Starting phenix.real_space_refine on Sun Jun 22 10:30:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ysg_34074/06_2025/7ysg_34074.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ysg_34074/06_2025/7ysg_34074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ysg_34074/06_2025/7ysg_34074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ysg_34074/06_2025/7ysg_34074.map" model { file = "/net/cci-nas-00/data/ceres_data/7ysg_34074/06_2025/7ysg_34074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ysg_34074/06_2025/7ysg_34074.cif" } resolution = 3.18 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= 0.000 sd= 0.048 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: 4 Type Number sf(0) Gaussians S 138 5.16 5 C 16155 2.51 5 N 4371 2.21 5 O 5012 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 125 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25676 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1786 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 212} Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1769 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 18, 'TRANS': 209} Chain: "C" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1763 Classifications: {'peptide': 227} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 18, 'TRANS': 208} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 18, 'TRANS': 205} Chain: "F" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 18, 'TRANS': 205} Chain: "G" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1742 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 18, 'TRANS': 205} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1798 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 18, 'TRANS': 213} Chain: "J" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 851 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain breaks: 1 Chain: "K" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1798 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 18, 'TRANS': 213} Chain: "L" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1798 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 18, 'TRANS': 213} Chain: "P" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3851 Classifications: {'peptide': 495} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 469} Chain breaks: 6 Chain: "R" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 766 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "S" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 785 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "U" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 766 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "V" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 805 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 16.42, per 1000 atoms: 0.64 Number of scatterers: 25676 At special positions: 0 Unit cell: (136.08, 185.76, 191.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 138 16.00 O 5012 8.00 N 4371 7.00 C 16155 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 536 " distance=2.03 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS J 68 " distance=2.23 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 426 " distance=2.04 Simple disulfide: pdb=" SG CYS B 414 " - pdb=" SG CYS C 414 " distance=2.51 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 536 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 426 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 536 " distance=2.03 Simple disulfide: pdb=" SG CYS D 367 " - pdb=" SG CYS D 426 " distance=2.03 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 536 " distance=1.97 Simple disulfide: pdb=" SG CYS E 474 " - pdb=" SG CYS E 536 " distance=1.98 Simple disulfide: pdb=" SG CYS F 367 " - pdb=" SG CYS F 426 " distance=2.03 Simple disulfide: pdb=" SG CYS F 474 " - pdb=" SG CYS F 536 " distance=2.03 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 426 " distance=2.03 Simple disulfide: pdb=" SG CYS G 474 " - pdb=" SG CYS G 536 " distance=1.98 Simple disulfide: pdb=" SG CYS H 367 " - pdb=" SG CYS H 426 " distance=2.03 Simple disulfide: pdb=" SG CYS H 474 " - pdb=" SG CYS H 536 " distance=1.98 Simple disulfide: pdb=" SG CYS H 575 " - pdb=" SG CYS K 575 " distance=2.03 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 100 " distance=2.03 Simple disulfide: pdb=" SG CYS J 14 " - pdb=" SG CYS L 575 " distance=2.06 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 133 " distance=2.03 Simple disulfide: pdb=" SG CYS K 367 " - pdb=" SG CYS K 426 " distance=2.03 Simple disulfide: pdb=" SG CYS K 474 " - pdb=" SG CYS K 536 " distance=1.95 Simple disulfide: pdb=" SG CYS L 367 " - pdb=" SG CYS L 426 " distance=2.03 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 536 " distance=2.01 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 38 " - pdb=" SG CYS P 46 " distance=2.04 Simple disulfide: pdb=" SG CYS P 134 " - pdb=" SG CYS P 202 " distance=2.02 Simple disulfide: pdb=" SG CYS P 239 " - pdb=" SG CYS P 307 " distance=2.02 Simple disulfide: pdb=" SG CYS P 253 " - pdb=" SG CYS P 261 " distance=2.05 Simple disulfide: pdb=" SG CYS P 353 " - pdb=" SG CYS P 423 " distance=1.95 Simple disulfide: pdb=" SG CYS P 367 " - pdb=" SG CYS P 377 " distance=2.02 Simple disulfide: pdb=" SG CYS P 464 " - pdb=" SG CYS P 526 " distance=2.06 Simple disulfide: pdb=" SG CYS P 478 " - pdb=" SG CYS P 485 " distance=2.02 Simple disulfide: pdb=" SG CYS R 37 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 49 " - pdb=" SG CYS R 58 " distance=2.03 Simple disulfide: pdb=" SG CYS S 37 " - pdb=" SG CYS S 104 " distance=2.03 Simple disulfide: pdb=" SG CYS S 49 " - pdb=" SG CYS S 58 " distance=2.03 Simple disulfide: pdb=" SG CYS U 37 " - pdb=" SG CYS U 104 " distance=2.03 Simple disulfide: pdb=" SG CYS U 49 " - pdb=" SG CYS U 58 " distance=2.03 Simple disulfide: pdb=" SG CYS V 37 " - pdb=" SG CYS V 104 " distance=2.03 Simple disulfide: pdb=" SG CYS V 49 " - pdb=" SG CYS V 58 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 601 " - " ASN A 563 " " NAG B 601 " - " ASN B 563 " " NAG C 601 " - " ASN C 563 " " NAG D 601 " - " ASN D 563 " " NAG E 601 " - " ASN E 563 " " NAG F 601 " - " ASN F 563 " " NAG H 601 " - " ASN H 563 " " NAG I 1 " - " ASN J 48 " " NAG L 601 " - " ASN L 563 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.28 Conformation dependent library (CDL) restraints added in 3.3 seconds 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6204 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 79 sheets defined 10.3% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.84 Creating SS restraints... Processing helix chain 'A' and resid 353 through 360 Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.514A pdb=" N TRP A 418 " --> pdb=" O CYS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 466 removed outlier: 3.674A pdb=" N LEU A 466 " --> pdb=" O GLU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 531 removed outlier: 3.952A pdb=" N GLY A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 460 through 465 removed outlier: 3.848A pdb=" N ASN B 465 " --> pdb=" O ARG B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 529 Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 414 through 421 removed outlier: 3.828A pdb=" N SER C 420 " --> pdb=" O ASP C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 465 Processing helix chain 'C' and resid 524 through 530 removed outlier: 3.674A pdb=" N THR C 530 " --> pdb=" O GLU C 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 361 Processing helix chain 'D' and resid 414 through 421 removed outlier: 4.144A pdb=" N GLY D 421 " --> pdb=" O ASP D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 467 Processing helix chain 'D' and resid 524 through 530 Processing helix chain 'E' and resid 353 through 360 Processing helix chain 'E' and resid 414 through 421 removed outlier: 3.983A pdb=" N TRP E 418 " --> pdb=" O CYS E 414 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY E 421 " --> pdb=" O ASP E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 467 removed outlier: 3.602A pdb=" N ARG E 467 " --> pdb=" O GLN E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 531 removed outlier: 3.785A pdb=" N TRP E 528 " --> pdb=" O SER E 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 361 Processing helix chain 'F' and resid 460 through 467 Processing helix chain 'F' and resid 524 through 530 removed outlier: 3.969A pdb=" N THR F 530 " --> pdb=" O GLU F 526 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 361 Processing helix chain 'G' and resid 414 through 420 Processing helix chain 'G' and resid 460 through 465 Processing helix chain 'G' and resid 524 through 530 Processing helix chain 'H' and resid 353 through 361 Processing helix chain 'H' and resid 414 through 421 removed outlier: 3.574A pdb=" N TRP H 418 " --> pdb=" O CYS H 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 460 through 467 Processing helix chain 'H' and resid 524 through 530 Processing helix chain 'J' and resid 64 through 69 removed outlier: 3.540A pdb=" N CYS J 68 " --> pdb=" O LEU J 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 353 through 361 Processing helix chain 'K' and resid 414 through 421 removed outlier: 3.938A pdb=" N TRP K 418 " --> pdb=" O CYS K 414 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY K 421 " --> pdb=" O ASP K 417 " (cutoff:3.500A) Processing helix chain 'K' and resid 460 through 466 removed outlier: 3.596A pdb=" N LEU K 466 " --> pdb=" O GLU K 462 " (cutoff:3.500A) Processing helix chain 'K' and resid 526 through 531 Processing helix chain 'L' and resid 353 through 361 Processing helix chain 'L' and resid 415 through 421 Processing helix chain 'L' and resid 460 through 467 removed outlier: 3.537A pdb=" N ARG L 467 " --> pdb=" O GLN L 463 " (cutoff:3.500A) Processing helix chain 'L' and resid 525 through 531 removed outlier: 3.504A pdb=" N GLY L 531 " --> pdb=" O GLU L 527 " (cutoff:3.500A) Processing helix chain 'L' and resid 553 through 557 removed outlier: 3.735A pdb=" N GLY L 557 " --> pdb=" O LYS L 554 " (cutoff:3.500A) Processing helix chain 'P' and resid 27 through 33 Processing helix chain 'P' and resid 96 through 100 removed outlier: 4.170A pdb=" N GLY P 100 " --> pdb=" O ASN P 97 " (cutoff:3.500A) Processing helix chain 'P' and resid 242 through 247 removed outlier: 3.880A pdb=" N ASN P 247 " --> pdb=" O PRO P 243 " (cutoff:3.500A) Processing helix chain 'P' and resid 272 through 276 removed outlier: 4.034A pdb=" N GLU P 276 " --> pdb=" O PRO P 273 " (cutoff:3.500A) Processing helix chain 'P' and resid 298 through 302 removed outlier: 3.727A pdb=" N ALA P 302 " --> pdb=" O LYS P 299 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 31 Processing helix chain 'V' and resid 69 through 73 Processing sheet with id=AA1, first strand: chain 'A' and resid 346 through 350 removed outlier: 3.722A pdb=" N THR A 366 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 372 " --> pdb=" O PHE A 405 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 381 through 383 removed outlier: 7.060A pdb=" N TRP A 382 " --> pdb=" O VAL A 390 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 424 through 427 Processing sheet with id=AA4, first strand: chain 'A' and resid 453 through 457 removed outlier: 3.611A pdb=" N VAL A 476 " --> pdb=" O ALA A 517 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 485 through 490 Processing sheet with id=AA6, first strand: chain 'A' and resid 561 through 563 Processing sheet with id=AA7, first strand: chain 'A' and resid 565 through 569 removed outlier: 3.504A pdb=" N PHE J 60 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR J 62 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 346 through 349 Processing sheet with id=AA9, first strand: chain 'B' and resid 364 through 365 Processing sheet with id=AB1, first strand: chain 'B' and resid 425 through 428 removed outlier: 3.584A pdb=" N GLN B 439 " --> pdb=" O CYS B 426 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 453 through 457 Processing sheet with id=AB3, first strand: chain 'B' and resid 453 through 457 Processing sheet with id=AB4, first strand: chain 'B' and resid 485 through 489 Processing sheet with id=AB5, first strand: chain 'C' and resid 347 through 350 removed outlier: 3.562A pdb=" N THR C 366 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LYS C 364 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE C 413 " --> pdb=" O LYS C 364 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N THR C 366 " --> pdb=" O ALA C 411 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ALA C 411 " --> pdb=" O THR C 366 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU C 368 " --> pdb=" O GLY C 409 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLY C 409 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N THR C 370 " --> pdb=" O ALA C 407 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ALA C 407 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU C 372 " --> pdb=" O PHE C 405 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 379 through 383 removed outlier: 3.541A pdb=" N THR C 379 " --> pdb=" O THR C 429 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 455 through 457 removed outlier: 3.725A pdb=" N SER C 519 " --> pdb=" O CYS C 474 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 455 through 457 removed outlier: 5.560A pdb=" N TYR C 515 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 493 through 494 removed outlier: 3.553A pdb=" N GLN C 490 " --> pdb=" O GLN C 493 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 347 through 350 removed outlier: 3.850A pdb=" N THR D 363 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA D 411 " --> pdb=" O LEU D 365 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 378 through 379 removed outlier: 3.831A pdb=" N THR D 425 " --> pdb=" O THR D 383 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 378 through 379 Processing sheet with id=AC4, first strand: chain 'D' and resid 453 through 457 removed outlier: 3.746A pdb=" N GLY D 478 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 453 through 457 removed outlier: 3.746A pdb=" N GLY D 478 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 493 through 494 removed outlier: 3.857A pdb=" N GLN D 493 " --> pdb=" O GLN D 490 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLN D 490 " --> pdb=" O GLN D 493 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 562 through 567 removed outlier: 6.826A pdb=" N TYR D 562 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER E 565 " --> pdb=" O TYR D 562 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL D 564 " --> pdb=" O SER E 565 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N VAL E 567 " --> pdb=" O VAL D 564 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU D 566 " --> pdb=" O VAL E 567 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'E' and resid 346 through 350 removed outlier: 3.669A pdb=" N ALA E 411 " --> pdb=" O LEU E 365 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 424 through 428 Processing sheet with id=AD1, first strand: chain 'E' and resid 453 through 457 Processing sheet with id=AD2, first strand: chain 'E' and resid 488 through 489 Processing sheet with id=AD3, first strand: chain 'F' and resid 382 through 384 Processing sheet with id=AD4, first strand: chain 'F' and resid 453 through 457 removed outlier: 5.045A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE F 520 " --> pdb=" O VAL F 501 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 493 through 494 removed outlier: 3.550A pdb=" N CYS F 536 " --> pdb=" O ARG F 550 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 347 through 350 removed outlier: 3.836A pdb=" N THR G 366 " --> pdb=" O ILE G 350 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 380 through 384 Processing sheet with id=AD8, first strand: chain 'G' and resid 453 through 457 removed outlier: 3.826A pdb=" N LEU G 457 " --> pdb=" O THR G 473 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA G 517 " --> pdb=" O VAL G 476 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 453 through 457 removed outlier: 3.826A pdb=" N LEU G 457 " --> pdb=" O THR G 473 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 493 through 494 Processing sheet with id=AE2, first strand: chain 'H' and resid 347 through 348 Processing sheet with id=AE3, first strand: chain 'H' and resid 381 through 382 removed outlier: 3.558A pdb=" N SER H 381 " --> pdb=" O THR H 427 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR H 427 " --> pdb=" O SER H 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'H' and resid 453 through 457 Processing sheet with id=AE5, first strand: chain 'H' and resid 453 through 457 removed outlier: 5.303A pdb=" N TYR H 515 " --> pdb=" O GLY H 478 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 493 through 494 removed outlier: 3.562A pdb=" N ARG H 550 " --> pdb=" O CYS H 536 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 5 through 10 removed outlier: 5.414A pdb=" N VAL J 6 " --> pdb=" O SER J 19 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N SER J 19 " --> pdb=" O VAL J 6 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR J 18 " --> pdb=" O ASN J 36 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 21 through 22 Processing sheet with id=AE9, first strand: chain 'J' and resid 103 through 104 removed outlier: 6.607A pdb=" N TYR J 103 " --> pdb=" O CYS L 575 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'J' and resid 110 through 114 Processing sheet with id=AF2, first strand: chain 'K' and resid 346 through 347 removed outlier: 3.779A pdb=" N ARG K 346 " --> pdb=" O THR K 370 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 363 through 364 removed outlier: 3.930A pdb=" N ILE K 413 " --> pdb=" O THR K 363 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 380 through 383 removed outlier: 3.666A pdb=" N SER K 381 " --> pdb=" O THR K 427 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN K 439 " --> pdb=" O CYS K 426 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 454 through 457 Processing sheet with id=AF6, first strand: chain 'K' and resid 454 through 457 Processing sheet with id=AF7, first strand: chain 'K' and resid 493 through 494 removed outlier: 3.565A pdb=" N GLN K 493 " --> pdb=" O GLN K 490 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 561 through 562 removed outlier: 6.830A pdb=" N LEU K 561 " --> pdb=" O TYR L 562 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'L' and resid 349 through 350 removed outlier: 4.277A pdb=" N ILE L 350 " --> pdb=" O THR L 366 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N THR L 366 " --> pdb=" O ILE L 350 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'L' and resid 454 through 457 Processing sheet with id=AG2, first strand: chain 'L' and resid 454 through 457 Processing sheet with id=AG3, first strand: chain 'L' and resid 493 through 494 removed outlier: 3.642A pdb=" N MET L 489 " --> pdb=" O THR L 535 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 11 through 13 removed outlier: 6.486A pdb=" N SER P 12 " --> pdb=" O SER P 110 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ARG P 89 " --> pdb=" O GLN P 40 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG P 39 " --> pdb=" O THR P 48 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N THR P 48 " --> pdb=" O ARG P 39 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLY P 41 " --> pdb=" O CYS P 46 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N CYS P 46 " --> pdb=" O GLY P 41 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'P' and resid 18 through 23 Processing sheet with id=AG6, first strand: chain 'P' and resid 121 through 125 removed outlier: 3.530A pdb=" N LEU P 220 " --> pdb=" O VAL P 124 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 130 through 133 Processing sheet with id=AG8, first strand: chain 'P' and resid 202 through 203 Processing sheet with id=AG9, first strand: chain 'P' and resid 225 through 230 removed outlier: 6.684A pdb=" N GLU P 225 " --> pdb=" O GLN P 325 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N PHE P 327 " --> pdb=" O GLU P 225 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL P 227 " --> pdb=" O PHE P 327 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ASN P 329 " --> pdb=" O VAL P 227 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N GLU P 229 " --> pdb=" O ASN P 329 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'P' and resid 234 through 240 removed outlier: 4.051A pdb=" N PHE P 290 " --> pdb=" O CYS P 239 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'P' and resid 251 through 252 removed outlier: 3.775A pdb=" N VAL P 265 " --> pdb=" O LEU P 252 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'P' and resid 343 through 344 removed outlier: 5.706A pdb=" N GLY P 343 " --> pdb=" O ILE P 440 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'P' and resid 351 through 352 Processing sheet with id=AH5, first strand: chain 'P' and resid 419 through 422 Processing sheet with id=AH6, first strand: chain 'P' and resid 463 through 464 removed outlier: 3.854A pdb=" N CYS P 464 " --> pdb=" O ARG P 507 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'P' and resid 486 through 487 removed outlier: 3.561A pdb=" N GLN P 486 " --> pdb=" O LYS P 479 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'R' and resid 22 through 24 removed outlier: 5.479A pdb=" N VAL R 23 " --> pdb=" O THR R 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'R' and resid 34 through 38 Processing sheet with id=AI1, first strand: chain 'R' and resid 58 through 62 removed outlier: 5.274A pdb=" N THR R 60 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ARG R 50 " --> pdb=" O THR R 60 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL R 62 " --> pdb=" O LEU R 48 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'S' and resid 33 through 38 Processing sheet with id=AI3, first strand: chain 'S' and resid 58 through 63 removed outlier: 6.589A pdb=" N LEU S 48 " --> pdb=" O VAL S 61 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N SER S 63 " --> pdb=" O ILE S 46 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE S 46 " --> pdb=" O SER S 63 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA S 106 " --> pdb=" O LYS S 114 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LYS S 114 " --> pdb=" O ALA S 106 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'U' and resid 33 through 38 Processing sheet with id=AI5, first strand: chain 'U' and resid 58 through 63 removed outlier: 6.700A pdb=" N LEU U 48 " --> pdb=" O VAL U 61 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N SER U 63 " --> pdb=" O ILE U 46 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE U 46 " --> pdb=" O SER U 63 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY U 105 " --> pdb=" O TYR U 47 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TYR U 102 " --> pdb=" O LYS U 117 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LYS U 117 " --> pdb=" O TYR U 102 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N CYS U 104 " --> pdb=" O THR U 115 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'V' and resid 33 through 38 Processing sheet with id=AI7, first strand: chain 'V' and resid 60 through 62 removed outlier: 5.095A pdb=" N THR V 60 " --> pdb=" O ARG V 50 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ARG V 50 " --> pdb=" O THR V 60 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL V 62 " --> pdb=" O LEU V 48 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TYR V 102 " --> pdb=" O LYS V 117 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LYS V 117 " --> pdb=" O TYR V 102 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N CYS V 104 " --> pdb=" O THR V 115 " (cutoff:3.500A) 690 hydrogen bonds defined for protein. 1749 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: 9.25 Time building geometry restraints manager: 7.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 4210 1.26 - 1.40: 6218 1.40 - 1.55: 15572 1.55 - 1.69: 87 1.69 - 1.83: 180 Bond restraints: 26267 Sorted by residual: bond pdb=" C GLY P 404 " pdb=" N THR P 405 " ideal model delta sigma weight residual 1.332 1.523 -0.190 1.40e-02 5.10e+03 1.85e+02 bond pdb=" C CYS H 536 " pdb=" O CYS H 536 " ideal model delta sigma weight residual 1.235 1.123 0.112 1.13e-02 7.83e+03 9.90e+01 bond pdb=" C VAL L 567 " pdb=" O VAL L 567 " ideal model delta sigma weight residual 1.238 1.134 0.104 1.06e-02 8.90e+03 9.54e+01 bond pdb=" C TYR G 562 " pdb=" O TYR G 562 " ideal model delta sigma weight residual 1.234 1.127 0.108 1.11e-02 8.12e+03 9.45e+01 bond pdb=" CA THR B 477 " pdb=" C THR B 477 " ideal model delta sigma weight residual 1.520 1.404 0.116 1.20e-02 6.94e+03 9.41e+01 ... (remaining 26262 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.59: 35155 5.59 - 11.18: 581 11.18 - 16.78: 85 16.78 - 22.37: 15 22.37 - 27.96: 5 Bond angle restraints: 35841 Sorted by residual: angle pdb=" C GLN E 493 " pdb=" N PRO E 494 " pdb=" CA PRO E 494 " ideal model delta sigma weight residual 119.84 142.99 -23.15 1.25e+00 6.40e-01 3.43e+02 angle pdb=" N THR L 551 " pdb=" CA THR L 551 " pdb=" C THR L 551 " ideal model delta sigma weight residual 109.40 136.17 -26.77 1.63e+00 3.76e-01 2.70e+02 angle pdb=" C GLY P 404 " pdb=" N THR P 405 " pdb=" CA THR P 405 " ideal model delta sigma weight residual 121.54 149.50 -27.96 1.91e+00 2.74e-01 2.14e+02 angle pdb=" C SER B 496 " pdb=" N PRO B 497 " pdb=" CA PRO B 497 " ideal model delta sigma weight residual 119.84 137.59 -17.75 1.25e+00 6.40e-01 2.02e+02 angle pdb=" N VAL L 552 " pdb=" CA VAL L 552 " pdb=" C VAL L 552 " ideal model delta sigma weight residual 108.06 125.56 -17.50 1.28e+00 6.10e-01 1.87e+02 ... (remaining 35836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.59: 14780 26.59 - 53.19: 1109 53.19 - 79.78: 203 79.78 - 106.38: 21 106.38 - 132.97: 10 Dihedral angle restraints: 16123 sinusoidal: 6544 harmonic: 9579 Sorted by residual: dihedral pdb=" CA SER C 480 " pdb=" C SER C 480 " pdb=" N PRO C 481 " pdb=" CA PRO C 481 " ideal model delta harmonic sigma weight residual -180.00 -75.27 -104.73 0 5.00e+00 4.00e-02 4.39e+02 dihedral pdb=" C THR L 551 " pdb=" N THR L 551 " pdb=" CA THR L 551 " pdb=" CB THR L 551 " ideal model delta harmonic sigma weight residual -122.00 -151.42 29.42 0 2.50e+00 1.60e-01 1.39e+02 dihedral pdb=" N GLU C 525 " pdb=" C GLU C 525 " pdb=" CA GLU C 525 " pdb=" CB GLU C 525 " ideal model delta harmonic sigma weight residual 122.80 151.03 -28.23 0 2.50e+00 1.60e-01 1.28e+02 ... (remaining 16120 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.285: 4071 0.285 - 0.570: 113 0.570 - 0.855: 17 0.855 - 1.140: 1 1.140 - 1.425: 3 Chirality restraints: 4205 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN J 48 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.98 -1.42 2.00e-01 2.50e+01 5.07e+01 chirality pdb=" CA THR L 551 " pdb=" N THR L 551 " pdb=" C THR L 551 " pdb=" CB THR L 551 " both_signs ideal model delta sigma weight residual False 2.53 1.10 1.42 2.00e-01 2.50e+01 5.05e+01 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.80e+01 ... (remaining 4202 not shown) Planarity restraints: 4587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " 0.425 2.00e-02 2.50e+03 3.48e-01 1.51e+03 pdb=" C7 NAG I 2 " -0.128 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " 0.211 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " -0.596 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 601 " 0.358 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG H 601 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG H 601 " 0.096 2.00e-02 2.50e+03 pdb=" N2 NAG H 601 " -0.541 2.00e-02 2.50e+03 pdb=" O7 NAG H 601 " 0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 601 " -0.343 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG G 601 " 0.088 2.00e-02 2.50e+03 pdb=" C8 NAG G 601 " -0.183 2.00e-02 2.50e+03 pdb=" N2 NAG G 601 " 0.508 2.00e-02 2.50e+03 pdb=" O7 NAG G 601 " -0.070 2.00e-02 2.50e+03 ... (remaining 4584 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 44 1.93 - 2.67: 1979 2.67 - 3.42: 35351 3.42 - 4.16: 61860 4.16 - 4.90: 109196 Nonbonded interactions: 208430 Sorted by model distance: nonbonded pdb=" SG CYS P 261 " pdb=" CD2 LEU P 315 " model vdw 1.189 3.820 nonbonded pdb=" O VAL P 344 " pdb=" CD1 LEU P 413 " model vdw 1.253 3.460 nonbonded pdb=" OE2 GLU A 549 " pdb=" CG2 THR J 126 " model vdw 1.258 3.460 nonbonded pdb=" N HIS F 450 " pdb=" OG SER F 480 " model vdw 1.305 3.120 nonbonded pdb=" OE2 GLU A 525 " pdb=" ND2 ASN A 529 " model vdw 1.368 3.120 ... (remaining 208425 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 512 or (resid 513 and (name N \ or name CA or name C )) or resid 514 through 568 or resid 601)) selection = (chain 'B' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 512 or (resid 513 and (name N \ or name CA or name C )) or resid 514 through 568 or resid 601)) selection = (chain 'C' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 568 or resid 601)) selection = (chain 'D' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 512 or (resid 513 and (name N \ or name CA or name C )) or resid 514 through 568 or resid 601)) selection = (chain 'E' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 512 or (resid 513 and (name N \ or name CA or name C )) or resid 514 through 568 or resid 601)) selection = (chain 'F' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 512 or (resid 513 and (name N \ or name CA or name C )) or resid 514 through 568 or resid 601)) selection = (chain 'G' and (resid 345 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 568 or (resid 601 and (name C1 or name C2 or name C \ 3 or name C4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 o \ r name O4 or name O5 or name O6 or name O7 )))) selection = (chain 'H' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 512 or (resid 513 and (name N \ or name CA or name C )) or resid 514 through 568 or resid 601)) selection = (chain 'K' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 512 or (resid 513 and (name N \ or name CA or name C )) or resid 514 through 568 or resid 601)) selection = (chain 'L' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 512 or (resid 513 and (name N \ or name CA or name C )) or resid 514 through 568 or resid 601)) } ncs_group { reference = (chain 'R' and resid 20 through 119) selection = (chain 'S' and resid 20 through 119) selection = (chain 'U' and resid 20 through 119) selection = (chain 'V' and resid 20 through 119) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.030 Check model and map are aligned: 0.220 Set scattering table: 0.240 Process input model: 58.820 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 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 : 0.017 0.478 26320 Z= 1.120 Angle : 1.784 38.012 35955 Z= 1.061 Chirality : 0.113 1.425 4205 Planarity : 0.013 0.348 4578 Dihedral : 18.112 132.971 9793 Min Nonbonded Distance : 1.189 Molprobity Statistics. All-atom Clashscore : 44.73 Ramachandran Plot: Outliers : 3.30 % Allowed : 9.86 % Favored : 86.84 % Rotamer: Outliers : 11.57 % Allowed : 5.82 % Favored : 82.60 % Cbeta Deviations : 2.77 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 1.32 % 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: -2.31 (0.14), residues: 3244 helix: -1.22 (0.30), residues: 258 sheet: -0.76 (0.16), residues: 1052 loop : -2.10 (0.14), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP P 480 HIS 0.024 0.002 HIS B 450 PHE 0.069 0.003 PHE P 275 TYR 0.041 0.003 TYR K 576 ARG 0.029 0.001 ARG A 514 Details of bonding type rmsd link_NAG-ASN : bond 0.09920 ( 9) link_NAG-ASN : angle 10.38377 ( 27) link_BETA1-4 : bond 0.01303 ( 1) link_BETA1-4 : angle 7.09849 ( 3) hydrogen bonds : bond 0.18768 ( 629) hydrogen bonds : angle 8.50115 ( 1749) SS BOND : bond 0.08409 ( 42) SS BOND : angle 6.76351 ( 84) covalent geometry : bond 0.01665 (26267) covalent geometry : angle 1.73170 (35841) Misc. bond : bond 0.03913 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 336 poor density : 404 time to evaluate : 2.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7568 (mptt) REVERT: A 543 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9069 (mp) REVERT: B 375 TYR cc_start: 0.3261 (OUTLIER) cc_final: 0.2213 (m-80) REVERT: B 418 TRP cc_start: 0.6135 (t60) cc_final: 0.5836 (t60) REVERT: C 386 ASN cc_start: 0.8138 (t0) cc_final: 0.7921 (t0) REVERT: C 526 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7111 (mm-30) REVERT: D 424 PHE cc_start: 0.7553 (m-80) cc_final: 0.7297 (m-80) REVERT: E 445 LYS cc_start: 0.7232 (OUTLIER) cc_final: 0.6921 (mmtp) REVERT: F 364 LYS cc_start: 0.8169 (mmmt) cc_final: 0.7757 (mtpp) REVERT: F 376 ASP cc_start: 0.2528 (OUTLIER) cc_final: 0.2288 (t0) REVERT: F 414 CYS cc_start: 0.6217 (OUTLIER) cc_final: 0.5853 (m) REVERT: F 416 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7405 (p0) REVERT: F 554 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8665 (tmtm) REVERT: G 417 ASP cc_start: 0.7050 (m-30) cc_final: 0.6729 (m-30) REVERT: G 445 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.6581 (mmpt) REVERT: J 35 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8147 (ttm170) REVERT: K 368 LEU cc_start: 0.6466 (pt) cc_final: 0.5566 (tt) REVERT: K 391 LYS cc_start: 0.7488 (tptt) cc_final: 0.6883 (tptm) REVERT: K 490 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7291 (tp40) REVERT: L 453 ASP cc_start: 0.8095 (t0) cc_final: 0.7818 (t0) REVERT: L 479 PHE cc_start: 0.6800 (OUTLIER) cc_final: 0.5987 (m-80) REVERT: P 99 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8351 (tpt90) REVERT: P 358 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7912 (tptt) REVERT: P 390 GLN cc_start: 0.6985 (OUTLIER) cc_final: 0.6473 (tp40) REVERT: P 392 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7364 (mt-10) REVERT: P 400 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7122 (tp30) REVERT: P 432 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7998 (mpt180) REVERT: P 447 LYS cc_start: 0.4111 (OUTLIER) cc_final: 0.3549 (tptt) REVERT: P 469 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.6381 (pptt) REVERT: P 533 PHE cc_start: 0.6239 (OUTLIER) cc_final: 0.5609 (m-80) REVERT: P 541 TYR cc_start: 0.5291 (OUTLIER) cc_final: 0.5078 (m-80) REVERT: S 71 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7823 (pm20) REVERT: S 73 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7805 (mtpt) REVERT: U 44 VAL cc_start: 0.8416 (OUTLIER) cc_final: 0.8044 (t) REVERT: U 83 ARG cc_start: 0.8399 (mpp80) cc_final: 0.8156 (ptt90) REVERT: U 88 LEU cc_start: 0.7230 (mt) cc_final: 0.6953 (mt) REVERT: U 112 ARG cc_start: 0.7769 (ttp80) cc_final: 0.7529 (ttp80) REVERT: U 117 LYS cc_start: 0.5705 (OUTLIER) cc_final: 0.4897 (mttt) outliers start: 336 outliers final: 182 residues processed: 696 average time/residue: 0.4073 time to fit residues: 430.3567 Evaluate side-chains 540 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 331 time to evaluate : 3.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 467 ARG Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 499 LYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 546 ARG Chi-restraints excluded: chain C residue 451 ARG Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 526 GLU Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 565 SER Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 499 LYS Chi-restraints excluded: chain D residue 536 CYS Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain E residue 445 LYS Chi-restraints excluded: chain E residue 514 ARG Chi-restraints excluded: chain E residue 532 GLU Chi-restraints excluded: chain E residue 535 THR Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain F residue 376 ASP Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 406 SER Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 412 SER Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain F residue 439 GLN Chi-restraints excluded: chain F residue 440 THR Chi-restraints excluded: chain F residue 479 PHE Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain F residue 520 ILE Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 544 PRO Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 546 ARG Chi-restraints excluded: chain F residue 550 ARG Chi-restraints excluded: chain F residue 554 LYS Chi-restraints excluded: chain F residue 556 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 445 LYS Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 449 LEU Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 475 LEU Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 516 PHE Chi-restraints excluded: chain H residue 442 SER Chi-restraints excluded: chain H residue 443 ARG Chi-restraints excluded: chain H residue 444 PRO Chi-restraints excluded: chain H residue 449 LEU Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain H residue 519 SER Chi-restraints excluded: chain H residue 532 GLU Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 556 THR Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain H residue 563 ASN Chi-restraints excluded: chain H residue 566 LEU Chi-restraints excluded: chain H residue 568 MET Chi-restraints excluded: chain J residue 23 ARG Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 35 ARG Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 447 VAL Chi-restraints excluded: chain K residue 462 GLU Chi-restraints excluded: chain K residue 464 LEU Chi-restraints excluded: chain K residue 474 CYS Chi-restraints excluded: chain K residue 475 LEU Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 490 GLN Chi-restraints excluded: chain K residue 514 ARG Chi-restraints excluded: chain K residue 516 PHE Chi-restraints excluded: chain K residue 520 ILE Chi-restraints excluded: chain K residue 521 LEU Chi-restraints excluded: chain K residue 530 THR Chi-restraints excluded: chain K residue 543 LEU Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain K residue 556 THR Chi-restraints excluded: chain K residue 558 LYS Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain K residue 565 SER Chi-restraints excluded: chain K residue 568 MET Chi-restraints excluded: chain K residue 574 THR Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 443 ARG Chi-restraints excluded: chain L residue 445 LYS Chi-restraints excluded: chain L residue 450 HIS Chi-restraints excluded: chain L residue 479 PHE Chi-restraints excluded: chain L residue 480 SER Chi-restraints excluded: chain L residue 534 TYR Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 543 LEU Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 548 THR Chi-restraints excluded: chain L residue 551 THR Chi-restraints excluded: chain L residue 556 THR Chi-restraints excluded: chain L residue 558 LYS Chi-restraints excluded: chain L residue 566 LEU Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain P residue 10 VAL Chi-restraints excluded: chain P residue 60 TYR Chi-restraints excluded: chain P residue 99 ARG Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 132 ILE Chi-restraints excluded: chain P residue 151 ILE Chi-restraints excluded: chain P residue 245 VAL Chi-restraints excluded: chain P residue 247 ASN Chi-restraints excluded: chain P residue 259 GLU Chi-restraints excluded: chain P residue 260 ASN Chi-restraints excluded: chain P residue 275 PHE Chi-restraints excluded: chain P residue 287 ASP Chi-restraints excluded: chain P residue 290 PHE Chi-restraints excluded: chain P residue 314 GLN Chi-restraints excluded: chain P residue 315 LEU Chi-restraints excluded: chain P residue 317 GLU Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain P residue 349 VAL Chi-restraints excluded: chain P residue 358 LYS Chi-restraints excluded: chain P residue 361 LYS Chi-restraints excluded: chain P residue 379 LEU Chi-restraints excluded: chain P residue 390 GLN Chi-restraints excluded: chain P residue 392 GLU Chi-restraints excluded: chain P residue 398 LEU Chi-restraints excluded: chain P residue 400 GLU Chi-restraints excluded: chain P residue 405 THR Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 413 LEU Chi-restraints excluded: chain P residue 414 THR Chi-restraints excluded: chain P residue 431 TRP Chi-restraints excluded: chain P residue 432 ARG Chi-restraints excluded: chain P residue 439 ILE Chi-restraints excluded: chain P residue 446 LEU Chi-restraints excluded: chain P residue 447 LYS Chi-restraints excluded: chain P residue 462 VAL Chi-restraints excluded: chain P residue 469 LYS Chi-restraints excluded: chain P residue 470 PHE Chi-restraints excluded: chain P residue 475 LYS Chi-restraints excluded: chain P residue 478 CYS Chi-restraints excluded: chain P residue 533 PHE Chi-restraints excluded: chain P residue 540 VAL Chi-restraints excluded: chain P residue 541 TYR Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 93 GLN Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain S residue 39 LEU Chi-restraints excluded: chain S residue 71 GLU Chi-restraints excluded: chain S residue 72 TYR Chi-restraints excluded: chain S residue 73 LYS Chi-restraints excluded: chain S residue 92 THR Chi-restraints excluded: chain S residue 93 GLN Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 GLN Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 26 GLU Chi-restraints excluded: chain U residue 44 VAL Chi-restraints excluded: chain U residue 117 LYS Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain V residue 114 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 272 optimal weight: 4.9990 chunk 244 optimal weight: 0.7980 chunk 135 optimal weight: 30.0000 chunk 83 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 253 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 153 optimal weight: 1.9990 chunk 188 optimal weight: 10.0000 chunk 293 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 GLN ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN B 450 HIS ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 HIS C 465 ASN ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 44 ASN K 419 ASN ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 490 GLN P 30 ASN P 68 ASN P 111 GLN P 310 HIS P 426 ASN P 530 GLN R 93 GLN R 116 GLN S 116 GLN U 43 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.179457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.120666 restraints weight = 41951.202| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 3.29 r_work: 0.3318 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 26320 Z= 0.245 Angle : 0.865 22.017 35955 Z= 0.437 Chirality : 0.052 0.429 4205 Planarity : 0.007 0.115 4578 Dihedral : 13.859 179.147 4242 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.69 % Favored : 91.03 % Rotamer: Outliers : 6.96 % Allowed : 13.57 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.07 % 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: -2.17 (0.14), residues: 3244 helix: -1.34 (0.27), residues: 276 sheet: -0.80 (0.15), residues: 1130 loop : -1.91 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 382 HIS 0.010 0.001 HIS F 450 PHE 0.027 0.002 PHE K 354 TYR 0.020 0.002 TYR L 562 ARG 0.007 0.001 ARG H 443 Details of bonding type rmsd link_NAG-ASN : bond 0.00526 ( 9) link_NAG-ASN : angle 3.91262 ( 27) link_BETA1-4 : bond 0.02813 ( 1) link_BETA1-4 : angle 8.43947 ( 3) hydrogen bonds : bond 0.04344 ( 629) hydrogen bonds : angle 6.80970 ( 1749) SS BOND : bond 0.00760 ( 42) SS BOND : angle 1.56557 ( 84) covalent geometry : bond 0.00579 (26267) covalent geometry : angle 0.85277 (35841) Misc. bond : bond 0.01586 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 372 time to evaluate : 2.802 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 445 LYS cc_start: 0.8336 (tttm) cc_final: 0.7810 (mmtt) REVERT: B 375 TYR cc_start: 0.3509 (OUTLIER) cc_final: 0.3274 (p90) REVERT: B 441 ILE cc_start: 0.4760 (OUTLIER) cc_final: 0.4154 (mt) REVERT: B 499 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8324 (mttm) REVERT: B 506 MET cc_start: 0.8409 (mtp) cc_final: 0.8153 (mtm) REVERT: B 532 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7531 (mt-10) REVERT: C 348 PHE cc_start: 0.4366 (OUTLIER) cc_final: 0.3905 (m-80) REVERT: C 386 ASN cc_start: 0.8160 (t0) cc_final: 0.7869 (t0) REVERT: D 491 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8181 (mtm110) REVERT: E 364 LYS cc_start: 0.7679 (tppt) cc_final: 0.6827 (tppt) REVERT: E 489 MET cc_start: 0.7550 (tpp) cc_final: 0.7272 (tpp) REVERT: F 364 LYS cc_start: 0.7981 (mmmt) cc_final: 0.7600 (mmtm) REVERT: F 380 ILE cc_start: 0.4316 (mm) cc_final: 0.3933 (mp) REVERT: F 396 ILE cc_start: 0.5551 (OUTLIER) cc_final: 0.5309 (tt) REVERT: F 414 CYS cc_start: 0.6101 (OUTLIER) cc_final: 0.5427 (m) REVERT: F 416 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7262 (p0) REVERT: F 423 ARG cc_start: 0.7115 (mtm180) cc_final: 0.6631 (mtp180) REVERT: G 371 ASP cc_start: 0.6416 (t0) cc_final: 0.6131 (t0) REVERT: G 417 ASP cc_start: 0.7358 (m-30) cc_final: 0.7016 (m-30) REVERT: G 445 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.6520 (mmmt) REVERT: H 532 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7158 (mp0) REVERT: K 368 LEU cc_start: 0.6088 (pt) cc_final: 0.5550 (mt) REVERT: K 462 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7988 (mp0) REVERT: K 485 PHE cc_start: 0.8661 (t80) cc_final: 0.8455 (t80) REVERT: K 490 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7415 (tp40) REVERT: K 515 TYR cc_start: 0.8071 (m-80) cc_final: 0.7625 (m-10) REVERT: K 566 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8805 (tt) REVERT: L 453 ASP cc_start: 0.8250 (t0) cc_final: 0.8038 (t0) REVERT: L 483 ASP cc_start: 0.7270 (m-30) cc_final: 0.6382 (t0) REVERT: L 485 PHE cc_start: 0.5555 (t80) cc_final: 0.5319 (t80) REVERT: P 247 ASN cc_start: 0.8812 (m-40) cc_final: 0.7711 (t0) REVERT: P 392 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7265 (mt-10) REVERT: P 400 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6851 (tp30) REVERT: P 447 LYS cc_start: 0.4121 (OUTLIER) cc_final: 0.3373 (tptt) REVERT: P 469 LYS cc_start: 0.6532 (OUTLIER) cc_final: 0.5779 (pptt) REVERT: P 533 PHE cc_start: 0.6255 (OUTLIER) cc_final: 0.5784 (m-80) REVERT: S 71 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8441 (pm20) REVERT: S 81 TYR cc_start: 0.7792 (m-80) cc_final: 0.7514 (m-80) REVERT: U 44 VAL cc_start: 0.8318 (OUTLIER) cc_final: 0.8017 (t) REVERT: U 83 ARG cc_start: 0.8540 (mpp80) cc_final: 0.8202 (ptt90) REVERT: U 93 GLN cc_start: 0.7151 (mp10) cc_final: 0.6783 (mp10) outliers start: 202 outliers final: 123 residues processed: 541 average time/residue: 0.3897 time to fit residues: 320.9266 Evaluate side-chains 472 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 328 time to evaluate : 3.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 467 ARG Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 499 LYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 546 ARG Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain D residue 348 PHE Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 491 ARG Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 506 MET Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain E residue 532 GLU Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 377 SER Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain F residue 418 TRP Chi-restraints excluded: chain F residue 422 GLU Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 445 LYS Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 449 LEU Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 449 LEU Chi-restraints excluded: chain H residue 532 GLU Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 553 ASP Chi-restraints excluded: chain H residue 556 THR Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain H residue 566 LEU Chi-restraints excluded: chain H residue 568 MET Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 23 ARG Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 44 ASN Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 462 GLU Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 490 GLN Chi-restraints excluded: chain K residue 491 ARG Chi-restraints excluded: chain K residue 514 ARG Chi-restraints excluded: chain K residue 516 PHE Chi-restraints excluded: chain K residue 543 LEU Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain K residue 556 THR Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain K residue 566 LEU Chi-restraints excluded: chain K residue 574 THR Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 443 ARG Chi-restraints excluded: chain L residue 445 LYS Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 558 LYS Chi-restraints excluded: chain L residue 566 LEU Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain L residue 575 CYS Chi-restraints excluded: chain P residue 10 VAL Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 230 ASP Chi-restraints excluded: chain P residue 257 SER Chi-restraints excluded: chain P residue 260 ASN Chi-restraints excluded: chain P residue 262 ASP Chi-restraints excluded: chain P residue 287 ASP Chi-restraints excluded: chain P residue 290 PHE Chi-restraints excluded: chain P residue 317 GLU Chi-restraints excluded: chain P residue 344 VAL Chi-restraints excluded: chain P residue 349 VAL Chi-restraints excluded: chain P residue 361 LYS Chi-restraints excluded: chain P residue 379 LEU Chi-restraints excluded: chain P residue 392 GLU Chi-restraints excluded: chain P residue 400 GLU Chi-restraints excluded: chain P residue 405 THR Chi-restraints excluded: chain P residue 413 LEU Chi-restraints excluded: chain P residue 431 TRP Chi-restraints excluded: chain P residue 446 LEU Chi-restraints excluded: chain P residue 447 LYS Chi-restraints excluded: chain P residue 462 VAL Chi-restraints excluded: chain P residue 469 LYS Chi-restraints excluded: chain P residue 473 TYR Chi-restraints excluded: chain P residue 475 LYS Chi-restraints excluded: chain P residue 478 CYS Chi-restraints excluded: chain P residue 533 PHE Chi-restraints excluded: chain P residue 540 VAL Chi-restraints excluded: chain R residue 93 GLN Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain S residue 71 GLU Chi-restraints excluded: chain S residue 89 VAL Chi-restraints excluded: chain S residue 93 GLN Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 44 VAL Chi-restraints excluded: chain U residue 57 THR Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain V residue 46 ILE Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 60 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 191 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 291 optimal weight: 8.9990 chunk 150 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 147 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 HIS B 385 GLN ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 439 GLN ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 463 GLN L 529 ASN P 260 ASN P 314 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.181621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.117481 restraints weight = 41923.069| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.60 r_work: 0.3344 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 26320 Z= 0.149 Angle : 0.726 17.975 35955 Z= 0.363 Chirality : 0.047 0.408 4205 Planarity : 0.006 0.100 4578 Dihedral : 10.907 90.676 4003 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.80 % Favored : 91.95 % Rotamer: Outliers : 5.68 % Allowed : 16.71 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.03 % 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: -1.85 (0.14), residues: 3244 helix: -1.18 (0.28), residues: 277 sheet: -0.62 (0.15), residues: 1118 loop : -1.65 (0.14), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP P 477 HIS 0.006 0.001 HIS L 430 PHE 0.024 0.002 PHE D 424 TYR 0.028 0.002 TYR K 576 ARG 0.007 0.000 ARG B 423 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 9) link_NAG-ASN : angle 3.58447 ( 27) link_BETA1-4 : bond 0.01947 ( 1) link_BETA1-4 : angle 7.98956 ( 3) hydrogen bonds : bond 0.03633 ( 629) hydrogen bonds : angle 6.20840 ( 1749) SS BOND : bond 0.00406 ( 42) SS BOND : angle 1.35060 ( 84) covalent geometry : bond 0.00345 (26267) covalent geometry : angle 0.71358 (35841) Misc. bond : bond 0.01532 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 364 time to evaluate : 3.780 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 445 LYS cc_start: 0.8221 (tttm) cc_final: 0.7488 (mmtt) REVERT: B 375 TYR cc_start: 0.3588 (OUTLIER) cc_final: 0.3292 (p90) REVERT: B 441 ILE cc_start: 0.5388 (OUTLIER) cc_final: 0.4852 (mt) REVERT: B 499 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8518 (mttm) REVERT: B 506 MET cc_start: 0.8396 (mtp) cc_final: 0.8103 (mtm) REVERT: B 514 ARG cc_start: 0.8067 (mpt180) cc_final: 0.7599 (mmt90) REVERT: B 532 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7420 (mt-10) REVERT: B 545 ASN cc_start: 0.8466 (m-40) cc_final: 0.8233 (m-40) REVERT: C 348 PHE cc_start: 0.4416 (OUTLIER) cc_final: 0.4050 (m-80) REVERT: C 386 ASN cc_start: 0.8108 (t0) cc_final: 0.7830 (t0) REVERT: C 461 ARG cc_start: 0.8615 (tmm160) cc_final: 0.7992 (tpp-160) REVERT: D 532 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7151 (mt-10) REVERT: E 364 LYS cc_start: 0.7601 (tppt) cc_final: 0.6962 (tppt) REVERT: E 427 THR cc_start: 0.6764 (OUTLIER) cc_final: 0.6530 (p) REVERT: E 489 MET cc_start: 0.7519 (tpp) cc_final: 0.7080 (tpp) REVERT: F 364 LYS cc_start: 0.7635 (mmmt) cc_final: 0.7411 (mmtm) REVERT: F 384 ARG cc_start: 0.7811 (mtp-110) cc_final: 0.7503 (mtp-110) REVERT: F 414 CYS cc_start: 0.6238 (OUTLIER) cc_final: 0.5772 (t) REVERT: F 424 PHE cc_start: 0.6803 (m-80) cc_final: 0.6359 (m-80) REVERT: F 439 GLN cc_start: 0.5110 (OUTLIER) cc_final: 0.4300 (pm20) REVERT: G 371 ASP cc_start: 0.6743 (t0) cc_final: 0.6497 (t0) REVERT: G 417 ASP cc_start: 0.7621 (m-30) cc_final: 0.7058 (m-30) REVERT: G 445 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.6610 (mmmt) REVERT: H 532 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: J 120 GLU cc_start: 0.8769 (mp0) cc_final: 0.8292 (pt0) REVERT: K 368 LEU cc_start: 0.5917 (pt) cc_final: 0.5430 (mt) REVERT: K 450 HIS cc_start: 0.7792 (m170) cc_final: 0.7349 (m170) REVERT: K 462 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7869 (mp0) REVERT: K 485 PHE cc_start: 0.8734 (t80) cc_final: 0.8381 (t80) REVERT: K 489 MET cc_start: 0.8589 (mtp) cc_final: 0.8151 (mtp) REVERT: K 490 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.7029 (tp40) REVERT: K 515 TYR cc_start: 0.7702 (m-80) cc_final: 0.7241 (m-10) REVERT: L 453 ASP cc_start: 0.8237 (t0) cc_final: 0.7881 (t0) REVERT: L 455 TYR cc_start: 0.7666 (m-80) cc_final: 0.7332 (m-80) REVERT: L 485 PHE cc_start: 0.5754 (t80) cc_final: 0.5498 (t80) REVERT: P 247 ASN cc_start: 0.8941 (m-40) cc_final: 0.7832 (t0) REVERT: P 376 ARG cc_start: 0.7983 (tmt170) cc_final: 0.7408 (ptt90) REVERT: P 469 LYS cc_start: 0.6531 (OUTLIER) cc_final: 0.5856 (pptt) REVERT: P 533 PHE cc_start: 0.6296 (OUTLIER) cc_final: 0.5768 (m-80) REVERT: R 51 GLU cc_start: 0.6188 (tm-30) cc_final: 0.5806 (tm-30) REVERT: R 87 PHE cc_start: 0.6043 (t80) cc_final: 0.5731 (t80) REVERT: S 71 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8366 (pm20) REVERT: V 42 MET cc_start: 0.4945 (OUTLIER) cc_final: 0.4576 (tpt) outliers start: 165 outliers final: 100 residues processed: 497 average time/residue: 0.3953 time to fit residues: 300.2286 Evaluate side-chains 445 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 329 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 ARG Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 499 LYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 546 ARG Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 506 MET Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 532 GLU Chi-restraints excluded: chain F residue 377 SER Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 439 GLN Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 445 LYS Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain H residue 532 GLU Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 553 ASP Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain H residue 566 LEU Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 23 ARG Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 427 THR Chi-restraints excluded: chain K residue 462 GLU Chi-restraints excluded: chain K residue 474 CYS Chi-restraints excluded: chain K residue 490 GLN Chi-restraints excluded: chain K residue 514 ARG Chi-restraints excluded: chain K residue 516 PHE Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain K residue 556 THR Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain K residue 574 THR Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 443 ARG Chi-restraints excluded: chain L residue 445 LYS Chi-restraints excluded: chain L residue 476 VAL Chi-restraints excluded: chain L residue 533 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 551 THR Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 566 LEU Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain L residue 575 CYS Chi-restraints excluded: chain P residue 10 VAL Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 230 ASP Chi-restraints excluded: chain P residue 257 SER Chi-restraints excluded: chain P residue 260 ASN Chi-restraints excluded: chain P residue 262 ASP Chi-restraints excluded: chain P residue 290 PHE Chi-restraints excluded: chain P residue 344 VAL Chi-restraints excluded: chain P residue 379 LEU Chi-restraints excluded: chain P residue 405 THR Chi-restraints excluded: chain P residue 413 LEU Chi-restraints excluded: chain P residue 431 TRP Chi-restraints excluded: chain P residue 446 LEU Chi-restraints excluded: chain P residue 462 VAL Chi-restraints excluded: chain P residue 469 LYS Chi-restraints excluded: chain P residue 473 TYR Chi-restraints excluded: chain P residue 475 LYS Chi-restraints excluded: chain P residue 478 CYS Chi-restraints excluded: chain P residue 533 PHE Chi-restraints excluded: chain R residue 93 GLN Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain S residue 71 GLU Chi-restraints excluded: chain S residue 89 VAL Chi-restraints excluded: chain S residue 93 GLN Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 44 VAL Chi-restraints excluded: chain U residue 57 THR Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain V residue 42 MET Chi-restraints excluded: chain V residue 57 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 23 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 316 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 246 optimal weight: 7.9990 chunk 208 optimal weight: 2.9990 chunk 319 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 GLN ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 430 HIS ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 545 ASN K 385 GLN ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 282 ASN R 85 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.178486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.113385 restraints weight = 42147.923| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 3.50 r_work: 0.3285 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 26320 Z= 0.247 Angle : 0.749 17.959 35955 Z= 0.375 Chirality : 0.049 0.415 4205 Planarity : 0.006 0.098 4578 Dihedral : 10.252 83.920 3953 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.20 % Favored : 91.58 % Rotamer: Outliers : 6.03 % Allowed : 18.43 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.44 % 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: -1.86 (0.14), residues: 3244 helix: -1.18 (0.28), residues: 280 sheet: -0.68 (0.15), residues: 1132 loop : -1.62 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP P 369 HIS 0.011 0.001 HIS F 430 PHE 0.025 0.002 PHE B 354 TYR 0.019 0.002 TYR L 562 ARG 0.006 0.001 ARG J 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00525 ( 9) link_NAG-ASN : angle 3.78967 ( 27) link_BETA1-4 : bond 0.02242 ( 1) link_BETA1-4 : angle 7.82466 ( 3) hydrogen bonds : bond 0.03756 ( 629) hydrogen bonds : angle 6.18933 ( 1749) SS BOND : bond 0.00482 ( 42) SS BOND : angle 1.20397 ( 84) covalent geometry : bond 0.00592 (26267) covalent geometry : angle 0.73668 (35841) Misc. bond : bond 0.01586 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 337 time to evaluate : 3.373 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 LYS cc_start: 0.8340 (tttm) cc_final: 0.7737 (mmtt) REVERT: A 527 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: B 375 TYR cc_start: 0.3612 (OUTLIER) cc_final: 0.3278 (p90) REVERT: B 441 ILE cc_start: 0.5351 (OUTLIER) cc_final: 0.4673 (mt) REVERT: B 499 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8513 (mttm) REVERT: B 506 MET cc_start: 0.8501 (mtp) cc_final: 0.8173 (mtm) REVERT: C 348 PHE cc_start: 0.4459 (OUTLIER) cc_final: 0.4089 (m-80) REVERT: C 386 ASN cc_start: 0.8170 (t0) cc_final: 0.7889 (t0) REVERT: C 461 ARG cc_start: 0.8658 (tmm160) cc_final: 0.8169 (tpp-160) REVERT: E 364 LYS cc_start: 0.7671 (tppt) cc_final: 0.7045 (tppt) REVERT: E 427 THR cc_start: 0.6785 (OUTLIER) cc_final: 0.6522 (p) REVERT: E 489 MET cc_start: 0.7897 (tpp) cc_final: 0.7684 (tpp) REVERT: F 414 CYS cc_start: 0.6250 (OUTLIER) cc_final: 0.5908 (t) REVERT: G 371 ASP cc_start: 0.6790 (t0) cc_final: 0.6527 (t0) REVERT: G 417 ASP cc_start: 0.7721 (m-30) cc_final: 0.7157 (m-30) REVERT: G 445 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.6670 (mmmt) REVERT: H 384 ARG cc_start: 0.6896 (mtm180) cc_final: 0.6570 (ptp-170) REVERT: H 532 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: H 534 TYR cc_start: 0.9049 (m-80) cc_final: 0.8770 (m-80) REVERT: J 51 ASP cc_start: 0.8195 (t0) cc_final: 0.7928 (t0) REVERT: J 120 GLU cc_start: 0.8806 (mp0) cc_final: 0.8356 (pt0) REVERT: K 368 LEU cc_start: 0.5685 (pt) cc_final: 0.5086 (mt) REVERT: K 462 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7842 (mp0) REVERT: K 489 MET cc_start: 0.8708 (mtp) cc_final: 0.8184 (mtp) REVERT: K 490 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7142 (tp40) REVERT: K 515 TYR cc_start: 0.7917 (m-80) cc_final: 0.7430 (m-10) REVERT: K 566 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8890 (tt) REVERT: L 453 ASP cc_start: 0.8375 (t0) cc_final: 0.7857 (t0) REVERT: L 485 PHE cc_start: 0.5668 (t80) cc_final: 0.5430 (t80) REVERT: P 247 ASN cc_start: 0.8881 (m-40) cc_final: 0.7781 (t0) REVERT: P 469 LYS cc_start: 0.6502 (OUTLIER) cc_final: 0.5843 (pptt) REVERT: R 51 GLU cc_start: 0.6287 (tm-30) cc_final: 0.5897 (tm-30) REVERT: R 87 PHE cc_start: 0.5798 (t80) cc_final: 0.5577 (t80) REVERT: S 71 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8397 (pm20) REVERT: S 93 GLN cc_start: 0.7024 (OUTLIER) cc_final: 0.6184 (mp10) REVERT: U 73 LYS cc_start: 0.8119 (mmtt) cc_final: 0.7837 (mmmt) REVERT: U 93 GLN cc_start: 0.7398 (mp10) cc_final: 0.6857 (mp10) outliers start: 175 outliers final: 123 residues processed: 482 average time/residue: 0.4507 time to fit residues: 335.4781 Evaluate side-chains 460 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 322 time to evaluate : 3.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 ARG Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 499 LYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 546 ARG Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 506 MET Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 525 GLU Chi-restraints excluded: chain E residue 532 GLU Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain F residue 377 SER Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 445 LYS Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 441 ILE Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 532 GLU Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 553 ASP Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain H residue 563 ASN Chi-restraints excluded: chain H residue 566 LEU Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 427 THR Chi-restraints excluded: chain K residue 462 GLU Chi-restraints excluded: chain K residue 474 CYS Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 490 GLN Chi-restraints excluded: chain K residue 491 ARG Chi-restraints excluded: chain K residue 514 ARG Chi-restraints excluded: chain K residue 516 PHE Chi-restraints excluded: chain K residue 520 ILE Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain K residue 556 THR Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain K residue 566 LEU Chi-restraints excluded: chain K residue 574 THR Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 443 ARG Chi-restraints excluded: chain L residue 445 LYS Chi-restraints excluded: chain L residue 476 VAL Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 566 LEU Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain L residue 575 CYS Chi-restraints excluded: chain P residue 10 VAL Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 230 ASP Chi-restraints excluded: chain P residue 257 SER Chi-restraints excluded: chain P residue 260 ASN Chi-restraints excluded: chain P residue 262 ASP Chi-restraints excluded: chain P residue 275 PHE Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain P residue 344 VAL Chi-restraints excluded: chain P residue 379 LEU Chi-restraints excluded: chain P residue 405 THR Chi-restraints excluded: chain P residue 413 LEU Chi-restraints excluded: chain P residue 431 TRP Chi-restraints excluded: chain P residue 446 LEU Chi-restraints excluded: chain P residue 462 VAL Chi-restraints excluded: chain P residue 469 LYS Chi-restraints excluded: chain P residue 473 TYR Chi-restraints excluded: chain P residue 475 LYS Chi-restraints excluded: chain P residue 540 VAL Chi-restraints excluded: chain R residue 60 THR Chi-restraints excluded: chain R residue 93 GLN Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 96 GLU Chi-restraints excluded: chain S residue 71 GLU Chi-restraints excluded: chain S residue 89 VAL Chi-restraints excluded: chain S residue 93 GLN Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 44 VAL Chi-restraints excluded: chain U residue 57 THR Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain V residue 57 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 22 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 23 optimal weight: 20.0000 chunk 239 optimal weight: 1.9990 chunk 254 optimal weight: 2.9990 chunk 292 optimal weight: 20.0000 chunk 283 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 245 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 HIS B 545 ASN ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 ASN ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 393 HIS ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 463 GLN R 85 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.177349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.111116 restraints weight = 41981.893| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.27 r_work: 0.3286 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 26320 Z= 0.281 Angle : 0.761 16.928 35955 Z= 0.382 Chirality : 0.050 0.411 4205 Planarity : 0.006 0.096 4578 Dihedral : 9.824 80.848 3937 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.75 % Favored : 91.12 % Rotamer: Outliers : 6.48 % Allowed : 19.74 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.44 % 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 (0.14), residues: 3244 helix: -1.24 (0.28), residues: 281 sheet: -0.77 (0.15), residues: 1142 loop : -1.63 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP P 369 HIS 0.005 0.001 HIS A 450 PHE 0.032 0.002 PHE B 354 TYR 0.021 0.002 TYR L 562 ARG 0.008 0.001 ARG F 384 Details of bonding type rmsd link_NAG-ASN : bond 0.00491 ( 9) link_NAG-ASN : angle 3.88770 ( 27) link_BETA1-4 : bond 0.02559 ( 1) link_BETA1-4 : angle 7.64295 ( 3) hydrogen bonds : bond 0.03760 ( 629) hydrogen bonds : angle 6.25284 ( 1749) SS BOND : bond 0.00514 ( 42) SS BOND : angle 1.16781 ( 84) covalent geometry : bond 0.00671 (26267) covalent geometry : angle 0.74931 (35841) Misc. bond : bond 0.01518 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 334 time to evaluate : 5.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 LYS cc_start: 0.8369 (tttm) cc_final: 0.7773 (mmtt) REVERT: A 467 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8197 (mpp-170) REVERT: B 375 TYR cc_start: 0.3921 (OUTLIER) cc_final: 0.3485 (p90) REVERT: B 400 HIS cc_start: 0.3153 (t-90) cc_final: 0.2941 (m170) REVERT: B 402 ASN cc_start: 0.7334 (m-40) cc_final: 0.7043 (p0) REVERT: B 441 ILE cc_start: 0.5759 (OUTLIER) cc_final: 0.5090 (mt) REVERT: B 499 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8479 (mttm) REVERT: B 506 MET cc_start: 0.8526 (mtp) cc_final: 0.8197 (mtm) REVERT: C 348 PHE cc_start: 0.4499 (OUTLIER) cc_final: 0.4070 (m-80) REVERT: C 386 ASN cc_start: 0.8297 (t0) cc_final: 0.7999 (t0) REVERT: C 461 ARG cc_start: 0.8551 (tmm160) cc_final: 0.8063 (tpp-160) REVERT: E 427 THR cc_start: 0.6779 (OUTLIER) cc_final: 0.6533 (p) REVERT: E 489 MET cc_start: 0.8128 (tpp) cc_final: 0.7800 (tpp) REVERT: F 423 ARG cc_start: 0.7310 (mtm180) cc_final: 0.6843 (mpt180) REVERT: G 371 ASP cc_start: 0.6972 (t0) cc_final: 0.6766 (t0) REVERT: G 445 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.6699 (mmmt) REVERT: H 384 ARG cc_start: 0.6990 (mtm180) cc_final: 0.6590 (ptp-170) REVERT: H 532 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7070 (mp0) REVERT: H 534 TYR cc_start: 0.9083 (m-80) cc_final: 0.8873 (m-80) REVERT: J 51 ASP cc_start: 0.8164 (t0) cc_final: 0.7896 (t0) REVERT: J 120 GLU cc_start: 0.8800 (mp0) cc_final: 0.8524 (mp0) REVERT: K 368 LEU cc_start: 0.5797 (pt) cc_final: 0.5203 (mp) REVERT: K 462 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7857 (mp0) REVERT: K 489 MET cc_start: 0.8679 (mtp) cc_final: 0.8141 (mtp) REVERT: K 490 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7091 (tp40) REVERT: K 515 TYR cc_start: 0.8022 (m-80) cc_final: 0.7596 (m-10) REVERT: K 566 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8873 (tt) REVERT: L 453 ASP cc_start: 0.8295 (t0) cc_final: 0.7768 (t0) REVERT: L 485 PHE cc_start: 0.5631 (t80) cc_final: 0.5392 (t80) REVERT: P 225 GLU cc_start: 0.7550 (tt0) cc_final: 0.7204 (tt0) REVERT: P 247 ASN cc_start: 0.8890 (m-40) cc_final: 0.7808 (t0) REVERT: P 424 LEU cc_start: 0.6362 (OUTLIER) cc_final: 0.6150 (mp) REVERT: P 469 LYS cc_start: 0.6472 (OUTLIER) cc_final: 0.5844 (pptt) REVERT: P 475 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.6811 (mttt) REVERT: R 51 GLU cc_start: 0.6447 (tm-30) cc_final: 0.6046 (tm-30) REVERT: R 68 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7968 (tp) REVERT: S 71 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8314 (pm20) REVERT: S 93 GLN cc_start: 0.7022 (OUTLIER) cc_final: 0.6191 (mp10) REVERT: U 73 LYS cc_start: 0.8092 (mmtt) cc_final: 0.7847 (mmmt) REVERT: U 93 GLN cc_start: 0.7523 (mp10) cc_final: 0.6909 (mp10) outliers start: 188 outliers final: 137 residues processed: 488 average time/residue: 0.4522 time to fit residues: 346.1759 Evaluate side-chains 467 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 313 time to evaluate : 3.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 ARG Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 499 LYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 546 ARG Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 506 MET Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 525 GLU Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain F residue 377 SER Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 440 THR Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 503 SER Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain G residue 433 LEU Chi-restraints excluded: chain G residue 445 LYS Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 532 GLU Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain H residue 553 ASP Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain H residue 563 ASN Chi-restraints excluded: chain H residue 566 LEU Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 427 THR Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 462 GLU Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 490 GLN Chi-restraints excluded: chain K residue 491 ARG Chi-restraints excluded: chain K residue 514 ARG Chi-restraints excluded: chain K residue 516 PHE Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain K residue 566 LEU Chi-restraints excluded: chain K residue 574 THR Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 443 ARG Chi-restraints excluded: chain L residue 445 LYS Chi-restraints excluded: chain L residue 476 VAL Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 566 LEU Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain L residue 575 CYS Chi-restraints excluded: chain P residue 10 VAL Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 230 ASP Chi-restraints excluded: chain P residue 257 SER Chi-restraints excluded: chain P residue 260 ASN Chi-restraints excluded: chain P residue 262 ASP Chi-restraints excluded: chain P residue 315 LEU Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain P residue 344 VAL Chi-restraints excluded: chain P residue 379 LEU Chi-restraints excluded: chain P residue 405 THR Chi-restraints excluded: chain P residue 413 LEU Chi-restraints excluded: chain P residue 424 LEU Chi-restraints excluded: chain P residue 431 TRP Chi-restraints excluded: chain P residue 446 LEU Chi-restraints excluded: chain P residue 448 VAL Chi-restraints excluded: chain P residue 462 VAL Chi-restraints excluded: chain P residue 469 LYS Chi-restraints excluded: chain P residue 473 TYR Chi-restraints excluded: chain P residue 475 LYS Chi-restraints excluded: chain P residue 540 VAL Chi-restraints excluded: chain R residue 60 THR Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain R residue 93 GLN Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 96 GLU Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain S residue 39 LEU Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 71 GLU Chi-restraints excluded: chain S residue 89 VAL Chi-restraints excluded: chain S residue 93 GLN Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 57 THR Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain V residue 57 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 276 optimal weight: 2.9990 chunk 204 optimal weight: 0.7980 chunk 244 optimal weight: 0.8980 chunk 228 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 211 optimal weight: 30.0000 chunk 298 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 142 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 430 HIS ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 463 GLN R 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.178291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.112342 restraints weight = 41834.638| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 3.32 r_work: 0.3316 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26320 Z= 0.188 Angle : 0.701 16.899 35955 Z= 0.351 Chirality : 0.048 0.421 4205 Planarity : 0.006 0.093 4578 Dihedral : 9.307 89.271 3929 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.98 % Favored : 91.89 % Rotamer: Outliers : 6.44 % Allowed : 20.67 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.44 % 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: -1.81 (0.14), residues: 3244 helix: -1.15 (0.28), residues: 279 sheet: -0.69 (0.15), residues: 1144 loop : -1.55 (0.15), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP P 369 HIS 0.017 0.001 HIS F 430 PHE 0.023 0.002 PHE B 354 TYR 0.032 0.001 TYR D 562 ARG 0.009 0.001 ARG J 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 9) link_NAG-ASN : angle 3.65028 ( 27) link_BETA1-4 : bond 0.02550 ( 1) link_BETA1-4 : angle 7.06590 ( 3) hydrogen bonds : bond 0.03443 ( 629) hydrogen bonds : angle 6.03216 ( 1749) SS BOND : bond 0.00395 ( 42) SS BOND : angle 1.01449 ( 84) covalent geometry : bond 0.00447 (26267) covalent geometry : angle 0.68970 (35841) Misc. bond : bond 0.01548 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 332 time to evaluate : 3.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 LYS cc_start: 0.8386 (tttm) cc_final: 0.7780 (mmtt) REVERT: A 467 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8321 (mpp-170) REVERT: B 375 TYR cc_start: 0.3919 (OUTLIER) cc_final: 0.3500 (p90) REVERT: B 402 ASN cc_start: 0.7469 (m-40) cc_final: 0.7182 (p0) REVERT: B 441 ILE cc_start: 0.5735 (OUTLIER) cc_final: 0.5156 (mt) REVERT: B 443 ARG cc_start: 0.5961 (OUTLIER) cc_final: 0.5564 (pmt-80) REVERT: B 493 GLN cc_start: 0.8505 (pp30) cc_final: 0.8199 (pp30) REVERT: B 499 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8453 (mttm) REVERT: B 506 MET cc_start: 0.8547 (mtp) cc_final: 0.8220 (mtm) REVERT: C 348 PHE cc_start: 0.4499 (OUTLIER) cc_final: 0.4071 (m-80) REVERT: C 386 ASN cc_start: 0.8306 (t0) cc_final: 0.8020 (t0) REVERT: C 461 ARG cc_start: 0.8483 (tmm160) cc_final: 0.7978 (tpp-160) REVERT: E 427 THR cc_start: 0.6766 (OUTLIER) cc_final: 0.6520 (p) REVERT: E 489 MET cc_start: 0.8032 (tpp) cc_final: 0.7714 (tpp) REVERT: F 416 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.6982 (m-30) REVERT: G 371 ASP cc_start: 0.7011 (t0) cc_final: 0.6809 (t0) REVERT: G 445 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.6695 (mmmt) REVERT: H 384 ARG cc_start: 0.6937 (mtm180) cc_final: 0.6602 (ptp-170) REVERT: H 532 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7178 (mt-10) REVERT: H 534 TYR cc_start: 0.9103 (m-80) cc_final: 0.8793 (m-80) REVERT: J 51 ASP cc_start: 0.7977 (t0) cc_final: 0.7735 (t0) REVERT: J 120 GLU cc_start: 0.8768 (mp0) cc_final: 0.8468 (mp0) REVERT: K 354 PHE cc_start: 0.6737 (t80) cc_final: 0.6520 (t80) REVERT: K 368 LEU cc_start: 0.5668 (pt) cc_final: 0.5097 (mp) REVERT: K 489 MET cc_start: 0.8564 (mtp) cc_final: 0.8120 (mtp) REVERT: K 490 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.6888 (tp40) REVERT: K 515 TYR cc_start: 0.7950 (m-80) cc_final: 0.7578 (m-10) REVERT: K 558 LYS cc_start: 0.7436 (ptpt) cc_final: 0.6928 (tttm) REVERT: K 566 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8796 (tt) REVERT: L 453 ASP cc_start: 0.8228 (t0) cc_final: 0.7665 (t0) REVERT: P 225 GLU cc_start: 0.7468 (tt0) cc_final: 0.7132 (tt0) REVERT: P 247 ASN cc_start: 0.8894 (m-40) cc_final: 0.7835 (t0) REVERT: P 314 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7669 (mm-40) REVERT: P 447 LYS cc_start: 0.3341 (OUTLIER) cc_final: 0.2757 (tptt) REVERT: P 469 LYS cc_start: 0.6344 (OUTLIER) cc_final: 0.5696 (pptt) REVERT: P 475 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.6919 (mttt) REVERT: P 480 TRP cc_start: 0.6371 (t60) cc_final: 0.6062 (t60) REVERT: R 50 ARG cc_start: 0.6996 (ttt-90) cc_final: 0.6169 (mmm160) REVERT: R 51 GLU cc_start: 0.6404 (tm-30) cc_final: 0.6050 (tm-30) REVERT: R 68 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7915 (tp) REVERT: S 93 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.6162 (mp10) REVERT: S 102 TYR cc_start: 0.6572 (m-10) cc_final: 0.6133 (m-10) REVERT: U 22 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.5951 (pt0) REVERT: U 73 LYS cc_start: 0.8131 (mmtt) cc_final: 0.7831 (mmmt) REVERT: U 93 GLN cc_start: 0.7503 (mp10) cc_final: 0.7227 (mp10) REVERT: U 101 VAL cc_start: 0.8338 (m) cc_final: 0.7829 (p) outliers start: 187 outliers final: 128 residues processed: 490 average time/residue: 0.4158 time to fit residues: 315.9532 Evaluate side-chains 466 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 319 time to evaluate : 2.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 ARG Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 499 LYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 546 ARG Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain D residue 348 PHE Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 506 MET Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 525 GLU Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain F residue 377 SER Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 440 THR Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 503 SER Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain G residue 433 LEU Chi-restraints excluded: chain G residue 443 ARG Chi-restraints excluded: chain G residue 445 LYS Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 532 GLU Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 553 ASP Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 390 VAL Chi-restraints excluded: chain K residue 427 THR Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 490 GLN Chi-restraints excluded: chain K residue 491 ARG Chi-restraints excluded: chain K residue 514 ARG Chi-restraints excluded: chain K residue 516 PHE Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain K residue 566 LEU Chi-restraints excluded: chain K residue 574 THR Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 443 ARG Chi-restraints excluded: chain L residue 445 LYS Chi-restraints excluded: chain L residue 476 VAL Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 558 LYS Chi-restraints excluded: chain L residue 566 LEU Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain L residue 575 CYS Chi-restraints excluded: chain P residue 10 VAL Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 230 ASP Chi-restraints excluded: chain P residue 257 SER Chi-restraints excluded: chain P residue 260 ASN Chi-restraints excluded: chain P residue 262 ASP Chi-restraints excluded: chain P residue 314 GLN Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain P residue 379 LEU Chi-restraints excluded: chain P residue 405 THR Chi-restraints excluded: chain P residue 413 LEU Chi-restraints excluded: chain P residue 431 TRP Chi-restraints excluded: chain P residue 433 THR Chi-restraints excluded: chain P residue 446 LEU Chi-restraints excluded: chain P residue 447 LYS Chi-restraints excluded: chain P residue 462 VAL Chi-restraints excluded: chain P residue 469 LYS Chi-restraints excluded: chain P residue 473 TYR Chi-restraints excluded: chain P residue 475 LYS Chi-restraints excluded: chain P residue 540 VAL Chi-restraints excluded: chain R residue 60 THR Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain R residue 93 GLN Chi-restraints excluded: chain R residue 96 GLU Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 39 LEU Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 89 VAL Chi-restraints excluded: chain S residue 93 GLN Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain U residue 22 GLU Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 57 THR Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 119 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 60 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 147 optimal weight: 1.9990 chunk 302 optimal weight: 8.9990 chunk 265 optimal weight: 0.3980 chunk 295 optimal weight: 0.0870 chunk 103 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 300 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 439 GLN ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.180086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.114889 restraints weight = 41857.469| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.11 r_work: 0.3347 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26320 Z= 0.146 Angle : 0.677 17.679 35955 Z= 0.337 Chirality : 0.047 0.456 4205 Planarity : 0.005 0.088 4578 Dihedral : 8.718 83.221 3916 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.71 % Favored : 92.17 % Rotamer: Outliers : 5.55 % Allowed : 21.84 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.44 % 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: -1.69 (0.15), residues: 3244 helix: -1.10 (0.28), residues: 279 sheet: -0.59 (0.15), residues: 1146 loop : -1.48 (0.15), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP P 366 HIS 0.006 0.001 HIS F 430 PHE 0.030 0.002 PHE G 424 TYR 0.037 0.001 TYR D 562 ARG 0.009 0.000 ARG J 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 9) link_NAG-ASN : angle 3.53342 ( 27) link_BETA1-4 : bond 0.02286 ( 1) link_BETA1-4 : angle 6.70979 ( 3) hydrogen bonds : bond 0.03243 ( 629) hydrogen bonds : angle 5.84631 ( 1749) SS BOND : bond 0.00322 ( 42) SS BOND : angle 0.92224 ( 84) covalent geometry : bond 0.00345 (26267) covalent geometry : angle 0.66633 (35841) Misc. bond : bond 0.01639 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 348 time to evaluate : 3.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 LYS cc_start: 0.8436 (tttm) cc_final: 0.7825 (mmtt) REVERT: A 467 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8250 (mpp-170) REVERT: B 375 TYR cc_start: 0.3947 (OUTLIER) cc_final: 0.3624 (p90) REVERT: B 441 ILE cc_start: 0.5689 (OUTLIER) cc_final: 0.5054 (mt) REVERT: B 443 ARG cc_start: 0.6011 (OUTLIER) cc_final: 0.5630 (pmt-80) REVERT: B 493 GLN cc_start: 0.8527 (pp30) cc_final: 0.8271 (pp30) REVERT: B 499 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8459 (mttm) REVERT: B 506 MET cc_start: 0.8518 (mtp) cc_final: 0.8275 (mtm) REVERT: C 348 PHE cc_start: 0.4633 (OUTLIER) cc_final: 0.4202 (m-80) REVERT: C 386 ASN cc_start: 0.8326 (t0) cc_final: 0.8069 (t0) REVERT: C 461 ARG cc_start: 0.8496 (tmm160) cc_final: 0.8002 (tpp-160) REVERT: D 418 TRP cc_start: 0.6666 (t-100) cc_final: 0.5932 (t-100) REVERT: E 427 THR cc_start: 0.6738 (OUTLIER) cc_final: 0.6462 (p) REVERT: E 489 MET cc_start: 0.7993 (tpp) cc_final: 0.7515 (tpp) REVERT: F 416 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.6995 (m-30) REVERT: G 371 ASP cc_start: 0.6977 (t0) cc_final: 0.6716 (t0) REVERT: G 445 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.6781 (mmmt) REVERT: G 468 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8308 (mm-30) REVERT: H 384 ARG cc_start: 0.7086 (mtm180) cc_final: 0.6695 (ptp-170) REVERT: H 532 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: H 534 TYR cc_start: 0.9075 (m-80) cc_final: 0.8861 (m-80) REVERT: J 120 GLU cc_start: 0.8704 (mp0) cc_final: 0.8296 (pt0) REVERT: K 354 PHE cc_start: 0.6802 (t80) cc_final: 0.6538 (t80) REVERT: K 368 LEU cc_start: 0.5694 (pt) cc_final: 0.5109 (mp) REVERT: K 489 MET cc_start: 0.8567 (mtp) cc_final: 0.8188 (mtp) REVERT: K 490 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.6805 (tp40) REVERT: K 515 TYR cc_start: 0.7921 (m-80) cc_final: 0.7594 (m-10) REVERT: K 558 LYS cc_start: 0.7485 (ptpt) cc_final: 0.7110 (tttm) REVERT: K 566 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8758 (tt) REVERT: L 453 ASP cc_start: 0.8209 (t0) cc_final: 0.7668 (t0) REVERT: L 510 GLN cc_start: 0.7980 (mp10) cc_final: 0.7071 (pm20) REVERT: P 247 ASN cc_start: 0.8831 (m-40) cc_final: 0.7720 (t0) REVERT: P 314 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7616 (mm-40) REVERT: P 475 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.6970 (mttt) REVERT: P 480 TRP cc_start: 0.6497 (t60) cc_final: 0.6173 (t60) REVERT: R 50 ARG cc_start: 0.7188 (ttt-90) cc_final: 0.6528 (mmm160) REVERT: R 51 GLU cc_start: 0.6369 (tm-30) cc_final: 0.6010 (tm-30) REVERT: R 68 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7950 (tp) REVERT: R 81 TYR cc_start: 0.7453 (m-80) cc_final: 0.7215 (m-80) REVERT: S 93 GLN cc_start: 0.7065 (OUTLIER) cc_final: 0.6109 (mp10) REVERT: S 102 TYR cc_start: 0.6684 (m-10) cc_final: 0.6233 (m-10) REVERT: U 20 LEU cc_start: 0.6960 (OUTLIER) cc_final: 0.6284 (pp) REVERT: U 22 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.6481 (pt0) REVERT: U 73 LYS cc_start: 0.8116 (mmtt) cc_final: 0.7765 (mmmt) REVERT: U 93 GLN cc_start: 0.7483 (mp10) cc_final: 0.7206 (mp10) REVERT: U 101 VAL cc_start: 0.8350 (m) cc_final: 0.7869 (p) outliers start: 161 outliers final: 121 residues processed: 475 average time/residue: 0.3896 time to fit residues: 283.1275 Evaluate side-chains 464 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 325 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 467 ARG Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 499 LYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 546 ARG Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain D residue 348 PHE Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 506 MET Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 525 GLU Chi-restraints excluded: chain F residue 377 SER Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain F residue 423 ARG Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 440 THR Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 503 SER Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain F residue 556 THR Chi-restraints excluded: chain G residue 433 LEU Chi-restraints excluded: chain G residue 443 ARG Chi-restraints excluded: chain G residue 445 LYS Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain H residue 472 ILE Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 532 GLU Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 553 ASP Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 390 VAL Chi-restraints excluded: chain K residue 427 THR Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 490 GLN Chi-restraints excluded: chain K residue 491 ARG Chi-restraints excluded: chain K residue 514 ARG Chi-restraints excluded: chain K residue 516 PHE Chi-restraints excluded: chain K residue 520 ILE Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain K residue 566 LEU Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 443 ARG Chi-restraints excluded: chain L residue 445 LYS Chi-restraints excluded: chain L residue 476 VAL Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 558 LYS Chi-restraints excluded: chain L residue 566 LEU Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain L residue 575 CYS Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 230 ASP Chi-restraints excluded: chain P residue 257 SER Chi-restraints excluded: chain P residue 260 ASN Chi-restraints excluded: chain P residue 314 GLN Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain P residue 379 LEU Chi-restraints excluded: chain P residue 413 LEU Chi-restraints excluded: chain P residue 431 TRP Chi-restraints excluded: chain P residue 433 THR Chi-restraints excluded: chain P residue 446 LEU Chi-restraints excluded: chain P residue 448 VAL Chi-restraints excluded: chain P residue 462 VAL Chi-restraints excluded: chain P residue 473 TYR Chi-restraints excluded: chain P residue 475 LYS Chi-restraints excluded: chain R residue 60 THR Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 93 GLN Chi-restraints excluded: chain R residue 96 GLU Chi-restraints excluded: chain S residue 39 LEU Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 89 VAL Chi-restraints excluded: chain S residue 93 GLN Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 22 GLU Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 57 THR Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 119 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 202 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 215 optimal weight: 30.0000 chunk 245 optimal weight: 10.0000 chunk 264 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 252 optimal weight: 0.8980 chunk 298 optimal weight: 0.9990 chunk 259 optimal weight: 0.0670 chunk 200 optimal weight: 5.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 GLN ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.179582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.114591 restraints weight = 41886.486| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.42 r_work: 0.3322 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 26320 Z= 0.177 Angle : 0.686 18.060 35955 Z= 0.343 Chirality : 0.047 0.448 4205 Planarity : 0.006 0.090 4578 Dihedral : 8.531 81.011 3907 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.98 % Favored : 91.89 % Rotamer: Outliers : 5.41 % Allowed : 22.46 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.44 % 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: -1.66 (0.15), residues: 3244 helix: -1.16 (0.28), residues: 288 sheet: -0.54 (0.16), residues: 1127 loop : -1.45 (0.15), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 418 HIS 0.005 0.001 HIS H 450 PHE 0.021 0.002 PHE B 354 TYR 0.034 0.001 TYR D 562 ARG 0.010 0.000 ARG F 384 Details of bonding type rmsd link_NAG-ASN : bond 0.00422 ( 9) link_NAG-ASN : angle 3.57941 ( 27) link_BETA1-4 : bond 0.02386 ( 1) link_BETA1-4 : angle 6.51858 ( 3) hydrogen bonds : bond 0.03279 ( 629) hydrogen bonds : angle 5.80730 ( 1749) SS BOND : bond 0.00362 ( 42) SS BOND : angle 1.15734 ( 84) covalent geometry : bond 0.00423 (26267) covalent geometry : angle 0.67545 (35841) Misc. bond : bond 0.01604 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 336 time to evaluate : 2.916 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 GLU cc_start: 0.7289 (mp0) cc_final: 0.6964 (mp0) REVERT: A 445 LYS cc_start: 0.8445 (tttm) cc_final: 0.7842 (mmtt) REVERT: A 467 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8228 (mpp-170) REVERT: B 375 TYR cc_start: 0.4157 (OUTLIER) cc_final: 0.3730 (p90) REVERT: B 402 ASN cc_start: 0.7435 (m-40) cc_final: 0.7037 (p0) REVERT: B 441 ILE cc_start: 0.5668 (OUTLIER) cc_final: 0.5021 (mt) REVERT: B 443 ARG cc_start: 0.5935 (OUTLIER) cc_final: 0.5552 (pmt-80) REVERT: B 451 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8027 (ptm-80) REVERT: B 493 GLN cc_start: 0.8525 (pp30) cc_final: 0.8264 (pp30) REVERT: B 499 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8468 (mttm) REVERT: B 506 MET cc_start: 0.8545 (mtp) cc_final: 0.8296 (mtm) REVERT: C 348 PHE cc_start: 0.4644 (OUTLIER) cc_final: 0.4223 (m-80) REVERT: C 386 ASN cc_start: 0.8277 (t0) cc_final: 0.8030 (t0) REVERT: C 461 ARG cc_start: 0.8534 (tmm160) cc_final: 0.8023 (tpp-160) REVERT: C 498 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7737 (pm20) REVERT: D 380 ILE cc_start: 0.0590 (OUTLIER) cc_final: 0.0151 (mt) REVERT: D 418 TRP cc_start: 0.6645 (t-100) cc_final: 0.6178 (t-100) REVERT: E 364 LYS cc_start: 0.7767 (tppt) cc_final: 0.7110 (tppt) REVERT: E 427 THR cc_start: 0.6749 (OUTLIER) cc_final: 0.6500 (p) REVERT: E 489 MET cc_start: 0.8019 (tpp) cc_final: 0.7713 (tpp) REVERT: F 382 TRP cc_start: 0.6482 (m100) cc_final: 0.5424 (m100) REVERT: F 416 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.6824 (m-30) REVERT: F 423 ARG cc_start: 0.7543 (mtm180) cc_final: 0.7066 (mtt180) REVERT: G 371 ASP cc_start: 0.6981 (t0) cc_final: 0.6749 (t0) REVERT: G 445 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.6897 (mmmt) REVERT: H 384 ARG cc_start: 0.7157 (mtm180) cc_final: 0.6799 (ptp-170) REVERT: H 532 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7100 (mp0) REVERT: H 534 TYR cc_start: 0.9100 (m-80) cc_final: 0.8890 (m-80) REVERT: J 120 GLU cc_start: 0.8703 (mp0) cc_final: 0.8281 (pt0) REVERT: K 354 PHE cc_start: 0.6884 (t80) cc_final: 0.6657 (t80) REVERT: K 368 LEU cc_start: 0.5707 (pt) cc_final: 0.5080 (mp) REVERT: K 489 MET cc_start: 0.8583 (mtp) cc_final: 0.8183 (mtp) REVERT: K 515 TYR cc_start: 0.7979 (m-80) cc_final: 0.7761 (m-80) REVERT: K 558 LYS cc_start: 0.7462 (ptpt) cc_final: 0.7122 (tttm) REVERT: K 566 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8764 (tt) REVERT: L 453 ASP cc_start: 0.8247 (t0) cc_final: 0.7723 (t0) REVERT: L 510 GLN cc_start: 0.8002 (mp10) cc_final: 0.7069 (pm20) REVERT: P 247 ASN cc_start: 0.8829 (m-40) cc_final: 0.7738 (t0) REVERT: P 447 LYS cc_start: 0.3298 (OUTLIER) cc_final: 0.2770 (tptt) REVERT: P 475 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.6979 (mttt) REVERT: P 480 TRP cc_start: 0.6504 (t60) cc_final: 0.6160 (t60) REVERT: R 50 ARG cc_start: 0.7162 (ttt-90) cc_final: 0.6544 (mmm160) REVERT: R 51 GLU cc_start: 0.6375 (tm-30) cc_final: 0.6042 (tm-30) REVERT: R 68 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.7971 (tp) REVERT: S 93 GLN cc_start: 0.7040 (OUTLIER) cc_final: 0.6153 (mp10) REVERT: S 102 TYR cc_start: 0.6666 (m-10) cc_final: 0.6426 (m-80) REVERT: U 22 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.6017 (pt0) REVERT: U 73 LYS cc_start: 0.8102 (mmtt) cc_final: 0.7716 (mmmt) REVERT: U 83 ARG cc_start: 0.8666 (mpp80) cc_final: 0.8240 (ptt90) REVERT: U 93 GLN cc_start: 0.7510 (mp10) cc_final: 0.7221 (mp10) REVERT: U 101 VAL cc_start: 0.8327 (m) cc_final: 0.7850 (p) REVERT: V 42 MET cc_start: 0.4361 (tpp) cc_final: 0.4029 (tpt) REVERT: V 108 MET cc_start: 0.6079 (mmm) cc_final: 0.5864 (mmm) outliers start: 157 outliers final: 125 residues processed: 463 average time/residue: 0.4748 time to fit residues: 339.7293 Evaluate side-chains 470 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 326 time to evaluate : 4.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 467 ARG Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 499 LYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 546 ARG Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain D residue 348 PHE Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 506 MET Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 525 GLU Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain F residue 377 SER Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 503 SER Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 433 LEU Chi-restraints excluded: chain G residue 443 ARG Chi-restraints excluded: chain G residue 445 LYS Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 503 SER Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 472 ILE Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 532 GLU Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 553 ASP Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain H residue 564 VAL Chi-restraints excluded: chain H residue 566 LEU Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 390 VAL Chi-restraints excluded: chain K residue 427 THR Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 491 ARG Chi-restraints excluded: chain K residue 514 ARG Chi-restraints excluded: chain K residue 516 PHE Chi-restraints excluded: chain K residue 520 ILE Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain K residue 566 LEU Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 443 ARG Chi-restraints excluded: chain L residue 445 LYS Chi-restraints excluded: chain L residue 476 VAL Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 566 LEU Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain L residue 575 CYS Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 230 ASP Chi-restraints excluded: chain P residue 257 SER Chi-restraints excluded: chain P residue 260 ASN Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain P residue 379 LEU Chi-restraints excluded: chain P residue 413 LEU Chi-restraints excluded: chain P residue 431 TRP Chi-restraints excluded: chain P residue 433 THR Chi-restraints excluded: chain P residue 446 LEU Chi-restraints excluded: chain P residue 447 LYS Chi-restraints excluded: chain P residue 448 VAL Chi-restraints excluded: chain P residue 462 VAL Chi-restraints excluded: chain P residue 473 TYR Chi-restraints excluded: chain P residue 475 LYS Chi-restraints excluded: chain R residue 60 THR Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 93 GLN Chi-restraints excluded: chain R residue 96 GLU Chi-restraints excluded: chain S residue 39 LEU Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 89 VAL Chi-restraints excluded: chain S residue 93 GLN Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain U residue 22 GLU Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 57 THR Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 143 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 299 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 160 optimal weight: 0.0020 chunk 138 optimal weight: 9.9990 chunk 321 optimal weight: 8.9990 chunk 219 optimal weight: 30.0000 chunk 15 optimal weight: 0.9980 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 385 GLN ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 450 HIS ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 532 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.178708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.113276 restraints weight = 42103.897| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.45 r_work: 0.3306 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 26320 Z= 0.205 Angle : 0.699 17.699 35955 Z= 0.350 Chirality : 0.048 0.455 4205 Planarity : 0.006 0.090 4578 Dihedral : 8.384 80.746 3902 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.29 % Favored : 91.62 % Rotamer: Outliers : 5.37 % Allowed : 22.87 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.44 % 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: -1.71 (0.15), residues: 3244 helix: -1.20 (0.28), residues: 285 sheet: -0.65 (0.15), residues: 1144 loop : -1.43 (0.15), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP P 366 HIS 0.004 0.001 HIS A 450 PHE 0.023 0.002 PHE G 424 TYR 0.033 0.001 TYR D 562 ARG 0.009 0.000 ARG F 384 Details of bonding type rmsd link_NAG-ASN : bond 0.00401 ( 9) link_NAG-ASN : angle 3.65724 ( 27) link_BETA1-4 : bond 0.02380 ( 1) link_BETA1-4 : angle 6.36392 ( 3) hydrogen bonds : bond 0.03367 ( 629) hydrogen bonds : angle 5.85034 ( 1749) SS BOND : bond 0.00376 ( 42) SS BOND : angle 1.18374 ( 84) covalent geometry : bond 0.00489 (26267) covalent geometry : angle 0.68852 (35841) Misc. bond : bond 0.01615 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 329 time to evaluate : 2.898 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 GLU cc_start: 0.7167 (mp0) cc_final: 0.6788 (mp0) REVERT: A 445 LYS cc_start: 0.8528 (tttm) cc_final: 0.7946 (mmtt) REVERT: A 467 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8258 (mpp-170) REVERT: B 375 TYR cc_start: 0.4120 (OUTLIER) cc_final: 0.3717 (p90) REVERT: B 402 ASN cc_start: 0.7509 (t0) cc_final: 0.7095 (p0) REVERT: B 441 ILE cc_start: 0.5541 (OUTLIER) cc_final: 0.4183 (mt) REVERT: B 451 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.7664 (ptm-80) REVERT: B 493 GLN cc_start: 0.8521 (pp30) cc_final: 0.8253 (pp30) REVERT: B 499 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8737 (mtpp) REVERT: B 506 MET cc_start: 0.8587 (mtp) cc_final: 0.8339 (mtm) REVERT: C 348 PHE cc_start: 0.4616 (OUTLIER) cc_final: 0.4208 (m-80) REVERT: C 386 ASN cc_start: 0.8268 (t0) cc_final: 0.8019 (t0) REVERT: C 489 MET cc_start: 0.9043 (mtp) cc_final: 0.8817 (mtp) REVERT: C 498 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7705 (pm20) REVERT: D 380 ILE cc_start: 0.0642 (OUTLIER) cc_final: 0.0192 (mt) REVERT: E 364 LYS cc_start: 0.7808 (tppt) cc_final: 0.7138 (tppt) REVERT: E 427 THR cc_start: 0.6738 (OUTLIER) cc_final: 0.6484 (p) REVERT: E 489 MET cc_start: 0.8062 (tpp) cc_final: 0.7655 (tpp) REVERT: F 382 TRP cc_start: 0.6619 (m100) cc_final: 0.5444 (m100) REVERT: F 416 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.6827 (m-30) REVERT: G 445 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.6925 (mmmt) REVERT: H 384 ARG cc_start: 0.7197 (mtm180) cc_final: 0.6884 (ptp-170) REVERT: H 532 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7238 (mp0) REVERT: H 534 TYR cc_start: 0.9127 (m-80) cc_final: 0.8911 (m-80) REVERT: J 120 GLU cc_start: 0.8709 (mp0) cc_final: 0.8372 (mp0) REVERT: K 354 PHE cc_start: 0.6895 (t80) cc_final: 0.6662 (t80) REVERT: K 489 MET cc_start: 0.8585 (mtp) cc_final: 0.8170 (mtp) REVERT: K 490 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.6931 (tp40) REVERT: K 515 TYR cc_start: 0.8018 (m-80) cc_final: 0.7811 (m-80) REVERT: K 558 LYS cc_start: 0.7394 (ptpt) cc_final: 0.7049 (tttm) REVERT: K 566 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8821 (tt) REVERT: L 453 ASP cc_start: 0.8265 (t0) cc_final: 0.7735 (t0) REVERT: P 225 GLU cc_start: 0.7603 (tt0) cc_final: 0.7396 (tt0) REVERT: P 247 ASN cc_start: 0.8805 (m-40) cc_final: 0.7704 (t0) REVERT: P 447 LYS cc_start: 0.3358 (OUTLIER) cc_final: 0.2795 (tptt) REVERT: P 475 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7053 (mttt) REVERT: P 480 TRP cc_start: 0.6527 (t60) cc_final: 0.6175 (t60) REVERT: R 51 GLU cc_start: 0.6407 (tm-30) cc_final: 0.5999 (tm-30) REVERT: S 93 GLN cc_start: 0.7171 (OUTLIER) cc_final: 0.6255 (mp10) REVERT: S 102 TYR cc_start: 0.6707 (m-10) cc_final: 0.6402 (m-10) REVERT: U 20 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6365 (pt) REVERT: U 73 LYS cc_start: 0.8077 (mmtt) cc_final: 0.7690 (mmmt) REVERT: U 83 ARG cc_start: 0.8687 (mpp80) cc_final: 0.8250 (ptt90) REVERT: U 93 GLN cc_start: 0.7565 (mp10) cc_final: 0.7268 (mp10) REVERT: U 101 VAL cc_start: 0.8427 (m) cc_final: 0.7948 (p) outliers start: 156 outliers final: 126 residues processed: 454 average time/residue: 0.4068 time to fit residues: 286.3560 Evaluate side-chains 463 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 319 time to evaluate : 3.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 467 ARG Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 499 LYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 546 ARG Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain D residue 348 PHE Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 506 MET Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 525 GLU Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain F residue 377 SER Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 503 SER Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 433 LEU Chi-restraints excluded: chain G residue 443 ARG Chi-restraints excluded: chain G residue 445 LYS Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 503 SER Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 472 ILE Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 532 GLU Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 553 ASP Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain H residue 564 VAL Chi-restraints excluded: chain H residue 566 LEU Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 390 VAL Chi-restraints excluded: chain K residue 427 THR Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 490 GLN Chi-restraints excluded: chain K residue 491 ARG Chi-restraints excluded: chain K residue 514 ARG Chi-restraints excluded: chain K residue 516 PHE Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain K residue 566 LEU Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 443 ARG Chi-restraints excluded: chain L residue 445 LYS Chi-restraints excluded: chain L residue 476 VAL Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 566 LEU Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain L residue 575 CYS Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 230 ASP Chi-restraints excluded: chain P residue 257 SER Chi-restraints excluded: chain P residue 260 ASN Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain P residue 379 LEU Chi-restraints excluded: chain P residue 413 LEU Chi-restraints excluded: chain P residue 431 TRP Chi-restraints excluded: chain P residue 433 THR Chi-restraints excluded: chain P residue 446 LEU Chi-restraints excluded: chain P residue 447 LYS Chi-restraints excluded: chain P residue 448 VAL Chi-restraints excluded: chain P residue 462 VAL Chi-restraints excluded: chain P residue 473 TYR Chi-restraints excluded: chain P residue 475 LYS Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 93 GLN Chi-restraints excluded: chain R residue 96 GLU Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 89 VAL Chi-restraints excluded: chain S residue 93 GLN Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 22 GLU Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 57 THR Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 112 ARG Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain V residue 78 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 298 optimal weight: 0.2980 chunk 51 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 137 optimal weight: 8.9990 chunk 203 optimal weight: 0.9990 chunk 146 optimal weight: 0.6980 chunk 304 optimal weight: 10.0000 chunk 297 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 99 optimal weight: 0.0070 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.180812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.121484 restraints weight = 41665.784| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 3.68 r_work: 0.3348 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26320 Z= 0.131 Angle : 0.665 17.412 35955 Z= 0.332 Chirality : 0.046 0.456 4205 Planarity : 0.005 0.093 4578 Dihedral : 8.040 80.661 3902 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.18 % Favored : 92.73 % Rotamer: Outliers : 4.34 % Allowed : 23.94 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.44 % 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: -1.57 (0.15), residues: 3244 helix: -1.08 (0.28), residues: 285 sheet: -0.52 (0.15), residues: 1153 loop : -1.37 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP B 382 HIS 0.004 0.001 HIS A 450 PHE 0.018 0.002 PHE G 424 TYR 0.025 0.001 TYR D 562 ARG 0.010 0.000 ARG F 384 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 9) link_NAG-ASN : angle 3.46162 ( 27) link_BETA1-4 : bond 0.01769 ( 1) link_BETA1-4 : angle 5.86545 ( 3) hydrogen bonds : bond 0.03074 ( 629) hydrogen bonds : angle 5.60676 ( 1749) SS BOND : bond 0.00279 ( 42) SS BOND : angle 0.95494 ( 84) covalent geometry : bond 0.00308 (26267) covalent geometry : angle 0.65517 (35841) Misc. bond : bond 0.01619 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6488 Ramachandran restraints generated. 3244 Oldfield, 0 Emsley, 3244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 342 time to evaluate : 2.937 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 GLU cc_start: 0.7245 (mp0) cc_final: 0.6923 (mp0) REVERT: A 445 LYS cc_start: 0.8507 (tttm) cc_final: 0.7914 (mmtt) REVERT: B 375 TYR cc_start: 0.4041 (OUTLIER) cc_final: 0.3653 (p90) REVERT: B 402 ASN cc_start: 0.7508 (t0) cc_final: 0.7110 (p0) REVERT: B 441 ILE cc_start: 0.5043 (OUTLIER) cc_final: 0.4348 (mt) REVERT: B 451 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7861 (ptm-80) REVERT: B 493 GLN cc_start: 0.8549 (pp30) cc_final: 0.8264 (pp30) REVERT: B 499 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8790 (mtpp) REVERT: B 506 MET cc_start: 0.8540 (mtp) cc_final: 0.8308 (mtm) REVERT: B 532 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6794 (tt0) REVERT: B 546 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7477 (mtm110) REVERT: C 348 PHE cc_start: 0.4712 (OUTLIER) cc_final: 0.4300 (m-80) REVERT: C 386 ASN cc_start: 0.8212 (t0) cc_final: 0.8000 (t0) REVERT: C 489 MET cc_start: 0.9009 (mtp) cc_final: 0.8755 (mtp) REVERT: C 498 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7906 (pm20) REVERT: D 380 ILE cc_start: 0.0132 (OUTLIER) cc_final: -0.0243 (mt) REVERT: D 418 TRP cc_start: 0.6660 (t-100) cc_final: 0.5910 (t-100) REVERT: E 427 THR cc_start: 0.6680 (OUTLIER) cc_final: 0.6409 (p) REVERT: E 489 MET cc_start: 0.7958 (tpp) cc_final: 0.7492 (tpp) REVERT: F 382 TRP cc_start: 0.6530 (m100) cc_final: 0.5417 (m100) REVERT: F 416 ASP cc_start: 0.7623 (OUTLIER) cc_final: 0.6805 (m-30) REVERT: F 423 ARG cc_start: 0.7482 (mtm180) cc_final: 0.7002 (mtt180) REVERT: G 445 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.6967 (mmmt) REVERT: G 525 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7764 (tm-30) REVERT: H 384 ARG cc_start: 0.7221 (mtm180) cc_final: 0.6869 (ptp-170) REVERT: H 532 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: H 534 TYR cc_start: 0.9112 (m-80) cc_final: 0.8904 (m-80) REVERT: J 120 GLU cc_start: 0.8630 (mp0) cc_final: 0.8297 (mp0) REVERT: K 354 PHE cc_start: 0.6758 (t80) cc_final: 0.6546 (t80) REVERT: K 368 LEU cc_start: 0.5435 (pt) cc_final: 0.4782 (mp) REVERT: K 489 MET cc_start: 0.8572 (mtp) cc_final: 0.8232 (mtp) REVERT: K 558 LYS cc_start: 0.7341 (ptpt) cc_final: 0.7075 (tttm) REVERT: K 566 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8708 (tt) REVERT: L 453 ASP cc_start: 0.8212 (t0) cc_final: 0.7671 (t0) REVERT: P 225 GLU cc_start: 0.7574 (tt0) cc_final: 0.7359 (tt0) REVERT: P 247 ASN cc_start: 0.8788 (m-40) cc_final: 0.7691 (t0) REVERT: P 447 LYS cc_start: 0.3207 (OUTLIER) cc_final: 0.2680 (tptt) REVERT: P 475 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7146 (mttt) REVERT: P 480 TRP cc_start: 0.6574 (t60) cc_final: 0.6199 (t60) REVERT: R 51 GLU cc_start: 0.6420 (tm-30) cc_final: 0.5994 (tm-30) REVERT: S 81 TYR cc_start: 0.7756 (m-80) cc_final: 0.7434 (m-80) REVERT: S 93 GLN cc_start: 0.7217 (OUTLIER) cc_final: 0.6196 (mp10) REVERT: S 102 TYR cc_start: 0.6584 (m-10) cc_final: 0.6168 (m-10) REVERT: U 22 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.5980 (pt0) REVERT: U 73 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7802 (mmmt) REVERT: U 83 ARG cc_start: 0.8742 (mpp80) cc_final: 0.8262 (ptt90) REVERT: U 93 GLN cc_start: 0.7511 (mp10) cc_final: 0.7235 (mp10) REVERT: U 101 VAL cc_start: 0.8277 (m) cc_final: 0.7854 (p) REVERT: V 52 MET cc_start: 0.4506 (tpt) cc_final: 0.4173 (tpt) REVERT: V 108 MET cc_start: 0.6031 (mmm) cc_final: 0.5821 (mmm) outliers start: 126 outliers final: 99 residues processed: 441 average time/residue: 0.4027 time to fit residues: 274.7352 Evaluate side-chains 442 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 325 time to evaluate : 2.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 499 LYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 546 ARG Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain D residue 348 PHE Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 506 MET Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 525 GLU Chi-restraints excluded: chain F residue 377 SER Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 503 SER Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 433 LEU Chi-restraints excluded: chain G residue 443 ARG Chi-restraints excluded: chain G residue 445 LYS Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 472 ILE Chi-restraints excluded: chain H residue 532 GLU Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 553 ASP Chi-restraints excluded: chain H residue 566 LEU Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 390 VAL Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 491 ARG Chi-restraints excluded: chain K residue 514 ARG Chi-restraints excluded: chain K residue 516 PHE Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain K residue 566 LEU Chi-restraints excluded: chain L residue 441 ILE Chi-restraints excluded: chain L residue 443 ARG Chi-restraints excluded: chain L residue 445 LYS Chi-restraints excluded: chain L residue 476 VAL Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 558 LYS Chi-restraints excluded: chain L residue 566 LEU Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain L residue 575 CYS Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 230 ASP Chi-restraints excluded: chain P residue 257 SER Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain P residue 379 LEU Chi-restraints excluded: chain P residue 413 LEU Chi-restraints excluded: chain P residue 431 TRP Chi-restraints excluded: chain P residue 433 THR Chi-restraints excluded: chain P residue 446 LEU Chi-restraints excluded: chain P residue 447 LYS Chi-restraints excluded: chain P residue 448 VAL Chi-restraints excluded: chain P residue 462 VAL Chi-restraints excluded: chain P residue 473 TYR Chi-restraints excluded: chain P residue 475 LYS Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 93 GLN Chi-restraints excluded: chain R residue 96 GLU Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 89 VAL Chi-restraints excluded: chain S residue 93 GLN Chi-restraints excluded: chain U residue 22 GLU Chi-restraints excluded: chain U residue 23 VAL Chi-restraints excluded: chain U residue 57 THR Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 112 ARG Chi-restraints excluded: chain U residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 25 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 246 optimal weight: 9.9990 chunk 208 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 122 optimal weight: 0.1980 chunk 280 optimal weight: 0.0070 chunk 242 optimal weight: 0.9990 chunk 313 optimal weight: 0.0170 chunk 302 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.182452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.123080 restraints weight = 42034.649| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 3.79 r_work: 0.3385 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26320 Z= 0.117 Angle : 0.642 16.990 35955 Z= 0.320 Chirality : 0.046 0.462 4205 Planarity : 0.005 0.087 4578 Dihedral : 7.597 80.760 3886 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.94 % Favored : 92.97 % Rotamer: Outliers : 4.00 % Allowed : 24.32 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.44 % 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: -1.38 (0.15), residues: 3244 helix: -0.93 (0.29), residues: 283 sheet: -0.30 (0.16), residues: 1114 loop : -1.30 (0.14), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 382 HIS 0.005 0.001 HIS L 518 PHE 0.022 0.002 PHE R 87 TYR 0.015 0.001 TYR D 562 ARG 0.009 0.000 ARG F 384 Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 9) link_NAG-ASN : angle 3.33214 ( 27) link_BETA1-4 : bond 0.01892 ( 1) link_BETA1-4 : angle 5.55921 ( 3) hydrogen bonds : bond 0.02969 ( 629) hydrogen bonds : angle 5.40299 ( 1749) SS BOND : bond 0.00244 ( 42) SS BOND : angle 0.86037 ( 84) covalent geometry : bond 0.00272 (26267) covalent geometry : angle 0.63260 (35841) Misc. bond : bond 0.01611 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17471.49 seconds wall clock time: 304 minutes 34.77 seconds (18274.77 seconds total)