Starting phenix.real_space_refine on Tue Oct 15 06:46:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekm_28207/10_2024/8ekm_28207.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekm_28207/10_2024/8ekm_28207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekm_28207/10_2024/8ekm_28207.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekm_28207/10_2024/8ekm_28207.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekm_28207/10_2024/8ekm_28207.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekm_28207/10_2024/8ekm_28207.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.069 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 14 9.91 5 S 35 5.16 5 C 12275 2.51 5 N 3276 2.21 5 O 4172 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 19772 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2820 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 14, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 2821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2821 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 14, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2819 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 14, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "D" Number of atoms: 2821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2821 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 14, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "E" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2827 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 14, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 22 Chain: "F" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2823 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 14, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "G" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2827 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 14, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.15, per 1000 atoms: 0.61 Number of scatterers: 19772 At special positions: 0 Unit cell: (139.573, 139.573, 144.018, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 14 19.99 S 35 16.00 O 4172 8.00 N 3276 7.00 C 12275 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.54 Conformation dependent library (CDL) restraints added in 2.6 seconds 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4844 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 52 sheets defined 19.7% alpha, 35.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 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: 7.27 Time building geometry restraints manager: 5.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6625 1.34 - 1.46: 3857 1.46 - 1.58: 9513 1.58 - 1.69: 1 1.69 - 1.81: 63 Bond restraints: 20059 Sorted by residual: bond pdb=" CB PRO C 538 " pdb=" CG PRO C 538 " ideal model delta sigma weight residual 1.492 1.601 -0.109 5.00e-02 4.00e+02 4.72e+00 bond pdb=" CB ASP A 239 " pdb=" CG ASP A 239 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.55e+00 bond pdb=" CA ASN B 225 " pdb=" CB ASN B 225 " ideal model delta sigma weight residual 1.527 1.543 -0.016 1.36e-02 5.41e+03 1.44e+00 bond pdb=" CB ASP B 239 " pdb=" CG ASP B 239 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.43e+00 bond pdb=" CA ASP A 239 " pdb=" CB ASP A 239 " ideal model delta sigma weight residual 1.529 1.547 -0.018 1.58e-02 4.01e+03 1.29e+00 ... (remaining 20054 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 26484 1.44 - 2.89: 573 2.89 - 4.33: 162 4.33 - 5.77: 25 5.77 - 7.22: 9 Bond angle restraints: 27253 Sorted by residual: angle pdb=" N GLU D 539 " pdb=" CA GLU D 539 " pdb=" C GLU D 539 " ideal model delta sigma weight residual 114.62 107.55 7.07 1.14e+00 7.69e-01 3.84e+01 angle pdb=" N ASN B 225 " pdb=" CA ASN B 225 " pdb=" C ASN B 225 " ideal model delta sigma weight residual 111.30 104.74 6.56 1.43e+00 4.89e-01 2.11e+01 angle pdb=" CA PRO C 538 " pdb=" N PRO C 538 " pdb=" CD PRO C 538 " ideal model delta sigma weight residual 112.00 106.28 5.72 1.40e+00 5.10e-01 1.67e+01 angle pdb=" CA GLU D 539 " pdb=" C GLU D 539 " pdb=" N ASP D 540 " ideal model delta sigma weight residual 119.71 115.60 4.11 1.17e+00 7.31e-01 1.23e+01 angle pdb=" N ASP A 239 " pdb=" CA ASP A 239 " pdb=" C ASP A 239 " ideal model delta sigma weight residual 111.39 107.10 4.29 1.38e+00 5.25e-01 9.65e+00 ... (remaining 27248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 10245 17.93 - 35.86: 1524 35.86 - 53.79: 382 53.79 - 71.73: 45 71.73 - 89.66: 25 Dihedral angle restraints: 12221 sinusoidal: 4675 harmonic: 7546 Sorted by residual: dihedral pdb=" CA PRO F 538 " pdb=" C PRO F 538 " pdb=" N GLU F 539 " pdb=" CA GLU F 539 " ideal model delta harmonic sigma weight residual 180.00 155.67 24.33 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA PRO E 538 " pdb=" C PRO E 538 " pdb=" N GLU E 539 " pdb=" CA GLU E 539 " ideal model delta harmonic sigma weight residual 180.00 156.53 23.47 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA ASP C 228 " pdb=" C ASP C 228 " pdb=" N SER C 229 " pdb=" CA SER C 229 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 12218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2041 0.035 - 0.070: 716 0.070 - 0.105: 261 0.105 - 0.140: 135 0.140 - 0.176: 4 Chirality restraints: 3157 Sorted by residual: chirality pdb=" CB THR A 480 " pdb=" CA THR A 480 " pdb=" OG1 THR A 480 " pdb=" CG2 THR A 480 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CA ASP A 247 " pdb=" N ASP A 247 " pdb=" C ASP A 247 " pdb=" CB ASP A 247 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.63e-01 chirality pdb=" CB ILE F 299 " pdb=" CA ILE F 299 " pdb=" CG1 ILE F 299 " pdb=" CG2 ILE F 299 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 3154 not shown) Planarity restraints: 3568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 388 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C TYR B 388 " -0.057 2.00e-02 2.50e+03 pdb=" O TYR B 388 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE B 389 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 388 " 0.016 2.00e-02 2.50e+03 3.26e-02 1.07e+01 pdb=" C TYR A 388 " -0.056 2.00e-02 2.50e+03 pdb=" O TYR A 388 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE A 389 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR G 388 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.05e+01 pdb=" C TYR G 388 " -0.056 2.00e-02 2.50e+03 pdb=" O TYR G 388 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE G 389 " 0.019 2.00e-02 2.50e+03 ... (remaining 3565 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1764 2.74 - 3.28: 18561 3.28 - 3.82: 30132 3.82 - 4.36: 34954 4.36 - 4.90: 64783 Nonbonded interactions: 150194 Sorted by model distance: nonbonded pdb=" OD1 ASP B 222 " pdb="CA CA B 901 " model vdw 2.199 2.510 nonbonded pdb=" OD2 ASP F 282 " pdb=" OH TYR F 404 " model vdw 2.206 3.040 nonbonded pdb=" OD1 ASP E 222 " pdb="CA CA E 901 " model vdw 2.207 2.510 nonbonded pdb=" NE2 GLN C 425 " pdb=" OG1 THR C 451 " model vdw 2.214 3.120 nonbonded pdb=" OD1 ASP A 222 " pdb="CA CA A 902 " model vdw 2.215 2.510 ... (remaining 150189 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 217 or (resid 218 and (name N or name CA or name C or name \ O or name CB )) or resid 219 through 329 or (resid 330 and (name N or name CA o \ r name C or name O or name CB )) or resid 331 through 363 or (resid 364 and (nam \ e N or name CA or name C or name O or name CB )) or resid 365 through 416 or (re \ sid 417 and (name N or name CA or name C or name O or name CB )) or resid 418 th \ rough 617 or resid 901 through 902)) selection = (chain 'B' and (resid 217 through 227 or (resid 228 and (name N or name CA or na \ me C or name O or name CB )) or resid 229 through 329 or (resid 330 and (name N \ or name CA or name C or name O or name CB )) or resid 331 through 363 or (resid \ 364 and (name N or name CA or name C or name O or name CB )) or resid 365 throug \ h 384 or (resid 385 and (name N or name CA or name C or name O or name CB )) or \ resid 386 through 617 or resid 901 through 902)) selection = (chain 'C' and (resid 217 through 384 or (resid 385 and (name N or name CA or na \ me C or name O or name CB )) or resid 386 through 416 or (resid 417 and (name N \ or name CA or name C or name O or name CB )) or resid 418 through 617 or resid 9 \ 01 through 902)) selection = (chain 'D' and (resid 217 through 329 or (resid 330 and (name N or name CA or na \ me C or name O or name CB )) or resid 331 through 363 or (resid 364 and (name N \ or name CA or name C or name O or name CB )) or resid 365 through 384 or (resid \ 385 and (name N or name CA or name C or name O or name CB )) or resid 386 throug \ h 416 or (resid 417 and (name N or name CA or name C or name O or name CB )) or \ resid 418 through 617 or resid 901 through 902)) selection = (chain 'E' and (resid 217 or (resid 218 and (name N or name CA or name C or name \ O or name CB )) or resid 219 through 227 or (resid 228 and (name N or name CA o \ r name C or name O or name CB )) or resid 229 through 329 or (resid 330 and (nam \ e N or name CA or name C or name O or name CB )) or resid 331 through 363 or (re \ sid 364 and (name N or name CA or name C or name O or name CB )) or resid 365 th \ rough 384 or (resid 385 and (name N or name CA or name C or name O or name CB )) \ or resid 386 through 416 or (resid 417 and (name N or name CA or name C or name \ O or name CB )) or resid 418 through 617 or resid 901 through 902)) selection = (chain 'F' and (resid 217 or (resid 218 and (name N or name CA or name C or name \ O or name CB )) or resid 219 through 329 or (resid 330 and (name N or name CA o \ r name C or name O or name CB )) or resid 331 through 384 or (resid 385 and (nam \ e N or name CA or name C or name O or name CB )) or resid 386 through 416 or (re \ sid 417 and (name N or name CA or name C or name O or name CB )) or resid 418 th \ rough 617 or resid 901 through 902)) selection = (chain 'G' and (resid 217 or (resid 218 and (name N or name CA or name C or name \ O or name CB )) or resid 219 through 227 or (resid 228 and (name N or name CA o \ r name C or name O or name CB )) or resid 229 through 329 or (resid 330 and (nam \ e N or name CA or name C or name O or name CB )) or resid 331 through 363 or (re \ sid 364 and (name N or name CA or name C or name O or name CB )) or resid 365 th \ rough 384 or (resid 385 and (name N or name CA or name C or name O or name CB )) \ or resid 386 through 416 or (resid 417 and (name N or name CA or name C or name \ O or name CB )) or resid 418 through 617 or resid 901 through 902)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.910 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 45.400 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.340 ------------------------------------------------------------------------------- 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= 0.152 Angle : 0.587 7.217 27253 Z= 0.322 Chirality : 0.044 0.176 3157 Planarity : 0.004 0.081 3568 Dihedral : 17.683 89.657 7377 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 0.37 % Allowed : 39.05 % Favored : 60.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.15), residues: 2562 helix: -0.62 (0.24), residues: 448 sheet: -0.55 (0.19), residues: 686 loop : -2.13 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 245 HIS 0.001 0.000 HIS G 314 PHE 0.009 0.001 PHE A 281 TYR 0.013 0.001 TYR B 257 ARG 0.004 0.000 ARG F 290 *********************** 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 fitting. rotamer outliers: 8 poor density : 270 time to evaluate : 2.198 Fit side-chains REVERT: B 466 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7928 (mt0) REVERT: B 511 ASP cc_start: 0.7727 (m-30) cc_final: 0.7300 (m-30) REVERT: F 498 THR cc_start: 0.9343 (p) cc_final: 0.9133 (p) outliers start: 8 outliers final: 4 residues processed: 277 average time/residue: 0.2665 time to fit residues: 121.1584 Evaluate side-chains 253 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 248 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain C residue 427 ASN Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain F residue 385 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 0.7980 chunk 196 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 104 optimal weight: 0.0570 chunk 203 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 151 optimal weight: 0.8980 chunk 235 optimal weight: 6.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN A 427 ASN B 265 ASN B 371 ASN B 382 ASN C 265 ASN ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN D 314 HIS D 431 ASN E 260 ASN F 314 HIS F 432 ASN F 586 ASN G 428 GLN G 583 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20059 Z= 0.220 Angle : 0.562 6.476 27253 Z= 0.301 Chirality : 0.045 0.169 3157 Planarity : 0.003 0.039 3568 Dihedral : 5.140 54.622 2769 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 3.26 % Allowed : 36.30 % Favored : 60.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.16), residues: 2562 helix: -0.50 (0.24), residues: 448 sheet: -0.54 (0.19), residues: 686 loop : -1.99 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 245 HIS 0.002 0.001 HIS G 314 PHE 0.017 0.002 PHE F 281 TYR 0.011 0.001 TYR C 230 ARG 0.002 0.000 ARG E 394 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 270 time to evaluate : 2.157 Fit side-chains REVERT: A 239 ASP cc_start: 0.7891 (t0) cc_final: 0.7611 (t0) REVERT: A 304 MET cc_start: 0.8798 (tpp) cc_final: 0.8583 (tmm) REVERT: A 388 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.7761 (m-10) REVERT: B 225 ASN cc_start: 0.7661 (t0) cc_final: 0.7414 (t0) REVERT: B 263 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7862 (mt-10) REVERT: B 388 TYR cc_start: 0.8827 (OUTLIER) cc_final: 0.7613 (m-10) REVERT: C 388 TYR cc_start: 0.8837 (OUTLIER) cc_final: 0.7464 (m-10) REVERT: D 304 MET cc_start: 0.8801 (tmm) cc_final: 0.8482 (ttt) REVERT: E 394 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7575 (ttm170) REVERT: F 260 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8532 (t0) REVERT: F 314 HIS cc_start: 0.6138 (OUTLIER) cc_final: 0.5578 (t70) REVERT: F 388 TYR cc_start: 0.8927 (OUTLIER) cc_final: 0.7384 (m-10) REVERT: F 480 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.9024 (t) REVERT: F 533 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7468 (tttt) REVERT: G 225 ASN cc_start: 0.7790 (t0) cc_final: 0.7413 (t0) REVERT: G 388 TYR cc_start: 0.8894 (OUTLIER) cc_final: 0.7556 (m-10) REVERT: G 428 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.8778 (mp-120) outliers start: 71 outliers final: 34 residues processed: 322 average time/residue: 0.2740 time to fit residues: 144.1297 Evaluate side-chains 299 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 253 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 427 ASN Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 388 TYR Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 574 SER Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 394 ARG Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 535 LEU Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain F residue 260 ASN Chi-restraints excluded: chain F residue 314 HIS Chi-restraints excluded: chain F residue 388 TYR Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 533 LYS Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain G residue 388 TYR Chi-restraints excluded: chain G residue 428 GLN Chi-restraints excluded: chain G residue 535 LEU Chi-restraints excluded: chain G residue 605 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 130 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 195 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 235 optimal weight: 9.9990 chunk 254 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 chunk 233 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 189 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 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 F 314 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20059 Z= 0.190 Angle : 0.547 6.407 27253 Z= 0.291 Chirality : 0.044 0.171 3157 Planarity : 0.003 0.037 3568 Dihedral : 4.766 23.751 2758 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 4.54 % Allowed : 35.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.16), residues: 2562 helix: -0.46 (0.24), residues: 448 sheet: -0.48 (0.19), residues: 693 loop : -2.01 (0.15), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 245 HIS 0.010 0.001 HIS F 314 PHE 0.015 0.002 PHE F 281 TYR 0.010 0.001 TYR C 230 ARG 0.003 0.000 ARG F 290 *********************** 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 376 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 277 time to evaluate : 2.282 Fit side-chains REVERT: A 225 ASN cc_start: 0.8074 (t0) cc_final: 0.7235 (t0) REVERT: A 239 ASP cc_start: 0.7942 (t0) cc_final: 0.7643 (t0) REVERT: A 246 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6721 (tt0) REVERT: A 281 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8158 (p90) REVERT: A 388 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.8107 (m-10) REVERT: B 217 GLU cc_start: 0.5590 (OUTLIER) cc_final: 0.5029 (mm-30) REVERT: B 225 ASN cc_start: 0.7777 (t0) cc_final: 0.7446 (t0) REVERT: B 263 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7882 (mt-10) REVERT: B 281 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.8329 (p90) REVERT: B 388 TYR cc_start: 0.8813 (OUTLIER) cc_final: 0.7547 (m-10) REVERT: C 225 ASN cc_start: 0.8016 (t0) cc_final: 0.7743 (t0) REVERT: C 388 TYR cc_start: 0.8858 (OUTLIER) cc_final: 0.7633 (m-10) REVERT: D 281 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.8150 (p90) REVERT: D 304 MET cc_start: 0.8769 (tmm) cc_final: 0.8516 (ttt) REVERT: E 394 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7578 (ttm170) REVERT: F 225 ASN cc_start: 0.7784 (t0) cc_final: 0.7481 (t0) REVERT: F 239 ASP cc_start: 0.7781 (t0) cc_final: 0.7553 (t0) REVERT: F 260 ASN cc_start: 0.8810 (OUTLIER) cc_final: 0.8533 (t0) REVERT: F 388 TYR cc_start: 0.8927 (OUTLIER) cc_final: 0.7614 (m-10) REVERT: F 533 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7471 (tttt) REVERT: G 225 ASN cc_start: 0.7887 (t0) cc_final: 0.7493 (t0) REVERT: G 388 TYR cc_start: 0.8871 (OUTLIER) cc_final: 0.7842 (m-10) REVERT: G 601 TYR cc_start: 0.9114 (OUTLIER) cc_final: 0.8787 (m-10) outliers start: 99 outliers final: 51 residues processed: 353 average time/residue: 0.2634 time to fit residues: 153.1802 Evaluate side-chains 330 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 264 time to evaluate : 2.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 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 272 THR Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 407 THR 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 272 THR 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 535 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 601 TYR 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 489 THR Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 574 SER Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 272 THR 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 F residue 221 THR Chi-restraints excluded: chain F residue 260 ASN Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 388 TYR Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 533 LYS Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 388 TYR Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 535 LEU Chi-restraints excluded: chain G residue 601 TYR Chi-restraints excluded: chain G residue 605 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 232 optimal weight: 7.9990 chunk 177 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 158 optimal weight: 8.9990 chunk 236 optimal weight: 1.9990 chunk 250 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 224 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: