Starting phenix.real_space_refine on Sun Jul 5 05:18:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ysg_34074/07_2026/7ysg_34074.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ysg_34074/07_2026/7ysg_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_34074/07_2026/7ysg_34074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ysg_34074/07_2026/7ysg_34074.map" model { file = "/net/cci-nas-00/data/ceres_data/7ysg_34074/07_2026/7ysg_34074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ysg_34074/07_2026/7ysg_34074.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ysg_34074/07_2026/7ysg_34074.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ysg_34074/07_2026/7ysg_34074.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 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 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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 6.88, per 1000 atoms: 0.27 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: 2.37 Conformation dependent library (CDL) restraints added in 1.0 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: 0.92 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: 4.61 Time building geometry restraints manager: 3.12 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 - 20.95: 14098 20.95 - 41.89: 1294 41.89 - 62.84: 415 62.84 - 83.79: 48 83.79 - 104.73: 13 Dihedral angle restraints: 15868 sinusoidal: 6289 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 15865 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 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 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 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: 3.400 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: 0.040 Extract box with map and model: 0.570 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.740 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 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 : 17.533 104.733 9538 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.029 0.001 ARG A 514 TYR 0.041 0.003 TYR K 576 PHE 0.069 0.003 PHE P 275 TRP 0.043 0.003 TRP P 480 HIS 0.024 0.002 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.01665 / 1.10 (26267) covalent geometry : angle 1.73170 / 1.05 (35841) SS BOND : bond 0.08409 / 6.01 ( 42) SS BOND : angle 6.76351 / 4.57 ( 84) hydrogen bonds : bond 0.18768 / 13.11 ( 629) hydrogen bonds : angle 8.50115 / 6.00 ( 1749) Misc. bond : bond 0.03913 / 2.06 ( 1) link_BETA1-4 : bond 0.01303 / 0.69 ( 1) link_BETA1-4 : angle 7.09849 / 3.43 ( 3) link_NAG-ASN : bond 0.09920 / 3.52 ( 9) link_NAG-ASN : angle 10.38377 / 7.14 ( 27) *********************** 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 : 1.126 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: 0.8316 (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 410 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6854 (tt0) 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: 0.7110 (mm-30) REVERT: D 424 PHE cc_start: 0.7553 (m-80) cc_final: 0.7298 (m-80) REVERT: E 445 LYS cc_start: 0.7232 (OUTLIER) cc_final: 0.6922 (mmtp) REVERT: F 364 LYS cc_start: 0.8169 (mmmt) cc_final: 0.7750 (mtpp) REVERT: F 376 ASP cc_start: 0.2528 (OUTLIER) cc_final: 0.2287 (t0) REVERT: F 414 CYS cc_start: 0.6217 (OUTLIER) cc_final: 0.5994 (m) REVERT: F 416 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7367 (p0) REVERT: F 554 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8664 (tmtm) REVERT: G 417 ASP cc_start: 0.7050 (m-30) cc_final: 0.6710 (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: 0.7819 (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: 0.6474 (tp40) REVERT: P 392 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7363 (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: 0.8045 (t) REVERT: U 83 ARG cc_start: 0.8399 (mpp80) cc_final: 0.8158 (ptt90) REVERT: U 88 LEU cc_start: 0.7230 (mt) cc_final: 0.6957 (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: 0.1695 time to fit residues: 182.2687 Evaluate side-chains 540 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 330 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 410 GLU 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 197 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 510 GLN ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN B 385 GLN 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** J 44 ASN K 419 ASN ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 463 GLN L 490 GLN L 529 ASN 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 V 121 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.181836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.122440 restraints weight = 42110.702| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 3.39 r_work: 0.3347 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 26320 Z= 0.184 Angle : 0.824 20.535 35955 Z= 0.417 Chirality : 0.050 0.406 4205 Planarity : 0.007 0.108 4578 Dihedral : 13.137 174.952 3990 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.42 % Favored : 91.31 % Rotamer: Outliers : 6.68 % Allowed : 13.23 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.14), residues: 3244 helix: -1.31 (0.27), residues: 277 sheet: -0.69 (0.15), residues: 1131 loop : -1.87 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 467 TYR 0.021 0.002 TYR L 562 PHE 0.027 0.002 PHE K 354 TRP 0.033 0.002 TRP B 418 HIS 0.006 0.001 HIS K 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (26267) covalent geometry : angle 0.81435 / 0.41 (35841) SS BOND : bond 0.00686 / 0.50 ( 42) SS BOND : angle 1.48746 / 1.19 ( 84) hydrogen bonds : bond 0.04109 / 2.86 ( 629) hydrogen bonds : angle 6.64618 / 4.65 ( 1749) Misc. bond : bond 0.01954 / 1.03 ( 1) link_BETA1-4 : bond 0.02919 / 1.54 ( 1) link_BETA1-4 : angle 5.56524 / 2.42 ( 3) link_NAG-ASN : bond 0.00422 / 0.20 ( 9) link_NAG-ASN : angle 3.76114 / 2.52 ( 27) *********************** 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 586 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 392 time to evaluate : 0.973 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: A 445 LYS cc_start: 0.8357 (tttm) cc_final: 0.7793 (mmtt) REVERT: A 519 SER cc_start: 0.8699 (OUTLIER) cc_final: 0.8485 (t) REVERT: B 441 ILE cc_start: 0.4936 (OUTLIER) cc_final: 0.4408 (mt) REVERT: B 499 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8305 (mttm) REVERT: B 506 MET cc_start: 0.8456 (mtp) cc_final: 0.8203 (mtm) REVERT: B 532 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7469 (mt-10) REVERT: C 348 PHE cc_start: 0.4366 (OUTLIER) cc_final: 0.3892 (m-80) REVERT: C 386 ASN cc_start: 0.8131 (t0) cc_final: 0.7845 (t0) REVERT: D 491 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8198 (mtm110) REVERT: E 364 LYS cc_start: 0.7667 (tppt) cc_final: 0.6791 (tppt) REVERT: F 364 LYS cc_start: 0.7973 (mmmt) cc_final: 0.7578 (mmtm) REVERT: F 380 ILE cc_start: 0.4173 (mm) cc_final: 0.3849 (mp) REVERT: F 396 ILE cc_start: 0.5475 (OUTLIER) cc_final: 0.5202 (tt) REVERT: F 416 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7248 (p0) REVERT: F 424 PHE cc_start: 0.7197 (m-80) cc_final: 0.6446 (m-80) REVERT: G 371 ASP cc_start: 0.6480 (t0) cc_final: 0.6192 (t0) REVERT: G 445 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.6490 (mmmt) REVERT: H 532 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: K 368 LEU cc_start: 0.6068 (pt) cc_final: 0.5544 (mt) REVERT: K 462 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8004 (mp0) REVERT: K 464 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8358 (mm) REVERT: K 490 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7507 (tp40) REVERT: K 515 TYR cc_start: 0.8001 (m-80) cc_final: 0.7586 (m-10) REVERT: L 455 TYR cc_start: 0.7900 (m-80) cc_final: 0.7629 (m-80) REVERT: L 483 ASP cc_start: 0.7282 (m-30) cc_final: 0.6359 (t0) REVERT: L 485 PHE cc_start: 0.5504 (t80) cc_final: 0.5262 (t80) REVERT: L 545 ASN cc_start: 0.8018 (t0) cc_final: 0.7793 (t0) REVERT: P 247 ASN cc_start: 0.8812 (m-40) cc_final: 0.7733 (t0) REVERT: P 376 ARG cc_start: 0.7799 (tmt170) cc_final: 0.7304 (ptt90) REVERT: P 388 LYS cc_start: 0.5719 (tppt) cc_final: 0.5461 (ttpp) REVERT: P 400 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6529 (tm-30) REVERT: P 447 LYS cc_start: 0.4136 (OUTLIER) cc_final: 0.3347 (tptt) REVERT: P 469 LYS cc_start: 0.6520 (OUTLIER) cc_final: 0.5792 (pptt) REVERT: P 533 PHE cc_start: 0.6392 (OUTLIER) cc_final: 0.5864 (m-80) REVERT: S 71 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8474 (pm20) REVERT: S 81 TYR cc_start: 0.7677 (m-80) cc_final: 0.7377 (m-80) REVERT: U 83 ARG cc_start: 0.8565 (mpp80) cc_final: 0.8225 (ptt90) REVERT: U 93 GLN cc_start: 0.7077 (mp10) cc_final: 0.6737 (mp10) outliers start: 194 outliers final: 110 residues processed: 554 average time/residue: 0.1902 time to fit residues: 161.6510 Evaluate side-chains 463 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 335 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 519 SER 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 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 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 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 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 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 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 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 K residue 383 THR Chi-restraints excluded: chain K residue 462 GLU Chi-restraints excluded: chain K residue 464 LEU 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 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 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 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 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 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 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 286 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 296 optimal weight: 0.6980 chunk 298 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 321 optimal weight: 10.0000 chunk 306 optimal weight: 0.5980 chunk 260 optimal weight: 0.9990 chunk 250 optimal weight: 8.9990 chunk 293 optimal weight: 9.9990 chunk 110 optimal weight: 0.0770 overall best weight: 1.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 540 HIS ** 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 439 GLN ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 393 HIS ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 385 GLN ** K 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 260 ASN R 85 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.181198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.115636 restraints weight = 42131.928| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 3.31 r_work: 0.3359 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 26320 Z= 0.169 Angle : 0.724 18.350 35955 Z= 0.363 Chirality : 0.047 0.416 4205 Planarity : 0.006 0.101 4578 Dihedral : 10.168 89.355 3741 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.98 % Favored : 91.77 % Rotamer: Outliers : 5.99 % Allowed : 16.57 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.14), residues: 3244 helix: -1.23 (0.28), residues: 277 sheet: -0.56 (0.15), residues: 1115 loop : -1.60 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 423 TYR 0.018 0.002 TYR L 562 PHE 0.026 0.002 PHE D 424 TRP 0.045 0.002 TRP B 418 HIS 0.008 0.001 HIS G 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (26267) covalent geometry : angle 0.71474 / 0.36 (35841) SS BOND : bond 0.00565 / 0.44 ( 42) SS BOND : angle 1.15225 / 0.88 ( 84) hydrogen bonds : bond 0.03728 / 2.55 ( 629) hydrogen bonds : angle 6.23556 / 4.32 ( 1749) Misc. bond : bond 0.01536 / 0.81 ( 1) link_BETA1-4 : bond 0.01420 / 0.75 ( 1) link_BETA1-4 : angle 5.00985 / 2.27 ( 3) link_NAG-ASN : bond 0.00395 / 0.19 ( 9) link_NAG-ASN : angle 3.66613 / 2.41 ( 27) *********************** 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 535 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 361 time to evaluate : 1.002 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: 0.8180 (tttm) cc_final: 0.7467 (mmtt) REVERT: A 490 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.7212 (tp-100) REVERT: B 441 ILE cc_start: 0.5535 (OUTLIER) cc_final: 0.4938 (mt) REVERT: B 443 ARG cc_start: 0.5263 (OUTLIER) cc_final: 0.4719 (ptt-90) REVERT: B 499 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8459 (mttm) REVERT: B 506 MET cc_start: 0.8350 (mtp) cc_final: 0.8041 (mtm) REVERT: C 348 PHE cc_start: 0.4418 (OUTLIER) cc_final: 0.4046 (m-80) REVERT: C 386 ASN cc_start: 0.8137 (t0) cc_final: 0.7855 (t0) REVERT: C 461 ARG cc_start: 0.8583 (tmm160) cc_final: 0.8066 (tpp-160) REVERT: E 364 LYS cc_start: 0.7600 (tppt) cc_final: 0.6946 (tppt) REVERT: F 364 LYS cc_start: 0.7688 (mmmt) cc_final: 0.7440 (mmtm) REVERT: F 424 PHE cc_start: 0.6614 (m-80) cc_final: 0.6178 (m-10) REVERT: F 439 GLN cc_start: 0.4974 (OUTLIER) cc_final: 0.4295 (pm20) REVERT: G 371 ASP cc_start: 0.6623 (t0) cc_final: 0.6377 (t0) REVERT: G 445 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.6613 (mmmt) REVERT: G 525 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7592 (tm-30) REVERT: H 532 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: H 534 TYR cc_start: 0.9024 (m-80) cc_final: 0.8811 (m-80) REVERT: J 120 GLU cc_start: 0.7498 (pt0) cc_final: 0.7238 (mp0) REVERT: K 368 LEU cc_start: 0.5925 (pt) cc_final: 0.5432 (mt) REVERT: K 450 HIS cc_start: 0.7737 (m170) cc_final: 0.7358 (m170) REVERT: K 462 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7893 (mp0) REVERT: K 489 MET cc_start: 0.8645 (mtp) cc_final: 0.8147 (mtp) REVERT: K 490 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7058 (tp40) REVERT: K 515 TYR cc_start: 0.7692 (m-80) cc_final: 0.7351 (m-80) REVERT: L 453 ASP cc_start: 0.8279 (t0) cc_final: 0.7921 (t0) REVERT: L 483 ASP cc_start: 0.7017 (m-30) cc_final: 0.6045 (t0) REVERT: L 485 PHE cc_start: 0.5761 (t80) cc_final: 0.5537 (t80) REVERT: L 545 ASN cc_start: 0.7855 (t0) cc_final: 0.7637 (t0) REVERT: P 247 ASN cc_start: 0.8929 (m-40) cc_final: 0.7827 (t0) REVERT: P 314 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7764 (mm-40) REVERT: P 469 LYS cc_start: 0.6566 (OUTLIER) cc_final: 0.5877 (pptt) REVERT: P 533 PHE cc_start: 0.6291 (OUTLIER) cc_final: 0.5756 (m-80) REVERT: R 51 GLU cc_start: 0.6129 (tm-30) cc_final: 0.5729 (tm-30) REVERT: R 87 PHE cc_start: 0.6020 (t80) cc_final: 0.5687 (t80) REVERT: S 71 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8318 (pm20) REVERT: S 85 ASN cc_start: 0.9136 (p0) cc_final: 0.8931 (p0) outliers start: 174 outliers final: 116 residues processed: 501 average time/residue: 0.1870 time to fit residues: 144.7447 Evaluate side-chains 465 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 335 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 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 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 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 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 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 429 THR Chi-restraints excluded: chain F residue 439 GLN 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 556 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 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 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 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 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 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 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 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 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 290 PHE Chi-restraints excluded: chain P residue 314 GLN Chi-restraints excluded: chain P residue 344 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 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 57 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 242 optimal weight: 8.9990 chunk 114 optimal weight: 20.0000 chunk 250 optimal weight: 0.4980 chunk 256 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 180 optimal weight: 0.3980 chunk 312 optimal weight: 10.0000 chunk 252 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 5 optimal weight: 9.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 393 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 487 GLN ** 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 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 510 GLN R 85 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.179379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.115530 restraints weight = 41990.780| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 3.57 r_work: 0.3315 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 26320 Z= 0.204 Angle : 0.720 17.946 35955 Z= 0.361 Chirality : 0.048 0.420 4205 Planarity : 0.006 0.094 4578 Dihedral : 9.473 83.572 3703 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.80 % Favored : 92.02 % Rotamer: Outliers : 5.75 % Allowed : 18.22 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.14), residues: 3244 helix: -1.24 (0.28), residues: 280 sheet: -0.52 (0.15), residues: 1119 loop : -1.56 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 59 TYR 0.027 0.002 TYR K 576 PHE 0.028 0.002 PHE B 354 TRP 0.027 0.002 TRP P 369 HIS 0.012 0.001 HIS F 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.20 (26267) covalent geometry : angle 0.70965 / 0.36 (35841) SS BOND : bond 0.00479 / 0.34 ( 42) SS BOND : angle 1.28443 / 0.89 ( 84) hydrogen bonds : bond 0.03589 / 2.46 ( 629) hydrogen bonds : angle 6.06937 / 4.18 ( 1749) Misc. bond : bond 0.01593 / 0.84 ( 1) link_BETA1-4 : bond 0.01143 / 0.60 ( 1) link_BETA1-4 : angle 4.70607 / 2.17 ( 3) link_NAG-ASN : bond 0.00407 / 0.20 ( 9) link_NAG-ASN : angle 3.67821 / 2.39 ( 27) *********************** 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 506 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 339 time to evaluate : 0.993 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: A 445 LYS cc_start: 0.8331 (tttm) cc_final: 0.7692 (mmtt) REVERT: A 490 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8289 (tt0) REVERT: B 441 ILE cc_start: 0.5646 (OUTLIER) cc_final: 0.4939 (mt) REVERT: B 499 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8501 (mttm) REVERT: B 506 MET cc_start: 0.8463 (mtp) cc_final: 0.8161 (mtm) REVERT: C 348 PHE cc_start: 0.4434 (OUTLIER) cc_final: 0.4047 (m-80) REVERT: C 386 ASN cc_start: 0.8151 (t0) cc_final: 0.7870 (t0) REVERT: C 461 ARG cc_start: 0.8607 (tmm160) cc_final: 0.8034 (tpp-160) REVERT: E 427 THR cc_start: 0.6764 (OUTLIER) cc_final: 0.6494 (p) REVERT: G 371 ASP cc_start: 0.6861 (t0) cc_final: 0.6612 (t0) REVERT: G 445 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.6674 (mmmt) REVERT: H 532 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: H 534 TYR cc_start: 0.9059 (m-80) cc_final: 0.8829 (m-80) REVERT: J 51 ASP cc_start: 0.8198 (t0) cc_final: 0.7924 (t0) REVERT: J 120 GLU cc_start: 0.7392 (pt0) cc_final: 0.7165 (mp0) REVERT: K 354 PHE cc_start: 0.6695 (t80) cc_final: 0.6361 (t80) REVERT: K 368 LEU cc_start: 0.5672 (pt) cc_final: 0.5101 (mp) REVERT: K 450 HIS cc_start: 0.7805 (m170) cc_final: 0.7314 (m170) REVERT: K 462 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: K 489 MET cc_start: 0.8619 (mtp) cc_final: 0.8106 (mtp) REVERT: K 490 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7048 (tp40) REVERT: K 515 TYR cc_start: 0.7801 (m-80) cc_final: 0.7330 (m-10) REVERT: L 453 ASP cc_start: 0.8264 (t0) cc_final: 0.7829 (t0) REVERT: L 483 ASP cc_start: 0.6877 (m-30) cc_final: 0.6027 (t0) REVERT: L 485 PHE cc_start: 0.5674 (t80) cc_final: 0.5433 (t80) REVERT: L 545 ASN cc_start: 0.7936 (t0) cc_final: 0.7712 (t0) REVERT: P 247 ASN cc_start: 0.8884 (m-40) cc_final: 0.7807 (t0) REVERT: P 314 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7681 (mm-40) REVERT: P 392 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: P 469 LYS cc_start: 0.6481 (OUTLIER) cc_final: 0.5835 (pptt) REVERT: P 475 LYS cc_start: 0.7400 (OUTLIER) cc_final: 0.6542 (mttt) REVERT: R 51 GLU cc_start: 0.6359 (tm-30) cc_final: 0.5946 (tm-30) REVERT: R 87 PHE cc_start: 0.5857 (t80) cc_final: 0.5610 (t80) REVERT: S 71 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8454 (pm20) REVERT: U 22 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.6098 (pp20) REVERT: U 93 GLN cc_start: 0.7345 (mp10) cc_final: 0.6816 (mp10) outliers start: 167 outliers final: 120 residues processed: 474 average time/residue: 0.1861 time to fit residues: 136.6309 Evaluate side-chains 460 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 325 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 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 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 566 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 380 ILE 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 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 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 416 ASP 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 449 LEU 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 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 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 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 575 CYS Chi-restraints excluded: chain P residue 10 VAL Chi-restraints excluded: chain P residue 47 ILE 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 314 GLN 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 392 GLU 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 22 GLU 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 60 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 232 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 244 optimal weight: 2.9990 chunk 47 optimal weight: 30.0000 chunk 210 optimal weight: 0.9980 chunk 127 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 229 optimal weight: 1.9990 chunk 303 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** E 400 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** P 282 ASN R 85 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.180886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.116397 restraints weight = 42031.338| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 3.56 r_work: 0.3341 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26320 Z= 0.143 Angle : 0.666 16.564 35955 Z= 0.334 Chirality : 0.046 0.416 4205 Planarity : 0.005 0.089 4578 Dihedral : 8.829 82.144 3678 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.55 % Favored : 92.32 % Rotamer: Outliers : 5.51 % Allowed : 19.70 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.15), residues: 3244 helix: -1.14 (0.28), residues: 279 sheet: -0.42 (0.15), residues: 1108 loop : -1.46 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 443 TYR 0.018 0.001 TYR L 562 PHE 0.025 0.002 PHE G 424 TRP 0.029 0.001 TRP P 369 HIS 0.008 0.001 HIS L 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (26267) covalent geometry : angle 0.65693 / 0.33 (35841) SS BOND : bond 0.00320 / 0.23 ( 42) SS BOND : angle 0.93599 / 0.67 ( 84) hydrogen bonds : bond 0.03241 / 2.22 ( 629) hydrogen bonds : angle 5.79560 / 3.98 ( 1749) Misc. bond : bond 0.01531 / 0.81 ( 1) link_BETA1-4 : bond 0.01059 / 0.56 ( 1) link_BETA1-4 : angle 4.28883 / 1.99 ( 3) link_NAG-ASN : bond 0.00388 / 0.19 ( 9) link_NAG-ASN : angle 3.54685 / 2.28 ( 27) *********************** 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 510 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 350 time to evaluate : 1.004 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: 0.8287 (tttm) cc_final: 0.7709 (mmtt) REVERT: A 467 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8232 (mpp-170) REVERT: A 549 GLU cc_start: 0.9131 (OUTLIER) cc_final: 0.8275 (pm20) REVERT: B 376 ASP cc_start: 0.4266 (p0) cc_final: 0.4021 (p0) REVERT: B 440 THR cc_start: 0.6301 (OUTLIER) cc_final: 0.6085 (t) REVERT: B 441 ILE cc_start: 0.5839 (OUTLIER) cc_final: 0.5358 (mt) REVERT: B 499 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8522 (mttm) REVERT: B 506 MET cc_start: 0.8520 (mtp) cc_final: 0.8243 (mtm) REVERT: B 525 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8658 (tm-30) REVERT: C 348 PHE cc_start: 0.4542 (OUTLIER) cc_final: 0.4146 (m-80) REVERT: C 386 ASN cc_start: 0.8190 (t0) cc_final: 0.7930 (t0) REVERT: C 461 ARG cc_start: 0.8533 (tmm160) cc_final: 0.7994 (tpp-160) REVERT: D 418 TRP cc_start: 0.6666 (t-100) cc_final: 0.6413 (t-100) REVERT: D 445 LYS cc_start: 0.8115 (mttm) cc_final: 0.7868 (mmtt) REVERT: E 427 THR cc_start: 0.6733 (OUTLIER) cc_final: 0.6463 (p) REVERT: F 375 TYR cc_start: 0.4352 (m-10) cc_final: 0.4045 (m-10) REVERT: G 371 ASP cc_start: 0.6956 (t0) cc_final: 0.6741 (t0) REVERT: G 445 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.6683 (mmmt) REVERT: H 532 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7215 (mp0) REVERT: J 51 ASP cc_start: 0.8179 (t0) cc_final: 0.7910 (t0) REVERT: J 120 GLU cc_start: 0.7348 (pt0) cc_final: 0.7103 (mp0) REVERT: K 354 PHE cc_start: 0.6716 (t80) cc_final: 0.6460 (t80) REVERT: K 368 LEU cc_start: 0.5828 (pt) cc_final: 0.5226 (mp) REVERT: K 450 HIS cc_start: 0.7768 (m170) cc_final: 0.7506 (m170) REVERT: K 462 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: K 489 MET cc_start: 0.8574 (mtp) cc_final: 0.8146 (mtp) REVERT: K 490 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.6502 (tp40) REVERT: K 491 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7597 (ttm170) REVERT: K 515 TYR cc_start: 0.7847 (m-80) cc_final: 0.7458 (m-10) REVERT: K 545 ASN cc_start: 0.8587 (OUTLIER) cc_final: 0.8382 (m-40) REVERT: K 558 LYS cc_start: 0.7476 (ptpt) cc_final: 0.7082 (tttm) REVERT: L 453 ASP cc_start: 0.8206 (t0) cc_final: 0.7771 (t0) REVERT: L 483 ASP cc_start: 0.6852 (m-30) cc_final: 0.6095 (t0) REVERT: L 485 PHE cc_start: 0.5654 (t80) cc_final: 0.5438 (t80) REVERT: L 545 ASN cc_start: 0.7924 (t0) cc_final: 0.7692 (t0) REVERT: P 85 ASP cc_start: 0.7818 (t0) cc_final: 0.7607 (t0) REVERT: P 247 ASN cc_start: 0.8857 (m-40) cc_final: 0.7780 (t0) REVERT: P 314 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7555 (mm-40) REVERT: P 469 LYS cc_start: 0.6364 (OUTLIER) cc_final: 0.5780 (pptt) REVERT: P 475 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.6768 (mttt) REVERT: R 51 GLU cc_start: 0.6405 (tm-30) cc_final: 0.5998 (tm-30) REVERT: R 68 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7918 (tp) REVERT: S 71 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8392 (pm20) REVERT: S 93 GLN cc_start: 0.7081 (OUTLIER) cc_final: 0.6176 (mp10) REVERT: U 44 VAL cc_start: 0.7965 (OUTLIER) cc_final: 0.7738 (t) REVERT: U 93 GLN cc_start: 0.7380 (mp10) cc_final: 0.6768 (mp10) REVERT: V 42 MET cc_start: 0.5248 (tpt) cc_final: 0.4789 (tpt) outliers start: 160 outliers final: 101 residues processed: 481 average time/residue: 0.1832 time to fit residues: 137.0831 Evaluate side-chains 451 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 330 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 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 549 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 380 ILE Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 440 THR 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 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 552 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 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 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 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 502 THR 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 350 ILE Chi-restraints excluded: chain G residue 433 LEU 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 456 LEU 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 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 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 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 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 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 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 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 68 ILE 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 71 GLU 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 60 THR Chi-restraints excluded: chain U residue 88 LEU Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 236 optimal weight: 1.9990 chunk 233 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 254 optimal weight: 3.9990 chunk 91 optimal weight: 30.0000 chunk 245 optimal weight: 0.0870 chunk 28 optimal weight: 0.0170 chunk 141 optimal weight: 7.9990 chunk 286 optimal weight: 9.9990 chunk 115 optimal weight: 0.0000 chunk 196 optimal weight: 20.0000 overall best weight: 0.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 395 ASN ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.182283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.118307 restraints weight = 42086.155| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.55 r_work: 0.3371 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26320 Z= 0.121 Angle : 0.653 17.188 35955 Z= 0.326 Chirality : 0.046 0.454 4205 Planarity : 0.005 0.085 4578 Dihedral : 8.253 81.259 3663 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.87 % Favored : 93.00 % Rotamer: Outliers : 4.86 % Allowed : 21.18 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.15), residues: 3244 helix: -1.06 (0.28), residues: 282 sheet: -0.27 (0.16), residues: 1098 loop : -1.37 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 443 TYR 0.019 0.001 TYR D 562 PHE 0.022 0.002 PHE B 354 TRP 0.031 0.001 TRP P 369 HIS 0.017 0.001 HIS F 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (26267) covalent geometry : angle 0.64452 / 0.32 (35841) SS BOND : bond 0.00306 / 0.22 ( 42) SS BOND : angle 0.80403 / 0.58 ( 84) hydrogen bonds : bond 0.03098 / 2.13 ( 629) hydrogen bonds : angle 5.57402 / 3.82 ( 1749) Misc. bond : bond 0.01577 / 0.83 ( 1) link_BETA1-4 : bond 0.00834 / 0.44 ( 1) link_BETA1-4 : angle 4.08378 / 1.91 ( 3) link_NAG-ASN : bond 0.00411 / 0.20 ( 9) link_NAG-ASN : angle 3.44135 / 2.19 ( 27) *********************** 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 500 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 359 time to evaluate : 1.067 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: 0.8380 (tttm) cc_final: 0.7770 (mmtt) REVERT: A 467 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8279 (mpp-170) REVERT: A 549 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8208 (pm20) REVERT: B 376 ASP cc_start: 0.4483 (p0) cc_final: 0.4233 (p0) REVERT: B 440 THR cc_start: 0.6203 (OUTLIER) cc_final: 0.5942 (t) REVERT: B 441 ILE cc_start: 0.5855 (OUTLIER) cc_final: 0.4859 (mt) REVERT: B 499 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8648 (mtpp) REVERT: B 506 MET cc_start: 0.8467 (mtp) cc_final: 0.8217 (mtm) REVERT: C 348 PHE cc_start: 0.4490 (OUTLIER) cc_final: 0.4073 (m-80) REVERT: C 386 ASN cc_start: 0.8161 (t0) cc_final: 0.7898 (t0) REVERT: C 461 ARG cc_start: 0.8518 (tmm160) cc_final: 0.7995 (tpp-160) REVERT: C 489 MET cc_start: 0.8937 (mtt) cc_final: 0.8726 (mtp) REVERT: C 498 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7936 (pm20) REVERT: E 427 THR cc_start: 0.6717 (OUTLIER) cc_final: 0.6446 (p) REVERT: F 416 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7229 (p0) REVERT: G 445 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.6701 (mmmt) REVERT: H 532 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7245 (mp0) REVERT: J 51 ASP cc_start: 0.8176 (t0) cc_final: 0.7895 (t0) REVERT: J 117 TYR cc_start: 0.8847 (t80) cc_final: 0.8586 (t80) REVERT: J 120 GLU cc_start: 0.7398 (pt0) cc_final: 0.7046 (mp0) REVERT: K 368 LEU cc_start: 0.5825 (pt) cc_final: 0.5203 (mp) REVERT: K 489 MET cc_start: 0.8558 (mtp) cc_final: 0.8194 (mtp) REVERT: K 491 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7909 (ttm170) REVERT: K 515 TYR cc_start: 0.7830 (m-80) cc_final: 0.7489 (m-10) REVERT: K 554 LYS cc_start: 0.8552 (ttpp) cc_final: 0.8331 (ttpp) REVERT: K 558 LYS cc_start: 0.7404 (ptpt) cc_final: 0.7204 (tttm) REVERT: L 453 ASP cc_start: 0.8253 (t0) cc_final: 0.7849 (t0) REVERT: L 483 ASP cc_start: 0.6875 (m-30) cc_final: 0.6167 (t0) REVERT: L 545 ASN cc_start: 0.7903 (t0) cc_final: 0.7652 (t0) REVERT: P 247 ASN cc_start: 0.8857 (m-40) cc_final: 0.7788 (t0) REVERT: P 366 TRP cc_start: 0.7393 (OUTLIER) cc_final: 0.7105 (t60) REVERT: P 392 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.6263 (tp30) REVERT: P 469 LYS cc_start: 0.6308 (OUTLIER) cc_final: 0.5745 (pptt) REVERT: P 475 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.6891 (mttt) REVERT: R 50 ARG cc_start: 0.7079 (ttt-90) cc_final: 0.6412 (mmm160) REVERT: R 51 GLU cc_start: 0.6354 (tm-30) cc_final: 0.6019 (tm-30) REVERT: S 51 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7365 (tp30) REVERT: S 81 TYR cc_start: 0.7729 (m-80) cc_final: 0.7412 (m-80) REVERT: S 93 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.6258 (mp10) REVERT: U 22 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.6117 (pt0) REVERT: U 44 VAL cc_start: 0.7949 (OUTLIER) cc_final: 0.7740 (t) REVERT: U 93 GLN cc_start: 0.7415 (mp10) cc_final: 0.6798 (mp10) REVERT: U 101 VAL cc_start: 0.8201 (m) cc_final: 0.7727 (p) REVERT: V 42 MET cc_start: 0.5027 (tpt) cc_final: 0.4554 (tpt) outliers start: 141 outliers final: 91 residues processed: 469 average time/residue: 0.1834 time to fit residues: 133.5852 Evaluate side-chains 436 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 326 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 501 VAL Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 440 THR 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 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 552 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 502 THR 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 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 427 THR 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 502 THR Chi-restraints excluded: chain F residue 503 SER Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 433 LEU 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 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 564 VAL Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 116 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 522 THR Chi-restraints excluded: chain K residue 561 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 489 MET Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 521 LEU Chi-restraints excluded: chain L residue 522 THR 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 575 CYS 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 230 ASP Chi-restraints excluded: chain P residue 260 ASN Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain P residue 366 TRP Chi-restraints excluded: chain P residue 379 LEU Chi-restraints excluded: chain P residue 392 GLU 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 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 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 44 VAL Chi-restraints excluded: chain U residue 57 THR Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 88 LEU 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 306 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 50.0000 chunk 116 optimal weight: 0.8980 chunk 227 optimal weight: 9.9990 chunk 184 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 197 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 430 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 = 0.4417 r_free = 0.4417 target = 0.181063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.115221 restraints weight = 41719.136| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 3.35 r_work: 0.3365 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3360 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= 0.148 Angle : 0.657 17.390 35955 Z= 0.329 Chirality : 0.046 0.440 4205 Planarity : 0.005 0.085 4578 Dihedral : 7.770 81.215 3645 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.34 % Favored : 92.57 % Rotamer: Outliers : 4.79 % Allowed : 21.63 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.15), residues: 3244 helix: -1.02 (0.28), residues: 281 sheet: -0.26 (0.16), residues: 1114 loop : -1.33 (0.15), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 59 TYR 0.019 0.001 TYR D 562 PHE 0.021 0.002 PHE B 354 TRP 0.032 0.002 TRP B 382 HIS 0.009 0.001 HIS F 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (26267) covalent geometry : angle 0.64857 / 0.33 (35841) SS BOND : bond 0.00331 / 0.23 ( 42) SS BOND : angle 0.85329 / 0.60 ( 84) hydrogen bonds : bond 0.03138 / 2.15 ( 629) hydrogen bonds : angle 5.51947 / 3.78 ( 1749) Misc. bond : bond 0.01568 / 0.83 ( 1) link_BETA1-4 : bond 0.00803 / 0.42 ( 1) link_BETA1-4 : angle 4.20578 / 1.95 ( 3) link_NAG-ASN : bond 0.00413 / 0.21 ( 9) link_NAG-ASN : angle 3.46215 / 2.19 ( 27) *********************** 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 473 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 334 time to evaluate : 1.082 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: 0.8412 (tttm) cc_final: 0.7757 (mmtt) REVERT: A 467 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8217 (mpp-170) REVERT: A 549 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8173 (pm20) REVERT: B 375 TYR cc_start: 0.3935 (OUTLIER) cc_final: 0.3690 (p90) REVERT: B 376 ASP cc_start: 0.4739 (p0) cc_final: 0.4292 (p0) REVERT: B 441 ILE cc_start: 0.5539 (OUTLIER) cc_final: 0.4873 (mt) REVERT: B 493 GLN cc_start: 0.8512 (pp30) cc_final: 0.8254 (pp30) REVERT: B 499 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8823 (mtpp) REVERT: B 506 MET cc_start: 0.8478 (mtp) cc_final: 0.8207 (mtm) REVERT: C 348 PHE cc_start: 0.4494 (OUTLIER) cc_final: 0.4060 (m-80) REVERT: C 386 ASN cc_start: 0.8171 (t0) cc_final: 0.7952 (t0) REVERT: C 461 ARG cc_start: 0.8525 (tmm160) cc_final: 0.7989 (tpp-160) REVERT: C 498 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7874 (pm20) REVERT: D 380 ILE cc_start: 0.0202 (OUTLIER) cc_final: -0.0155 (mt) REVERT: E 427 THR cc_start: 0.6688 (OUTLIER) cc_final: 0.6416 (p) REVERT: E 489 MET cc_start: 0.7519 (tpp) cc_final: 0.7255 (tpp) REVERT: F 384 ARG cc_start: 0.7538 (mtp-110) cc_final: 0.7318 (mtp-110) REVERT: F 417 ASP cc_start: 0.8466 (t0) cc_final: 0.7651 (m-30) REVERT: G 445 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.6871 (mmmt) REVERT: H 532 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.6893 (mp0) REVERT: H 534 TYR cc_start: 0.9086 (m-80) cc_final: 0.8659 (m-80) REVERT: J 51 ASP cc_start: 0.8220 (t0) cc_final: 0.7933 (t0) REVERT: J 120 GLU cc_start: 0.7405 (pt0) cc_final: 0.7043 (mp0) REVERT: K 368 LEU cc_start: 0.5723 (pt) cc_final: 0.5148 (mp) REVERT: K 489 MET cc_start: 0.8559 (mtp) cc_final: 0.8180 (mtp) REVERT: K 491 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7875 (ttm170) REVERT: K 515 TYR cc_start: 0.7872 (m-80) cc_final: 0.7527 (m-10) REVERT: K 554 LYS cc_start: 0.8588 (ttpp) cc_final: 0.8353 (ttpp) REVERT: K 558 LYS cc_start: 0.7526 (ptpt) cc_final: 0.7208 (tttm) REVERT: L 453 ASP cc_start: 0.8235 (t0) cc_final: 0.7808 (t0) REVERT: L 483 ASP cc_start: 0.6838 (m-30) cc_final: 0.6129 (t0) REVERT: L 545 ASN cc_start: 0.7946 (t0) cc_final: 0.7711 (t0) REVERT: P 247 ASN cc_start: 0.8855 (m-40) cc_final: 0.7795 (t0) REVERT: P 314 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7476 (mm-40) REVERT: P 366 TRP cc_start: 0.7381 (OUTLIER) cc_final: 0.7129 (t60) REVERT: P 392 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6293 (tp30) REVERT: P 447 LYS cc_start: 0.3237 (OUTLIER) cc_final: 0.2560 (mmtt) REVERT: P 475 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.6991 (mttt) REVERT: R 51 GLU cc_start: 0.6334 (tm-30) cc_final: 0.5956 (tm-30) REVERT: R 68 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7948 (tp) REVERT: S 51 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7409 (tp30) REVERT: S 81 TYR cc_start: 0.7665 (m-80) cc_final: 0.7414 (m-80) REVERT: S 93 GLN cc_start: 0.7163 (OUTLIER) cc_final: 0.6201 (mp10) REVERT: U 22 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.6073 (pt0) REVERT: U 44 VAL cc_start: 0.7956 (OUTLIER) cc_final: 0.7756 (t) REVERT: U 93 GLN cc_start: 0.7333 (mp10) cc_final: 0.7050 (mp10) REVERT: U 101 VAL cc_start: 0.8267 (m) cc_final: 0.7796 (p) outliers start: 139 outliers final: 102 residues processed: 444 average time/residue: 0.1827 time to fit residues: 126.4420 Evaluate side-chains 441 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 318 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 501 VAL 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 549 GLU Chi-restraints excluded: chain A residue 564 VAL 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 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 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 502 THR 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 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 427 THR Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 483 ASP 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 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 350 ILE Chi-restraints excluded: chain G residue 433 LEU 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 456 LEU 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 564 VAL 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 522 THR Chi-restraints excluded: chain K residue 561 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 489 MET Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 521 LEU 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 551 THR Chi-restraints excluded: chain L residue 552 VAL 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 314 GLN Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain P residue 366 TRP Chi-restraints excluded: chain P residue 379 LEU Chi-restraints excluded: chain P residue 392 GLU 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 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 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 33 VAL 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 44 VAL Chi-restraints excluded: chain U residue 57 THR Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 88 LEU 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 257 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 104 optimal weight: 0.0070 chunk 164 optimal weight: 10.0000 chunk 317 optimal weight: 0.9980 chunk 214 optimal weight: 8.9990 chunk 149 optimal weight: 0.0470 chunk 118 optimal weight: 7.9990 chunk 202 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 198 optimal weight: 0.9980 overall best weight: 0.6096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 430 HIS ** 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 = 0.4434 r_free = 0.4434 target = 0.182538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.117238 restraints weight = 41863.963| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.39 r_work: 0.3395 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26320 Z= 0.117 Angle : 0.631 17.181 35955 Z= 0.316 Chirality : 0.045 0.446 4205 Planarity : 0.005 0.081 4578 Dihedral : 7.464 81.273 3639 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.94 % Favored : 92.97 % Rotamer: Outliers : 4.68 % Allowed : 21.94 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.15), residues: 3244 helix: -0.93 (0.28), residues: 284 sheet: -0.16 (0.16), residues: 1117 loop : -1.23 (0.15), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 59 TYR 0.023 0.001 TYR J 117 PHE 0.021 0.002 PHE B 354 TRP 0.032 0.001 TRP P 369 HIS 0.007 0.001 HIS F 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (26267) covalent geometry : angle 0.62311 / 0.31 (35841) SS BOND : bond 0.00270 / 0.20 ( 42) SS BOND : angle 0.75430 / 0.55 ( 84) hydrogen bonds : bond 0.03009 / 2.07 ( 629) hydrogen bonds : angle 5.34636 / 3.67 ( 1749) Misc. bond : bond 0.01573 / 0.83 ( 1) link_BETA1-4 : bond 0.00851 / 0.45 ( 1) link_BETA1-4 : angle 4.27660 / 1.96 ( 3) link_NAG-ASN : bond 0.00426 / 0.20 ( 9) link_NAG-ASN : angle 3.31515 / 2.11 ( 27) *********************** 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 475 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 339 time to evaluate : 1.016 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: A 445 LYS cc_start: 0.8399 (tttm) cc_final: 0.7769 (mmtt) REVERT: A 549 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8162 (pm20) REVERT: B 375 TYR cc_start: 0.3965 (OUTLIER) cc_final: 0.3649 (p90) REVERT: B 376 ASP cc_start: 0.4883 (p0) cc_final: 0.4485 (p0) REVERT: B 441 ILE cc_start: 0.5326 (OUTLIER) cc_final: 0.4619 (mt) REVERT: B 451 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7768 (ptm-80) REVERT: B 493 GLN cc_start: 0.8536 (pp30) cc_final: 0.8279 (pp30) REVERT: B 499 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8862 (mtpp) REVERT: B 506 MET cc_start: 0.8498 (mtp) cc_final: 0.8273 (mtm) REVERT: C 348 PHE cc_start: 0.4624 (OUTLIER) cc_final: 0.4185 (m-80) REVERT: C 461 ARG cc_start: 0.8500 (tmm160) cc_final: 0.7972 (tpp-160) REVERT: D 380 ILE cc_start: -0.0104 (OUTLIER) cc_final: -0.0408 (mt) REVERT: E 427 THR cc_start: 0.6646 (OUTLIER) cc_final: 0.6378 (p) REVERT: E 489 MET cc_start: 0.7308 (tpp) cc_final: 0.7103 (tpp) REVERT: E 490 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7905 (pp30) REVERT: F 382 TRP cc_start: 0.6438 (m100) cc_final: 0.5943 (m100) REVERT: F 417 ASP cc_start: 0.8480 (t0) cc_final: 0.7643 (m-30) REVERT: G 445 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.6927 (mmmt) REVERT: H 532 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: H 534 TYR cc_start: 0.9058 (m-80) cc_final: 0.8679 (m-80) REVERT: H 541 GLU cc_start: 0.8472 (mp0) cc_final: 0.8179 (mp0) REVERT: J 51 ASP cc_start: 0.8281 (t0) cc_final: 0.7963 (t0) REVERT: J 120 GLU cc_start: 0.7335 (pt0) cc_final: 0.6965 (mp0) REVERT: K 368 LEU cc_start: 0.5689 (pt) cc_final: 0.5121 (mp) REVERT: K 489 MET cc_start: 0.8544 (mtp) cc_final: 0.8225 (mtp) REVERT: K 491 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7842 (ttm170) REVERT: K 515 TYR cc_start: 0.7809 (m-80) cc_final: 0.7602 (m-80) REVERT: K 554 LYS cc_start: 0.8632 (ttpp) cc_final: 0.8394 (ttpp) REVERT: K 558 LYS cc_start: 0.7435 (ptpt) cc_final: 0.7185 (tttm) REVERT: L 453 ASP cc_start: 0.8269 (t0) cc_final: 0.7830 (t0) REVERT: L 545 ASN cc_start: 0.7939 (t0) cc_final: 0.7703 (t0) REVERT: P 247 ASN cc_start: 0.8816 (m-40) cc_final: 0.7757 (t0) REVERT: P 314 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7486 (mm-40) REVERT: P 366 TRP cc_start: 0.7344 (OUTLIER) cc_final: 0.7081 (t60) REVERT: P 392 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6259 (tp30) REVERT: P 431 TRP cc_start: 0.6888 (OUTLIER) cc_final: 0.6279 (m-10) REVERT: P 447 LYS cc_start: 0.3460 (OUTLIER) cc_final: 0.2887 (mmtt) REVERT: R 51 GLU cc_start: 0.6386 (tm-30) cc_final: 0.5991 (tm-30) REVERT: R 68 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7903 (tp) REVERT: S 51 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7343 (tp30) REVERT: S 65 THR cc_start: 0.8440 (m) cc_final: 0.8055 (p) REVERT: S 93 GLN cc_start: 0.7247 (OUTLIER) cc_final: 0.6236 (mp10) REVERT: U 22 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.6119 (pt0) REVERT: U 83 ARG cc_start: 0.8657 (mpp80) cc_final: 0.8191 (ptt90) REVERT: U 93 GLN cc_start: 0.7238 (mp10) cc_final: 0.6986 (mp10) REVERT: U 101 VAL cc_start: 0.8230 (m) cc_final: 0.7806 (p) REVERT: V 42 MET cc_start: 0.4992 (tpt) cc_final: 0.4571 (tpp) outliers start: 136 outliers final: 95 residues processed: 440 average time/residue: 0.1853 time to fit residues: 127.4271 Evaluate side-chains 442 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 327 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 506 MET 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 549 GLU Chi-restraints excluded: chain A residue 564 VAL 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 451 ARG Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 499 LYS 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 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 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 427 THR Chi-restraints excluded: chain E residue 490 GLN Chi-restraints excluded: chain F residue 377 SER Chi-restraints excluded: chain F residue 383 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 551 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 433 LEU 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 456 LEU 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 564 VAL 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 520 ILE Chi-restraints excluded: chain K residue 522 THR Chi-restraints excluded: chain K residue 561 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 489 MET Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 521 LEU Chi-restraints excluded: chain L residue 522 THR 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 567 VAL Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain L residue 575 CYS 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 314 GLN Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain P residue 366 TRP Chi-restraints excluded: chain P residue 379 LEU Chi-restraints excluded: chain P residue 392 GLU 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 473 TYR 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 33 VAL Chi-restraints excluded: chain S residue 61 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 88 LEU 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 72 optimal weight: 8.9990 chunk 180 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 216 optimal weight: 9.9990 chunk 173 optimal weight: 0.5980 chunk 270 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 chunk 239 optimal weight: 1.9990 chunk 279 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 518 HIS C 385 GLN ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 545 ASN ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 532 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.180617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.116471 restraints weight = 41962.970| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 3.69 r_work: 0.3345 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26320 Z= 0.166 Angle : 0.656 17.054 35955 Z= 0.330 Chirality : 0.046 0.444 4205 Planarity : 0.005 0.092 4578 Dihedral : 7.249 80.812 3623 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.24 % Favored : 92.66 % Rotamer: Outliers : 4.37 % Allowed : 22.12 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.15), residues: 3244 helix: -0.96 (0.28), residues: 289 sheet: -0.27 (0.16), residues: 1125 loop : -1.18 (0.15), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 384 TYR 0.025 0.001 TYR D 562 PHE 0.024 0.002 PHE G 424 TRP 0.026 0.002 TRP P 369 HIS 0.004 0.001 HIS A 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (26267) covalent geometry : angle 0.64778 / 0.33 (35841) SS BOND : bond 0.00340 / 0.24 ( 42) SS BOND : angle 0.84039 / 0.60 ( 84) hydrogen bonds : bond 0.03188 / 2.20 ( 629) hydrogen bonds : angle 5.41302 / 3.71 ( 1749) Misc. bond : bond 0.01581 / 0.83 ( 1) link_BETA1-4 : bond 0.00688 / 0.36 ( 1) link_BETA1-4 : angle 4.34827 / 2.04 ( 3) link_NAG-ASN : bond 0.00512 / 0.27 ( 9) link_NAG-ASN : angle 3.33744 / 2.08 ( 27) *********************** 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 458 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 331 time to evaluate : 1.035 Fit side-chains revert: symmetry clash 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: A 445 LYS cc_start: 0.8443 (tttm) cc_final: 0.7859 (mmtt) REVERT: A 549 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8185 (pm20) REVERT: B 375 TYR cc_start: 0.3870 (OUTLIER) cc_final: 0.3578 (p90) REVERT: B 376 ASP cc_start: 0.5100 (p0) cc_final: 0.4802 (p0) REVERT: B 402 ASN cc_start: 0.7471 (t0) cc_final: 0.7066 (p0) REVERT: B 441 ILE cc_start: 0.5501 (OUTLIER) cc_final: 0.4800 (mt) REVERT: B 451 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8008 (ptm-80) REVERT: B 493 GLN cc_start: 0.8517 (pp30) cc_final: 0.8254 (pp30) REVERT: B 499 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8867 (mtpp) REVERT: B 506 MET cc_start: 0.8529 (mtp) cc_final: 0.8261 (mtm) REVERT: C 348 PHE cc_start: 0.4616 (OUTLIER) cc_final: 0.4235 (m-80) REVERT: C 461 ARG cc_start: 0.8517 (tmm160) cc_final: 0.7977 (tpp-160) REVERT: D 380 ILE cc_start: 0.0101 (OUTLIER) cc_final: -0.0266 (mt) REVERT: E 427 THR cc_start: 0.6687 (OUTLIER) cc_final: 0.6414 (p) REVERT: E 489 MET cc_start: 0.7614 (tpp) cc_final: 0.7373 (tpp) REVERT: F 417 ASP cc_start: 0.8409 (t0) cc_final: 0.7692 (m-30) REVERT: G 445 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.6958 (mmmt) REVERT: H 532 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: H 534 TYR cc_start: 0.9101 (m-80) cc_final: 0.8674 (m-80) REVERT: H 541 GLU cc_start: 0.8499 (mp0) cc_final: 0.8210 (mp0) REVERT: J 51 ASP cc_start: 0.8310 (t0) cc_final: 0.8017 (t0) REVERT: J 120 GLU cc_start: 0.7339 (pt0) cc_final: 0.6920 (mp0) REVERT: K 368 LEU cc_start: 0.5701 (pt) cc_final: 0.5085 (mp) REVERT: K 489 MET cc_start: 0.8581 (mtp) cc_final: 0.8182 (mtp) REVERT: K 515 TYR cc_start: 0.7915 (m-80) cc_final: 0.7687 (m-80) REVERT: K 554 LYS cc_start: 0.8571 (ttpp) cc_final: 0.8271 (ttpp) REVERT: K 558 LYS cc_start: 0.7454 (ptpt) cc_final: 0.7171 (tttm) REVERT: L 453 ASP cc_start: 0.8284 (t0) cc_final: 0.7843 (t0) REVERT: L 545 ASN cc_start: 0.7941 (t0) cc_final: 0.7726 (t0) REVERT: P 247 ASN cc_start: 0.8826 (m-40) cc_final: 0.7772 (t0) REVERT: P 282 ASN cc_start: 0.7622 (m-40) cc_final: 0.7257 (m-40) REVERT: P 392 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.6279 (tp30) REVERT: P 447 LYS cc_start: 0.3357 (OUTLIER) cc_final: 0.2943 (tptt) REVERT: P 475 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7013 (mttt) REVERT: R 51 GLU cc_start: 0.6435 (tm-30) cc_final: 0.6029 (tm-30) REVERT: S 51 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7362 (tp30) REVERT: S 65 THR cc_start: 0.8440 (m) cc_final: 0.8060 (p) REVERT: S 81 TYR cc_start: 0.7435 (m-80) cc_final: 0.6917 (m-80) REVERT: S 88 LEU cc_start: 0.7668 (mt) cc_final: 0.7426 (mt) REVERT: S 93 GLN cc_start: 0.7113 (OUTLIER) cc_final: 0.6200 (mp10) REVERT: U 22 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.6070 (pt0) REVERT: U 73 LYS cc_start: 0.8153 (mmtt) cc_final: 0.7835 (mmmt) REVERT: U 83 ARG cc_start: 0.8652 (mpp80) cc_final: 0.8191 (ptt90) REVERT: U 93 GLN cc_start: 0.7306 (mp10) cc_final: 0.7046 (mp10) REVERT: U 101 VAL cc_start: 0.8249 (m) cc_final: 0.7824 (p) REVERT: V 42 MET cc_start: 0.4938 (tpt) cc_final: 0.4667 (tpp) outliers start: 127 outliers final: 98 residues processed: 427 average time/residue: 0.1843 time to fit residues: 121.9563 Evaluate side-chains 438 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 325 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 501 VAL 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 549 GLU Chi-restraints excluded: chain A residue 564 VAL 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 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 462 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 499 LYS 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 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 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 427 THR 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 429 THR Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 433 LEU 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 390 VAL 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 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 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 484 VAL 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 522 THR Chi-restraints excluded: chain K residue 561 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 489 MET Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 521 LEU 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 551 THR Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain L residue 575 CYS 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 392 GLU 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 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 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 88 LEU Chi-restraints excluded: chain U residue 89 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 192 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 285 optimal weight: 8.9990 chunk 262 optimal weight: 3.9990 chunk 280 optimal weight: 10.0000 chunk 81 optimal weight: 0.6980 chunk 50 optimal weight: 30.0000 chunk 150 optimal weight: 2.9990 chunk 214 optimal weight: 40.0000 chunk 273 optimal weight: 10.0000 chunk 266 optimal weight: 2.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** 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 529 ASN ** J 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.176681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.109498 restraints weight = 41999.922| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.15 r_work: 0.3294 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 26320 Z= 0.295 Angle : 0.755 16.867 35955 Z= 0.383 Chirality : 0.050 0.437 4205 Planarity : 0.006 0.092 4578 Dihedral : 7.592 80.533 3621 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.38 % Favored : 91.49 % Rotamer: Outliers : 4.20 % Allowed : 22.43 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.15), residues: 3244 helix: -1.22 (0.28), residues: 287 sheet: -0.60 (0.15), residues: 1149 loop : -1.36 (0.15), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 384 TYR 0.031 0.002 TYR D 562 PHE 0.029 0.002 PHE B 354 TRP 0.046 0.002 TRP P 366 HIS 0.008 0.001 HIS A 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00708 / 0.29 (26267) covalent geometry : angle 0.74603 / 0.38 (35841) SS BOND : bond 0.00541 / 0.38 ( 42) SS BOND : angle 1.09796 / 0.75 ( 84) hydrogen bonds : bond 0.03777 / 2.61 ( 629) hydrogen bonds : angle 5.89533 / 4.03 ( 1749) Misc. bond : bond 0.01587 / 0.84 ( 1) link_BETA1-4 : bond 0.01085 / 0.57 ( 1) link_BETA1-4 : angle 4.42244 / 2.10 ( 3) link_NAG-ASN : bond 0.00563 / 0.30 ( 9) link_NAG-ASN : angle 3.81924 / 2.39 ( 27) ********************** 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 453 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 331 time to evaluate : 1.235 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: A 445 LYS cc_start: 0.8532 (tttm) cc_final: 0.7922 (mmtt) REVERT: A 549 GLU cc_start: 0.9342 (OUTLIER) cc_final: 0.8491 (pm20) REVERT: B 375 TYR cc_start: 0.3907 (OUTLIER) cc_final: 0.3623 (p90) REVERT: B 402 ASN cc_start: 0.7525 (t0) cc_final: 0.7055 (p0) REVERT: B 441 ILE cc_start: 0.4940 (OUTLIER) cc_final: 0.4218 (mt) REVERT: B 451 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7959 (ptm-80) REVERT: B 493 GLN cc_start: 0.8508 (pp30) cc_final: 0.8188 (pp30) REVERT: B 499 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8689 (mttm) REVERT: B 506 MET cc_start: 0.8819 (mtp) cc_final: 0.8486 (mtm) REVERT: B 546 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8202 (mpt180) REVERT: C 348 PHE cc_start: 0.5031 (OUTLIER) cc_final: 0.4549 (m-80) REVERT: D 380 ILE cc_start: 0.0560 (OUTLIER) cc_final: 0.0159 (mt) REVERT: E 427 THR cc_start: 0.6659 (OUTLIER) cc_final: 0.6407 (p) REVERT: E 489 MET cc_start: 0.8261 (tpp) cc_final: 0.8015 (tpp) REVERT: F 382 TRP cc_start: 0.6634 (m100) cc_final: 0.5549 (m100) REVERT: F 416 ASP cc_start: 0.7633 (t70) cc_final: 0.7412 (p0) REVERT: F 568 MET cc_start: 0.8038 (mmt) cc_final: 0.7528 (tmm) REVERT: G 418 TRP cc_start: 0.7218 (t-100) cc_final: 0.7003 (t-100) REVERT: G 445 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7022 (mmmt) REVERT: H 532 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7029 (mp0) REVERT: J 51 ASP cc_start: 0.8411 (t0) cc_final: 0.8148 (t0) REVERT: J 120 GLU cc_start: 0.7506 (pt0) cc_final: 0.7044 (mp0) REVERT: K 489 MET cc_start: 0.8865 (mtp) cc_final: 0.8461 (mtp) REVERT: K 490 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7243 (tp40) REVERT: K 515 TYR cc_start: 0.8048 (m-80) cc_final: 0.7620 (m-10) REVERT: K 554 LYS cc_start: 0.8693 (ttpp) cc_final: 0.8430 (ttpp) REVERT: K 558 LYS cc_start: 0.7492 (ptpt) cc_final: 0.7126 (tttm) REVERT: L 483 ASP cc_start: 0.6908 (m-30) cc_final: 0.6080 (t0) REVERT: P 247 ASN cc_start: 0.8892 (m-40) cc_final: 0.7870 (t0) REVERT: P 392 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.6328 (tp30) REVERT: P 447 LYS cc_start: 0.3354 (OUTLIER) cc_final: 0.2901 (tptt) REVERT: P 475 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7131 (mttt) REVERT: R 51 GLU cc_start: 0.6478 (tm-30) cc_final: 0.6067 (tm-30) REVERT: S 51 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7385 (tp30) REVERT: S 81 TYR cc_start: 0.7452 (m-80) cc_final: 0.7173 (m-80) REVERT: S 93 GLN cc_start: 0.7072 (OUTLIER) cc_final: 0.6149 (mp10) REVERT: S 102 TYR cc_start: 0.6556 (m-10) cc_final: 0.6336 (m-80) REVERT: U 73 LYS cc_start: 0.8076 (mmtt) cc_final: 0.7751 (mmmt) REVERT: U 83 ARG cc_start: 0.8748 (mpp80) cc_final: 0.8224 (ptt90) REVERT: U 93 GLN cc_start: 0.7542 (mp10) cc_final: 0.6804 (mp10) REVERT: U 101 VAL cc_start: 0.8374 (m) cc_final: 0.7943 (p) REVERT: V 72 TYR cc_start: 0.7049 (m-80) cc_final: 0.6773 (m-10) outliers start: 122 outliers final: 96 residues processed: 422 average time/residue: 0.1836 time to fit residues: 120.7784 Evaluate side-chains 432 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 320 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 549 GLU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 371 ASP 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 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 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 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 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 429 THR 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 433 LEU 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 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 553 ASP Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain H residue 564 VAL 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 390 VAL Chi-restraints excluded: chain K residue 484 VAL 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 522 THR Chi-restraints excluded: chain K residue 561 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 489 MET Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 521 LEU 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 567 VAL Chi-restraints excluded: chain L residue 575 CYS 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 392 GLU 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 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 86 LEU Chi-restraints excluded: chain R residue 93 GLN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 264 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 255 optimal weight: 2.9990 chunk 208 optimal weight: 0.9990 chunk 204 optimal weight: 0.0870 chunk 292 optimal weight: 0.9980 chunk 309 optimal weight: 0.3980 chunk 217 optimal weight: 30.0000 chunk 102 optimal weight: 0.6980 chunk 222 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 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** R 80 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.181016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.116616 restraints weight = 41806.445| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.42 r_work: 0.3366 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26320 Z= 0.124 Angle : 0.654 16.158 35955 Z= 0.330 Chirality : 0.046 0.440 4205 Planarity : 0.005 0.088 4578 Dihedral : 7.210 80.601 3621 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.75 % Favored : 93.16 % Rotamer: Outliers : 3.65 % Allowed : 23.25 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.15), residues: 3244 helix: -1.12 (0.28), residues: 290 sheet: -0.31 (0.16), residues: 1110 loop : -1.28 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 50 TYR 0.022 0.001 TYR J 117 PHE 0.023 0.002 PHE F 424 TRP 0.032 0.002 TRP P 366 HIS 0.004 0.001 HIS F 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (26267) covalent geometry : angle 0.64604 / 0.33 (35841) SS BOND : bond 0.00294 / 0.18 ( 42) SS BOND : angle 1.02093 / 0.75 ( 84) hydrogen bonds : bond 0.03122 / 2.14 ( 629) hydrogen bonds : angle 5.46846 / 3.75 ( 1749) Misc. bond : bond 0.01613 / 0.85 ( 1) link_BETA1-4 : bond 0.00541 / 0.28 ( 1) link_BETA1-4 : angle 4.06506 / 1.87 ( 3) link_NAG-ASN : bond 0.00420 / 0.20 ( 9) link_NAG-ASN : angle 3.28892 / 2.04 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8682.00 seconds wall clock time: 149 minutes 30.98 seconds (8970.98 seconds total)