Starting phenix.real_space_refine on Sat Feb 17 20:44:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekm_28207/02_2024/8ekm_28207.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekm_28207/02_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_28207/02_2024/8ekm_28207.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekm_28207/02_2024/8ekm_28207.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekm_28207/02_2024/8ekm_28207.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekm_28207/02_2024/8ekm_28207.pdb" } 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 Residue "A GLU 246": "OE1" <-> "OE2" Residue "A ASP 247": "OD1" <-> "OD2" Residue "A ASP 269": "OD1" <-> "OD2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 465": "OD1" <-> "OD2" Residue "B GLU 524": "OE1" <-> "OE2" Residue "B ASP 561": "OD1" <-> "OD2" Residue "C ASP 239": "OD1" <-> "OD2" Residue "C ASP 269": "OD1" <-> "OD2" Residue "C GLU 385": "OE1" <-> "OE2" Residue "C GLU 499": "OE1" <-> "OE2" Residue "C GLU 552": "OE1" <-> "OE2" Residue "D ASP 239": "OD1" <-> "OD2" Residue "D TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 417": "OD1" <-> "OD2" Residue "D GLU 499": "OE1" <-> "OE2" Residue "D ASP 520": "OD1" <-> "OD2" Residue "E ASP 239": "OD1" <-> "OD2" Residue "E ASP 247": "OD1" <-> "OD2" Residue "E ASP 269": "OD1" <-> "OD2" Residue "E TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 385": "OE1" <-> "OE2" Residue "E TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 499": "OE1" <-> "OE2" Residue "E ASP 520": "OD1" <-> "OD2" Residue "E GLU 524": "OE1" <-> "OE2" Residue "E GLU 539": "OE1" <-> "OE2" Residue "F ASP 239": "OD1" <-> "OD2" Residue "F PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 269": "OD1" <-> "OD2" Residue "F GLU 499": "OE1" <-> "OE2" Residue "F GLU 524": "OE1" <-> "OE2" Residue "G ASP 239": "OD1" <-> "OD2" Residue "G TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 385": "OE1" <-> "OE2" Residue "G ASP 465": "OD1" <-> "OD2" Residue "G GLU 499": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 11.20, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 8.64 Conformation dependent library (CDL) restraints added in 4.0 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: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 229 through 234 Processing helix chain 'A' and resid 249 through 253 removed outlier: 3.991A pdb=" N GLY A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 463 through 473 removed outlier: 3.621A pdb=" N GLY A 473 " --> pdb=" O LYS A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 513 removed outlier: 4.860A pdb=" N SER A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLN A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 555 Processing helix chain 'A' and resid 581 through 594 removed outlier: 3.708A pdb=" N THR A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 234 Processing helix chain 'B' and resid 246 through 253 removed outlier: 3.897A pdb=" N GLU B 251 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 252 " --> pdb=" O PHE B 249 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY B 253 " --> pdb=" O ALA B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 463 through 473 removed outlier: 3.649A pdb=" N GLY B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 513 removed outlier: 4.761A pdb=" N SER B 508 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N GLN B 509 " --> pdb=" O ASP B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 581 through 594 removed outlier: 3.737A pdb=" N THR B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 603 Processing helix chain 'C' and resid 229 through 234 Processing helix chain 'C' and resid 247 through 253 removed outlier: 4.164A pdb=" N GLU C 251 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY C 253 " --> pdb=" O ALA C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 279 Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 463 through 473 removed outlier: 3.641A pdb=" N GLY C 473 " --> pdb=" O LYS C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 513 removed outlier: 4.821A pdb=" N SER C 508 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N GLN C 509 " --> pdb=" O ASP C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 555 Processing helix chain 'C' and resid 581 through 591 Processing helix chain 'D' and resid 229 through 234 Processing helix chain 'D' and resid 249 through 253 removed outlier: 4.149A pdb=" N GLY D 253 " --> pdb=" O ALA D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 279 Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 463 through 473 removed outlier: 3.678A pdb=" N GLY D 473 " --> pdb=" O LYS D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 513 removed outlier: 4.816A pdb=" N SER D 508 " --> pdb=" O SER D 504 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLN D 509 " --> pdb=" O ASP D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 555 Processing helix chain 'D' and resid 581 through 593 Processing helix chain 'D' and resid 599 through 603 Processing helix chain 'E' and resid 227 through 234 Processing helix chain 'E' and resid 246 through 253 removed outlier: 3.905A pdb=" N GLU E 251 " --> pdb=" O SER E 248 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN E 252 " --> pdb=" O PHE E 249 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY E 253 " --> pdb=" O ALA E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 279 Processing helix chain 'E' and resid 286 through 290 Processing helix chain 'E' and resid 463 through 473 removed outlier: 3.692A pdb=" N GLY E 473 " --> pdb=" O LYS E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'E' and resid 506 through 513 Processing helix chain 'E' and resid 546 through 555 Processing helix chain 'E' and resid 581 through 594 removed outlier: 3.773A pdb=" N THR E 594 " --> pdb=" O ASP E 590 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 234 Processing helix chain 'F' and resid 249 through 253 removed outlier: 4.131A pdb=" N GLY F 253 " --> pdb=" O ALA F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 279 Processing helix chain 'F' and resid 286 through 290 Processing helix chain 'F' and resid 463 through 473 removed outlier: 3.634A pdb=" N GLY F 473 " --> pdb=" O LYS F 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 502 through 505 Processing helix chain 'F' and resid 506 through 513 Processing helix chain 'F' and resid 546 through 555 Processing helix chain 'F' and resid 581 through 591 Processing helix chain 'G' and resid 227 through 234 Processing helix chain 'G' and resid 249 through 253 removed outlier: 4.155A pdb=" N GLY G 253 " --> pdb=" O ALA G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 279 Processing helix chain 'G' and resid 286 through 290 Processing helix chain 'G' and resid 463 through 473 removed outlier: 3.637A pdb=" N GLY G 473 " --> pdb=" O LYS G 469 " (cutoff:3.500A) Processing helix chain 'G' and resid 503 through 513 removed outlier: 4.783A pdb=" N SER G 508 " --> pdb=" O SER G 504 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLN G 509 " --> pdb=" O ASP G 505 " (cutoff:3.500A) Processing helix chain 'G' and resid 546 through 555 Processing helix chain 'G' and resid 581 through 593 Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 238 Processing sheet with id=AA2, first strand: chain 'A' and resid 301 through 311 removed outlier: 6.673A pdb=" N ASN A 392 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU A 307 " --> pdb=" O ASN A 390 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASN A 390 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ILE A 309 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N TYR A 388 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 314 through 331 Processing sheet with id=AA4, first strand: chain 'A' and resid 418 through 423 removed outlier: 6.835A pdb=" N TYR A 404 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN A 432 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 418 through 423 removed outlier: 7.059A pdb=" N LYS A 405 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY A 485 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR A 407 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N VAL A 483 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR A 409 " --> pdb=" O THR A 481 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AA7, first strand: chain 'A' and resid 526 through 531 removed outlier: 9.658A pdb=" N ILE A 611 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N SER A 516 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE A 613 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE A 518 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 558 through 559 removed outlier: 3.704A pdb=" N LEU A 564 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 235 through 238 Processing sheet with id=AB1, first strand: chain 'B' and resid 301 through 311 removed outlier: 6.657A pdb=" N ASN B 392 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU B 307 " --> pdb=" O ASN B 390 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN B 390 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ILE B 309 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N TYR B 388 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 418 through 423 removed outlier: 6.560A pdb=" N LEU B 412 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR B 421 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR B 410 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS B 423 " --> pdb=" O PRO B 408 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TYR B 404 " --> pdb=" O ASN B 432 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASN B 432 " --> pdb=" O TYR B 404 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 418 through 423 removed outlier: 6.560A pdb=" N LEU B 412 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR B 421 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR B 410 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS B 423 " --> pdb=" O PRO B 408 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LYS B 405 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLY B 485 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR B 407 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N VAL B 483 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR B 409 " --> pdb=" O THR B 481 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB5, first strand: chain 'B' and resid 526 through 531 removed outlier: 9.680A pdb=" N ILE B 611 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER B 516 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ILE B 613 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE B 518 " --> pdb=" O ILE B 613 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 558 through 559 removed outlier: 3.914A pdb=" N LEU B 564 " --> pdb=" O ILE B 571 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 235 through 238 Processing sheet with id=AB8, first strand: chain 'C' and resid 301 through 311 removed outlier: 6.612A pdb=" N ASN C 392 " --> pdb=" O GLU C 305 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU C 307 " --> pdb=" O ASN C 390 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN C 390 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ILE C 309 " --> pdb=" O TYR C 388 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N TYR C 388 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 418 through 423 removed outlier: 6.780A pdb=" N TYR C 404 " --> pdb=" O ASN C 432 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN C 432 " --> pdb=" O TYR C 404 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 418 through 423 removed outlier: 6.935A pdb=" N LYS C 405 " --> pdb=" O GLY C 485 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY C 485 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR C 407 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N VAL C 483 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N THR C 409 " --> pdb=" O THR C 481 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 489 through 490 Processing sheet with id=AC3, first strand: chain 'C' and resid 526 through 531 removed outlier: 9.636A pdb=" N ILE C 611 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER C 516 " --> pdb=" O ILE C 611 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ILE C 613 " --> pdb=" O SER C 516 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE C 518 " --> pdb=" O ILE C 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 558 through 559 removed outlier: 4.024A pdb=" N LEU C 564 " --> pdb=" O ILE C 571 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 235 through 238 Processing sheet with id=AC6, first strand: chain 'D' and resid 301 through 311 removed outlier: 6.683A pdb=" N ASN D 392 " --> pdb=" O GLU D 305 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU D 307 " --> pdb=" O ASN D 390 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN D 390 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE D 309 " --> pdb=" O TYR D 388 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR D 388 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 301 through 311 removed outlier: 6.683A pdb=" N ASN D 392 " --> pdb=" O GLU D 305 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU D 307 " --> pdb=" O ASN D 390 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN D 390 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE D 309 " --> pdb=" O TYR D 388 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR D 388 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ILE D 460 " --> pdb=" O ILE D 389 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 418 through 423 removed outlier: 6.830A pdb=" N TYR D 404 " --> pdb=" O ASN D 432 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASN D 432 " --> pdb=" O TYR D 404 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 418 through 423 removed outlier: 7.009A pdb=" N LYS D 405 " --> pdb=" O GLY D 485 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLY D 485 " --> pdb=" O LYS D 405 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR D 407 " --> pdb=" O VAL D 483 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL D 483 " --> pdb=" O THR D 407 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR D 409 " --> pdb=" O THR D 481 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AD2, first strand: chain 'D' and resid 526 through 531 removed outlier: 9.648A pdb=" N ILE D 611 " --> pdb=" O SER D 514 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N SER D 516 " --> pdb=" O ILE D 611 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ILE D 613 " --> pdb=" O SER D 516 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE D 518 " --> pdb=" O ILE D 613 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 558 through 559 removed outlier: 4.032A pdb=" N LEU D 564 " --> pdb=" O ILE D 571 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 235 through 238 Processing sheet with id=AD5, first strand: chain 'E' and resid 301 through 311 removed outlier: 5.231A pdb=" N VAL E 302 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYR E 396 " --> pdb=" O VAL E 302 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N MET E 304 " --> pdb=" O ARG E 394 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG E 394 " --> pdb=" O MET E 304 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 301 through 311 removed outlier: 5.231A pdb=" N VAL E 302 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYR E 396 " --> pdb=" O VAL E 302 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N MET E 304 " --> pdb=" O ARG E 394 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG E 394 " --> pdb=" O MET E 304 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE E 460 " --> pdb=" O ILE E 389 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 418 through 423 removed outlier: 6.776A pdb=" N TYR E 404 " --> pdb=" O ASN E 432 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ASN E 432 " --> pdb=" O TYR E 404 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 418 through 423 removed outlier: 6.891A pdb=" N LYS E 405 " --> pdb=" O GLY E 485 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLY E 485 " --> pdb=" O LYS E 405 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR E 407 " --> pdb=" O VAL E 483 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL E 483 " --> pdb=" O THR E 407 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR E 409 " --> pdb=" O THR E 481 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 489 through 490 Processing sheet with id=AE1, first strand: chain 'E' and resid 526 through 531 removed outlier: 9.670A pdb=" N ILE E 611 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N SER E 516 " --> pdb=" O ILE E 611 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ILE E 613 " --> pdb=" O SER E 516 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE E 518 " --> pdb=" O ILE E 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 558 through 559 removed outlier: 4.233A pdb=" N LEU E 564 " --> pdb=" O ILE E 571 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 235 through 238 Processing sheet with id=AE4, first strand: chain 'F' and resid 301 through 311 removed outlier: 6.661A pdb=" N ASN F 392 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU F 307 " --> pdb=" O ASN F 390 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASN F 390 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ILE F 309 " --> pdb=" O TYR F 388 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N TYR F 388 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 418 through 423 removed outlier: 6.822A pdb=" N TYR F 404 " --> pdb=" O ASN F 432 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASN F 432 " --> pdb=" O TYR F 404 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 418 through 423 removed outlier: 7.064A pdb=" N LYS F 405 " --> pdb=" O GLY F 485 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLY F 485 " --> pdb=" O LYS F 405 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR F 407 " --> pdb=" O VAL F 483 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL F 483 " --> pdb=" O THR F 407 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR F 409 " --> pdb=" O THR F 481 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 489 through 490 Processing sheet with id=AE8, first strand: chain 'F' and resid 526 through 531 removed outlier: 9.584A pdb=" N ILE F 611 " --> pdb=" O SER F 514 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N SER F 516 " --> pdb=" O ILE F 611 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ILE F 613 " --> pdb=" O SER F 516 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE F 518 " --> pdb=" O ILE F 613 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 558 through 559 removed outlier: 3.918A pdb=" N LEU F 564 " --> pdb=" O ILE F 571 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 235 through 238 Processing sheet with id=AF2, first strand: chain 'G' and resid 301 through 311 removed outlier: 6.662A pdb=" N ASN G 392 " --> pdb=" O GLU G 305 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU G 307 " --> pdb=" O ASN G 390 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASN G 390 " --> pdb=" O LEU G 307 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE G 309 " --> pdb=" O TYR G 388 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N TYR G 388 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 418 through 423 removed outlier: 6.787A pdb=" N TYR G 404 " --> pdb=" O ASN G 432 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASN G 432 " --> pdb=" O TYR G 404 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 418 through 423 removed outlier: 6.994A pdb=" N LYS G 405 " --> pdb=" O GLY G 485 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLY G 485 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR G 407 " --> pdb=" O VAL G 483 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N VAL G 483 " --> pdb=" O THR G 407 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR G 409 " --> pdb=" O THR G 481 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 489 through 490 Processing sheet with id=AF6, first strand: chain 'G' and resid 526 through 531 removed outlier: 9.678A pdb=" N ILE G 611 " --> pdb=" O SER G 514 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N SER G 516 " --> pdb=" O ILE G 611 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ILE G 613 " --> pdb=" O SER G 516 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE G 518 " --> pdb=" O ILE G 613 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 558 through 559 removed outlier: 3.726A pdb=" N LEU G 564 " --> pdb=" O ILE G 571 " (cutoff:3.500A) 820 hydrogen bonds defined for protein. 2133 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.30 Time building geometry restraints manager: 8.44 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: 98.88 - 105.91: 389 105.91 - 112.93: 10939 112.93 - 119.96: 6564 119.96 - 126.98: 9210 126.98 - 134.00: 151 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 2.440 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 2.520 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 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: 3.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 14.900 Check model and map are aligned: 0.270 Set scattering table: 0.220 Process input model: 54.240 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.010 ------------------------------------------------------------------------------- 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 : 2.398 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: 0.2645 time to fit residues: 120.0183 Evaluate side-chains 253 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 248 time to evaluate : 2.356 ------------------------------------------------------------------------------- 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: 3.9990 chunk 196 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 104 optimal weight: 0.0970 chunk 203 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 329 ASN E 363 ASN F 314 HIS F 329 ASN F 586 ASN G 583 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 20059 Z= 0.334 Angle : 0.606 7.108 27253 Z= 0.325 Chirality : 0.047 0.161 3157 Planarity : 0.004 0.036 3568 Dihedral : 5.522 77.926 2769 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 6.01 % Allowed : 35.38 % Favored : 58.60 % 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: -2.13 (0.15), residues: 2562 helix: -0.40 (0.25), residues: 406 sheet: -0.79 (0.19), residues: 707 loop : -2.10 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 245 HIS 0.001 0.001 HIS B 314 PHE 0.025 0.003 PHE A 281 TYR 0.013 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 393 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 262 time to evaluate : 2.229 Fit side-chains REVERT: A 239 ASP cc_start: 0.7861 (t0) cc_final: 0.7604 (t0) REVERT: A 281 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8412 (p90) REVERT: A 304 MET cc_start: 0.8731 (tpp) cc_final: 0.8530 (tmm) REVERT: A 388 TYR cc_start: 0.8955 (OUTLIER) cc_final: 0.7950 (m-10) REVERT: B 225 ASN cc_start: 0.7738 (t0) cc_final: 0.7346 (t0) REVERT: B 239 ASP cc_start: 0.7865 (t0) cc_final: 0.7566 (t0) REVERT: B 263 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7830 (mt-10) REVERT: B 281 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.8431 (p90) REVERT: B 363 ASN cc_start: 0.2177 (OUTLIER) cc_final: 0.1715 (p0) REVERT: B 388 TYR cc_start: 0.8892 (OUTLIER) cc_final: 0.7855 (m-10) REVERT: C 388 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.7485 (m-10) REVERT: D 281 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.8482 (p90) REVERT: D 304 MET cc_start: 0.8799 (tmm) cc_final: 0.8518 (ttt) REVERT: E 225 ASN cc_start: 0.7977 (t0) cc_final: 0.7651 (t0) REVERT: E 265 ASN cc_start: 0.8900 (OUTLIER) cc_final: 0.8510 (m-40) REVERT: E 394 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7694 (ttm170) REVERT: F 260 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8631 (t0) REVERT: F 388 TYR cc_start: 0.8966 (OUTLIER) cc_final: 0.7464 (m-10) REVERT: F 480 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8949 (t) REVERT: F 533 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7464 (tttt) REVERT: G 225 ASN cc_start: 0.7851 (t0) cc_final: 0.7461 (t0) REVERT: G 388 TYR cc_start: 0.8962 (OUTLIER) cc_final: 0.7648 (m-10) outliers start: 131 outliers final: 76 residues processed: 363 average time/residue: 0.2545 time to fit residues: 150.8662 Evaluate side-chains 347 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 256 time to evaluate : 2.317 ------------------------------------------------------------------------------- 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 486 ASN Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 610 ASN 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 363 ASN 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 486 ASN 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 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 486 ASN Chi-restraints excluded: chain C residue 498 THR 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 C residue 610 ASN 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 310 SER Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 427 ASN Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 486 ASN 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 567 ASN 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 265 ASN Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 363 ASN Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 394 ARG Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 486 ASN Chi-restraints excluded: chain E residue 535 LEU Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 610 ASN 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 427 ASN Chi-restraints excluded: chain F residue 463 ASN Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 486 ASN 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 265 ASN 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 427 ASN Chi-restraints excluded: chain G residue 438 THR Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 453 ASP Chi-restraints excluded: chain G residue 486 ASN Chi-restraints excluded: chain G residue 535 LEU Chi-restraints excluded: chain G residue 605 LEU Chi-restraints excluded: chain G residue 610 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 130 optimal weight: 0.2980 chunk 72 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 235 optimal weight: 9.9990 chunk 254 optimal weight: 4.9990 chunk 209 optimal weight: 3.9990 chunk 233 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 ASN F 314 HIS F 586 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20059 Z= 0.274 Angle : 0.577 6.798 27253 Z= 0.308 Chirality : 0.046 0.167 3157 Planarity : 0.003 0.035 3568 Dihedral : 5.064 24.751 2760 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 6.29 % Allowed : 36.03 % Favored : 57.69 % 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 (0.16), residues: 2562 helix: -0.41 (0.25), residues: 406 sheet: -0.76 (0.19), residues: 707 loop : -2.07 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 503 HIS 0.001 0.000 HIS B 314 PHE 0.022 0.002 PHE A 281 TYR 0.012 0.001 TYR C 230 ARG 0.002 0.000 ARG E 394 *********************** 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 398 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 261 time to evaluate : 2.372 Fit side-chains REVERT: A 239 ASP cc_start: 0.8011 (t0) cc_final: 0.7763 (t0) REVERT: A 281 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8122 (p90) REVERT: A 388 TYR cc_start: 0.8903 (OUTLIER) cc_final: 0.8160 (m-10) REVERT: A 559 LYS cc_start: 0.7006 (OUTLIER) cc_final: 0.6782 (ttmt) REVERT: B 217 GLU cc_start: 0.5606 (OUTLIER) cc_final: 0.5082 (mm-30) REVERT: B 225 ASN cc_start: 0.7849 (t0) cc_final: 0.7535 (t0) REVERT: B 239 ASP cc_start: 0.7882 (t0) cc_final: 0.7606 (t0) REVERT: B 263 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7882 (mt-10) REVERT: B 281 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.8223 (p90) REVERT: B 363 ASN cc_start: 0.2149 (OUTLIER) cc_final: 0.1697 (p0) REVERT: B 388 TYR cc_start: 0.8866 (OUTLIER) cc_final: 0.7561 (m-10) REVERT: C 225 ASN cc_start: 0.8048 (t0) cc_final: 0.7572 (t0) REVERT: C 388 TYR cc_start: 0.8904 (OUTLIER) cc_final: 0.7708 (m-10) REVERT: D 281 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.8056 (p90) REVERT: D 304 MET cc_start: 0.8778 (tmm) cc_final: 0.8544 (ttt) REVERT: E 225 ASN cc_start: 0.7959 (t0) cc_final: 0.7597 (t0) REVERT: E 265 ASN cc_start: 0.8882 (OUTLIER) cc_final: 0.8664 (m-40) REVERT: E 394 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7729 (ttm170) REVERT: F 260 ASN cc_start: 0.8921 (OUTLIER) cc_final: 0.8618 (t0) REVERT: F 388 TYR cc_start: 0.8923 (OUTLIER) cc_final: 0.7852 (m-10) REVERT: F 480 THR cc_start: 0.9144 (OUTLIER) cc_final: 0.8925 (t) REVERT: F 533 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7469 (tttt) REVERT: G 225 ASN cc_start: 0.7907 (t0) cc_final: 0.7407 (t0) REVERT: G 281 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.7863 (p90) REVERT: G 388 TYR cc_start: 0.8912 (OUTLIER) cc_final: 0.7921 (m-10) REVERT: G 458 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7610 (ttt90) outliers start: 137 outliers final: 81 residues processed: 370 average time/residue: 0.2629 time to fit residues: 158.5604 Evaluate side-chains 354 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 254 time to evaluate : 2.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 265 ASN 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 476 ILE Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 559 LYS Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 610 ASN 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 363 ASN Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 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 427 ASN Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 549 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 291 ASP Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain D residue 574 SER Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 265 ASN 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 486 ASN Chi-restraints excluded: chain E residue 535 LEU Chi-restraints excluded: chain E residue 549 GLU Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain E residue 610 ASN 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 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 463 ASN Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 486 ASN 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 272 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 388 TYR Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 453 ASP Chi-restraints excluded: chain G residue 458 ARG Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 486 ASN Chi-restraints excluded: chain G residue 535 LEU Chi-restraints excluded: chain G residue 549 GLU Chi-restraints excluded: chain G residue 610 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 232 optimal weight: 9.9990 chunk 177 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 158 optimal weight: 7.9990 chunk 236 optimal weight: 0.9990 chunk 250 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 224 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 ASN E 390 ASN F 586 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 : 0.003 0.047 20059 Z= 0.210 Angle : 0.549 6.654 27253 Z= 0.291 Chirality : 0.045 0.184 3157 Planarity : 0.003 0.033 3568 Dihedral : 4.911 24.197 2760 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 6.52 % Allowed : 35.66 % Favored : 57.82 % 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: -1.98 (0.16), residues: 2562 helix: -0.38 (0.25), residues: 406 sheet: -0.67 (0.19), residues: 707 loop : -1.98 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 503 HIS 0.000 0.000 HIS B 314 PHE 0.018 0.002 PHE A 281 TYR 0.011 0.001 TYR C 230 ARG 0.002 0.000 ARG C 290 *********************** 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 406 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 264 time to evaluate : 2.553 Fit side-chains REVERT: A 225 ASN cc_start: 0.8089 (t0) cc_final: 0.7343 (t0) REVERT: A 239 ASP cc_start: 0.7988 (t0) cc_final: 0.7733 (t0) REVERT: A 244 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8026 (mtpp) REVERT: B 217 GLU cc_start: 0.5563 (OUTLIER) cc_final: 0.5030 (mm-30) REVERT: B 225 ASN cc_start: 0.7909 (t0) cc_final: 0.7558 (t0) REVERT: B 239 ASP cc_start: 0.7920 (t0) cc_final: 0.7644 (t0) REVERT: B 263 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7908 (mt-10) REVERT: B 363 ASN cc_start: 0.2159 (OUTLIER) cc_final: 0.1609 (p0) REVERT: B 388 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.7508 (m-10) REVERT: C 225 ASN cc_start: 0.8045 (t0) cc_final: 0.7588 (t0) REVERT: C 244 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7915 (mtpp) REVERT: C 388 TYR cc_start: 0.8858 (OUTLIER) cc_final: 0.7939 (m-10) REVERT: C 541 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7943 (mmtp) REVERT: E 225 ASN cc_start: 0.7969 (t0) cc_final: 0.7593 (t0) REVERT: E 239 ASP cc_start: 0.7397 (t0) cc_final: 0.7149 (t0) REVERT: E 394 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7718 (ttm170) REVERT: F 260 ASN cc_start: 0.8920 (OUTLIER) cc_final: 0.8617 (t0) REVERT: F 388 TYR cc_start: 0.8876 (OUTLIER) cc_final: 0.8223 (m-10) REVERT: F 480 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8950 (t) REVERT: F 533 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7460 (tttt) REVERT: G 225 ASN cc_start: 0.7966 (t0) cc_final: 0.7509 (t0) REVERT: G 388 TYR cc_start: 0.8859 (OUTLIER) cc_final: 0.7487 (m-10) outliers start: 142 outliers final: 91 residues processed: 378 average time/residue: 0.2763 time to fit residues: 170.1524 Evaluate side-chains 356 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 251 time to evaluate : 2.474 ------------------------------------------------------------------------------- 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 265 ASN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 379 LEU 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 498 THR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 610 ASN 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 316 SER Chi-restraints excluded: chain B residue 363 ASN 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 486 ASN Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 388 TYR Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 427 ASN Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 498 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 605 LEU Chi-restraints excluded: chain C residue 610 ASN Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 291 ASP Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 310 SER 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 486 ASN Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 567 ASN 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 281 PHE Chi-restraints excluded: chain E residue 363 ASN 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 486 ASN 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 365 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 463 ASN Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 486 ASN 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 265 ASN Chi-restraints excluded: chain G residue 363 ASN Chi-restraints excluded: chain G residue 388 TYR Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 438 THR Chi-restraints excluded: chain G residue 453 ASP Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 486 ASN Chi-restraints excluded: chain G residue 535 LEU Chi-restraints excluded: chain G residue 610 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 208 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 186 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 213 optimal weight: 0.9980 chunk 173 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 224 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN B 463 ASN ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 ASN ** E 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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 : 0.003 0.039 20059 Z= 0.198 Angle : 0.543 6.416 27253 Z= 0.287 Chirality : 0.044 0.176 3157 Planarity : 0.003 0.032 3568 Dihedral : 4.834 24.044 2760 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 7.30 % Allowed : 35.38 % Favored : 57.32 % 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: -1.98 (0.16), residues: 2562 helix: -0.36 (0.25), residues: 406 sheet: -0.75 (0.20), residues: 651 loop : -1.90 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 375 HIS 0.000 0.000 HIS B 314 PHE 0.017 0.002 PHE A 281 TYR 0.010 0.001 TYR C 230 ARG 0.003 0.000 ARG F 290 *********************** 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 430 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 271 time to evaluate : 2.325 Fit side-chains REVERT: A 225 ASN cc_start: 0.8089 (t0) cc_final: 0.7331 (t0) REVERT: A 239 ASP cc_start: 0.8008 (t0) cc_final: 0.7767 (t0) REVERT: A 244 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8034 (mtpp) REVERT: A 281 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.8245 (p90) REVERT: A 601 TYR cc_start: 0.9114 (OUTLIER) cc_final: 0.8750 (m-10) REVERT: B 217 GLU cc_start: 0.5555 (OUTLIER) cc_final: 0.5030 (mm-30) REVERT: B 225 ASN cc_start: 0.7945 (t0) cc_final: 0.7558 (t0) REVERT: B 239 ASP cc_start: 0.7906 (t0) cc_final: 0.7628 (t0) REVERT: B 263 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7924 (mt-10) REVERT: B 281 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.8292 (p90) REVERT: B 363 ASN cc_start: 0.2167 (OUTLIER) cc_final: 0.1622 (p0) REVERT: B 388 TYR cc_start: 0.8794 (OUTLIER) cc_final: 0.7535 (m-10) REVERT: C 225 ASN cc_start: 0.8063 (t0) cc_final: 0.7615 (t0) REVERT: C 244 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7881 (mtpp) REVERT: C 541 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7944 (mmtp) REVERT: D 281 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.8181 (p90) REVERT: D 535 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7416 (mp) REVERT: D 541 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7941 (mmtp) REVERT: E 225 ASN cc_start: 0.7971 (t0) cc_final: 0.7576 (t0) REVERT: E 265 ASN cc_start: 0.8982 (OUTLIER) cc_final: 0.8583 (m-40) REVERT: E 394 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7641 (ttm170) REVERT: F 225 ASN cc_start: 0.7783 (t0) cc_final: 0.7422 (t0) REVERT: F 260 ASN cc_start: 0.8896 (OUTLIER) cc_final: 0.8583 (t0) REVERT: F 388 TYR cc_start: 0.8828 (OUTLIER) cc_final: 0.8268 (m-10) REVERT: F 480 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8946 (t) REVERT: F 533 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7454 (tttt) REVERT: G 225 ASN cc_start: 0.7977 (t0) cc_final: 0.7506 (t0) REVERT: G 281 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.7864 (p90) REVERT: G 286 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7891 (mtmm) REVERT: G 601 TYR cc_start: 0.9068 (OUTLIER) cc_final: 0.8755 (m-10) outliers start: 159 outliers final: 109 residues processed: 395 average time/residue: 0.2619 time to fit residues: 169.0145 Evaluate side-chains 395 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 264 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 601 TYR Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 222 ASP 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 311 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 463 ASN Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 291 ASP 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 427 ASN Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 498 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 C residue 605 LEU Chi-restraints excluded: chain C residue 610 ASN Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 263 GLU 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 291 ASP Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 427 ASN Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 486 ASN 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 222 ASP Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 394 ARG Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 486 ASN 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 E residue 610 ASN Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 260 ASN Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain F residue 388 TYR Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 427 ASN Chi-restraints excluded: chain F residue 463 ASN Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 486 ASN 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 265 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 363 ASN Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 438 THR Chi-restraints excluded: chain G residue 453 ASP Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 486 ASN Chi-restraints excluded: chain G residue 535 LEU Chi-restraints excluded: chain G residue 549 GLU Chi-restraints excluded: chain G residue 601 TYR Chi-restraints excluded: chain G residue 610 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 84 optimal weight: 8.9990 chunk 225 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 250 optimal weight: 3.9990 chunk 208 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 131 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN E 363 ASN E 390 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20059 Z= 0.201 Angle : 0.541 6.375 27253 Z= 0.286 Chirality : 0.045 0.173 3157 Planarity : 0.003 0.032 3568 Dihedral : 4.788 23.516 2760 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 7.48 % Allowed : 35.52 % Favored : 57.00 % 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: -1.93 (0.16), residues: 2562 helix: -0.31 (0.25), residues: 406 sheet: -0.60 (0.20), residues: 637 loop : -1.93 (0.15), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 503 HIS 0.000 0.000 HIS A 314 PHE 0.017 0.002 PHE A 281 TYR 0.009 0.001 TYR C 230 ARG 0.001 0.000 ARG G 458 *********************** 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 437 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 274 time to evaluate : 2.108 Fit side-chains REVERT: A 225 ASN cc_start: 0.8098 (t0) cc_final: 0.7328 (t0) REVERT: A 239 ASP cc_start: 0.8010 (t0) cc_final: 0.7760 (t0) REVERT: A 244 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8044 (mtpp) REVERT: A 246 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6547 (tt0) REVERT: A 281 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.8246 (p90) REVERT: A 394 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7461 (ttm170) REVERT: A 601 TYR cc_start: 0.9111 (OUTLIER) cc_final: 0.8768 (m-10) REVERT: B 225 ASN cc_start: 0.8017 (t0) cc_final: 0.7620 (t0) REVERT: B 239 ASP cc_start: 0.7905 (t0) cc_final: 0.7633 (t0) REVERT: B 263 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7929 (mt-10) REVERT: B 281 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.8283 (p90) REVERT: B 363 ASN cc_start: 0.2205 (OUTLIER) cc_final: 0.1584 (p0) REVERT: B 388 TYR cc_start: 0.8786 (OUTLIER) cc_final: 0.7567 (m-10) REVERT: C 225 ASN cc_start: 0.8063 (t0) cc_final: 0.7619 (t0) REVERT: C 244 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7904 (mtpp) REVERT: C 388 TYR cc_start: 0.8775 (OUTLIER) cc_final: 0.8043 (m-10) REVERT: C 541 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7938 (mmtp) REVERT: D 265 ASN cc_start: 0.8963 (OUTLIER) cc_final: 0.8659 (m-40) REVERT: D 281 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.8161 (p90) REVERT: D 535 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7422 (mp) REVERT: D 541 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7926 (mmtp) REVERT: E 225 ASN cc_start: 0.7959 (t0) cc_final: 0.7561 (t0) REVERT: E 265 ASN cc_start: 0.8965 (OUTLIER) cc_final: 0.8560 (m-40) REVERT: E 390 ASN cc_start: 0.9049 (OUTLIER) cc_final: 0.8689 (p0) REVERT: E 394 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7592 (ttm170) REVERT: F 225 ASN cc_start: 0.7812 (t0) cc_final: 0.7432 (t0) REVERT: F 249 PHE cc_start: 0.8420 (m-10) cc_final: 0.8215 (m-10) REVERT: F 260 ASN cc_start: 0.8892 (OUTLIER) cc_final: 0.8587 (t0) REVERT: F 388 TYR cc_start: 0.8833 (OUTLIER) cc_final: 0.8449 (m-10) REVERT: F 480 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8965 (t) REVERT: F 533 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7457 (tttt) REVERT: G 225 ASN cc_start: 0.8002 (t0) cc_final: 0.7515 (t0) REVERT: G 281 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.8073 (p90) REVERT: G 286 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7887 (mtmm) REVERT: G 388 TYR cc_start: 0.8791 (OUTLIER) cc_final: 0.7450 (m-10) REVERT: G 601 TYR cc_start: 0.9059 (OUTLIER) cc_final: 0.8741 (m-10) outliers start: 163 outliers final: 114 residues processed: 403 average time/residue: 0.2682 time to fit residues: 174.6836 Evaluate side-chains 405 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 264 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 394 ARG Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 498 THR 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 A residue 610 ASN Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 486 ASN 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 265 ASN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 291 ASP 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 427 ASN Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 498 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 C residue 605 LEU Chi-restraints excluded: chain C residue 610 ASN Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 291 ASP Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 427 ASN Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 486 ASN 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 D residue 578 LEU Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 291 ASP Chi-restraints excluded: chain E residue 363 ASN Chi-restraints excluded: chain E residue 365 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 486 ASN 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 E residue 610 ASN Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 222 ASP Chi-restraints excluded: chain F residue 260 ASN Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain F residue 388 TYR Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 427 ASN Chi-restraints excluded: chain F residue 463 ASN Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 486 ASN Chi-restraints excluded: chain F residue 533 LYS Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 610 ASN Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 265 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 363 ASN Chi-restraints excluded: chain G residue 388 TYR Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 438 THR Chi-restraints excluded: chain G residue 453 ASP Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 486 ASN Chi-restraints excluded: chain G residue 535 LEU Chi-restraints excluded: chain G residue 549 GLU Chi-restraints excluded: chain G residue 578 LEU Chi-restraints excluded: chain G residue 601 TYR Chi-restraints excluded: chain G residue 610 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 241 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 182 optimal weight: 10.0000 chunk 141 optimal weight: 0.7980 chunk 210 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 249 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 ASN ** E 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1079 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= 0.159 Angle : 0.529 6.143 27253 Z= 0.280 Chirality : 0.044 0.176 3157 Planarity : 0.003 0.032 3568 Dihedral : 4.682 23.165 2760 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 6.70 % Allowed : 36.35 % Favored : 56.95 % 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: -1.84 (0.16), residues: 2562 helix: -0.26 (0.25), residues: 406 sheet: -0.51 (0.20), residues: 651 loop : -1.90 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 503 HIS 0.000 0.000 HIS B 314 PHE 0.015 0.002 PHE G 249 TYR 0.009 0.001 TYR C 230 ARG 0.001 0.000 ARG C 290 *********************** 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 422 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 276 time to evaluate : 2.270 Fit side-chains REVERT: A 239 ASP cc_start: 0.8050 (t0) cc_final: 0.7830 (t0) REVERT: A 244 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8037 (mtpp) REVERT: A 246 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6393 (tt0) REVERT: A 281 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8172 (p90) REVERT: A 394 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.7412 (ttm170) REVERT: A 601 TYR cc_start: 0.9099 (OUTLIER) cc_final: 0.8760 (m-10) REVERT: B 217 GLU cc_start: 0.5597 (OUTLIER) cc_final: 0.5035 (mm-30) REVERT: B 225 ASN cc_start: 0.8016 (t0) cc_final: 0.7594 (t0) REVERT: B 239 ASP cc_start: 0.7947 (t0) cc_final: 0.7690 (t0) REVERT: B 263 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7899 (mt-10) REVERT: B 281 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.8211 (p90) REVERT: B 363 ASN cc_start: 0.2136 (OUTLIER) cc_final: 0.1534 (p0) REVERT: C 225 ASN cc_start: 0.8066 (t0) cc_final: 0.7779 (t0) REVERT: C 244 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7899 (mtpp) REVERT: C 541 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7920 (mmtp) REVERT: D 265 ASN cc_start: 0.8943 (OUTLIER) cc_final: 0.8631 (m-40) REVERT: D 281 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8079 (p90) REVERT: D 363 ASN cc_start: 0.2162 (OUTLIER) cc_final: 0.1651 (p0) REVERT: D 541 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7912 (mmtp) REVERT: E 225 ASN cc_start: 0.7907 (t0) cc_final: 0.7495 (t0) REVERT: E 265 ASN cc_start: 0.8934 (OUTLIER) cc_final: 0.8546 (m-40) REVERT: E 363 ASN cc_start: 0.2610 (OUTLIER) cc_final: 0.2208 (p0) REVERT: E 394 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7526 (ttm170) REVERT: F 225 ASN cc_start: 0.7853 (t0) cc_final: 0.7466 (t0) REVERT: F 260 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8533 (t0) REVERT: F 480 THR cc_start: 0.9200 (OUTLIER) cc_final: 0.8981 (t) REVERT: F 533 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7435 (tttt) REVERT: G 225 ASN cc_start: 0.8007 (t0) cc_final: 0.7507 (t0) REVERT: G 281 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.7856 (p90) REVERT: G 286 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7883 (mtmm) REVERT: G 601 TYR cc_start: 0.9046 (OUTLIER) cc_final: 0.8726 (m-10) outliers start: 146 outliers final: 98 residues processed: 392 average time/residue: 0.2590 time to fit residues: 164.4658 Evaluate side-chains 386 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 264 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 394 ARG Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 498 THR 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 A residue 610 ASN Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 363 ASN 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 486 ASN Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 291 ASP 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 427 ASN Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 498 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 C residue 605 LEU Chi-restraints excluded: chain C residue 610 ASN Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 291 ASP Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 363 ASN Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 486 ASN Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 541 LYS Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 574 SER Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 291 ASP Chi-restraints excluded: chain E residue 363 ASN Chi-restraints excluded: chain E residue 394 ARG Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 486 ASN 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 E residue 610 ASN Chi-restraints excluded: chain F residue 222 ASP 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 308 ILE Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 427 ASN Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 463 ASN Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 486 ASN 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 265 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 363 ASN Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 438 THR Chi-restraints excluded: chain G residue 453 ASP Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 486 ASN Chi-restraints excluded: chain G residue 535 LEU Chi-restraints excluded: chain G residue 549 GLU Chi-restraints excluded: chain G residue 601 TYR Chi-restraints excluded: chain G residue 610 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 154 optimal weight: 0.4980 chunk 99 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 158 optimal weight: 7.9990 chunk 170 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 196 optimal weight: 9.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 428 GLN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 ASN E 390 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 20059 Z= 0.472 Angle : 0.677 7.711 27253 Z= 0.361 Chirality : 0.049 0.266 3157 Planarity : 0.004 0.033 3568 Dihedral : 5.376 24.178 2760 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.71 % Favored : 88.29 % Rotamer: Outliers : 7.57 % Allowed : 35.66 % Favored : 56.77 % 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: -2.20 (0.15), residues: 2562 helix: -0.47 (0.25), residues: 406 sheet: -0.91 (0.20), residues: 651 loop : -2.06 (0.14), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 375 HIS 0.002 0.001 HIS B 314 PHE 0.033 0.004 PHE G 281 TYR 0.016 0.002 TYR A 257 ARG 0.006 0.000 ARG F 290 *********************** 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 433 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 268 time to evaluate : 2.493 Fit side-chains REVERT: A 225 ASN cc_start: 0.8113 (t0) cc_final: 0.7366 (t0) REVERT: A 244 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8024 (mtpp) REVERT: A 246 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6596 (tt0) REVERT: A 394 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7119 (ttm-80) REVERT: A 601 TYR cc_start: 0.9106 (OUTLIER) cc_final: 0.8822 (m-10) REVERT: B 217 GLU cc_start: 0.5589 (OUTLIER) cc_final: 0.5096 (mm-30) REVERT: B 225 ASN cc_start: 0.8073 (t0) cc_final: 0.7658 (t0) REVERT: B 239 ASP cc_start: 0.8005 (t0) cc_final: 0.7747 (t0) REVERT: B 263 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7848 (mt-10) REVERT: B 363 ASN cc_start: 0.1926 (OUTLIER) cc_final: 0.1631 (p0) REVERT: B 388 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.7551 (m-10) REVERT: C 225 ASN cc_start: 0.8199 (t0) cc_final: 0.7704 (t0) REVERT: C 388 TYR cc_start: 0.8786 (OUTLIER) cc_final: 0.7934 (m-10) REVERT: C 541 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7982 (mmtp) REVERT: D 265 ASN cc_start: 0.8983 (OUTLIER) cc_final: 0.8698 (m-40) REVERT: D 363 ASN cc_start: 0.2061 (OUTLIER) cc_final: 0.1695 (p0) REVERT: E 225 ASN cc_start: 0.8027 (t0) cc_final: 0.7605 (t0) REVERT: E 265 ASN cc_start: 0.8973 (OUTLIER) cc_final: 0.8686 (m-40) REVERT: E 363 ASN cc_start: 0.2622 (OUTLIER) cc_final: 0.2360 (p0) REVERT: E 390 ASN cc_start: 0.9104 (OUTLIER) cc_final: 0.8723 (p0) REVERT: E 394 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.7987 (ttm170) REVERT: F 225 ASN cc_start: 0.8004 (t0) cc_final: 0.7387 (t0) REVERT: F 239 ASP cc_start: 0.7883 (t0) cc_final: 0.7677 (t0) REVERT: F 260 ASN cc_start: 0.8954 (OUTLIER) cc_final: 0.8647 (t0) REVERT: F 363 ASN cc_start: 0.2574 (OUTLIER) cc_final: 0.1895 (p0) REVERT: F 388 TYR cc_start: 0.8823 (OUTLIER) cc_final: 0.8361 (m-10) REVERT: F 480 THR cc_start: 0.9199 (OUTLIER) cc_final: 0.8983 (t) REVERT: F 514 SER cc_start: 0.9337 (m) cc_final: 0.9108 (m) REVERT: F 533 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7492 (tttt) REVERT: G 225 ASN cc_start: 0.8090 (t0) cc_final: 0.7448 (t0) REVERT: G 286 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7925 (mtmm) REVERT: G 388 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.7419 (m-10) REVERT: G 601 TYR cc_start: 0.9066 (OUTLIER) cc_final: 0.8795 (m-10) outliers start: 165 outliers final: 117 residues processed: 400 average time/residue: 0.2571 time to fit residues: 169.3344 Evaluate side-chains 403 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 262 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 394 ARG Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 601 TYR Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 291 ASP 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 413 VAL Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 427 ASN Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 486 ASN 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 549 GLU Chi-restraints excluded: chain C residue 567 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 610 ASN Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 291 ASP Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 363 ASN Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 396 TYR Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 427 ASN Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 486 ASN Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain D residue 567 ASN 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 265 ASN Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 363 ASN 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 486 ASN Chi-restraints excluded: chain E residue 535 LEU Chi-restraints excluded: chain E residue 549 GLU Chi-restraints excluded: chain E residue 561 ASP Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 610 ASN Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 260 ASN Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 363 ASN Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 388 TYR Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 427 ASN Chi-restraints excluded: chain F residue 463 ASN Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 486 ASN 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 265 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 363 ASN 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 427 ASN Chi-restraints excluded: chain G residue 438 THR Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 453 ASP Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 486 ASN Chi-restraints excluded: chain G residue 535 LEU Chi-restraints excluded: chain G residue 549 GLU Chi-restraints excluded: chain G residue 578 LEU Chi-restraints excluded: chain G residue 601 TYR Chi-restraints excluded: chain G residue 610 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 227 optimal weight: 0.9990 chunk 239 optimal weight: 0.8980 chunk 218 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 182 optimal weight: 8.9990 chunk 71 optimal weight: 0.9980 chunk 210 optimal weight: 0.9980 chunk 220 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 463 ASN ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 ASN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20059 Z= 0.182 Angle : 0.562 6.229 27253 Z= 0.299 Chirality : 0.045 0.235 3157 Planarity : 0.003 0.033 3568 Dihedral : 4.914 23.130 2760 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 5.32 % Allowed : 38.32 % Favored : 56.36 % 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: -1.96 (0.16), residues: 2562 helix: -0.35 (0.25), residues: 406 sheet: -0.72 (0.20), residues: 651 loop : -1.90 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 245 HIS 0.000 0.000 HIS A 314 PHE 0.017 0.002 PHE G 249 TYR 0.010 0.001 TYR C 230 ARG 0.004 0.000 ARG F 290 *********************** 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 378 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 262 time to evaluate : 2.495 Fit side-chains REVERT: A 225 ASN cc_start: 0.7968 (t0) cc_final: 0.7296 (t0) REVERT: A 244 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8045 (mtpp) REVERT: A 281 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.8105 (p90) REVERT: A 394 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.7558 (ttm170) REVERT: A 601 TYR cc_start: 0.9096 (OUTLIER) cc_final: 0.8787 (m-10) REVERT: B 217 GLU cc_start: 0.5602 (OUTLIER) cc_final: 0.5087 (mm-30) REVERT: B 225 ASN cc_start: 0.8002 (t0) cc_final: 0.7609 (t0) REVERT: B 239 ASP cc_start: 0.8033 (t0) cc_final: 0.7813 (t0) REVERT: B 263 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7844 (mt-10) REVERT: B 281 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.8049 (p90) REVERT: B 297 TYR cc_start: 0.8732 (t80) cc_final: 0.8027 (t80) REVERT: B 363 ASN cc_start: 0.2201 (OUTLIER) cc_final: 0.1555 (p0) REVERT: B 388 TYR cc_start: 0.8734 (OUTLIER) cc_final: 0.7544 (m-10) REVERT: C 225 ASN cc_start: 0.8086 (t0) cc_final: 0.7633 (t0) REVERT: C 541 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7934 (mmtp) REVERT: D 281 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.8156 (p90) REVERT: D 363 ASN cc_start: 0.2109 (OUTLIER) cc_final: 0.1674 (p0) REVERT: D 541 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7940 (mmtp) REVERT: E 225 ASN cc_start: 0.7961 (t0) cc_final: 0.7555 (t0) REVERT: E 265 ASN cc_start: 0.8965 (OUTLIER) cc_final: 0.8600 (m-40) REVERT: E 363 ASN cc_start: 0.2082 (OUTLIER) cc_final: 0.1729 (t0) REVERT: E 394 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7692 (ttm170) REVERT: F 225 ASN cc_start: 0.7915 (t0) cc_final: 0.7553 (t0) REVERT: F 239 ASP cc_start: 0.7904 (t0) cc_final: 0.7703 (t0) REVERT: F 260 ASN cc_start: 0.8825 (OUTLIER) cc_final: 0.8553 (t0) REVERT: F 290 ARG cc_start: 0.8284 (ptm-80) cc_final: 0.7321 (ptm-80) REVERT: F 388 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.8477 (m-10) REVERT: F 480 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8963 (t) REVERT: F 533 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7505 (tttt) REVERT: G 225 ASN cc_start: 0.8011 (t0) cc_final: 0.7414 (t0) REVERT: G 281 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.7837 (p90) REVERT: G 286 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7907 (mtmm) REVERT: G 541 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8268 (mmtp) REVERT: G 601 TYR cc_start: 0.9031 (OUTLIER) cc_final: 0.8748 (m-10) outliers start: 116 outliers final: 79 residues processed: 352 average time/residue: 0.2684 time to fit residues: 152.9495 Evaluate side-chains 364 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 261 time to evaluate : 2.264 ------------------------------------------------------------------------------- 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 398 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 601 TYR Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 363 ASN 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 486 ASN 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 278 SER Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 541 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 601 TYR Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 610 ASN Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 291 ASP Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 363 ASN Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 486 ASN Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 541 LYS 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 265 ASN Chi-restraints excluded: chain E residue 363 ASN Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 394 ARG Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 476 ILE Chi-restraints excluded: chain E residue 486 ASN 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 610 ASN 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 413 VAL Chi-restraints excluded: chain F residue 463 ASN Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 486 ASN 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 281 PHE Chi-restraints excluded: chain G residue 286 LYS Chi-restraints excluded: chain G residue 363 ASN Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 453 ASP Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 486 ASN Chi-restraints excluded: chain G residue 535 LEU Chi-restraints excluded: chain G residue 541 LYS Chi-restraints excluded: chain G residue 578 LEU Chi-restraints excluded: chain G residue 601 TYR Chi-restraints excluded: chain G residue 610 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 152 optimal weight: 2.9990 chunk 245 optimal weight: 0.2980 chunk 150 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 171 optimal weight: 0.8980 chunk 258 optimal weight: 5.9990 chunk 237 optimal weight: 0.9980 chunk 205 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 158 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 ASN E 390 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1231 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= 0.188 Angle : 0.557 6.493 27253 Z= 0.295 Chirality : 0.045 0.231 3157 Planarity : 0.003 0.033 3568 Dihedral : 4.804 22.875 2760 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 5.23 % Allowed : 38.27 % Favored : 56.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.16), residues: 2562 helix: -0.29 (0.25), residues: 406 sheet: -0.53 (0.20), residues: 637 loop : -1.91 (0.15), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 245 HIS 0.000 0.000 HIS B 314 PHE 0.016 0.002 PHE A 281 TYR 0.010 0.001 TYR C 230 ARG 0.004 0.000 ARG F 290 ********************** 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 383 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 269 time to evaluate : 2.265 Fit side-chains REVERT: A 225 ASN cc_start: 0.7985 (t0) cc_final: 0.7320 (t0) REVERT: A 244 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8062 (mtpp) REVERT: A 281 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8268 (p90) REVERT: A 394 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7523 (ttm170) REVERT: A 520 ASP cc_start: 0.7856 (t0) cc_final: 0.7524 (t0) REVERT: A 601 TYR cc_start: 0.9079 (OUTLIER) cc_final: 0.8767 (m-10) REVERT: B 217 GLU cc_start: 0.5588 (OUTLIER) cc_final: 0.5078 (mm-30) REVERT: B 225 ASN cc_start: 0.7993 (t0) cc_final: 0.7581 (t0) REVERT: B 239 ASP cc_start: 0.8033 (t0) cc_final: 0.7812 (t0) REVERT: B 263 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7845 (mt-10) REVERT: B 281 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.8224 (p90) REVERT: B 297 TYR cc_start: 0.8744 (t80) cc_final: 0.8014 (t80) REVERT: B 363 ASN cc_start: 0.2176 (OUTLIER) cc_final: 0.1553 (p0) REVERT: C 225 ASN cc_start: 0.8112 (t0) cc_final: 0.7640 (t0) REVERT: C 541 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7930 (mmtp) REVERT: D 281 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.8204 (p90) REVERT: D 363 ASN cc_start: 0.2092 (OUTLIER) cc_final: 0.1706 (p0) REVERT: D 541 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7936 (mmtp) REVERT: E 225 ASN cc_start: 0.7984 (t0) cc_final: 0.7574 (t0) REVERT: E 265 ASN cc_start: 0.8962 (OUTLIER) cc_final: 0.8573 (m-40) REVERT: E 363 ASN cc_start: 0.2720 (OUTLIER) cc_final: 0.2399 (t0) REVERT: E 390 ASN cc_start: 0.9057 (OUTLIER) cc_final: 0.8672 (p0) REVERT: E 394 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7129 (ttm170) REVERT: F 225 ASN cc_start: 0.7961 (t0) cc_final: 0.7586 (t0) REVERT: F 260 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8552 (t0) REVERT: F 290 ARG cc_start: 0.8269 (ptm-80) cc_final: 0.7328 (ptm-80) REVERT: F 388 TYR cc_start: 0.8714 (OUTLIER) cc_final: 0.8501 (m-10) REVERT: F 480 THR cc_start: 0.9190 (OUTLIER) cc_final: 0.8975 (t) REVERT: F 533 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7480 (tttt) REVERT: G 225 ASN cc_start: 0.8013 (t0) cc_final: 0.7383 (t0) REVERT: G 281 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.7838 (p90) REVERT: G 286 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7924 (mtmm) REVERT: G 541 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8259 (mmtp) REVERT: G 601 TYR cc_start: 0.9032 (OUTLIER) cc_final: 0.8750 (m-10) outliers start: 114 outliers final: 84 residues processed: 362 average time/residue: 0.2590 time to fit residues: 152.1427 Evaluate side-chains 371 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 263 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 394 ARG Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 601 TYR Chi-restraints excluded: chain A residue 610 ASN Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 363 ASN 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 486 ASN Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 291 ASP 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 486 ASN Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 498 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 C residue 605 LEU Chi-restraints excluded: chain C residue 610 ASN Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 291 ASP Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 363 ASN Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 427 ASN Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 486 ASN Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 541 LYS Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 574 SER Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 363 ASN Chi-restraints excluded: chain E residue 379 LEU 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 486 ASN 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 610 ASN 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 413 VAL Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 463 ASN Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 486 ASN Chi-restraints excluded: chain F residue 533 LYS Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 260 ASN Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 286 LYS Chi-restraints excluded: chain G residue 363 ASN Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 453 ASP Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 486 ASN Chi-restraints excluded: chain G residue 535 LEU Chi-restraints excluded: chain G residue 541 LYS Chi-restraints excluded: chain G residue 578 LEU Chi-restraints excluded: chain G residue 601 TYR Chi-restraints excluded: chain G residue 610 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 163 optimal weight: 0.6980 chunk 218 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 189 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 205 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 211 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 ASN E 390 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.135359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.106909 restraints weight = 29880.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.110310 restraints weight = 15086.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.112459 restraints weight = 10026.704| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 20059 Z= 0.350 Angle : 0.624 7.160 27253 Z= 0.332 Chirality : 0.047 0.241 3157 Planarity : 0.004 0.046 3568 Dihedral : 5.096 23.492 2760 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % Rotamer: Outliers : 6.20 % Allowed : 37.08 % Favored : 56.72 % 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: -2.05 (0.16), residues: 2562 helix: -0.34 (0.25), residues: 406 sheet: -0.79 (0.20), residues: 651 loop : -1.98 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 245 HIS 0.001 0.001 HIS B 314 PHE 0.026 0.003 PHE A 281 TYR 0.012 0.001 TYR C 230 ARG 0.004 0.000 ARG F 290 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4113.24 seconds wall clock time: 76 minutes 42.65 seconds (4602.65 seconds total)