.7422 (t0) REVERT: B 263 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7864 (mt-10) REVERT: B 388 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.7610 (m-10) REVERT: C 385 GLU cc_start: 0.8124 (mp0) cc_final: 0.7915 (mp0) REVERT: C 388 TYR cc_start: 0.8834 (OUTLIER) cc_final: 0.7461 (m-10) REVERT: D 304 MET cc_start: 0.8791 (tmm) cc_final: 0.8468 (ttt) REVERT: E 394 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7561 (ttm170) REVERT: F 260 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8520 (t0) REVERT: F 314 HIS cc_start: 0.6135 (OUTLIER) cc_final: 0.5579 (t70) REVERT: F 388 TYR cc_start: 0.8924 (OUTLIER) cc_final: 0.7382 (m-10) REVERT: F 480 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.9022 (t) REVERT: F 533 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7460 (tttt) REVERT: G 225 ASN cc_start: 0.7792 (t0) cc_final: 0.7411 (t0) REVERT: G 388 TYR cc_start: 0.8892 (OUTLIER) cc_final: 0.7552 (m-10) REVERT: G 428 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.8768 (mp-120) outliers start: 71 outliers final: 34 residues processed: 322 average time/residue: 0.2657 time to fit residues: 139.5964 Evaluate side-chains 299 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 253 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 427 ASN Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 388 TYR Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 574 SER Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 394 ARG Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 535 LEU Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain F residue 260 ASN Chi-restraints excluded: chain F residue 314 HIS Chi-restraints excluded: chain F residue 388 TYR Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 533 LYS Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain G residue 388 TYR Chi-restraints excluded: chain G residue 428 GLN Chi-restraints excluded: chain G residue 535 LEU Chi-restraints excluded: chain G residue 605 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 170 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 134 optimal weight: 0.0000 chunk 9 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 3 optimal weight: 0.3980 chunk 220 optimal weight: 0.0040 chunk 198 optimal weight: 8.9990 overall best weight: 2.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 ASN B 428 GLN B 431 ASN ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 509 GLN F 314 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.131453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.102174 restraints weight = 29724.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.105609 restraints weight = 15287.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.107830 restraints weight = 10210.023| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 20059 Z= 0.216 Angle : 0.609 7.105 27253 Z= 0.326 Chirality : 0.047 0.170 3157 Planarity : 0.004 0.039 3568 Dihedral : 5.090 24.676 2758 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer: Outliers : 5.28 % Allowed : 34.97 % Favored : 59.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.16), residues: 2562 helix: -0.34 (0.26), residues: 406 sheet: -0.74 (0.19), residues: 707 loop : -2.03 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 245 HIS 0.018 0.002 HIS F 314 PHE 0.023 0.003 PHE F 281 TYR 0.013 0.001 TYR C 230 ARG 0.004 0.000 ARG F 290 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 784) hydrogen bonds : angle 4.81851 ( 2133) covalent geometry : bond 0.00520 (20059) covalent geometry : angle 0.60909 (27253) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 258 time to evaluate : 2.107 Fit side-chains REVERT: A 239 ASP cc_start: 0.7958 (t0) cc_final: 0.7691 (t0) REVERT: A 246 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6797 (tt0) REVERT: A 388 TYR cc_start: 0.8929 (OUTLIER) cc_final: 0.8150 (m-10) REVERT: B 225 ASN cc_start: 0.7867 (t0) cc_final: 0.7540 (t0) REVERT: B 263 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7851 (mt-10) REVERT: B 388 TYR cc_start: 0.8869 (OUTLIER) cc_final: 0.7519 (m-10) REVERT: C 388 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.7718 (m-10) REVERT: D 304 MET cc_start: 0.8802 (tmm) cc_final: 0.8513 (ttt) REVERT: D 417 ASP cc_start: 0.8005 (m-30) cc_final: 0.7550 (m-30) REVERT: E 385 GLU cc_start: 0.8243 (mp0) cc_final: 0.8029 (mp0) REVERT: E 394 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7793 (ttm170) REVERT: F 260 ASN cc_start: 0.8916 (OUTLIER) cc_final: 0.8611 (t0) REVERT: F 290 ARG cc_start: 0.8334 (ptm-80) cc_final: 0.8134 (ptm-80) REVERT: F 388 TYR cc_start: 0.8938 (OUTLIER) cc_final: 0.7622 (m-10) REVERT: F 480 THR cc_start: 0.9172 (OUTLIER) cc_final: 0.8954 (t) REVERT: F 533 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7476 (tttt) REVERT: G 225 ASN cc_start: 0.7942 (t0) cc_final: 0.7547 (t0) REVERT: G 388 TYR cc_start: 0.8923 (OUTLIER) cc_final: 0.7911 (m-10) outliers start: 115 outliers final: 66 residues processed: 351 average time/residue: 0.2746 time to fit residues: 157.5403 Evaluate side-chains 331 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 254 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 427 ASN Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 388 TYR Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 396 TYR Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 574 SER Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 394 ARG Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 535 LEU Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 260 ASN Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 388 TYR Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 396 TYR Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 533 LYS Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 388 TYR Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 535 LEU Chi-restraints excluded: chain G residue 605 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 179 optimal weight: 4.9990 chunk 183 optimal weight: 0.0770 chunk 134 optimal weight: 3.9990 chunk 216 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 199 optimal weight: 0.6980 chunk 78 optimal weight: 0.0980 chunk 3 optimal weight: 4.9990 chunk 159 optimal weight: 7.9990 chunk 180 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN B 428 GLN C 425 GLN C 428 GLN E 390 ASN F 586 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.134194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.104940 restraints weight = 29637.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.108511 restraints weight = 15024.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.110783 restraints weight = 9920.118| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20059 Z= 0.118 Angle : 0.545 7.273 27253 Z= 0.289 Chirality : 0.045 0.181 3157 Planarity : 0.003 0.038 3568 Dihedral : 4.808 24.277 2758 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 4.86 % Allowed : 34.92 % Favored : 60.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.16), residues: 2562 helix: -0.29 (0.25), residues: 406 sheet: -0.59 (0.19), residues: 707 loop : -1.93 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 503 HIS 0.002 0.000 HIS F 314 PHE 0.014 0.002 PHE G 281 TYR 0.010 0.001 TYR C 230 ARG 0.002 0.000 ARG F 290 Details of bonding type rmsd hydrogen bonds : bond 0.02990 ( 784) hydrogen bonds : angle 4.63448 ( 2133) covalent geometry : bond 0.00276 (20059) covalent geometry : angle 0.54454 (27253) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 284 time to evaluate : 2.041 Fit side-chains REVERT: A 225 ASN cc_start: 0.8101 (t0) cc_final: 0.7333 (t0) REVERT: A 239 ASP cc_start: 0.8004 (t0) cc_final: 0.7728 (t0) REVERT: A 244 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8029 (mtpp) REVERT: A 246 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6543 (tm-30) REVERT: A 281 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8190 (p90) REVERT: A 601 TYR cc_start: 0.9109 (OUTLIER) cc_final: 0.8694 (m-10) REVERT: B 217 GLU cc_start: 0.5556 (OUTLIER) cc_final: 0.5034 (mm-30) REVERT: B 225 ASN cc_start: 0.7921 (t0) cc_final: 0.7542 (t0) REVERT: B 263 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7883 (mt-10) REVERT: B 281 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.8224 (p90) REVERT: B 388 TYR cc_start: 0.8791 (OUTLIER) cc_final: 0.7506 (m-10) REVERT: C 225 ASN cc_start: 0.8108 (t0) cc_final: 0.7626 (t0) REVERT: C 244 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7953 (mtpp) REVERT: C 541 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7900 (mmtp) REVERT: D 239 ASP cc_start: 0.7612 (t0) cc_final: 0.7401 (t0) REVERT: D 281 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.8127 (p90) REVERT: D 417 ASP cc_start: 0.7967 (m-30) cc_final: 0.7502 (m-30) REVERT: D 535 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7292 (mp) REVERT: E 239 ASP cc_start: 0.7535 (t0) cc_final: 0.7286 (t0) REVERT: E 394 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7662 (ttm170) REVERT: F 225 ASN cc_start: 0.7802 (t0) cc_final: 0.7448 (t0) REVERT: F 260 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8560 (t0) REVERT: F 480 THR cc_start: 0.9163 (OUTLIER) cc_final: 0.8943 (t) REVERT: F 533 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7474 (tttt) REVERT: G 225 ASN cc_start: 0.7969 (t0) cc_final: 0.7515 (t0) REVERT: G 281 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.7843 (p90) REVERT: G 601 TYR cc_start: 0.9107 (OUTLIER) cc_final: 0.8786 (m-10) outliers start: 106 outliers final: 55 residues processed: 362 average time/residue: 0.2648 time to fit residues: 156.6035 Evaluate side-chains 342 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 269 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 601 TYR Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 541 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 601 TYR Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 390 ASN Chi-restraints excluded: chain E residue 394 ARG Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 535 LEU Chi-restraints excluded: chain E residue 561 ASP Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 260 ASN Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 533 LYS Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 535 LEU Chi-restraints excluded: chain G residue 601 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 141 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 208 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 117 optimal weight: 0.0670 chunk 58 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.130630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.101537 restraints weight = 30068.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.104977 restraints weight = 15366.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.107181 restraints weight = 10222.622| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 20059 Z= 0.229 Angle : 0.619 7.172 27253 Z= 0.330 Chirality : 0.047 0.176 3157 Planarity : 0.003 0.039 3568 Dihedral : 5.139 24.150 2758 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer: Outliers : 5.46 % Allowed : 34.69 % Favored : 59.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.15), residues: 2562 helix: -0.37 (0.25), residues: 406 sheet: -0.86 (0.20), residues: 651 loop : -1.98 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 375 HIS 0.002 0.001 HIS F 314 PHE 0.025 0.003 PHE G 281 TYR 0.013 0.002 TYR A 257 ARG 0.003 0.000 ARG F 290 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 784) hydrogen bonds : angle 4.74976 ( 2133) covalent geometry : bond 0.00552 (20059) covalent geometry : angle 0.61877 (27253) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 270 time to evaluate : 2.185 Fit side-chains REVERT: A 225 ASN cc_start: 0.8208 (t0) cc_final: 0.7453 (t0) REVERT: A 239 ASP cc_start: 0.8085 (t0) cc_final: 0.7848 (t0) REVERT: A 246 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6627 (tm-30) REVERT: A 388 TYR cc_start: 0.8846 (OUTLIER) cc_final: 0.8174 (m-10) REVERT: A 394 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7421 (ttm170) REVERT: A 552 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7896 (pt0) REVERT: A 559 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6817 (ttmt) REVERT: A 601 TYR cc_start: 0.9117 (OUTLIER) cc_final: 0.8766 (m-10) REVERT: B 217 GLU cc_start: 0.5614 (OUTLIER) cc_final: 0.5099 (mm-30) REVERT: B 225 ASN cc_start: 0.8006 (t0) cc_final: 0.7613 (t0) REVERT: B 263 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7872 (mt-10) REVERT: B 388 TYR cc_start: 0.8793 (OUTLIER) cc_final: 0.7519 (m-10) REVERT: C 225 ASN cc_start: 0.8169 (t0) cc_final: 0.7655 (t0) REVERT: C 385 GLU cc_start: 0.8139 (mp0) cc_final: 0.7923 (mp0) REVERT: C 388 TYR cc_start: 0.8855 (OUTLIER) cc_final: 0.7959 (m-10) REVERT: D 417 ASP cc_start: 0.8043 (m-30) cc_final: 0.7560 (m-30) REVERT: D 535 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7282 (mp) REVERT: E 394 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7936 (ttm170) REVERT: F 225 ASN cc_start: 0.7877 (t0) cc_final: 0.7540 (t0) REVERT: F 239 ASP cc_start: 0.7863 (t0) cc_final: 0.7656 (t0) REVERT: F 245 TRP cc_start: 0.8573 (t-100) cc_final: 0.8268 (t-100) REVERT: F 260 ASN cc_start: 0.8948 (OUTLIER) cc_final: 0.8646 (t0) REVERT: F 388 TYR cc_start: 0.8875 (OUTLIER) cc_final: 0.8282 (m-10) REVERT: F 480 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8935 (t) REVERT: F 533 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7476 (tttt) REVERT: G 225 ASN cc_start: 0.8087 (t0) cc_final: 0.7619 (t0) REVERT: G 281 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8449 (p90) REVERT: G 388 TYR cc_start: 0.8851 (OUTLIER) cc_final: 0.7463 (m-10) REVERT: G 601 TYR cc_start: 0.9087 (OUTLIER) cc_final: 0.8814 (m-10) outliers start: 119 outliers final: 80 residues processed: 361 average time/residue: 0.2752 time to fit residues: 162.6903 Evaluate side-chains 356 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 257 time to evaluate : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 394 ARG Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 427 ASN Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 559 LYS Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 601 TYR Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 388 TYR Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 549 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 574 SER Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 394 ARG Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 535 LEU Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 260 ASN Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain F residue 388 TYR Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 533 LYS Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 260 ASN Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 388 TYR Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 535 LEU Chi-restraints excluded: chain G residue 549 GLU Chi-restraints excluded: chain G residue 601 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 247 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 245 optimal weight: 0.8980 chunk 119 optimal weight: 0.3980 chunk 3 optimal weight: 5.9990 chunk 213 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 390 ASN F 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.132076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.102940 restraints weight = 29769.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.106413 restraints weight = 15216.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.108643 restraints weight = 10100.318| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20059 Z= 0.165 Angle : 0.580 6.761 27253 Z= 0.309 Chirality : 0.046 0.179 3157 Planarity : 0.003 0.038 3568 Dihedral : 5.025 24.193 2758 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 5.78 % Allowed : 35.20 % Favored : 59.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.15), residues: 2562 helix: -0.35 (0.25), residues: 406 sheet: -0.81 (0.20), residues: 651 loop : -1.96 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 375 HIS 0.001 0.000 HIS A 314 PHE 0.020 0.002 PHE G 281 TYR 0.011 0.001 TYR A 257 ARG 0.004 0.000 ARG F 290 Details of bonding type rmsd hydrogen bonds : bond 0.03447 ( 784) hydrogen bonds : angle 4.69036 ( 2133) covalent geometry : bond 0.00396 (20059) covalent geometry : angle 0.57985 (27253) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 272 time to evaluate : 2.629 Fit side-chains REVERT: A 225 ASN cc_start: 0.8178 (t0) cc_final: 0.7442 (t0) REVERT: A 239 ASP cc_start: 0.8096 (t0) cc_final: 0.7862 (t0) REVERT: A 244 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8039 (mtpp) REVERT: A 246 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6492 (tm-30) REVERT: A 394 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7350 (ttm170) REVERT: A 552 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7879 (pt0) REVERT: A 559 LYS cc_start: 0.7007 (OUTLIER) cc_final: 0.6796 (ttmt) REVERT: A 601 TYR cc_start: 0.9110 (OUTLIER) cc_final: 0.8752 (m-10) REVERT: B 217 GLU cc_start: 0.5610 (OUTLIER) cc_final: 0.5092 (mm-30) REVERT: B 225 ASN cc_start: 0.8008 (t0) cc_final: 0.7613 (t0) REVERT: B 263 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7865 (mt-10) REVERT: B 388 TYR cc_start: 0.8766 (OUTLIER) cc_final: 0.7539 (m-10) REVERT: C 225 ASN cc_start: 0.8197 (t0) cc_final: 0.7703 (t0) REVERT: C 244 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8051 (mtpp) REVERT: C 388 TYR cc_start: 0.8780 (OUTLIER) cc_final: 0.8026 (m-10) REVERT: C 541 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7934 (mmtp) REVERT: D 417 ASP cc_start: 0.7999 (m-30) cc_final: 0.7517 (m-30) REVERT: D 541 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7926 (mmtp) REVERT: E 394 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.7906 (ttm170) REVERT: F 225 ASN cc_start: 0.7872 (t0) cc_final: 0.7517 (t0) REVERT: F 239 ASP cc_start: 0.7944 (t0) cc_final: 0.7731 (t0) REVERT: F 245 TRP cc_start: 0.8546 (t-100) cc_final: 0.8220 (t-100) REVERT: F 260 ASN cc_start: 0.8942 (OUTLIER) cc_final: 0.8643 (t0) REVERT: F 388 TYR cc_start: 0.8832 (OUTLIER) cc_final: 0.8333 (m-10) REVERT: F 480 THR cc_start: 0.9169 (OUTLIER) cc_final: 0.8949 (t) REVERT: F 533 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7480 (tttt) REVERT: G 225 ASN cc_start: 0.8069 (t0) cc_final: 0.7587 (t0) REVERT: G 281 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8113 (p90) REVERT: G 286 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7932 (mtmm) REVERT: G 388 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.7384 (m-10) REVERT: G 601 TYR cc_start: 0.9071 (OUTLIER) cc_final: 0.8796 (m-10) outliers start: 126 outliers final: 86 residues processed: 371 average time/residue: 0.3308 time to fit residues: 200.1174 Evaluate side-chains 370 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 262 time to evaluate : 5.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 394 ARG Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 559 LYS Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 601 TYR Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 388 TYR Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 541 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 601 TYR Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 541 LYS Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 574 SER Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 390 ASN Chi-restraints excluded: chain E residue 394 ARG Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 535 LEU Chi-restraints excluded: chain E residue 561 ASP Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 260 ASN Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 388 TYR Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 533 LYS Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 260 ASN Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 286 LYS Chi-restraints excluded: chain G residue 388 TYR Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 535 LEU Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 578 LEU Chi-restraints excluded: chain G residue 601 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 246 optimal weight: 0.9980 chunk 160 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 chunk 54 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 238 optimal weight: 0.5980 chunk 156 optimal weight: 0.0060 chunk 167 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 212 optimal weight: 0.6980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.135253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.106291 restraints weight = 29375.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.109812 restraints weight = 15062.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.112062 restraints weight = 10021.816| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20059 Z= 0.100 Angle : 0.541 6.962 27253 Z= 0.287 Chirality : 0.044 0.184 3157 Planarity : 0.003 0.037 3568 Dihedral : 4.706 23.267 2758 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 4.31 % Allowed : 36.39 % Favored : 59.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.16), residues: 2562 helix: -0.23 (0.25), residues: 406 sheet: -0.50 (0.19), residues: 707 loop : -1.87 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 245 HIS 0.000 0.000 HIS A 314 PHE 0.011 0.002 PHE A 281 TYR 0.009 0.001 TYR D 297 ARG 0.004 0.000 ARG F 290 Details of bonding type rmsd hydrogen bonds : bond 0.02724 ( 784) hydrogen bonds : angle 4.52959 ( 2133) covalent geometry : bond 0.00227 (20059) covalent geometry : angle 0.54058 (27253) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 282 time to evaluate : 2.368 Fit side-chains REVERT: A 239 ASP cc_start: 0.8066 (t0) cc_final: 0.7814 (t0) REVERT: A 244 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8039 (mtpp) REVERT: A 246 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6424 (tm-30) REVERT: A 281 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.8081 (p90) REVERT: A 394 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.7494 (ttm170) REVERT: A 601 TYR cc_start: 0.9103 (OUTLIER) cc_final: 0.8732 (m-10) REVERT: B 217 GLU cc_start: 0.5642 (OUTLIER) cc_final: 0.5092 (mm-30) REVERT: B 225 ASN cc_start: 0.8051 (t0) cc_final: 0.7688 (t0) REVERT: B 263 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7891 (mt-10) REVERT: B 281 PHE cc_start: 0.8592 (OUTLIER) cc_final: 0.8092 (p90) REVERT: B 297 TYR cc_start: 0.8653 (t80) cc_final: 0.7821 (t80) REVERT: C 225 ASN cc_start: 0.8124 (t0) cc_final: 0.7806 (t0) REVERT: C 244 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7926 (mtpp) REVERT: C 541 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7881 (mmtp) REVERT: D 281 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.8129 (p90) REVERT: D 417 ASP cc_start: 0.7921 (m-30) cc_final: 0.7438 (m-30) REVERT: D 541 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7877 (mmtp) REVERT: E 225 ASN cc_start: 0.7974 (t0) cc_final: 0.7577 (t0) REVERT: E 394 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.6965 (ttm170) REVERT: F 225 ASN cc_start: 0.7867 (t0) cc_final: 0.7485 (t0) REVERT: F 239 ASP cc_start: 0.8012 (t0) cc_final: 0.7809 (t0) REVERT: F 260 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8542 (t0) REVERT: F 388 TYR cc_start: 0.8759 (OUTLIER) cc_final: 0.8477 (m-10) REVERT: F 480 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8978 (t) REVERT: F 533 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7461 (tttt) REVERT: G 225 ASN cc_start: 0.8040 (t0) cc_final: 0.7545 (t0) REVERT: G 286 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7859 (mtmm) REVERT: G 601 TYR cc_start: 0.9046 (OUTLIER) cc_final: 0.8753 (m-10) outliers start: 94 outliers final: 61 residues processed: 351 average time/residue: 0.3372 time to fit residues: 195.2688 Evaluate side-chains 347 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 267 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 394 ARG Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 601 TYR Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 541 LYS Chi-restraints excluded: chain C residue 549 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 601 TYR Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 541 LYS Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 394 ARG Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 476 ILE Chi-restraints excluded: chain E residue 535 LEU Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 260 ASN Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain F residue 388 TYR Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 533 LYS Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 286 LYS Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 535 LEU Chi-restraints excluded: chain G residue 601 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 225 optimal weight: 0.5980 chunk 141 optimal weight: 0.2980 chunk 54 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 221 optimal weight: 0.7980 chunk 130 optimal weight: 0.3980 chunk 215 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 235 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 GLN ** E 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.136842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.108051 restraints weight = 29112.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.111478 restraints weight = 15493.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.113691 restraints weight = 10485.847| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20059 Z= 0.100 Angle : 0.539 6.949 27253 Z= 0.285 Chirality : 0.044 0.232 3157 Planarity : 0.003 0.038 3568 Dihedral : 4.516 22.314 2758 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 4.45 % Allowed : 36.16 % Favored : 59.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.16), residues: 2562 helix: -0.10 (0.26), residues: 406 sheet: -0.30 (0.21), residues: 623 loop : -1.71 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 503 HIS 0.000 0.000 HIS G 314 PHE 0.016 0.002 PHE G 249 TYR 0.010 0.001 TYR D 506 ARG 0.002 0.000 ARG F 290 Details of bonding type rmsd hydrogen bonds : bond 0.02545 ( 784) hydrogen bonds : angle 4.42591 ( 2133) covalent geometry : bond 0.00230 (20059) covalent geometry : angle 0.53948 (27253) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 281 time to evaluate : 2.216 Fit side-chains REVERT: A 239 ASP cc_start: 0.8189 (t0) cc_final: 0.7899 (t0) REVERT: A 244 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7968 (mtpp) REVERT: A 246 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6393 (tm-30) REVERT: A 281 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.7961 (p90) REVERT: A 394 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7354 (ttm170) REVERT: A 601 TYR cc_start: 0.9030 (OUTLIER) cc_final: 0.8591 (m-10) REVERT: B 217 GLU cc_start: 0.5618 (OUTLIER) cc_final: 0.5065 (mm-30) REVERT: B 225 ASN cc_start: 0.8065 (t0) cc_final: 0.7645 (t0) REVERT: B 263 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7899 (mt-10) REVERT: B 281 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.7989 (p90) REVERT: B 297 TYR cc_start: 0.8600 (t80) cc_final: 0.7737 (t80) REVERT: C 225 ASN cc_start: 0.8104 (t0) cc_final: 0.7836 (t0) REVERT: C 244 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8047 (mtpp) REVERT: C 541 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7759 (mmtp) REVERT: D 281 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.8026 (p90) REVERT: D 410 THR cc_start: 0.9103 (p) cc_final: 0.8796 (t) REVERT: D 417 ASP cc_start: 0.8000 (m-30) cc_final: 0.7474 (m-30) REVERT: D 522 GLU cc_start: 0.7328 (mm-30) cc_final: 0.7045 (pm20) REVERT: D 541 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7738 (mmtp) REVERT: E 225 ASN cc_start: 0.7944 (t0) cc_final: 0.7517 (t0) REVERT: E 394 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7533 (ttm170) REVERT: E 445 SER cc_start: 0.8970 (m) cc_final: 0.8440 (p) REVERT: F 225 ASN cc_start: 0.7961 (t0) cc_final: 0.7617 (t0) REVERT: F 239 ASP cc_start: 0.8149 (t0) cc_final: 0.7891 (t0) REVERT: F 260 ASN cc_start: 0.8648 (OUTLIER) cc_final: 0.8342 (t0) REVERT: F 290 ARG cc_start: 0.8239 (ptm-80) cc_final: 0.7997 (ptm-80) REVERT: F 533 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7288 (tttt) REVERT: G 225 ASN cc_start: 0.8105 (t0) cc_final: 0.7590 (t0) REVERT: G 601 TYR cc_start: 0.8932 (OUTLIER) cc_final: 0.8553 (m-10) outliers start: 97 outliers final: 62 residues processed: 355 average time/residue: 0.2741 time to fit residues: 157.0101 Evaluate side-chains 347 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 269 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 394 ARG Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 601 TYR Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 541 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 601 TYR Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 541 LYS Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 394 ARG Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 476 ILE Chi-restraints excluded: chain E residue 535 LEU Chi-restraints excluded: chain E residue 561 ASP Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 260 ASN Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 533 LYS Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 535 LEU Chi-restraints excluded: chain G residue 601 TYR Chi-restraints excluded: chain G residue 605 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 93 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 159 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 227 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.132813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.104653 restraints weight = 29530.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.108077 restraints weight = 15035.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.110284 restraints weight = 9945.624| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20059 Z= 0.173 Angle : 0.589 7.419 27253 Z= 0.312 Chirality : 0.046 0.218 3157 Planarity : 0.003 0.036 3568 Dihedral : 4.804 22.419 2758 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 4.45 % Allowed : 36.21 % Favored : 59.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.16), residues: 2562 helix: -0.19 (0.26), residues: 406 sheet: -0.55 (0.20), residues: 651 loop : -1.81 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 503 HIS 0.001 0.000 HIS F 314 PHE 0.021 0.002 PHE G 281 TYR 0.012 0.001 TYR A 257 ARG 0.002 0.000 ARG F 290 Details of bonding type rmsd hydrogen bonds : bond 0.03289 ( 784) hydrogen bonds : angle 4.51267 ( 2133) covalent geometry : bond 0.00416 (20059) covalent geometry : angle 0.58912 (27253) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 273 time to evaluate : 2.150 Fit side-chains REVERT: A 239 ASP cc_start: 0.8091 (t0) cc_final: 0.7850 (t0) REVERT: A 244 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7993 (mtpp) REVERT: A 246 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6397 (tm-30) REVERT: A 394 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7318 (ttm170) REVERT: A 601 TYR cc_start: 0.9053 (OUTLIER) cc_final: 0.8635 (m-10) REVERT: B 217 GLU cc_start: 0.5669 (OUTLIER) cc_final: 0.5089 (mm-30) REVERT: B 225 ASN cc_start: 0.8024 (t0) cc_final: 0.7593 (t0) REVERT: B 263 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7890 (mt-10) REVERT: B 297 TYR cc_start: 0.8755 (t80) cc_final: 0.7996 (t80) REVERT: C 225 ASN cc_start: 0.8155 (t0) cc_final: 0.7838 (t0) REVERT: C 541 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7874 (mmtp) REVERT: D 417 ASP cc_start: 0.7996 (m-30) cc_final: 0.7494 (m-30) REVERT: D 541 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7887 (mmtp) REVERT: E 225 ASN cc_start: 0.7997 (t0) cc_final: 0.7589 (t0) REVERT: E 394 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7877 (ttm170) REVERT: F 225 ASN cc_start: 0.8022 (t0) cc_final: 0.7622 (t0) REVERT: F 260 ASN cc_start: 0.8900 (OUTLIER) cc_final: 0.8587 (t0) REVERT: F 533 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7460 (tttt) REVERT: G 225 ASN cc_start: 0.8087 (t0) cc_final: 0.7421 (t0) REVERT: G 281 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.7802 (p90) REVERT: G 601 TYR cc_start: 0.8982 (OUTLIER) cc_final: 0.8640 (m-10) outliers start: 97 outliers final: 73 residues processed: 347 average time/residue: 0.3348 time to fit residues: 188.6418 Evaluate side-chains 355 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 269 time to evaluate : 2.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 394 ARG Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 601 TYR Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 541 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 601 TYR Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 541 LYS Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 394 ARG Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 476 ILE Chi-restraints excluded: chain E residue 535 LEU Chi-restraints excluded: chain E residue 561 ASP Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 260 ASN Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 533 LYS Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 535 LEU Chi-restraints excluded: chain G residue 578 LEU Chi-restraints excluded: chain G residue 601 TYR Chi-restraints excluded: chain G residue 605 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 45 optimal weight: 0.5980 chunk 126 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 130 optimal weight: 0.2980 chunk 82 optimal weight: 0.5980 chunk 87 optimal weight: 0.4980 chunk 256 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 221 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 390 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.136290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.107772 restraints weight = 28843.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.111137 restraints weight = 15383.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.113316 restraints weight = 10440.446| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20059 Z= 0.105 Angle : 0.554 8.171 27253 Z= 0.293 Chirality : 0.044 0.206 3157 Planarity : 0.003 0.037 3568 Dihedral : 4.547 21.857 2758 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 3.95 % Allowed : 36.67 % Favored : 59.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.16), residues: 2562 helix: -0.11 (0.26), residues: 406 sheet: -0.27 (0.21), residues: 623 loop : -1.72 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 503 HIS 0.001 0.000 HIS B 314 PHE 0.014 0.002 PHE D 249 TYR 0.008 0.001 TYR A 257 ARG 0.001 0.000 ARG E 394 Details of bonding type rmsd hydrogen bonds : bond 0.02606 ( 784) hydrogen bonds : angle 4.41741 ( 2133) covalent geometry : bond 0.00246 (20059) covalent geometry : angle 0.55448 (27253) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 275 time to evaluate : 2.851 Fit side-chains REVERT: A 225 ASN cc_start: 0.7954 (t0) cc_final: 0.7558 (t0) REVERT: A 239 ASP cc_start: 0.8225 (t0) cc_final: 0.7930 (t0) REVERT: A 244 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.7954 (mtpp) REVERT: A 281 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7956 (p90) REVERT: A 394 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7379 (ttm170) REVERT: A 601 TYR cc_start: 0.9011 (OUTLIER) cc_final: 0.8542 (m-10) REVERT: B 217 GLU cc_start: 0.5638 (OUTLIER) cc_final: 0.5080 (mm-30) REVERT: B 225 ASN cc_start: 0.8027 (t0) cc_final: 0.7599 (t0) REVERT: B 263 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7908 (mt-10) REVERT: B 281 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.8000 (p90) REVERT: B 297 TYR cc_start: 0.8630 (t80) cc_final: 0.7800 (t80) REVERT: B 419 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8637 (mp) REVERT: C 225 ASN cc_start: 0.8129 (t0) cc_final: 0.7877 (t0) REVERT: C 244 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8051 (mtpp) REVERT: C 541 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7733 (mmtp) REVERT: D 225 ASN cc_start: 0.7523 (t0) cc_final: 0.7297 (t0) REVERT: D 281 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8026 (p90) REVERT: D 417 ASP cc_start: 0.7994 (m-30) cc_final: 0.7478 (m-30) REVERT: D 522 GLU cc_start: 0.7306 (mm-30) cc_final: 0.7044 (pm20) REVERT: D 541 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7715 (mmtp) REVERT: E 225 ASN cc_start: 0.7968 (t0) cc_final: 0.7543 (t0) REVERT: E 394 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7022 (ttm170) REVERT: E 445 SER cc_start: 0.8986 (m) cc_final: 0.8449 (p) REVERT: F 225 ASN cc_start: 0.7970 (t0) cc_final: 0.7619 (t0) REVERT: F 260 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8367 (t0) REVERT: F 533 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7291 (tttt) REVERT: G 225 ASN cc_start: 0.8092 (t0) cc_final: 0.7553 (t0) REVERT: G 601 TYR cc_start: 0.8902 (OUTLIER) cc_final: 0.8516 (m-10) outliers start: 86 outliers final: 64 residues processed: 345 average time/residue: 0.3893 time to fit residues: 215.3395 Evaluate side-chains 351 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 271 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 394 ARG Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 601 TYR Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 541 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 601 TYR Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 541 LYS Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 390 ASN Chi-restraints excluded: chain E residue 394 ARG Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 476 ILE Chi-restraints excluded: chain E residue 535 LEU Chi-restraints excluded: chain E residue 561 ASP Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 260 ASN Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 533 LYS Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 535 LEU Chi-restraints excluded: chain G residue 578 LEU Chi-restraints excluded: chain G residue 601 TYR Chi-restraints excluded: chain G residue 605 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 156 optimal weight: 0.6980 chunk 211 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 216 optimal weight: 7.9990 chunk 244 optimal weight: 3.9990 chunk 245 optimal weight: 2.9990 chunk 186 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.136045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.107334 restraints weight = 29165.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.110780 restraints weight = 15396.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.112947 restraints weight = 10344.021| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.120 20059 Z= 0.158 Angle : 0.721 59.165 27253 Z= 0.413 Chirality : 0.048 0.887 3157 Planarity : 0.003 0.037 3568 Dihedral : 4.548 21.864 2758 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 4.04 % Allowed : 36.39 % Favored : 59.57 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.16), residues: 2562 helix: -0.12 (0.25), residues: 406 sheet: -0.26 (0.21), residues: 623 loop : -1.72 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 503 HIS 0.001 0.000 HIS B 314 PHE 0.011 0.002 PHE A 281 TYR 0.009 0.001 TYR A 257 ARG 0.002 0.000 ARG C 529 Details of bonding type rmsd hydrogen bonds : bond 0.02731 ( 784) hydrogen bonds : angle 4.43813 ( 2133) covalent geometry : bond 0.00344 (20059) covalent geometry : angle 0.72114 (27253) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6877.14 seconds wall clock time: 125 minutes 11.82 seconds (7511.82 seconds total)