Starting phenix.real_space_refine on Sun Aug 24 12:37:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ekm_28207/08_2025/8ekm_28207.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ekm_28207/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ekm_28207/08_2025/8ekm_28207.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ekm_28207/08_2025/8ekm_28207.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ekm_28207/08_2025/8ekm_28207.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ekm_28207/08_2025/8ekm_28207.map" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASP:plan': 1, 'GLU:plan': 5, 'PHE: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: {'ASP:plan': 2, 'GLU:plan': 4, 'PHE:plan': 1} 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: {'ASP:plan': 2, 'GLU:plan': 4, 'PHE:plan': 1} 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: {'ASP:plan': 2, 'GLU:plan': 4, 'PHE:plan': 1} 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: {'GLU:plan': 4, 'PHE:plan': 1} 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: {'ASP:plan': 1, 'GLU:plan': 4, 'PHE: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: {'GLU:plan': 4, 'PHE:plan': 1} 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: 4.48, per 1000 atoms: 0.23 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: 1.44 Conformation dependent library (CDL) restraints added in 871.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.56 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: 3.62 Time building geometry restraints manager: 1.81 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 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 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 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 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 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 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 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: 0.000 Normalize map: mean=0, sd=1: 4.300 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: 0.030 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 18.330 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.980 ------------------------------------------------------------------------------- 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 : 8.96 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG F 290 TYR 0.013 0.001 TYR B 257 PHE 0.009 0.001 PHE A 281 TRP 0.015 0.002 TRP B 245 HIS 0.001 0.000 HIS G 314 Details of bonding type rmsd covalent geometry : bond 0.00246 (20059) covalent geometry : angle 0.58736 (27253) hydrogen bonds : bond 0.08070 ( 784) hydrogen bonds : angle 5.99780 ( 2133) *********************** 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 : 0.612 Fit side-chains 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: 0.1134 time to fit residues: 52.1401 Evaluate side-chains 252 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 248 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 ASN 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 197 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 258 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 B 397 ASN B 428 GLN 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 583 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.129057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.100084 restraints weight = 30009.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.103452 restraints weight = 15401.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.105615 restraints weight = 10279.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.106877 restraints weight = 8030.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.107784 restraints weight = 6942.265| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 20059 Z= 0.295 Angle : 0.685 7.597 27253 Z= 0.369 Chirality : 0.049 0.162 3157 Planarity : 0.004 0.042 3568 Dihedral : 5.532 35.958 2766 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 5.14 % Allowed : 35.29 % Favored : 59.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.24 (0.15), residues: 2562 helix: -0.45 (0.25), residues: 406 sheet: -0.90 (0.19), residues: 707 loop : -2.17 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 290 TYR 0.015 0.002 TYR A 257 PHE 0.031 0.003 PHE G 281 TRP 0.016 0.002 TRP B 245 HIS 0.001 0.001 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00710 (20059) covalent geometry : angle 0.68506 (27253) hydrogen bonds : bond 0.04473 ( 784) hydrogen bonds : angle 5.07576 ( 2133) *********************** 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 373 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 261 time to evaluate : 0.695 Fit side-chains REVERT: A 239 ASP cc_start: 0.7840 (t0) cc_final: 0.7570 (t0) REVERT: A 304 MET cc_start: 0.8756 (tpp) cc_final: 0.8544 (tmm) REVERT: A 388 TYR cc_start: 0.8975 (OUTLIER) cc_final: 0.8019 (m-10) REVERT: B 225 ASN cc_start: 0.7816 (t0) cc_final: 0.7429 (t0) REVERT: B 239 ASP cc_start: 0.7850 (t0) cc_final: 0.7580 (t0) REVERT: B 263 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7841 (mt-10) REVERT: B 388 TYR cc_start: 0.8915 (OUTLIER) cc_final: 0.7795 (m-10) REVERT: B 466 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8027 (mt0) REVERT: C 388 TYR cc_start: 0.8941 (OUTLIER) cc_final: 0.7550 (m-10) REVERT: D 304 MET cc_start: 0.8836 (tmm) cc_final: 0.8482 (ttt) REVERT: E 394 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.7842 (ttm170) REVERT: F 260 ASN cc_start: 0.8965 (OUTLIER) cc_final: 0.8674 (t0) REVERT: F 388 TYR cc_start: 0.8975 (OUTLIER) cc_final: 0.7473 (m-10) REVERT: F 480 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8954 (t) REVERT: F 514 SER cc_start: 0.9338 (m) cc_final: 0.9108 (m) REVERT: F 533 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7538 (tttt) REVERT: G 225 ASN cc_start: 0.7921 (t0) cc_final: 0.7558 (t0) REVERT: G 388 TYR cc_start: 0.8977 (OUTLIER) cc_final: 0.7734 (m-10) REVERT: G 394 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7911 (ttm170) REVERT: G 458 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7481 (ttt90) outliers start: 112 outliers final: 63 residues processed: 347 average time/residue: 0.1109 time to fit residues: 63.5988 Evaluate side-chains 327 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 251 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 365 THR Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 466 GLN 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 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 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 272 THR Chi-restraints excluded: chain E residue 365 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 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 272 THR Chi-restraints excluded: chain G residue 388 TYR Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 394 ARG Chi-restraints excluded: chain G residue 396 TYR Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 458 ARG Chi-restraints excluded: chain G residue 535 LEU Chi-restraints excluded: chain G residue 569 ILE 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 108 optimal weight: 0.8980 chunk 180 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 206 optimal weight: 7.9990 chunk 244 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 239 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 242 optimal weight: 0.2980 chunk 125 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 428 GLN C 425 GLN C 428 GLN E 390 ASN F 586 ASN G 428 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.133776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.104498 restraints weight = 29804.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.108056 restraints weight = 15073.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.110341 restraints weight = 9962.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.111771 restraints weight = 7744.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.112596 restraints weight = 6633.221| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.0986 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= 0.113 Angle : 0.555 6.254 27253 Z= 0.296 Chirality : 0.045 0.177 3157 Planarity : 0.003 0.040 3568 Dihedral : 4.937 24.796 2758 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 4.36 % Allowed : 36.12 % Favored : 59.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (0.16), residues: 2562 helix: -0.33 (0.25), residues: 406 sheet: -0.71 (0.19), residues: 707 loop : -2.00 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 394 TYR 0.011 0.001 TYR C 230 PHE 0.016 0.002 PHE A 281 TRP 0.006 0.001 TRP B 245 HIS 0.001 0.000 HIS G 314 Details of bonding type rmsd covalent geometry : bond 0.00261 (20059) covalent geometry : angle 0.55468 (27253) hydrogen bonds : bond 0.03105 ( 784) hydrogen bonds : angle 4.77760 ( 2133) *********************** 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 371 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 276 time to evaluate : 0.509 Fit side-chains REVERT: A 225 ASN cc_start: 0.8088 (t0) cc_final: 0.7356 (t0) REVERT: A 239 ASP cc_start: 0.7945 (t0) cc_final: 0.7668 (t0) REVERT: B 217 GLU cc_start: 0.5544 (OUTLIER) cc_final: 0.4999 (mm-30) REVERT: B 225 ASN cc_start: 0.7782 (t0) cc_final: 0.7455 (t0) REVERT: B 239 ASP cc_start: 0.7800 (t0) cc_final: 0.7533 (t0) REVERT: B 263 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7836 (mt-10) REVERT: B 388 TYR cc_start: 0.8821 (OUTLIER) cc_final: 0.7464 (m-10) REVERT: B 466 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7982 (mt0) REVERT: C 225 ASN cc_start: 0.8049 (t0) cc_final: 0.7591 (t0) REVERT: D 304 MET cc_start: 0.8747 (tmm) cc_final: 0.8516 (ttt) REVERT: D 417 ASP cc_start: 0.7909 (m-30) cc_final: 0.7427 (m-30) REVERT: E 394 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7623 (ttm170) REVERT: F 260 ASN cc_start: 0.8894 (OUTLIER) cc_final: 0.8626 (t0) REVERT: F 290 ARG cc_start: 0.8212 (ptm-80) cc_final: 0.7397 (ptm-80) REVERT: F 314 HIS cc_start: 0.6225 (OUTLIER) cc_final: 0.5703 (t70) REVERT: F 388 TYR cc_start: 0.8892 (OUTLIER) cc_final: 0.7967 (m-10) REVERT: F 480 THR cc_start: 0.9148 (OUTLIER) cc_final: 0.8942 (t) REVERT: F 533 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7517 (tttt) REVERT: G 225 ASN cc_start: 0.7930 (t0) cc_final: 0.7440 (t0) REVERT: G 281 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.7824 (p90) REVERT: G 388 TYR cc_start: 0.8862 (OUTLIER) cc_final: 0.7892 (m-10) REVERT: G 428 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.8805 (mp-120) outliers start: 95 outliers final: 47 residues processed: 351 average time/residue: 0.0995 time to fit residues: 57.2944 Evaluate side-chains 315 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 255 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 427 ASN Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 578 LEU 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 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 433 LEU Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain C residue 226 ILE 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 569 ILE Chi-restraints excluded: chain D residue 221 THR 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 489 THR Chi-restraints excluded: chain D residue 535 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 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 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 287 THR Chi-restraints excluded: chain F residue 308 ILE 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 221 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 388 TYR Chi-restraints excluded: chain G residue 428 GLN Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 535 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 114 optimal weight: 0.9990 chunk 80 optimal weight: 0.4980 chunk 116 optimal weight: 2.9990 chunk 19 optimal weight: 0.0470 chunk 128 optimal weight: 5.9990 chunk 196 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 243 optimal weight: 0.0010 chunk 201 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 overall best weight: 0.7088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN B 431 ASN ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 509 GLN ** E 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.134925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.105844 restraints weight = 29697.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.109376 restraints weight = 15173.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.111625 restraints weight = 10086.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.113022 restraints weight = 7860.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.113921 restraints weight = 6739.500| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20059 Z= 0.105 Angle : 0.537 6.223 27253 Z= 0.286 Chirality : 0.044 0.183 3157 Planarity : 0.003 0.038 3568 Dihedral : 4.733 23.894 2758 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 4.54 % Allowed : 35.06 % Favored : 60.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.86 (0.16), residues: 2562 helix: -0.27 (0.25), residues: 406 sheet: -0.58 (0.19), residues: 707 loop : -1.92 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 394 TYR 0.010 0.001 TYR D 297 PHE 0.012 0.002 PHE A 281 TRP 0.006 0.001 TRP C 503 HIS 0.001 0.000 HIS G 314 Details of bonding type rmsd covalent geometry : bond 0.00239 (20059) covalent geometry : angle 0.53704 (27253) hydrogen bonds : bond 0.02820 ( 784) hydrogen bonds : angle 4.61818 ( 2133) *********************** 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 380 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 281 time to evaluate : 0.610 Fit side-chains REVERT: A 225 ASN cc_start: 0.8072 (t0) cc_final: 0.7279 (t0) REVERT: A 239 ASP cc_start: 0.7980 (t0) cc_final: 0.7715 (t0) REVERT: A 246 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6370 (tm-30) REVERT: A 281 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.8054 (p90) REVERT: B 217 GLU cc_start: 0.5590 (OUTLIER) cc_final: 0.5020 (mm-30) REVERT: B 225 ASN cc_start: 0.7913 (t0) cc_final: 0.7552 (t0) REVERT: B 239 ASP cc_start: 0.7835 (t0) cc_final: 0.7569 (t0) REVERT: B 246 GLU cc_start: 0.8199 (pm20) cc_final: 0.7999 (pm20) REVERT: B 263 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: B 281 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.8029 (p90) REVERT: B 388 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.7480 (m-10) REVERT: C 225 ASN cc_start: 0.8101 (t0) cc_final: 0.7619 (t0) REVERT: C 244 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7946 (mtpp) REVERT: C 541 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7881 (mmtp) REVERT: D 239 ASP cc_start: 0.7534 (t0) cc_final: 0.7326 (t0) REVERT: D 417 ASP cc_start: 0.7958 (m-30) cc_final: 0.7465 (m-30) REVERT: E 394 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7535 (ttm170) REVERT: F 225 ASN cc_start: 0.7787 (t0) cc_final: 0.7421 (t0) REVERT: F 260 ASN cc_start: 0.8821 (OUTLIER) cc_final: 0.8541 (t0) REVERT: F 314 HIS cc_start: 0.6167 (OUTLIER) cc_final: 0.5590 (t70) REVERT: F 480 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8932 (t) REVERT: F 533 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7490 (tttt) REVERT: G 225 ASN cc_start: 0.7962 (t0) cc_final: 0.7504 (t0) REVERT: G 281 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.7829 (p90) REVERT: G 601 TYR cc_start: 0.9083 (OUTLIER) cc_final: 0.8751 (m-10) outliers start: 99 outliers final: 47 residues processed: 356 average time/residue: 0.1043 time to fit residues: 61.2108 Evaluate side-chains 329 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 267 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 263 GLU 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 400 THR Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain C residue 226 ILE 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 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 541 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 601 TYR 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 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 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 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 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 287 THR Chi-restraints excluded: chain F residue 314 HIS 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 G residue 221 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 389 ILE 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 54 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 chunk 249 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 105 optimal weight: 0.3980 chunk 82 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 163 optimal weight: 0.5980 chunk 158 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 118 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 466 GLN C 425 GLN C 428 GLN E 390 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.136498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.107913 restraints weight = 28914.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.111320 restraints weight = 15393.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.113524 restraints weight = 10418.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.114908 restraints weight = 8162.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.115796 restraints weight = 7026.932| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20059 Z= 0.096 Angle : 0.524 6.029 27253 Z= 0.277 Chirality : 0.044 0.193 3157 Planarity : 0.003 0.038 3568 Dihedral : 4.576 23.817 2758 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 4.13 % Allowed : 34.88 % Favored : 60.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.16), residues: 2562 helix: -0.19 (0.25), residues: 406 sheet: -0.42 (0.20), residues: 637 loop : -1.83 (0.15), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 290 TYR 0.008 0.001 TYR D 506 PHE 0.014 0.002 PHE F 249 TRP 0.006 0.001 TRP A 503 HIS 0.001 0.000 HIS G 314 Details of bonding type rmsd covalent geometry : bond 0.00219 (20059) covalent geometry : angle 0.52384 (27253) hydrogen bonds : bond 0.02597 ( 784) hydrogen bonds : angle 4.48602 ( 2133) *********************** 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 370 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 280 time to evaluate : 0.682 Fit side-chains REVERT: A 225 ASN cc_start: 0.8118 (t0) cc_final: 0.7653 (t0) REVERT: A 239 ASP cc_start: 0.8090 (t0) cc_final: 0.7793 (t0) REVERT: A 244 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.7976 (mtpp) REVERT: A 281 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.7785 (p90) REVERT: A 394 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7284 (ttm170) REVERT: A 601 TYR cc_start: 0.9074 (OUTLIER) cc_final: 0.8616 (m-10) REVERT: B 225 ASN cc_start: 0.7962 (t0) cc_final: 0.7571 (t0) REVERT: B 239 ASP cc_start: 0.7989 (t0) cc_final: 0.7713 (t0) REVERT: B 263 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7877 (mt-10) REVERT: C 225 ASN cc_start: 0.8109 (t0) cc_final: 0.7616 (t0) REVERT: C 244 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7858 (mtpp) REVERT: C 541 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7769 (mmtp) REVERT: D 239 ASP cc_start: 0.7741 (t0) cc_final: 0.7464 (t0) REVERT: D 281 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.8000 (p90) REVERT: D 417 ASP cc_start: 0.8050 (m-30) cc_final: 0.7583 (m-30) REVERT: D 522 GLU cc_start: 0.7297 (mm-30) cc_final: 0.7039 (pm20) REVERT: D 535 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7356 (mp) REVERT: D 541 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7795 (mmtp) REVERT: E 225 ASN cc_start: 0.7967 (t0) cc_final: 0.7536 (t0) REVERT: E 239 ASP cc_start: 0.7443 (t0) cc_final: 0.7215 (t0) REVERT: E 390 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8457 (p0) REVERT: E 394 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7433 (ttm170) REVERT: F 225 ASN cc_start: 0.7815 (t0) cc_final: 0.7411 (t0) REVERT: F 260 ASN cc_start: 0.8644 (OUTLIER) cc_final: 0.8372 (t0) REVERT: F 388 TYR cc_start: 0.8817 (OUTLIER) cc_final: 0.8448 (m-10) REVERT: F 405 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8395 (tttm) REVERT: F 480 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8944 (t) REVERT: G 225 ASN cc_start: 0.8061 (t0) cc_final: 0.7590 (t0) REVERT: G 286 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7611 (mtmm) REVERT: G 601 TYR cc_start: 0.9042 (OUTLIER) cc_final: 0.8659 (m-10) outliers start: 90 outliers final: 47 residues processed: 347 average time/residue: 0.1112 time to fit residues: 62.5216 Evaluate side-chains 332 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 267 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 281 PHE 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 B residue 226 ILE Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 311 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 433 LEU 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 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 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 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 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 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 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 405 LYS Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 535 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 113 optimal weight: 2.9990 chunk 177 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 185 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 225 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.133735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.104530 restraints weight = 29652.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.108045 restraints weight = 15080.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.110310 restraints weight = 10006.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.111703 restraints weight = 7769.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.112600 restraints weight = 6658.194| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20059 Z= 0.156 Angle : 0.558 6.593 27253 Z= 0.296 Chirality : 0.045 0.171 3157 Planarity : 0.003 0.036 3568 Dihedral : 4.749 22.936 2758 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 4.82 % Allowed : 34.79 % Favored : 60.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.16), residues: 2562 helix: -0.23 (0.25), residues: 406 sheet: -0.51 (0.20), residues: 637 loop : -1.85 (0.15), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 290 TYR 0.010 0.001 TYR A 257 PHE 0.019 0.002 PHE G 281 TRP 0.006 0.001 TRP A 375 HIS 0.000 0.000 HIS D 314 Details of bonding type rmsd covalent geometry : bond 0.00373 (20059) covalent geometry : angle 0.55837 (27253) hydrogen bonds : bond 0.03149 ( 784) hydrogen bonds : angle 4.50873 ( 2133) *********************** 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 374 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 269 time to evaluate : 0.750 Fit side-chains REVERT: A 239 ASP cc_start: 0.8021 (t0) cc_final: 0.7800 (t0) REVERT: A 244 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8052 (mtpp) REVERT: A 281 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.8408 (p90) REVERT: A 394 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7324 (ttm170) REVERT: A 601 TYR cc_start: 0.9082 (OUTLIER) cc_final: 0.8725 (m-10) REVERT: B 217 GLU cc_start: 0.5626 (OUTLIER) cc_final: 0.5061 (mm-30) REVERT: B 225 ASN cc_start: 0.7998 (t0) cc_final: 0.7589 (t0) REVERT: B 239 ASP cc_start: 0.7919 (t0) cc_final: 0.7689 (t0) REVERT: B 263 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7877 (mt-10) REVERT: B 281 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.8350 (p90) REVERT: B 388 TYR cc_start: 0.8786 (OUTLIER) cc_final: 0.7572 (m-10) REVERT: C 225 ASN cc_start: 0.8134 (t0) cc_final: 0.7828 (t0) REVERT: C 244 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7932 (mtpp) REVERT: C 388 TYR cc_start: 0.8777 (OUTLIER) cc_final: 0.8037 (m-10) REVERT: C 541 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7892 (mmtp) REVERT: D 417 ASP cc_start: 0.7949 (m-30) cc_final: 0.7575 (m-30) REVERT: D 535 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7216 (mp) REVERT: D 541 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7860 (mmtp) REVERT: E 394 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7813 (ttm170) REVERT: F 225 ASN cc_start: 0.7836 (t0) cc_final: 0.7438 (t0) REVERT: F 260 ASN cc_start: 0.8854 (OUTLIER) cc_final: 0.8577 (t0) REVERT: F 388 TYR cc_start: 0.8827 (OUTLIER) cc_final: 0.8490 (m-10) REVERT: F 480 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8947 (t) REVERT: F 533 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7501 (tttt) REVERT: G 225 ASN cc_start: 0.8086 (t0) cc_final: 0.7586 (t0) REVERT: G 281 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8197 (p90) REVERT: G 388 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.7391 (m-10) REVERT: G 458 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7579 (ttt90) REVERT: G 601 TYR cc_start: 0.9013 (OUTLIER) cc_final: 0.8706 (m-10) outliers start: 105 outliers final: 68 residues processed: 347 average time/residue: 0.1207 time to fit residues: 68.5100 Evaluate side-chains 352 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 262 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 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 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 226 ILE Chi-restraints excluded: chain B residue 263 GLU 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 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 433 LEU 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 226 ILE Chi-restraints excluded: chain C residue 244 LYS 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 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 240 LEU Chi-restraints excluded: chain D residue 260 ASN 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 400 THR Chi-restraints excluded: chain D residue 419 LEU 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 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 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 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 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 287 THR 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 G residue 221 THR Chi-restraints excluded: chain G residue 260 ASN 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 396 TYR Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 458 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 50 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 118 optimal weight: 0.3980 chunk 201 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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** E 390 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.134168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.104884 restraints weight = 29603.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.108410 restraints weight = 15062.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.110700 restraints weight = 9985.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112168 restraints weight = 7741.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.112925 restraints weight = 6612.261| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20059 Z= 0.134 Angle : 0.553 6.505 27253 Z= 0.294 Chirality : 0.045 0.178 3157 Planarity : 0.003 0.036 3568 Dihedral : 4.733 22.805 2758 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 4.77 % Allowed : 34.74 % Favored : 60.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.16), residues: 2562 helix: -0.24 (0.25), residues: 406 sheet: -0.57 (0.20), residues: 651 loop : -1.79 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 290 TYR 0.010 0.001 TYR A 257 PHE 0.016 0.002 PHE D 281 TRP 0.006 0.001 TRP A 375 HIS 0.000 0.000 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00320 (20059) covalent geometry : angle 0.55328 (27253) hydrogen bonds : bond 0.03019 ( 784) hydrogen bonds : angle 4.49235 ( 2133) *********************** 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 382 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 278 time to evaluate : 0.846 Fit side-chains REVERT: A 239 ASP cc_start: 0.8035 (t0) cc_final: 0.7805 (t0) REVERT: A 244 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8042 (mtpp) REVERT: A 281 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8189 (p90) REVERT: A 394 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7490 (ttm170) REVERT: A 601 TYR cc_start: 0.9063 (OUTLIER) cc_final: 0.8698 (m-10) REVERT: B 217 GLU cc_start: 0.5636 (OUTLIER) cc_final: 0.5068 (mm-30) REVERT: B 225 ASN cc_start: 0.7984 (t0) cc_final: 0.7581 (t0) REVERT: B 239 ASP cc_start: 0.7924 (t0) cc_final: 0.7698 (t0) REVERT: B 263 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7864 (mt-10) REVERT: B 281 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8260 (p90) REVERT: B 297 TYR cc_start: 0.8688 (t80) cc_final: 0.7905 (t80) REVERT: B 388 TYR cc_start: 0.8754 (OUTLIER) cc_final: 0.7531 (m-10) REVERT: C 225 ASN cc_start: 0.8126 (t0) cc_final: 0.7817 (t0) REVERT: C 244 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7908 (mtpp) REVERT: C 541 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7901 (mmtp) REVERT: D 417 ASP cc_start: 0.7950 (m-30) cc_final: 0.7531 (m-30) REVERT: D 535 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7350 (mp) REVERT: D 541 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7889 (mmtp) REVERT: E 225 ASN cc_start: 0.7953 (t0) cc_final: 0.7532 (t0) REVERT: E 394 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7805 (ttm170) REVERT: F 225 ASN cc_start: 0.7915 (t0) cc_final: 0.7524 (t0) REVERT: F 239 ASP cc_start: 0.7646 (t0) cc_final: 0.7438 (t0) REVERT: F 260 ASN cc_start: 0.8880 (OUTLIER) cc_final: 0.8588 (t0) REVERT: F 290 ARG cc_start: 0.8294 (ptm-80) cc_final: 0.7496 (ptm-80) REVERT: F 388 TYR cc_start: 0.8800 (OUTLIER) cc_final: 0.8541 (m-10) REVERT: F 480 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8955 (t) REVERT: F 533 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7491 (tttt) REVERT: G 225 ASN cc_start: 0.8105 (t0) cc_final: 0.7604 (t0) REVERT: G 281 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.7846 (p90) REVERT: G 286 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7877 (mtmm) REVERT: G 601 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.8656 (m-10) outliers start: 104 outliers final: 71 residues processed: 353 average time/residue: 0.1064 time to fit residues: 61.8442 Evaluate side-chains 359 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 268 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 281 PHE Chi-restraints excluded: chain A residue 379 LEU 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 476 ILE Chi-restraints excluded: chain A residue 552 GLU 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 226 ILE Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 278 SER 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 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 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 549 GLU Chi-restraints excluded: chain C residue 569 ILE 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 281 PHE 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 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 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 287 THR 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 563 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 389 ILE Chi-restraints excluded: chain G residue 396 TYR Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 452 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 33 optimal weight: 4.9990 chunk 225 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 chunk 157 optimal weight: 8.9990 chunk 118 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 52 optimal weight: 0.0570 overall best weight: 0.5500 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.136674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.108005 restraints weight = 28915.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.111375 restraints weight = 15426.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.113587 restraints weight = 10463.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.114971 restraints weight = 8244.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.115766 restraints weight = 7103.573| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20059 Z= 0.100 Angle : 0.537 5.978 27253 Z= 0.285 Chirality : 0.044 0.226 3157 Planarity : 0.003 0.036 3568 Dihedral : 4.529 21.739 2758 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 4.22 % Allowed : 35.47 % Favored : 60.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.16), residues: 2562 helix: -0.15 (0.25), residues: 406 sheet: -0.27 (0.21), residues: 623 loop : -1.67 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 290 TYR 0.008 0.001 TYR E 388 PHE 0.016 0.002 PHE D 281 TRP 0.007 0.001 TRP B 503 HIS 0.000 0.000 HIS E 314 Details of bonding type rmsd covalent geometry : bond 0.00228 (20059) covalent geometry : angle 0.53701 (27253) hydrogen bonds : bond 0.02573 ( 784) hydrogen bonds : angle 4.40553 ( 2133) *********************** 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 373 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 281 time to evaluate : 0.590 Fit side-chains REVERT: A 239 ASP cc_start: 0.8157 (t0) cc_final: 0.7879 (t0) REVERT: A 244 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.7966 (mtpp) REVERT: A 394 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7254 (ttm170) REVERT: A 601 TYR cc_start: 0.9010 (OUTLIER) cc_final: 0.8547 (m-10) REVERT: B 217 GLU cc_start: 0.5614 (OUTLIER) cc_final: 0.5056 (mm-30) REVERT: B 225 ASN cc_start: 0.8042 (t0) cc_final: 0.7629 (t0) REVERT: B 239 ASP cc_start: 0.8050 (t0) cc_final: 0.7833 (t0) REVERT: B 263 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7875 (mt-10) REVERT: B 281 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7906 (p90) REVERT: B 297 TYR cc_start: 0.8573 (t80) cc_final: 0.7615 (t80) REVERT: C 225 ASN cc_start: 0.8110 (t0) cc_final: 0.7831 (t0) REVERT: C 244 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7839 (mtpp) REVERT: C 541 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7765 (mmtp) REVERT: D 410 THR cc_start: 0.9101 (p) cc_final: 0.8782 (t) REVERT: D 417 ASP cc_start: 0.8043 (m-30) cc_final: 0.7582 (m-30) REVERT: D 522 GLU cc_start: 0.7283 (mm-30) cc_final: 0.7046 (pm20) REVERT: D 535 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7304 (mp) REVERT: D 541 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7790 (mmtp) REVERT: E 225 ASN cc_start: 0.7986 (t0) cc_final: 0.7543 (t0) REVERT: E 304 MET cc_start: 0.8828 (tmm) cc_final: 0.8586 (tpp) REVERT: E 390 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.8256 (p0) REVERT: E 394 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.6906 (ttm170) REVERT: E 445 SER cc_start: 0.8979 (m) cc_final: 0.8444 (p) REVERT: F 225 ASN cc_start: 0.7942 (t0) cc_final: 0.7591 (t0) REVERT: F 239 ASP cc_start: 0.7826 (t0) cc_final: 0.7558 (t0) REVERT: F 260 ASN cc_start: 0.8652 (OUTLIER) cc_final: 0.8370 (t0) REVERT: F 290 ARG cc_start: 0.8262 (ptm-80) cc_final: 0.7655 (ptm-80) REVERT: G 225 ASN cc_start: 0.8150 (t0) cc_final: 0.7633 (t0) REVERT: G 281 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.7611 (p90) REVERT: G 286 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7612 (mtmm) REVERT: G 601 TYR cc_start: 0.8898 (OUTLIER) cc_final: 0.8523 (m-10) outliers start: 92 outliers final: 56 residues processed: 350 average time/residue: 0.1170 time to fit residues: 66.8777 Evaluate side-chains 340 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 268 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 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 263 GLU 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 476 ILE 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 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 281 PHE 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 535 LEU 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 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 272 THR Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 260 ASN Chi-restraints excluded: chain G residue 281 PHE 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 569 ILE 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 1 optimal weight: 0.0770 chunk 119 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 227 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 186 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- 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 = 0.3577 r_free = 0.3577 target = 0.136614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.107777 restraints weight = 28845.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.111150 restraints weight = 15519.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.113329 restraints weight = 10590.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.114712 restraints weight = 8349.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.115363 restraints weight = 7210.610| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20059 Z= 0.109 Angle : 0.546 8.460 27253 Z= 0.287 Chirality : 0.045 0.207 3157 Planarity : 0.003 0.035 3568 Dihedral : 4.516 21.491 2758 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 4.13 % Allowed : 35.80 % Favored : 60.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.16), residues: 2562 helix: -0.13 (0.25), residues: 406 sheet: -0.25 (0.21), residues: 623 loop : -1.65 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 290 TYR 0.009 0.001 TYR D 506 PHE 0.019 0.002 PHE D 249 TRP 0.007 0.001 TRP B 503 HIS 0.000 0.000 HIS G 314 Details of bonding type rmsd covalent geometry : bond 0.00256 (20059) covalent geometry : angle 0.54632 (27253) hydrogen bonds : bond 0.02650 ( 784) hydrogen bonds : angle 4.38268 ( 2133) *********************** 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 356 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 266 time to evaluate : 0.828 Fit side-chains REVERT: A 239 ASP cc_start: 0.8177 (t0) cc_final: 0.7905 (t0) REVERT: A 244 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.7976 (mtpp) REVERT: A 394 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7277 (ttm170) REVERT: A 601 TYR cc_start: 0.9003 (OUTLIER) cc_final: 0.8544 (m-10) REVERT: B 217 GLU cc_start: 0.5587 (OUTLIER) cc_final: 0.5060 (mm-30) REVERT: B 225 ASN cc_start: 0.8076 (t0) cc_final: 0.7642 (t0) REVERT: B 239 ASP cc_start: 0.8075 (t0) cc_final: 0.7869 (t0) REVERT: B 263 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7877 (mt-10) REVERT: B 281 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.7992 (p90) REVERT: B 297 TYR cc_start: 0.8586 (t80) cc_final: 0.7682 (t80) REVERT: C 225 ASN cc_start: 0.8107 (t0) cc_final: 0.7822 (t0) REVERT: C 244 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7847 (mtpp) REVERT: C 541 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7765 (mmtp) REVERT: D 410 THR cc_start: 0.9108 (p) cc_final: 0.8778 (t) REVERT: D 417 ASP cc_start: 0.8053 (m-30) cc_final: 0.7595 (m-30) REVERT: D 535 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7330 (mp) REVERT: D 541 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7780 (mmtp) REVERT: E 225 ASN cc_start: 0.7983 (t0) cc_final: 0.7525 (t0) REVERT: E 304 MET cc_start: 0.8830 (tmm) cc_final: 0.8596 (tpp) REVERT: E 394 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7028 (ttm170) REVERT: E 445 SER cc_start: 0.8980 (m) cc_final: 0.8450 (p) REVERT: F 225 ASN cc_start: 0.7970 (t0) cc_final: 0.7604 (t0) REVERT: F 239 ASP cc_start: 0.7921 (t0) cc_final: 0.7658 (t0) REVERT: F 260 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.8371 (t0) REVERT: F 290 ARG cc_start: 0.8264 (ptm-80) cc_final: 0.7655 (ptm-80) REVERT: G 225 ASN cc_start: 0.8145 (t0) cc_final: 0.7642 (t0) REVERT: G 281 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.7637 (p90) REVERT: G 286 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7634 (mtmm) REVERT: G 601 TYR cc_start: 0.8907 (OUTLIER) cc_final: 0.8527 (m-10) outliers start: 90 outliers final: 63 residues processed: 333 average time/residue: 0.1218 time to fit residues: 66.4297 Evaluate side-chains 343 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 265 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 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 263 GLU 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 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 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 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 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 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 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 281 PHE Chi-restraints excluded: chain E residue 389 ILE 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 272 THR Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 476 ILE 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 260 ASN Chi-restraints excluded: chain G residue 281 PHE 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 569 ILE 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 107 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 120 optimal weight: 0.5980 chunk 50 optimal weight: 10.0000 chunk 165 optimal weight: 4.9990 chunk 159 optimal weight: 0.0970 chunk 123 optimal weight: 7.9990 chunk 203 optimal weight: 0.5980 chunk 209 optimal weight: 0.0050 overall best weight: 0.4392 ------------------------------------------------------------------------------- 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 = 0.3602 r_free = 0.3602 target = 0.138713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.109710 restraints weight = 28911.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.113155 restraints weight = 15538.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.115354 restraints weight = 10588.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.116744 restraints weight = 8352.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.117585 restraints weight = 7202.455| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20059 Z= 0.097 Angle : 0.537 8.497 27253 Z= 0.283 Chirality : 0.044 0.197 3157 Planarity : 0.003 0.036 3568 Dihedral : 4.346 20.321 2758 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 3.44 % Allowed : 36.30 % Favored : 60.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.16), residues: 2562 helix: 0.03 (0.26), residues: 399 sheet: -0.14 (0.21), residues: 637 loop : -1.60 (0.15), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 290 TYR 0.007 0.001 TYR D 261 PHE 0.014 0.002 PHE D 249 TRP 0.007 0.001 TRP B 503 HIS 0.000 0.000 HIS C 314 Details of bonding type rmsd covalent geometry : bond 0.00224 (20059) covalent geometry : angle 0.53741 (27253) hydrogen bonds : bond 0.02377 ( 784) hydrogen bonds : angle 4.32630 ( 2133) ********************** 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 355 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 280 time to evaluate : 0.563 Fit side-chains REVERT: A 225 ASN cc_start: 0.7996 (t0) cc_final: 0.7351 (t0) REVERT: A 239 ASP cc_start: 0.8166 (t0) cc_final: 0.7866 (t0) REVERT: A 244 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7963 (mtpp) REVERT: A 394 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7211 (ttm170) REVERT: A 601 TYR cc_start: 0.8946 (OUTLIER) cc_final: 0.8482 (m-10) REVERT: B 217 GLU cc_start: 0.5558 (OUTLIER) cc_final: 0.5046 (mm-30) REVERT: B 225 ASN cc_start: 0.7991 (t0) cc_final: 0.7534 (t0) REVERT: B 263 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7860 (mt-10) REVERT: B 281 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.7957 (p90) REVERT: B 297 TYR cc_start: 0.8586 (t80) cc_final: 0.7601 (t80) REVERT: C 225 ASN cc_start: 0.8070 (t0) cc_final: 0.7619 (t0) REVERT: C 244 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7832 (mtpp) REVERT: C 495 GLN cc_start: 0.8058 (mp10) cc_final: 0.7120 (tt0) REVERT: C 541 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7753 (mmtp) REVERT: D 410 THR cc_start: 0.9084 (p) cc_final: 0.8758 (t) REVERT: D 417 ASP cc_start: 0.8006 (m-30) cc_final: 0.7555 (m-30) REVERT: D 522 GLU cc_start: 0.7246 (mm-30) cc_final: 0.7020 (pm20) REVERT: D 535 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7376 (mp) REVERT: D 541 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7756 (mmtp) REVERT: E 225 ASN cc_start: 0.7915 (t0) cc_final: 0.7450 (t0) REVERT: E 304 MET cc_start: 0.8759 (tmm) cc_final: 0.8558 (tpp) REVERT: E 390 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8391 (p0) REVERT: E 445 SER cc_start: 0.8955 (m) cc_final: 0.8445 (p) REVERT: F 225 ASN cc_start: 0.7965 (t0) cc_final: 0.7583 (t0) REVERT: F 239 ASP cc_start: 0.7990 (t0) cc_final: 0.7742 (t0) REVERT: G 225 ASN cc_start: 0.8097 (t0) cc_final: 0.7640 (t0) REVERT: G 281 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.7648 (p90) REVERT: G 286 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7629 (mtmm) REVERT: G 601 TYR cc_start: 0.8898 (OUTLIER) cc_final: 0.8517 (m-10) outliers start: 75 outliers final: 53 residues processed: 338 average time/residue: 0.1211 time to fit residues: 67.3375 Evaluate side-chains 338 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 271 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 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 263 GLU 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 476 ILE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 272 THR 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 311 THR 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 535 LEU 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 574 SER 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 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 272 THR Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 476 ILE 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 260 ASN Chi-restraints excluded: chain G residue 281 PHE 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 569 ILE 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 179 optimal weight: 3.9990 chunk 166 optimal weight: 0.7980 chunk 175 optimal weight: 2.9990 chunk 118 optimal weight: 0.0060 chunk 19 optimal weight: 0.0370 chunk 132 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.6676 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.138467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.109479 restraints weight = 28952.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.112935 restraints weight = 15601.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.115166 restraints weight = 10617.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.116536 restraints weight = 8353.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.117415 restraints weight = 7190.182| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.158 20059 Z= 0.139 Angle : 0.714 59.200 27253 Z= 0.410 Chirality : 0.048 1.133 3157 Planarity : 0.003 0.036 3568 Dihedral : 4.345 20.278 2758 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 3.44 % Allowed : 36.35 % Favored : 60.21 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.16), residues: 2562 helix: 0.03 (0.26), residues: 399 sheet: -0.13 (0.21), residues: 637 loop : -1.59 (0.15), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 290 TYR 0.007 0.001 TYR D 261 PHE 0.014 0.002 PHE D 281 TRP 0.006 0.001 TRP B 503 HIS 0.001 0.000 HIS C 314 Details of bonding type rmsd covalent geometry : bond 0.00296 (20059) covalent geometry : angle 0.71386 (27253) hydrogen bonds : bond 0.02441 ( 784) hydrogen bonds : angle 4.34865 ( 2133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3069.30 seconds wall clock time: 53 minutes 54.39 seconds (3234.39 seconds total)