Starting phenix.real_space_refine on Sat Jul 4 15:35:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ytd_34086/07_2026/7ytd_34086.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ytd_34086/07_2026/7ytd_34086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ytd_34086/07_2026/7ytd_34086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ytd_34086/07_2026/7ytd_34086.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ytd_34086/07_2026/7ytd_34086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ytd_34086/07_2026/7ytd_34086.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ytd_34086/07_2026/7ytd_34086.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ytd_34086/07_2026/7ytd_34086.cif" } resolution = 3.71 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= 0.006 sd= 0.030 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 116 5.16 5 C 13645 2.51 5 N 3696 2.21 5 O 4236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s 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: 21693 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1773 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 18, 'TRANS': 210} Chain: "B" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1749 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 18, 'TRANS': 206} Chain: "C" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1748 Classifications: {'peptide': 225} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 206} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1749 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 18, 'TRANS': 206} Chain: "E" 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: "F" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1723 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 18, 'TRANS': 202} Chain breaks: 1 Chain: "G" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1742 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1730 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 18, 'TRANS': 203} Chain breaks: 1 Chain: "J" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 834 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 7, 'TRANS': 96} Chain breaks: 1 Chain: "K" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1737 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 18, 'TRANS': 204} Chain breaks: 1 Chain: "L" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1761 Classifications: {'peptide': 227} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 208} Chain breaks: 1 Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "S" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "U" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "V" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} 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: 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: "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: 4.68, per 1000 atoms: 0.22 Number of scatterers: 21693 At special positions: 0 Unit cell: (121.716, 187.128, 164.772, 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 116 16.00 O 4236 8.00 N 3696 7.00 C 13645 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, 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=2.04 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 414 " - pdb=" SG CYS C 414 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS D 414 " - pdb=" SG CYS E 414 " distance=2.03 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 536 " distance=2.04 Simple disulfide: pdb=" SG CYS E 367 " - pdb=" SG CYS E 426 " distance=2.03 Simple disulfide: pdb=" SG CYS E 474 " - pdb=" SG CYS E 536 " distance=2.04 Simple disulfide: pdb=" SG CYS F 367 " - pdb=" SG CYS F 426 " distance=2.03 Simple disulfide: pdb=" SG CYS F 414 " - pdb=" SG CYS G 414 " distance=2.03 Simple disulfide: pdb=" SG CYS F 474 " - pdb=" SG CYS F 536 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS H 367 " - pdb=" SG CYS H 426 " distance=2.04 Simple disulfide: pdb=" SG CYS H 474 " - pdb=" SG CYS H 536 " distance=2.05 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 100 " distance=1.99 Simple disulfide: pdb=" SG CYS J 14 " - pdb=" SG CYS L 575 " distance=1.88 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=2.04 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=2.04 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=2.02 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=2.02 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=2, symmetry=0 Links applied 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 G 601 " - " ASN G 563 " " NAG H 601 " - " ASN H 563 " " NAG K 601 " - " ASN K 563 " " NAG L 601 " - " ASN L 563 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 780.0 milliseconds 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5284 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 65 sheets defined 11.2% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 353 through 360 Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 461 through 466 removed outlier: 3.933A pdb=" N LEU A 466 " --> pdb=" O GLN A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.585A pdb=" N TRP A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.678A pdb=" N LEU B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 421 Processing helix chain 'B' and resid 462 through 467 removed outlier: 4.111A pdb=" N LEU B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG B 467 " --> pdb=" O GLN B 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 462 through 467' Processing helix chain 'B' and resid 524 through 530 Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 524 through 530 removed outlier: 3.785A pdb=" N TRP C 528 " --> pdb=" O SER C 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 360 removed outlier: 3.817A pdb=" N THR D 360 " --> pdb=" O SER D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 419 removed outlier: 4.103A pdb=" N TRP D 418 " --> pdb=" O CYS D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 467 removed outlier: 3.530A pdb=" N LEU D 464 " --> pdb=" O ALA D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 531 Processing helix chain 'E' and resid 353 through 360 removed outlier: 3.812A pdb=" N THR E 360 " --> pdb=" O SER E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 419 removed outlier: 3.850A pdb=" N TRP E 418 " --> pdb=" O CYS E 414 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 414 through 419' Processing helix chain 'E' and resid 462 through 467 removed outlier: 4.193A pdb=" N LEU E 466 " --> pdb=" O GLU E 462 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG E 467 " --> pdb=" O GLN E 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 462 through 467' Processing helix chain 'E' and resid 524 through 529 Processing helix chain 'F' and resid 353 through 361 Processing helix chain 'F' and resid 414 through 419 removed outlier: 4.015A pdb=" N TRP F 418 " --> pdb=" O CYS F 414 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN F 419 " --> pdb=" O GLU F 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 414 through 419' Processing helix chain 'F' and resid 462 through 466 removed outlier: 3.696A pdb=" N ASN F 465 " --> pdb=" O GLU F 462 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU F 466 " --> pdb=" O GLN F 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 462 through 466' Processing helix chain 'F' and resid 524 through 531 removed outlier: 3.546A pdb=" N TRP F 528 " --> pdb=" O SER F 524 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 359 removed outlier: 3.882A pdb=" N LEU G 359 " --> pdb=" O ALA G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 421 Processing helix chain 'G' and resid 462 through 466 removed outlier: 3.545A pdb=" N ASN G 465 " --> pdb=" O GLU G 462 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU G 466 " --> pdb=" O GLN G 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 462 through 466' Processing helix chain 'G' and resid 524 through 531 removed outlier: 3.813A pdb=" N TRP G 528 " --> pdb=" O SER G 524 " (cutoff:3.500A) Processing helix chain 'G' and resid 553 through 557 removed outlier: 3.527A pdb=" N THR G 556 " --> pdb=" O ASP G 553 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY G 557 " --> pdb=" O LYS G 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 553 through 557' Processing helix chain 'H' and resid 353 through 361 Processing helix chain 'H' and resid 414 through 421 Processing helix chain 'H' and resid 462 through 466 removed outlier: 3.510A pdb=" N ASN H 465 " --> pdb=" O GLU H 462 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU H 466 " --> pdb=" O GLN H 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 462 through 466' Processing helix chain 'H' and resid 524 through 530 Processing helix chain 'J' and resid 65 through 69 removed outlier: 3.714A pdb=" N CYS J 68 " --> pdb=" O SER J 65 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS J 69 " --> pdb=" O ASP J 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 65 through 69' Processing helix chain 'K' and resid 353 through 361 removed outlier: 3.706A pdb=" N LEU K 359 " --> pdb=" O ALA K 355 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR K 360 " --> pdb=" O SER K 356 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 419 removed outlier: 3.663A pdb=" N ASN K 419 " --> pdb=" O GLU K 415 " (cutoff:3.500A) Processing helix chain 'K' and resid 460 through 465 Processing helix chain 'K' and resid 496 through 498 No H-bonds generated for 'chain 'K' and resid 496 through 498' Processing helix chain 'K' and resid 525 through 531 removed outlier: 4.260A pdb=" N ASN K 529 " --> pdb=" O GLU K 525 " (cutoff:3.500A) Processing helix chain 'K' and resid 553 through 558 removed outlier: 3.896A pdb=" N GLY K 557 " --> pdb=" O ASP K 553 " (cutoff:3.500A) Processing helix chain 'L' and resid 353 through 358 Processing helix chain 'L' and resid 414 through 418 removed outlier: 3.946A pdb=" N TRP L 418 " --> pdb=" O GLU L 415 " (cutoff:3.500A) Processing helix chain 'L' and resid 460 through 465 removed outlier: 3.551A pdb=" N LEU L 464 " --> pdb=" O ALA L 460 " (cutoff:3.500A) Processing helix chain 'L' and resid 525 through 531 Processing helix chain 'R' and resid 109 through 113 Processing helix chain 'U' and resid 69 through 73 removed outlier: 3.567A pdb=" N LYS U 73 " --> pdb=" O ALA U 70 " (cutoff:3.500A) Processing helix chain 'U' and resid 109 through 113 removed outlier: 3.662A pdb=" N GLY U 113 " --> pdb=" O ASN U 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 109 through 113' Processing helix chain 'V' and resid 109 through 113 removed outlier: 3.602A pdb=" N GLY V 113 " --> pdb=" O ASN V 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 109 through 113' Processing sheet with id=AA1, first strand: chain 'A' and resid 346 through 347 removed outlier: 3.667A pdb=" N ALA A 407 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASP A 371 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N PHE A 405 " --> pdb=" O ASP A 371 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 379 through 383 removed outlier: 6.314A pdb=" N HIS A 430 " --> pdb=" O SER A 435 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N SER A 435 " --> pdb=" O HIS A 430 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 453 through 457 Processing sheet with id=AA4, first strand: chain 'A' and resid 453 through 457 Processing sheet with id=AA5, first strand: chain 'A' and resid 493 through 494 Processing sheet with id=AA6, first strand: chain 'A' and resid 568 through 569 Processing sheet with id=AA7, first strand: chain 'B' and resid 346 through 350 removed outlier: 3.777A pdb=" N THR B 366 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR B 363 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU B 365 " --> pdb=" O ALA B 411 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA B 411 " --> pdb=" O LEU B 365 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 381 through 383 removed outlier: 4.127A pdb=" N VAL B 428 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU B 437 " --> pdb=" O VAL B 428 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 381 through 383 Processing sheet with id=AB1, first strand: chain 'B' and resid 453 through 457 removed outlier: 3.549A pdb=" N GLY B 478 " --> pdb=" O TYR B 515 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 453 through 457 removed outlier: 3.549A pdb=" N GLY B 478 " --> pdb=" O TYR B 515 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AB4, first strand: chain 'C' and resid 346 through 350 removed outlier: 5.305A pdb=" N THR C 370 " --> pdb=" O ALA C 407 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ALA C 407 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR C 404 " --> pdb=" O HIS C 400 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 346 through 350 Processing sheet with id=AB6, first strand: chain 'C' and resid 380 through 383 Processing sheet with id=AB7, first strand: chain 'C' and resid 453 through 457 removed outlier: 3.727A pdb=" N THR C 477 " --> pdb=" O ASP C 453 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER C 519 " --> pdb=" O CYS C 474 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 453 through 457 removed outlier: 3.727A pdb=" N THR C 477 " --> pdb=" O ASP C 453 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TYR C 515 " --> pdb=" O GLY C 478 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG C 514 " --> pdb=" O GLU C 508 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 493 through 494 Processing sheet with id=AC1, first strand: chain 'D' and resid 346 through 350 removed outlier: 3.739A pdb=" N ALA D 407 " --> pdb=" O VAL D 369 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 379 through 383 removed outlier: 3.575A pdb=" N THR D 425 " --> pdb=" O THR D 383 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 453 through 457 removed outlier: 6.065A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 453 through 457 removed outlier: 6.065A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 493 through 494 Processing sheet with id=AC6, first strand: chain 'E' and resid 346 through 350 removed outlier: 5.763A pdb=" N THR E 366 " --> pdb=" O ALA E 411 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ALA E 411 " --> pdb=" O THR E 366 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU E 368 " --> pdb=" O GLY E 409 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLY E 409 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N THR E 370 " --> pdb=" O ALA E 407 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ALA E 407 " --> pdb=" O THR E 370 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU E 372 " --> pdb=" O PHE E 405 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 379 through 383 Processing sheet with id=AC8, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.661A pdb=" N ASP E 453 " --> pdb=" O THR E 477 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR E 477 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.661A pdb=" N ASP E 453 " --> pdb=" O THR E 477 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR E 477 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 485 through 489 Processing sheet with id=AD2, first strand: chain 'F' and resid 347 through 350 Processing sheet with id=AD3, first strand: chain 'F' and resid 379 through 383 Processing sheet with id=AD4, first strand: chain 'F' and resid 455 through 457 removed outlier: 3.545A pdb=" N ILE F 472 " --> pdb=" O LEU F 521 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL F 476 " --> pdb=" O ALA F 517 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 455 through 457 removed outlier: 3.545A pdb=" N ILE F 472 " --> pdb=" O LEU F 521 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL F 476 " --> pdb=" O ALA F 517 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 493 through 494 Processing sheet with id=AD7, first strand: chain 'F' and resid 565 through 567 removed outlier: 6.284A pdb=" N SER F 565 " --> pdb=" O LEU G 566 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'G' and resid 347 through 350 removed outlier: 3.539A pdb=" N GLY G 409 " --> pdb=" O CYS G 367 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA G 407 " --> pdb=" O VAL G 369 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N PHE G 405 " --> pdb=" O ASP G 371 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 379 through 383 Processing sheet with id=AE1, first strand: chain 'G' and resid 453 through 457 removed outlier: 5.332A pdb=" N TYR G 515 " --> pdb=" O GLY G 478 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 453 through 457 removed outlier: 5.332A pdb=" N TYR G 515 " --> pdb=" O GLY G 478 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 493 through 494 removed outlier: 3.528A pdb=" N GLN G 493 " --> pdb=" O GLN G 490 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN G 490 " --> pdb=" O GLN G 493 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 346 through 350 Processing sheet with id=AE5, first strand: chain 'H' and resid 379 through 383 removed outlier: 3.651A pdb=" N PHE H 424 " --> pdb=" O ILE H 441 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU H 437 " --> pdb=" O VAL H 428 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 455 through 457 removed outlier: 3.647A pdb=" N THR H 473 " --> pdb=" O LEU H 457 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 493 through 494 Processing sheet with id=AE8, first strand: chain 'H' and resid 506 through 507 Processing sheet with id=AE9, first strand: chain 'J' and resid 40 through 41 removed outlier: 3.577A pdb=" N VAL J 41 " --> pdb=" O VAL L 567 " (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 113 Processing sheet with id=AF2, first strand: chain 'K' and resid 347 through 350 Processing sheet with id=AF3, first strand: chain 'K' and resid 378 through 384 Processing sheet with id=AF4, first strand: chain 'K' and resid 453 through 457 removed outlier: 3.581A pdb=" N VAL K 476 " --> pdb=" O ALA K 517 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N TYR K 515 " --> pdb=" O GLY K 478 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 453 through 457 removed outlier: 3.581A pdb=" N VAL K 476 " --> pdb=" O ALA K 517 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N TYR K 515 " --> pdb=" O GLY K 478 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 485 through 489 Processing sheet with id=AF7, first strand: chain 'K' and resid 564 through 565 Processing sheet with id=AF8, first strand: chain 'L' and resid 346 through 350 removed outlier: 3.823A pdb=" N ASP L 371 " --> pdb=" O PHE L 405 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N PHE L 405 " --> pdb=" O ASP L 371 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 381 through 384 removed outlier: 3.564A pdb=" N PHE L 424 " --> pdb=" O ILE L 441 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 453 through 457 removed outlier: 3.797A pdb=" N THR L 473 " --> pdb=" O LEU L 457 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N TYR L 515 " --> pdb=" O GLY L 478 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 453 through 457 removed outlier: 3.797A pdb=" N THR L 473 " --> pdb=" O LEU L 457 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N TYR L 515 " --> pdb=" O GLY L 478 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 493 through 494 Processing sheet with id=AG4, first strand: chain 'R' and resid 33 through 38 Processing sheet with id=AG5, first strand: chain 'R' and resid 57 through 62 removed outlier: 6.939A pdb=" N LEU R 48 " --> pdb=" O VAL R 61 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N VAL R 101 " --> pdb=" O GLU R 51 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR R 102 " --> pdb=" O LYS R 117 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYS R 117 " --> pdb=" O TYR R 102 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N CYS R 104 " --> pdb=" O THR R 115 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'S' and resid 33 through 38 Processing sheet with id=AG7, first strand: chain 'S' and resid 57 through 62 removed outlier: 7.069A pdb=" N LEU S 48 " --> pdb=" O VAL S 61 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS S 104 " --> pdb=" O GLN S 116 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN S 116 " --> pdb=" O CYS S 104 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'U' and resid 33 through 38 Processing sheet with id=AG9, first strand: chain 'U' and resid 57 through 63 removed outlier: 7.029A pdb=" N LEU U 48 " --> pdb=" O VAL U 61 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N SER U 63 " --> pdb=" O ILE U 46 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE U 46 " --> pdb=" O SER U 63 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N VAL U 101 " --> pdb=" O GLU U 51 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TYR U 102 " --> pdb=" O LYS U 117 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LYS U 117 " --> pdb=" O TYR U 102 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N CYS U 104 " --> pdb=" O THR U 115 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'V' and resid 33 through 38 Processing sheet with id=AH2, first strand: chain 'V' and resid 57 through 62 removed outlier: 7.071A pdb=" N LEU V 48 " --> pdb=" O VAL V 61 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS V 104 " --> pdb=" O THR V 115 " (cutoff:3.500A) 770 hydrogen bonds defined for protein. 1941 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.46 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3549 1.31 - 1.44: 5882 1.44 - 1.57: 12606 1.57 - 1.70: 0 1.70 - 1.83: 159 Bond restraints: 22196 Sorted by residual: bond pdb=" C ASN V 85 " pdb=" N LEU V 86 " ideal model delta sigma weight residual 1.331 1.552 -0.221 1.41e-02 5.03e+03 2.47e+02 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.541 -0.135 2.00e-02 2.50e+03 4.58e+01 bond pdb=" C THR L 574 " pdb=" N CYS L 575 " ideal model delta sigma weight residual 1.329 1.421 -0.092 1.40e-02 5.10e+03 4.28e+01 bond pdb=" C SER A 569 " pdb=" N ASP A 570 " ideal model delta sigma weight residual 1.333 1.402 -0.069 1.39e-02 5.18e+03 2.47e+01 bond pdb=" CA TYR C 455 " pdb=" C TYR C 455 " ideal model delta sigma weight residual 1.520 1.467 0.052 1.12e-02 7.97e+03 2.19e+01 ... (remaining 22191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.58: 30113 4.58 - 9.17: 183 9.17 - 13.75: 16 13.75 - 18.33: 1 18.33 - 22.92: 1 Bond angle restraints: 30314 Sorted by residual: angle pdb=" C ASN V 85 " pdb=" N LEU V 86 " pdb=" CA LEU V 86 " ideal model delta sigma weight residual 122.59 99.67 22.92 1.57e+00 4.06e-01 2.13e+02 angle pdb=" C THR L 574 " pdb=" N CYS L 575 " pdb=" CA CYS L 575 " ideal model delta sigma weight residual 121.70 105.63 16.07 1.80e+00 3.09e-01 7.97e+01 angle pdb=" CA SER A 569 " pdb=" C SER A 569 " pdb=" O SER A 569 " ideal model delta sigma weight residual 121.44 111.32 10.12 1.17e+00 7.31e-01 7.48e+01 angle pdb=" N VAL V 122 " pdb=" CA VAL V 122 " pdb=" C VAL V 122 " ideal model delta sigma weight residual 110.30 118.08 -7.78 9.70e-01 1.06e+00 6.44e+01 angle pdb=" N SER A 569 " pdb=" CA SER A 569 " pdb=" C SER A 569 " ideal model delta sigma weight residual 109.52 120.57 -11.05 1.55e+00 4.16e-01 5.09e+01 ... (remaining 30309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 12092 17.99 - 35.97: 1028 35.97 - 53.96: 262 53.96 - 71.94: 54 71.94 - 89.93: 21 Dihedral angle restraints: 13457 sinusoidal: 5334 harmonic: 8123 Sorted by residual: dihedral pdb=" CB CYS R 49 " pdb=" SG CYS R 49 " pdb=" SG CYS R 58 " pdb=" CB CYS R 58 " ideal model delta sinusoidal sigma weight residual -86.00 -159.92 73.92 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS V 49 " pdb=" SG CYS V 49 " pdb=" SG CYS V 58 " pdb=" CB CYS V 58 " ideal model delta sinusoidal sigma weight residual -86.00 -155.64 69.64 1 1.00e+01 1.00e-02 6.26e+01 dihedral pdb=" CB CYS U 49 " pdb=" SG CYS U 49 " pdb=" SG CYS U 58 " pdb=" CB CYS U 58 " ideal model delta sinusoidal sigma weight residual -86.00 -152.86 66.86 1 1.00e+01 1.00e-02 5.83e+01 ... (remaining 13454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.395: 3588 0.395 - 0.791: 9 0.791 - 1.186: 1 1.186 - 1.581: 0 1.581 - 1.977: 2 Chirality restraints: 3600 Sorted by residual: chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 563 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -0.42 -1.98 2.00e-01 2.50e+01 9.77e+01 chirality pdb=" C1 NAG E 601 " pdb=" ND2 ASN E 563 " pdb=" C2 NAG E 601 " pdb=" O5 NAG E 601 " both_signs ideal model delta sigma weight residual False -2.40 -0.54 -1.86 2.00e-01 2.50e+01 8.65e+01 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 563 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.22 -1.18 2.00e-01 2.50e+01 3.51e+01 ... (remaining 3597 not shown) Planarity restraints: 3873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN K 563 " -0.068 2.00e-02 2.50e+03 6.35e-02 5.04e+01 pdb=" CG ASN K 563 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN K 563 " 0.031 2.00e-02 2.50e+03 pdb=" ND2 ASN K 563 " 0.092 2.00e-02 2.50e+03 pdb=" C1 NAG K 601 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET K 489 " -0.021 2.00e-02 2.50e+03 4.20e-02 1.76e+01 pdb=" C MET K 489 " 0.073 2.00e-02 2.50e+03 pdb=" O MET K 489 " -0.028 2.00e-02 2.50e+03 pdb=" N GLN K 490 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 563 " 0.030 2.00e-02 2.50e+03 3.51e-02 1.54e+01 pdb=" CG ASN C 563 " -0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN C 563 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN C 563 " -0.061 2.00e-02 2.50e+03 pdb=" C1 NAG C 601 " 0.039 2.00e-02 2.50e+03 ... (remaining 3870 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.98: 31 1.98 - 2.71: 1381 2.71 - 3.44: 31553 3.44 - 4.17: 51340 4.17 - 4.90: 86840 Nonbonded interactions: 171145 Sorted by model distance: nonbonded pdb=" N TYR V 81 " pdb=" O LEU V 86 " model vdw 1.252 3.120 nonbonded pdb=" O VAL U 23 " pdb=" CB LEU U 120 " model vdw 1.262 3.440 nonbonded pdb=" OG1 THR J 102 " pdb=" N CYS L 575 " model vdw 1.331 3.120 nonbonded pdb=" CD1 ILE J 17 " pdb=" CA ILE J 37 " model vdw 1.332 3.890 nonbonded pdb=" O GLY S 27 " pdb=" O VAL S 122 " model vdw 1.341 3.040 ... (remaining 171140 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 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 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 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 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 444 or resid 449 through 568 o \ r 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 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 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 444 or resid 449 through 512 o \ r (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 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 601)) selection = (chain 'G' and (resid 345 through 444 or resid 449 through 512 or (resid 513 and \ (name N or name CA or name C )) or resid 514 through 601)) 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 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 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 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 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' selection = chain 'S' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.360 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.040 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 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 : 0.006 0.273 22242 Z= 0.405 Angle : 1.106 46.662 30412 Z= 0.591 Chirality : 0.079 1.977 3600 Planarity : 0.006 0.092 3863 Dihedral : 14.785 89.926 8071 Min Nonbonded Distance : 1.252 Molprobity Statistics. All-atom Clashscore : 29.55 Ramachandran Plot: Outliers : 0.91 % Allowed : 8.59 % Favored : 90.50 % Rotamer: Outliers : 4.37 % Allowed : 2.63 % Favored : 93.00 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.91 (0.16), residues: 2737 helix: -0.88 (0.37), residues: 180 sheet: -0.96 (0.16), residues: 1037 loop : -1.52 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG U 112 TYR 0.027 0.002 TYR B 455 PHE 0.019 0.002 PHE H 516 TRP 0.025 0.002 TRP K 528 HIS 0.009 0.001 HIS F 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.32 (22196) covalent geometry : angle 0.96340 / 0.56 (30314) SS BOND : bond 0.02779 / 2.27 ( 34) SS BOND : angle 4.52527 / 2.72 ( 68) hydrogen bonds : bond 0.18078 / 12.67 ( 647) hydrogen bonds : angle 8.26643 / 5.91 ( 1941) Misc. bond : bond 0.17356 / 9.11 ( 2) link_NAG-ASN : bond 0.16107 / 9.87 ( 10) link_NAG-ASN : angle 16.02283 / 11.55 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 388 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 529 ASN cc_start: 0.9264 (m110) cc_final: 0.9026 (m110) REVERT: C 395 ASN cc_start: 0.5686 (t0) cc_final: 0.5278 (t0) REVERT: C 561 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8741 (mm) REVERT: D 424 PHE cc_start: 0.8586 (m-80) cc_final: 0.8245 (m-80) REVERT: D 510 GLN cc_start: 0.8305 (pp30) cc_final: 0.8071 (pp30) REVERT: D 534 TYR cc_start: 0.8559 (m-80) cc_final: 0.7940 (m-80) REVERT: E 461 ARG cc_start: 0.8015 (mmm160) cc_final: 0.7737 (mmm160) REVERT: F 493 GLN cc_start: 0.8285 (pp30) cc_final: 0.7886 (pp30) REVERT: H 506 MET cc_start: 0.7857 (mmp) cc_final: 0.7603 (mmm) REVERT: J 16 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.6523 (tmm160) REVERT: L 520 ILE cc_start: 0.9135 (pt) cc_final: 0.8931 (pt) REVERT: R 36 LYS cc_start: 0.7196 (tptt) cc_final: 0.6964 (tppt) REVERT: R 46 ILE cc_start: 0.9213 (tp) cc_final: 0.8860 (tp) REVERT: R 52 MET cc_start: 0.8274 (tpt) cc_final: 0.8046 (tpp) REVERT: S 46 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8698 (tp) REVERT: U 26 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7648 (tp30) REVERT: U 66 ASN cc_start: 0.8082 (p0) cc_final: 0.7512 (t0) REVERT: U 87 PHE cc_start: 0.8080 (t80) cc_final: 0.7711 (t80) REVERT: U 111 ASP cc_start: 0.7822 (p0) cc_final: 0.7598 (p0) REVERT: U 112 ARG cc_start: 0.8211 (mmp80) cc_final: 0.7988 (mmp80) REVERT: V 43 HIS cc_start: 0.6836 (m-70) cc_final: 0.6610 (m-70) REVERT: V 83 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6511 (ptt-90) REVERT: V 87 PHE cc_start: 0.8110 (t80) cc_final: 0.7529 (t80) outliers start: 108 outliers final: 73 residues processed: 472 average time/residue: 0.1601 time to fit residues: 116.4314 Evaluate side-chains 362 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 284 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 562 TYR Chi-restraints excluded: chain C residue 563 ASN Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 568 MET Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain E residue 485 PHE Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain E residue 514 ARG Chi-restraints excluded: chain E residue 561 LEU Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 510 GLN Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 16 ARG Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 66 ASP Chi-restraints excluded: chain J residue 68 CYS Chi-restraints excluded: chain J residue 134 TYR Chi-restraints excluded: chain K residue 490 GLN Chi-restraints excluded: chain K residue 493 GLN Chi-restraints excluded: chain K residue 567 VAL Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain R residue 95 THR Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 122 VAL Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 28 GLU Chi-restraints excluded: chain S residue 41 GLU Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 94 LEU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 98 ASP Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain S residue 114 LYS Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 22 GLU Chi-restraints excluded: chain U residue 26 GLU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 122 VAL Chi-restraints excluded: chain V residue 19 ILE Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 23 VAL Chi-restraints excluded: chain V residue 26 GLU Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 80 GLN Chi-restraints excluded: chain V residue 81 TYR Chi-restraints excluded: chain V residue 83 ARG Chi-restraints excluded: chain V residue 84 LYS Chi-restraints excluded: chain V residue 85 ASN Chi-restraints excluded: chain V residue 96 GLU Chi-restraints excluded: chain V residue 118 VAL Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 123 HIS Chi-restraints excluded: chain V residue 124 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.0050 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 HIS ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 GLN ** F 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 463 GLN ** H 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 529 ASN ** H 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 ASN L 400 HIS ** S 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 116 GLN U 121 ASN V 80 GLN V 123 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.117692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.077261 restraints weight = 76748.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.079664 restraints weight = 40736.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.081122 restraints weight = 28748.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.081764 restraints weight = 23781.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.082341 restraints weight = 21614.202| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22242 Z= 0.189 Angle : 0.791 17.155 30412 Z= 0.388 Chirality : 0.051 0.643 3600 Planarity : 0.005 0.082 3863 Dihedral : 9.234 103.770 3136 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.86 % Favored : 92.07 % Rotamer: Outliers : 3.60 % Allowed : 11.69 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.92 (0.16), residues: 2737 helix: -1.32 (0.31), residues: 221 sheet: -0.90 (0.16), residues: 1060 loop : -1.51 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 461 TYR 0.020 0.002 TYR H 375 PHE 0.021 0.002 PHE B 354 TRP 0.021 0.002 TRP H 528 HIS 0.007 0.001 HIS C 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (22196) covalent geometry : angle 0.76574 / 0.38 (30314) SS BOND : bond 0.00685 / 0.34 ( 34) SS BOND : angle 1.55449 / 1.02 ( 68) hydrogen bonds : bond 0.04384 / 2.94 ( 647) hydrogen bonds : angle 6.50680 / 4.63 ( 1941) Misc. bond : bond 0.00021 / 0.01 ( 2) link_NAG-ASN : bond 0.00889 / 0.53 ( 10) link_NAG-ASN : angle 6.04179 / 4.20 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 314 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7760 (tp) REVERT: C 395 ASN cc_start: 0.5431 (t0) cc_final: 0.4990 (t0) REVERT: C 561 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7879 (mm) REVERT: D 424 PHE cc_start: 0.8454 (m-80) cc_final: 0.8212 (m-80) REVERT: D 510 GLN cc_start: 0.8254 (pp30) cc_final: 0.8044 (pp30) REVERT: D 534 TYR cc_start: 0.8804 (m-80) cc_final: 0.8113 (m-80) REVERT: E 461 ARG cc_start: 0.8080 (mmm160) cc_final: 0.7817 (mmm160) REVERT: E 483 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.7584 (t0) REVERT: F 493 GLN cc_start: 0.8272 (pp30) cc_final: 0.7994 (pp30) REVERT: J 8 VAL cc_start: 0.4456 (p) cc_final: 0.4147 (t) REVERT: J 37 ILE cc_start: 0.7076 (mm) cc_final: 0.6797 (mm) REVERT: J 66 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.8217 (p0) REVERT: K 463 GLN cc_start: 0.8393 (tp-100) cc_final: 0.8119 (tp-100) REVERT: K 475 LEU cc_start: 0.9067 (tp) cc_final: 0.8818 (tp) REVERT: K 483 ASP cc_start: 0.8141 (t0) cc_final: 0.7892 (t0) REVERT: L 489 MET cc_start: 0.7617 (ttm) cc_final: 0.7330 (tpp) REVERT: R 36 LYS cc_start: 0.7246 (tptt) cc_final: 0.6894 (tppt) REVERT: S 26 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7311 (tp30) REVERT: S 42 MET cc_start: 0.8330 (ptp) cc_final: 0.7025 (pmm) REVERT: S 51 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6528 (mp0) REVERT: S 94 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7546 (tp) REVERT: U 26 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7471 (tp30) REVERT: U 66 ASN cc_start: 0.8153 (p0) cc_final: 0.7632 (t0) REVERT: V 26 GLU cc_start: 0.6032 (OUTLIER) cc_final: 0.5680 (tt0) REVERT: V 81 TYR cc_start: 0.6930 (OUTLIER) cc_final: 0.5259 (m-80) REVERT: V 83 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.6589 (mtm180) REVERT: V 87 PHE cc_start: 0.7857 (t80) cc_final: 0.7413 (t80) outliers start: 89 outliers final: 56 residues processed: 381 average time/residue: 0.1519 time to fit residues: 91.1869 Evaluate side-chains 336 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 270 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 561 LEU Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 510 GLN Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 63 HIS Chi-restraints excluded: chain J residue 66 ASP Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 376 ASP Chi-restraints excluded: chain K residue 528 TRP Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 94 LEU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 98 ASP Chi-restraints excluded: chain S residue 114 LYS Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 22 GLU Chi-restraints excluded: chain U residue 26 GLU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 122 VAL Chi-restraints excluded: chain V residue 19 ILE Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 26 GLU Chi-restraints excluded: chain V residue 81 TYR Chi-restraints excluded: chain V residue 83 ARG Chi-restraints excluded: chain V residue 85 ASN Chi-restraints excluded: chain V residue 118 VAL Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 123 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 155 optimal weight: 8.9990 chunk 150 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 198 optimal weight: 7.9990 chunk 3 optimal weight: 50.0000 chunk 52 optimal weight: 50.0000 chunk 177 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 194 optimal weight: 30.0000 chunk 80 optimal weight: 4.9990 chunk 96 optimal weight: 30.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 510 GLN ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 ASN D 450 HIS F 419 ASN F 545 ASN ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 529 ASN K 463 GLN L 463 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.114960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.073932 restraints weight = 76968.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.076229 restraints weight = 41577.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.077639 restraints weight = 29625.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.078349 restraints weight = 24636.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.078636 restraints weight = 22433.853| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 22242 Z= 0.284 Angle : 0.814 19.864 30412 Z= 0.402 Chirality : 0.051 0.560 3600 Planarity : 0.005 0.086 3863 Dihedral : 7.889 85.648 3063 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.26 % Favored : 91.71 % Rotamer: Outliers : 4.53 % Allowed : 14.85 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.01 (0.16), residues: 2737 helix: -1.13 (0.32), residues: 216 sheet: -1.05 (0.16), residues: 1041 loop : -1.53 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 45 TYR 0.026 0.002 TYR E 455 PHE 0.024 0.002 PHE H 516 TRP 0.014 0.002 TRP G 488 HIS 0.007 0.001 HIS C 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.28 (22196) covalent geometry : angle 0.78883 / 0.40 (30314) SS BOND : bond 0.00632 / 0.34 ( 34) SS BOND : angle 1.69341 / 1.12 ( 68) hydrogen bonds : bond 0.04229 / 2.86 ( 647) hydrogen bonds : angle 6.39488 / 4.51 ( 1941) Misc. bond : bond 0.00332 / 0.17 ( 2) link_NAG-ASN : bond 0.00900 / 0.49 ( 10) link_NAG-ASN : angle 5.98204 / 4.49 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 281 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 521 LEU cc_start: 0.8695 (tp) cc_final: 0.8485 (tp) REVERT: B 415 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8334 (mp0) REVERT: C 395 ASN cc_start: 0.5375 (t0) cc_final: 0.5052 (t0) REVERT: D 489 MET cc_start: 0.8477 (tpp) cc_final: 0.8235 (mmt) REVERT: D 510 GLN cc_start: 0.8376 (pp30) cc_final: 0.8106 (pp30) REVERT: E 461 ARG cc_start: 0.8177 (mmm160) cc_final: 0.7864 (mmm160) REVERT: E 465 ASN cc_start: 0.8564 (m-40) cc_final: 0.7597 (m-40) REVERT: E 483 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.7677 (t0) REVERT: E 568 MET cc_start: 0.6685 (tmm) cc_final: 0.6137 (ppp) REVERT: F 493 GLN cc_start: 0.8122 (pp30) cc_final: 0.7755 (pp30) REVERT: J 66 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8174 (p0) REVERT: K 463 GLN cc_start: 0.8666 (tp40) cc_final: 0.8391 (tp-100) REVERT: K 483 ASP cc_start: 0.8174 (t0) cc_final: 0.7862 (t0) REVERT: K 506 MET cc_start: 0.7700 (mpp) cc_final: 0.7499 (mpp) REVERT: L 489 MET cc_start: 0.7608 (ttm) cc_final: 0.7264 (tpp) REVERT: R 36 LYS cc_start: 0.7140 (tptt) cc_final: 0.6820 (tppt) REVERT: S 96 GLU cc_start: 0.8529 (tp30) cc_final: 0.8292 (tm-30) REVERT: U 26 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7662 (tm-30) REVERT: U 42 MET cc_start: 0.7046 (tpt) cc_final: 0.6770 (tpp) REVERT: V 52 MET cc_start: 0.7718 (tpp) cc_final: 0.7484 (tpp) REVERT: V 81 TYR cc_start: 0.7284 (OUTLIER) cc_final: 0.5988 (m-80) REVERT: V 83 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.6877 (mtm180) REVERT: V 87 PHE cc_start: 0.7952 (t80) cc_final: 0.7486 (t80) outliers start: 112 outliers final: 71 residues processed: 373 average time/residue: 0.1462 time to fit residues: 87.8305 Evaluate side-chains 335 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 258 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 568 MET Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 561 LEU Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 533 THR Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 486 VAL Chi-restraints excluded: chain G residue 510 GLN Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 63 HIS Chi-restraints excluded: chain J residue 66 ASP Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 528 TRP Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain L residue 521 LEU Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 114 LYS Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 22 GLU Chi-restraints excluded: chain U residue 26 GLU Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 122 VAL Chi-restraints excluded: chain V residue 81 TYR Chi-restraints excluded: chain V residue 83 ARG Chi-restraints excluded: chain V residue 85 ASN Chi-restraints excluded: chain V residue 118 VAL Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 123 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 222 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 170 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 145 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 GLN ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 545 ASN ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 400 HIS ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.115761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.075738 restraints weight = 78312.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.078835 restraints weight = 42888.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.078946 restraints weight = 27159.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.079251 restraints weight = 23874.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.079446 restraints weight = 23955.699| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 22242 Z= 0.220 Angle : 0.765 16.021 30412 Z= 0.375 Chirality : 0.050 0.610 3600 Planarity : 0.005 0.088 3863 Dihedral : 7.290 83.378 3042 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.00 % Favored : 91.96 % Rotamer: Outliers : 4.57 % Allowed : 16.75 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.93 (0.16), residues: 2737 helix: -1.08 (0.33), residues: 213 sheet: -1.02 (0.16), residues: 1055 loop : -1.47 (0.16), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 45 TYR 0.022 0.002 TYR D 534 PHE 0.025 0.002 PHE H 485 TRP 0.013 0.002 TRP A 488 HIS 0.007 0.001 HIS E 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.22 (22196) covalent geometry : angle 0.74260 / 0.37 (30314) SS BOND : bond 0.00562 / 0.29 ( 34) SS BOND : angle 1.42839 / 0.93 ( 68) hydrogen bonds : bond 0.03880 / 2.63 ( 647) hydrogen bonds : angle 6.15029 / 4.36 ( 1941) Misc. bond : bond 0.00163 / 0.09 ( 2) link_NAG-ASN : bond 0.00778 / 0.45 ( 10) link_NAG-ASN : angle 5.55594 / 3.94 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 270 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 ASP cc_start: 0.6396 (t0) cc_final: 0.5983 (p0) REVERT: A 455 TYR cc_start: 0.7998 (m-10) cc_final: 0.7661 (m-10) REVERT: A 550 ARG cc_start: 0.8299 (mmm160) cc_final: 0.7867 (mmm160) REVERT: B 415 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8361 (mp0) REVERT: B 554 LYS cc_start: 0.9128 (ttmt) cc_final: 0.8883 (ttmt) REVERT: C 395 ASN cc_start: 0.5086 (t0) cc_final: 0.4719 (t0) REVERT: C 430 HIS cc_start: 0.4712 (OUTLIER) cc_final: 0.4482 (t70) REVERT: C 561 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8242 (mm) REVERT: D 510 GLN cc_start: 0.8348 (pp30) cc_final: 0.8094 (pp30) REVERT: E 483 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.7655 (t0) REVERT: K 463 GLN cc_start: 0.8769 (tp40) cc_final: 0.8539 (tp-100) REVERT: K 483 ASP cc_start: 0.8206 (t0) cc_final: 0.7894 (t0) REVERT: L 489 MET cc_start: 0.7408 (ttm) cc_final: 0.7126 (tpp) REVERT: S 52 MET cc_start: 0.7693 (pmm) cc_final: 0.7262 (pmm) REVERT: S 96 GLU cc_start: 0.8703 (tp30) cc_final: 0.8392 (tm-30) REVERT: S 114 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7329 (ptpt) REVERT: U 26 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7758 (tm-30) REVERT: V 52 MET cc_start: 0.7811 (tpp) cc_final: 0.7592 (tpp) REVERT: V 81 TYR cc_start: 0.7590 (OUTLIER) cc_final: 0.7321 (m-80) REVERT: V 83 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.6855 (ptt-90) REVERT: V 87 PHE cc_start: 0.8113 (t80) cc_final: 0.7639 (t80) outliers start: 113 outliers final: 75 residues processed: 366 average time/residue: 0.1450 time to fit residues: 84.8671 Evaluate side-chains 326 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 243 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain C residue 358 PHE Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 510 GLN Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 522 THR Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 63 HIS Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 375 TYR Chi-restraints excluded: chain K residue 474 CYS Chi-restraints excluded: chain K residue 528 TRP Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 562 TYR Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 114 LYS Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 22 GLU Chi-restraints excluded: chain U residue 26 GLU Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 122 VAL Chi-restraints excluded: chain V residue 81 TYR Chi-restraints excluded: chain V residue 83 ARG Chi-restraints excluded: chain V residue 118 VAL Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 123 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 166 optimal weight: 0.9990 chunk 226 optimal weight: 8.9990 chunk 188 optimal weight: 40.0000 chunk 142 optimal weight: 2.9990 chunk 216 optimal weight: 30.0000 chunk 121 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 217 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.116081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.077593 restraints weight = 77601.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.078608 restraints weight = 51207.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.079055 restraints weight = 35538.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.079541 restraints weight = 30310.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.079560 restraints weight = 27010.307| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22242 Z= 0.175 Angle : 0.742 14.865 30412 Z= 0.362 Chirality : 0.049 0.595 3600 Planarity : 0.005 0.087 3863 Dihedral : 6.897 72.502 3029 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 4.81 % Allowed : 17.88 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.81 (0.16), residues: 2737 helix: -0.98 (0.34), residues: 214 sheet: -0.91 (0.16), residues: 1048 loop : -1.41 (0.16), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 461 TYR 0.022 0.002 TYR R 72 PHE 0.017 0.002 PHE K 358 TRP 0.012 0.001 TRP H 528 HIS 0.005 0.001 HIS C 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (22196) covalent geometry : angle 0.72095 / 0.36 (30314) SS BOND : bond 0.00492 / 0.24 ( 34) SS BOND : angle 1.24013 / 0.79 ( 68) hydrogen bonds : bond 0.03716 / 2.51 ( 647) hydrogen bonds : angle 5.96542 / 4.24 ( 1941) Misc. bond : bond 0.00182 / 0.10 ( 2) link_NAG-ASN : bond 0.00759 / 0.44 ( 10) link_NAG-ASN : angle 5.35510 / 3.73 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 271 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 ASP cc_start: 0.6352 (t0) cc_final: 0.5927 (p0) REVERT: A 455 TYR cc_start: 0.8052 (m-10) cc_final: 0.7690 (m-10) REVERT: A 550 ARG cc_start: 0.8374 (mmm160) cc_final: 0.7905 (mmm160) REVERT: B 415 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8415 (mp0) REVERT: B 515 TYR cc_start: 0.7745 (m-80) cc_final: 0.7536 (t80) REVERT: B 554 LYS cc_start: 0.9139 (ttmt) cc_final: 0.8876 (ttmt) REVERT: C 395 ASN cc_start: 0.4953 (t0) cc_final: 0.4545 (t0) REVERT: C 430 HIS cc_start: 0.4562 (OUTLIER) cc_final: 0.4327 (t70) REVERT: C 561 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8261 (mm) REVERT: D 510 GLN cc_start: 0.8462 (pp30) cc_final: 0.8176 (pp30) REVERT: D 534 TYR cc_start: 0.8807 (m-80) cc_final: 0.8598 (m-80) REVERT: E 483 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.7784 (t0) REVERT: E 568 MET cc_start: 0.6369 (ppp) cc_final: 0.5896 (ppp) REVERT: F 430 HIS cc_start: 0.1115 (OUTLIER) cc_final: 0.0719 (m-70) REVERT: H 527 GLU cc_start: 0.8575 (tp30) cc_final: 0.8339 (tp30) REVERT: J 19 SER cc_start: 0.8296 (OUTLIER) cc_final: 0.7836 (p) REVERT: K 347 VAL cc_start: 0.0156 (OUTLIER) cc_final: -0.0209 (m) REVERT: K 463 GLN cc_start: 0.8886 (tp40) cc_final: 0.8657 (tp-100) REVERT: K 483 ASP cc_start: 0.8232 (t0) cc_final: 0.7870 (t0) REVERT: L 489 MET cc_start: 0.7448 (ttm) cc_final: 0.7237 (tpp) REVERT: R 36 LYS cc_start: 0.7220 (tptt) cc_final: 0.6870 (tppt) REVERT: S 40 PRO cc_start: 0.8869 (Cg_exo) cc_final: 0.8618 (Cg_endo) REVERT: S 96 GLU cc_start: 0.8655 (tp30) cc_final: 0.8423 (tm-30) REVERT: S 114 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7553 (ptpt) REVERT: U 42 MET cc_start: 0.6849 (tpt) cc_final: 0.6627 (tpp) REVERT: V 52 MET cc_start: 0.7815 (tpp) cc_final: 0.7600 (tpp) REVERT: V 87 PHE cc_start: 0.8171 (t80) cc_final: 0.7708 (t80) outliers start: 119 outliers final: 90 residues processed: 370 average time/residue: 0.1398 time to fit residues: 84.4827 Evaluate side-chains 349 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 251 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain C residue 358 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 430 HIS Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 487 GLN Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 63 HIS Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 375 TYR Chi-restraints excluded: chain K residue 474 CYS Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 528 TRP Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain K residue 567 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 562 TYR Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 114 LYS Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 22 GLU Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 122 VAL Chi-restraints excluded: chain V residue 83 ARG Chi-restraints excluded: chain V residue 85 ASN Chi-restraints excluded: chain V residue 118 VAL Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 123 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 19 optimal weight: 6.9990 chunk 159 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 185 optimal weight: 7.9990 chunk 46 optimal weight: 30.0000 chunk 1 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 247 optimal weight: 10.0000 chunk 191 optimal weight: 20.0000 chunk 219 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 545 ASN ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 116 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 = 0.4229 r_free = 0.4229 target = 0.115454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.075502 restraints weight = 77511.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.078591 restraints weight = 43080.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.078997 restraints weight = 25508.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.079167 restraints weight = 24978.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.079208 restraints weight = 23319.153| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 22242 Z= 0.213 Angle : 0.753 16.111 30412 Z= 0.370 Chirality : 0.050 0.672 3600 Planarity : 0.005 0.086 3863 Dihedral : 6.607 59.887 3021 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 5.14 % Allowed : 18.37 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.16), residues: 2737 helix: -0.95 (0.34), residues: 214 sheet: -0.92 (0.16), residues: 1048 loop : -1.38 (0.16), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 461 TYR 0.023 0.002 TYR K 455 PHE 0.015 0.002 PHE R 67 TRP 0.013 0.002 TRP K 528 HIS 0.008 0.001 HIS D 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.21 (22196) covalent geometry : angle 0.73149 / 0.36 (30314) SS BOND : bond 0.00551 / 0.29 ( 34) SS BOND : angle 1.55305 / 0.95 ( 68) hydrogen bonds : bond 0.03729 / 2.52 ( 647) hydrogen bonds : angle 5.94152 / 4.23 ( 1941) Misc. bond : bond 0.00210 / 0.11 ( 2) link_NAG-ASN : bond 0.00672 / 0.34 ( 10) link_NAG-ASN : angle 5.41885 / 3.91 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 268 time to evaluate : 0.869 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 376 ASP cc_start: 0.6466 (t0) cc_final: 0.6022 (p0) REVERT: A 550 ARG cc_start: 0.8351 (mmm160) cc_final: 0.7838 (mmm160) REVERT: B 415 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8338 (mp0) REVERT: B 554 LYS cc_start: 0.9185 (ttmt) cc_final: 0.8950 (ttmt) REVERT: C 395 ASN cc_start: 0.4864 (t0) cc_final: 0.4610 (t0) REVERT: C 561 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8298 (mm) REVERT: D 489 MET cc_start: 0.8424 (tpp) cc_final: 0.8154 (mmt) REVERT: D 510 GLN cc_start: 0.8354 (pp30) cc_final: 0.8070 (pp30) REVERT: D 534 TYR cc_start: 0.8829 (m-80) cc_final: 0.8269 (m-80) REVERT: F 358 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.7748 (t80) REVERT: F 365 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7110 (mm) REVERT: F 430 HIS cc_start: 0.1243 (OUTLIER) cc_final: 0.0859 (m-70) REVERT: J 19 SER cc_start: 0.8501 (OUTLIER) cc_final: 0.8104 (p) REVERT: K 347 VAL cc_start: 0.0163 (OUTLIER) cc_final: -0.0211 (m) REVERT: K 483 ASP cc_start: 0.8229 (t0) cc_final: 0.7905 (t0) REVERT: L 489 MET cc_start: 0.7481 (ttm) cc_final: 0.7022 (tpp) REVERT: R 36 LYS cc_start: 0.7211 (tptt) cc_final: 0.6879 (tptt) REVERT: S 96 GLU cc_start: 0.8527 (tp30) cc_final: 0.8308 (tm-30) REVERT: V 52 MET cc_start: 0.7851 (tpp) cc_final: 0.7635 (tpp) REVERT: V 87 PHE cc_start: 0.8050 (t80) cc_final: 0.7579 (t80) outliers start: 127 outliers final: 95 residues processed: 375 average time/residue: 0.1457 time to fit residues: 88.0835 Evaluate side-chains 350 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 248 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain C residue 358 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain D residue 348 PHE Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 430 HIS Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 487 GLN Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 553 ASP Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 486 VAL Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 394 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 522 THR Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 63 HIS Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 375 TYR Chi-restraints excluded: chain K residue 474 CYS Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 528 TRP Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain K residue 567 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 562 TYR Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 122 VAL Chi-restraints excluded: chain V residue 83 ARG Chi-restraints excluded: chain V residue 85 ASN Chi-restraints excluded: chain V residue 118 VAL Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 123 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 55 optimal weight: 3.9990 chunk 220 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 66 optimal weight: 30.0000 chunk 77 optimal weight: 0.4980 chunk 227 optimal weight: 6.9990 chunk 206 optimal weight: 6.9990 chunk 138 optimal weight: 0.0040 chunk 0 optimal weight: 60.0000 chunk 30 optimal weight: 30.0000 chunk 135 optimal weight: 8.9990 overall best weight: 2.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 HIS D 463 GLN ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 386 ASN ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.116772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.077162 restraints weight = 77138.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.079668 restraints weight = 42721.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.080129 restraints weight = 29571.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.080916 restraints weight = 23680.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.080838 restraints weight = 23185.136| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22242 Z= 0.150 Angle : 0.730 14.536 30412 Z= 0.356 Chirality : 0.049 0.725 3600 Planarity : 0.005 0.086 3863 Dihedral : 6.151 59.197 3010 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 4.37 % Allowed : 19.78 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.68 (0.16), residues: 2737 helix: -1.01 (0.32), residues: 228 sheet: -0.75 (0.16), residues: 1038 loop : -1.37 (0.16), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 461 TYR 0.024 0.002 TYR K 455 PHE 0.036 0.002 PHE S 87 TRP 0.012 0.001 TRP K 528 HIS 0.006 0.001 HIS C 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (22196) covalent geometry : angle 0.70967 / 0.35 (30314) SS BOND : bond 0.00464 / 0.24 ( 34) SS BOND : angle 1.26328 / 0.76 ( 68) hydrogen bonds : bond 0.03521 / 2.37 ( 647) hydrogen bonds : angle 5.71389 / 4.07 ( 1941) Misc. bond : bond 0.00112 / 0.06 ( 2) link_NAG-ASN : bond 0.00755 / 0.44 ( 10) link_NAG-ASN : angle 5.32633 / 3.69 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 269 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 ASP cc_start: 0.6491 (t0) cc_final: 0.6072 (p0) REVERT: A 455 TYR cc_start: 0.8016 (m-10) cc_final: 0.7646 (m-10) REVERT: A 550 ARG cc_start: 0.8367 (mmm160) cc_final: 0.7807 (mmm160) REVERT: A 558 LYS cc_start: 0.7798 (mmmt) cc_final: 0.7283 (ttpt) REVERT: B 415 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8320 (mp0) REVERT: B 489 MET cc_start: 0.7949 (mmt) cc_final: 0.7660 (mmm) REVERT: C 395 ASN cc_start: 0.4859 (t0) cc_final: 0.4438 (m-40) REVERT: D 429 THR cc_start: 0.4413 (OUTLIER) cc_final: 0.4197 (m) REVERT: D 510 GLN cc_start: 0.8343 (pp30) cc_final: 0.8078 (pp30) REVERT: D 534 TYR cc_start: 0.8651 (m-80) cc_final: 0.8266 (m-80) REVERT: E 465 ASN cc_start: 0.8531 (m-40) cc_final: 0.8240 (m-40) REVERT: E 483 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7695 (t0) REVERT: J 19 SER cc_start: 0.8468 (OUTLIER) cc_final: 0.8068 (p) REVERT: K 347 VAL cc_start: 0.0096 (OUTLIER) cc_final: -0.0293 (m) REVERT: K 483 ASP cc_start: 0.8203 (t0) cc_final: 0.7943 (t0) REVERT: K 506 MET cc_start: 0.7687 (mpp) cc_final: 0.7471 (mpp) REVERT: K 568 MET cc_start: 0.5861 (pmm) cc_final: 0.5470 (pmm) REVERT: R 36 LYS cc_start: 0.7275 (tptt) cc_final: 0.6816 (tppt) REVERT: U 42 MET cc_start: 0.6893 (tpp) cc_final: 0.6677 (tpt) REVERT: U 66 ASN cc_start: 0.7904 (p0) cc_final: 0.7365 (t0) REVERT: V 83 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7213 (mtm180) REVERT: V 87 PHE cc_start: 0.8081 (t80) cc_final: 0.7565 (t80) outliers start: 108 outliers final: 88 residues processed: 360 average time/residue: 0.1423 time to fit residues: 82.6058 Evaluate side-chains 348 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 254 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain C residue 358 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain D residue 348 PHE Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 563 ASN Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 430 HIS Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 487 GLN Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 533 THR Chi-restraints excluded: chain F residue 553 ASP Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 394 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 522 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 63 HIS Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 375 TYR Chi-restraints excluded: chain K residue 474 CYS Chi-restraints excluded: chain K residue 475 LEU Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 528 TRP Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain K residue 567 VAL Chi-restraints excluded: chain L residue 454 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 562 TYR Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 122 VAL Chi-restraints excluded: chain V residue 46 ILE Chi-restraints excluded: chain V residue 83 ARG Chi-restraints excluded: chain V residue 118 VAL Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 123 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 239 optimal weight: 7.9990 chunk 254 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 30 optimal weight: 30.0000 chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 87 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 55 optimal weight: 0.3980 chunk 195 optimal weight: 20.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.116728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.075846 restraints weight = 75954.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.078431 restraints weight = 38999.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.079974 restraints weight = 26922.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.080865 restraints weight = 22035.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.081234 restraints weight = 19768.790| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22242 Z= 0.137 Angle : 0.720 14.125 30412 Z= 0.351 Chirality : 0.049 0.651 3600 Planarity : 0.005 0.085 3863 Dihedral : 5.920 59.221 3010 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 4.45 % Allowed : 20.39 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.60 (0.16), residues: 2737 helix: -0.94 (0.32), residues: 228 sheet: -0.68 (0.16), residues: 1046 loop : -1.34 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 461 TYR 0.023 0.002 TYR K 455 PHE 0.032 0.002 PHE H 516 TRP 0.013 0.001 TRP H 528 HIS 0.006 0.001 HIS E 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (22196) covalent geometry : angle 0.70110 / 0.35 (30314) SS BOND : bond 0.00441 / 0.22 ( 34) SS BOND : angle 1.14909 / 0.70 ( 68) hydrogen bonds : bond 0.03443 / 2.30 ( 647) hydrogen bonds : angle 5.55750 / 3.95 ( 1941) Misc. bond : bond 0.00440 / 0.23 ( 2) link_NAG-ASN : bond 0.00803 / 0.50 ( 10) link_NAG-ASN : angle 5.14472 / 3.56 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 270 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 ASP cc_start: 0.6645 (t0) cc_final: 0.6194 (p0) REVERT: A 455 TYR cc_start: 0.8081 (m-10) cc_final: 0.7667 (m-10) REVERT: A 550 ARG cc_start: 0.8336 (mmm160) cc_final: 0.7796 (mmm160) REVERT: B 415 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8268 (mp0) REVERT: B 489 MET cc_start: 0.8065 (mmt) cc_final: 0.7688 (mmm) REVERT: C 395 ASN cc_start: 0.4847 (t0) cc_final: 0.4403 (m-40) REVERT: D 370 THR cc_start: 0.2267 (OUTLIER) cc_final: 0.1954 (m) REVERT: D 429 THR cc_start: 0.4434 (OUTLIER) cc_final: 0.4214 (m) REVERT: D 510 GLN cc_start: 0.8463 (pp30) cc_final: 0.8174 (pp30) REVERT: D 534 TYR cc_start: 0.8548 (m-80) cc_final: 0.8274 (m-80) REVERT: E 465 ASN cc_start: 0.8639 (m-40) cc_final: 0.8423 (m-40) REVERT: E 483 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.7601 (t0) REVERT: J 19 SER cc_start: 0.8606 (OUTLIER) cc_final: 0.8224 (p) REVERT: K 347 VAL cc_start: 0.0063 (OUTLIER) cc_final: -0.0325 (m) REVERT: K 453 ASP cc_start: 0.8486 (m-30) cc_final: 0.7478 (p0) REVERT: K 483 ASP cc_start: 0.8190 (t0) cc_final: 0.7880 (t0) REVERT: K 487 GLN cc_start: 0.8216 (tm-30) cc_final: 0.7468 (tm-30) REVERT: K 506 MET cc_start: 0.7774 (mpp) cc_final: 0.7532 (mpp) REVERT: K 568 MET cc_start: 0.5867 (pmm) cc_final: 0.5463 (pmm) REVERT: R 36 LYS cc_start: 0.7237 (tptt) cc_final: 0.6788 (tppt) REVERT: U 42 MET cc_start: 0.6727 (tpp) cc_final: 0.6464 (tpp) REVERT: U 66 ASN cc_start: 0.7878 (p0) cc_final: 0.7397 (t0) REVERT: V 87 PHE cc_start: 0.7836 (t80) cc_final: 0.7352 (t80) outliers start: 110 outliers final: 85 residues processed: 361 average time/residue: 0.1433 time to fit residues: 83.7132 Evaluate side-chains 346 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 255 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 515 TYR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 358 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain D residue 348 PHE Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 430 HIS Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 487 GLN Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 533 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 553 ASP Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 486 VAL Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 394 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 522 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 63 HIS Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 375 TYR Chi-restraints excluded: chain K residue 474 CYS Chi-restraints excluded: chain K residue 475 LEU Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 528 TRP Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain K residue 567 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 562 TYR Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 122 VAL Chi-restraints excluded: chain V residue 46 ILE Chi-restraints excluded: chain V residue 85 ASN Chi-restraints excluded: chain V residue 118 VAL Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 123 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 267 optimal weight: 10.0000 chunk 110 optimal weight: 30.0000 chunk 163 optimal weight: 20.0000 chunk 154 optimal weight: 50.0000 chunk 134 optimal weight: 40.0000 chunk 125 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 180 optimal weight: 9.9990 chunk 157 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 222 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 63 HIS L 386 ASN ** U 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.114336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.073409 restraints weight = 74711.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.075777 restraints weight = 39081.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.077221 restraints weight = 27228.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.077912 restraints weight = 22358.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.078467 restraints weight = 20200.684| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 22242 Z= 0.233 Angle : 0.784 16.646 30412 Z= 0.385 Chirality : 0.050 0.525 3600 Planarity : 0.005 0.086 3863 Dihedral : 5.955 58.694 3005 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 4.45 % Allowed : 20.47 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.64 (0.16), residues: 2737 helix: -0.62 (0.34), residues: 220 sheet: -0.77 (0.16), residues: 1032 loop : -1.36 (0.16), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 461 TYR 0.022 0.002 TYR K 455 PHE 0.032 0.002 PHE H 516 TRP 0.015 0.002 TRP K 528 HIS 0.005 0.001 HIS E 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.23 (22196) covalent geometry : angle 0.76480 / 0.38 (30314) SS BOND : bond 0.00559 / 0.29 ( 34) SS BOND : angle 1.44053 / 0.92 ( 68) hydrogen bonds : bond 0.03660 / 2.47 ( 647) hydrogen bonds : angle 5.81458 / 4.13 ( 1941) Misc. bond : bond 0.00028 / 0.01 ( 2) link_NAG-ASN : bond 0.00789 / 0.43 ( 10) link_NAG-ASN : angle 5.25266 / 3.85 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 251 time to evaluate : 0.996 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: symmetry clash revert: symmetry clash REVERT: A 376 ASP cc_start: 0.6622 (t0) cc_final: 0.6151 (p0) REVERT: A 455 TYR cc_start: 0.8001 (m-10) cc_final: 0.7564 (m-10) REVERT: A 550 ARG cc_start: 0.8352 (mmm160) cc_final: 0.7772 (mmm160) REVERT: B 415 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8273 (mp0) REVERT: C 395 ASN cc_start: 0.4934 (t0) cc_final: 0.4656 (t0) REVERT: D 370 THR cc_start: 0.2251 (OUTLIER) cc_final: 0.2034 (m) REVERT: D 429 THR cc_start: 0.4442 (OUTLIER) cc_final: 0.4201 (m) REVERT: D 510 GLN cc_start: 0.8425 (pp30) cc_final: 0.8100 (pp30) REVERT: D 534 TYR cc_start: 0.8827 (m-80) cc_final: 0.8337 (m-80) REVERT: J 19 SER cc_start: 0.8738 (OUTLIER) cc_final: 0.8420 (p) REVERT: K 483 ASP cc_start: 0.8250 (t0) cc_final: 0.7953 (t0) REVERT: K 506 MET cc_start: 0.7711 (mpp) cc_final: 0.7485 (mpp) REVERT: K 568 MET cc_start: 0.6151 (pmm) cc_final: 0.5859 (pmm) REVERT: R 36 LYS cc_start: 0.7208 (tptt) cc_final: 0.6899 (tptt) REVERT: U 42 MET cc_start: 0.6894 (tpp) cc_final: 0.6618 (tpp) REVERT: V 87 PHE cc_start: 0.7831 (t80) cc_final: 0.7314 (t80) outliers start: 110 outliers final: 90 residues processed: 347 average time/residue: 0.1378 time to fit residues: 78.2112 Evaluate side-chains 341 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 247 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 358 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain D residue 348 PHE Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 430 HIS Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 487 GLN Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 533 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 553 ASP Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 486 VAL Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 394 THR Chi-restraints excluded: chain H residue 449 LEU Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 522 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 474 CYS Chi-restraints excluded: chain K residue 475 LEU Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 528 TRP Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain L residue 454 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 562 TYR Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 122 VAL Chi-restraints excluded: chain V residue 26 GLU Chi-restraints excluded: chain V residue 85 ASN Chi-restraints excluded: chain V residue 118 VAL Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 123 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 171 optimal weight: 4.9990 chunk 190 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 235 optimal weight: 9.9990 chunk 91 optimal weight: 30.0000 chunk 121 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 94 optimal weight: 30.0000 chunk 137 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 175 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 393 HIS ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 465 ASN ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.115991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.075113 restraints weight = 74609.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.077634 restraints weight = 37558.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.079161 restraints weight = 25693.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.080045 restraints weight = 20916.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.080428 restraints weight = 18706.920| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22242 Z= 0.144 Angle : 0.742 14.067 30412 Z= 0.362 Chirality : 0.048 0.458 3600 Planarity : 0.005 0.085 3863 Dihedral : 5.627 57.998 3004 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 3.48 % Allowed : 21.72 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.53 (0.16), residues: 2737 helix: -0.83 (0.32), residues: 235 sheet: -0.61 (0.16), residues: 1025 loop : -1.31 (0.16), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 514 TYR 0.025 0.002 TYR K 455 PHE 0.033 0.002 PHE H 516 TRP 0.013 0.001 TRP K 528 HIS 0.005 0.001 HIS L 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (22196) covalent geometry : angle 0.72467 / 0.36 (30314) SS BOND : bond 0.00468 / 0.23 ( 34) SS BOND : angle 1.18408 / 0.74 ( 68) hydrogen bonds : bond 0.03438 / 2.30 ( 647) hydrogen bonds : angle 5.53713 / 3.93 ( 1941) Misc. bond : bond 0.00044 / 0.02 ( 2) link_NAG-ASN : bond 0.00675 / 0.37 ( 10) link_NAG-ASN : angle 4.93825 / 3.44 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 269 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 ASP cc_start: 0.6612 (t0) cc_final: 0.6156 (p0) REVERT: A 455 TYR cc_start: 0.8104 (m-10) cc_final: 0.7757 (m-10) REVERT: A 550 ARG cc_start: 0.8423 (mmm160) cc_final: 0.7798 (mmm160) REVERT: B 415 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8302 (mp0) REVERT: B 489 MET cc_start: 0.8083 (mmt) cc_final: 0.7757 (mmm) REVERT: C 395 ASN cc_start: 0.4948 (t0) cc_final: 0.4424 (m-40) REVERT: C 561 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8092 (mm) REVERT: D 370 THR cc_start: 0.2220 (OUTLIER) cc_final: 0.2002 (m) REVERT: D 429 THR cc_start: 0.4268 (OUTLIER) cc_final: 0.4063 (m) REVERT: D 510 GLN cc_start: 0.8524 (pp30) cc_final: 0.8180 (pp30) REVERT: D 534 TYR cc_start: 0.8615 (m-80) cc_final: 0.8249 (m-80) REVERT: F 568 MET cc_start: 0.7946 (tmm) cc_final: 0.7377 (tpp) REVERT: J 19 SER cc_start: 0.8620 (OUTLIER) cc_final: 0.8268 (p) REVERT: J 46 ARG cc_start: 0.7927 (mmt180) cc_final: 0.7135 (mmm160) REVERT: K 347 VAL cc_start: 0.0048 (OUTLIER) cc_final: -0.0360 (m) REVERT: K 453 ASP cc_start: 0.8516 (m-30) cc_final: 0.7569 (p0) REVERT: K 483 ASP cc_start: 0.8203 (t0) cc_final: 0.7881 (t0) REVERT: K 487 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7461 (tm-30) REVERT: K 506 MET cc_start: 0.7842 (mpp) cc_final: 0.7599 (mpp) REVERT: K 568 MET cc_start: 0.5996 (pmm) cc_final: 0.5546 (pmm) REVERT: R 36 LYS cc_start: 0.7227 (tptt) cc_final: 0.6766 (tppt) REVERT: U 42 MET cc_start: 0.6887 (tpp) cc_final: 0.6627 (tpp) REVERT: U 66 ASN cc_start: 0.7935 (p0) cc_final: 0.7418 (t0) REVERT: V 26 GLU cc_start: 0.6168 (OUTLIER) cc_final: 0.5872 (mm-30) REVERT: V 87 PHE cc_start: 0.7671 (t80) cc_final: 0.7171 (t80) outliers start: 86 outliers final: 72 residues processed: 341 average time/residue: 0.1386 time to fit residues: 77.0613 Evaluate side-chains 335 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 256 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 358 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 348 PHE Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 487 GLN Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 533 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 553 ASP Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 486 VAL Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 394 THR Chi-restraints excluded: chain H residue 449 LEU Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 522 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 474 CYS Chi-restraints excluded: chain K residue 475 LEU Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 528 TRP Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 545 ASN 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 562 TYR Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 122 VAL Chi-restraints excluded: chain V residue 26 GLU Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 123 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 80 optimal weight: 0.0040 chunk 2 optimal weight: 30.0000 chunk 51 optimal weight: 6.9990 chunk 110 optimal weight: 40.0000 chunk 67 optimal weight: 8.9990 chunk 245 optimal weight: 0.8980 chunk 161 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 193 optimal weight: 0.2980 chunk 107 optimal weight: 6.9990 chunk 137 optimal weight: 30.0000 overall best weight: 2.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.114942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.073907 restraints weight = 74484.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.076380 restraints weight = 37724.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.077874 restraints weight = 25970.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.078725 restraints weight = 21185.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.079089 restraints weight = 19001.515| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22242 Z= 0.179 Angle : 0.758 13.816 30412 Z= 0.370 Chirality : 0.048 0.473 3600 Planarity : 0.005 0.085 3863 Dihedral : 5.638 57.364 3002 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 3.64 % Allowed : 21.44 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.55 (0.16), residues: 2737 helix: -0.72 (0.33), residues: 232 sheet: -0.66 (0.16), residues: 1017 loop : -1.30 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 461 TYR 0.030 0.002 TYR H 375 PHE 0.031 0.002 PHE H 516 TRP 0.014 0.001 TRP K 528 HIS 0.005 0.001 HIS F 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (22196) covalent geometry : angle 0.74129 / 0.37 (30314) SS BOND : bond 0.00462 / 0.24 ( 34) SS BOND : angle 1.28611 / 0.81 ( 68) hydrogen bonds : bond 0.03461 / 2.31 ( 647) hydrogen bonds : angle 5.58436 / 3.96 ( 1941) Misc. bond : bond 0.00041 / 0.02 ( 2) link_NAG-ASN : bond 0.00658 / 0.36 ( 10) link_NAG-ASN : angle 4.80824 / 3.38 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5103.62 seconds wall clock time: 88 minutes 57.68 seconds (5337.68 seconds total)