Starting phenix.real_space_refine on Wed Jun 18 22:51:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ytd_34086/06_2025/7ytd_34086.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ytd_34086/06_2025/7ytd_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ytd_34086/06_2025/7ytd_34086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ytd_34086/06_2025/7ytd_34086.map" model { file = "/net/cci-nas-00/data/ceres_data/7ytd_34086/06_2025/7ytd_34086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ytd_34086/06_2025/7ytd_34086.cif" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 15.50, per 1000 atoms: 0.71 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: 5.98 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 3.70 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: 8.11 Time building geometry restraints manager: 7.09 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 - 18.66: 12352 18.66 - 37.31: 995 37.31 - 55.97: 260 55.97 - 74.63: 39 74.63 - 93.28: 21 Dihedral angle restraints: 13667 sinusoidal: 5544 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 13664 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 568 or res \ id 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 568 or res \ id 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 568 or resid 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 568 or res \ id 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: 2.220 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: 1.110 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 56.200 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 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 : 14.871 93.281 8281 Min Nonbonded Distance : 1.252 Molprobity Statistics. All-atom Clashscore : 29.57 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (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 TRP 0.025 0.002 TRP K 528 HIS 0.009 0.001 HIS F 518 PHE 0.019 0.002 PHE H 516 TYR 0.027 0.002 TYR B 455 ARG 0.012 0.000 ARG U 112 Details of bonding type rmsd link_NAG-ASN : bond 0.16107 ( 10) link_NAG-ASN : angle 16.02283 ( 30) hydrogen bonds : bond 0.18078 ( 647) hydrogen bonds : angle 8.26643 ( 1941) SS BOND : bond 0.02779 ( 34) SS BOND : angle 4.52527 ( 68) covalent geometry : bond 0.00516 (22196) covalent geometry : angle 0.96340 (30314) Misc. bond : bond 0.17356 ( 2) *********************** 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 : 2.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: 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: 0.5687 (t0) cc_final: 0.5277 (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: 0.7734 (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: 0.7602 (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: 0.8047 (tpp) REVERT: S 46 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8696 (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: 0.7511 (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: 0.3466 time to fit residues: 249.3247 Evaluate side-chains 360 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 282 time to evaluate : 2.729 ------------------------------------------------------------------------------- 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 227 optimal weight: 4.9990 chunk 204 optimal weight: 0.9980 chunk 113 optimal weight: 40.0000 chunk 69 optimal weight: 30.0000 chunk 138 optimal weight: 40.0000 chunk 109 optimal weight: 0.6980 chunk 211 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 157 optimal weight: 40.0000 chunk 245 optimal weight: 10.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 ASN 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 430 HIS ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.117346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.077819 restraints weight = 76281.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.080380 restraints weight = 44935.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.080875 restraints weight = 27986.959| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 22242 Z= 0.202 Angle : 0.796 17.351 30412 Z= 0.391 Chirality : 0.051 0.618 3600 Planarity : 0.005 0.082 3863 Dihedral : 9.553 103.692 3346 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.93 % Favored : 92.00 % Rotamer: Outliers : 3.64 % Allowed : 11.73 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.16), residues: 2737 helix: -1.31 (0.32), residues: 218 sheet: -0.92 (0.16), residues: 1057 loop : -1.49 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 528 HIS 0.007 0.001 HIS C 430 PHE 0.022 0.002 PHE B 354 TYR 0.020 0.002 TYR H 375 ARG 0.009 0.001 ARG S 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00801 ( 10) link_NAG-ASN : angle 6.09337 ( 30) hydrogen bonds : bond 0.04356 ( 647) hydrogen bonds : angle 6.52411 ( 1941) SS BOND : bond 0.00616 ( 34) SS BOND : angle 1.54383 ( 68) covalent geometry : bond 0.00451 (22196) covalent geometry : angle 0.77007 (30314) Misc. bond : bond 0.00164 ( 2) *********************** 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 398 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 308 time to evaluate : 2.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7851 (tp) REVERT: C 395 ASN cc_start: 0.5291 (t0) cc_final: 0.4846 (t0) REVERT: C 561 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7966 (mm) REVERT: D 424 PHE cc_start: 0.8673 (m-80) cc_final: 0.8413 (m-80) REVERT: D 510 GLN cc_start: 0.8289 (pp30) cc_final: 0.8056 (pp30) REVERT: E 461 ARG cc_start: 0.8137 (mmm160) cc_final: 0.7866 (mmm160) REVERT: E 483 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.7591 (t0) REVERT: F 493 GLN cc_start: 0.8286 (pp30) cc_final: 0.7968 (pp30) REVERT: F 508 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8533 (tm-30) REVERT: J 8 VAL cc_start: 0.4545 (p) cc_final: 0.4173 (t) REVERT: J 37 ILE cc_start: 0.7177 (mm) cc_final: 0.6899 (mm) REVERT: J 66 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8215 (p0) REVERT: K 463 GLN cc_start: 0.8484 (tp-100) cc_final: 0.8207 (tp-100) REVERT: K 475 LEU cc_start: 0.9081 (tp) cc_final: 0.8819 (tp) REVERT: K 483 ASP cc_start: 0.8163 (t0) cc_final: 0.7911 (t0) REVERT: L 489 MET cc_start: 0.7572 (ttm) cc_final: 0.7287 (tpp) REVERT: R 36 LYS cc_start: 0.7328 (tptt) cc_final: 0.6962 (tppt) REVERT: R 52 MET cc_start: 0.8493 (tpt) cc_final: 0.8240 (tpp) REVERT: S 51 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6357 (mp0) REVERT: S 94 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7752 (tp) REVERT: U 26 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7530 (tp30) REVERT: U 66 ASN cc_start: 0.8218 (p0) cc_final: 0.7659 (t0) REVERT: U 87 PHE cc_start: 0.8208 (t80) cc_final: 0.7892 (t80) REVERT: U 120 LEU cc_start: 0.8981 (pp) cc_final: 0.8737 (pp) REVERT: V 26 GLU cc_start: 0.6220 (OUTLIER) cc_final: 0.5993 (tt0) REVERT: V 41 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8210 (tm-30) REVERT: V 81 TYR cc_start: 0.7044 (OUTLIER) cc_final: 0.5916 (m-80) REVERT: V 83 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.6741 (mtm180) REVERT: V 87 PHE cc_start: 0.8106 (t80) cc_final: 0.7624 (t80) outliers start: 90 outliers final: 56 residues processed: 377 average time/residue: 0.3197 time to fit residues: 187.4363 Evaluate side-chains 338 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 272 time to evaluate : 2.473 ------------------------------------------------------------------------------- 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 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 19 SER 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 199 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 123 optimal weight: 0.0770 chunk 63 optimal weight: 6.9990 chunk 227 optimal weight: 0.0870 chunk 141 optimal weight: 0.5980 chunk 4 optimal weight: 40.0000 chunk 44 optimal weight: 40.0000 chunk 161 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 overall best weight: 0.9318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 GLN B 529 ASN D 450 HIS ** F 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 545 ASN ** H 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 529 ASN ** H 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 463 GLN ** S 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.118920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.078711 restraints weight = 75693.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.081205 restraints weight = 40331.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.082686 restraints weight = 28363.334| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22242 Z= 0.126 Angle : 0.722 18.225 30412 Z= 0.351 Chirality : 0.049 0.670 3600 Planarity : 0.005 0.085 3863 Dihedral : 7.810 82.524 3273 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.12 % Favored : 92.84 % Rotamer: Outliers : 3.80 % Allowed : 14.36 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.16), residues: 2737 helix: -0.99 (0.33), residues: 216 sheet: -0.81 (0.16), residues: 1049 loop : -1.53 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 528 HIS 0.010 0.001 HIS E 450 PHE 0.024 0.002 PHE H 516 TYR 0.017 0.002 TYR D 534 ARG 0.006 0.000 ARG S 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00626 ( 10) link_NAG-ASN : angle 5.91362 ( 30) hydrogen bonds : bond 0.03819 ( 647) hydrogen bonds : angle 5.96858 ( 1941) SS BOND : bond 0.00434 ( 34) SS BOND : angle 1.17754 ( 68) covalent geometry : bond 0.00279 (22196) covalent geometry : angle 0.69686 (30314) Misc. bond : bond 0.00325 ( 2) *********************** 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 405 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 311 time to evaluate : 2.797 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: symmetry clash revert: symmetry clash REVERT: A 376 ASP cc_start: 0.6507 (t0) cc_final: 0.6031 (p0) REVERT: A 449 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7748 (tp) REVERT: A 455 TYR cc_start: 0.8003 (m-10) cc_final: 0.7613 (m-10) REVERT: A 475 LEU cc_start: 0.9297 (tp) cc_final: 0.9085 (tp) REVERT: B 415 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8270 (mp0) REVERT: C 395 ASN cc_start: 0.5499 (t0) cc_final: 0.5050 (t0) REVERT: C 521 LEU cc_start: 0.9150 (tt) cc_final: 0.8941 (tt) REVERT: D 424 PHE cc_start: 0.8432 (m-80) cc_final: 0.8136 (m-10) REVERT: D 510 GLN cc_start: 0.8315 (pp30) cc_final: 0.8111 (pp30) REVERT: D 534 TYR cc_start: 0.8654 (m-80) cc_final: 0.8173 (m-80) REVERT: E 354 PHE cc_start: 0.8604 (t80) cc_final: 0.8221 (t80) REVERT: E 461 ARG cc_start: 0.8092 (mmm160) cc_final: 0.7766 (mmm160) REVERT: E 465 ASN cc_start: 0.8448 (m-40) cc_final: 0.7441 (m-40) REVERT: E 483 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.7760 (t0) REVERT: E 568 MET cc_start: 0.6550 (tmm) cc_final: 0.6156 (ppp) REVERT: F 461 ARG cc_start: 0.8122 (mmm160) cc_final: 0.7761 (mmm160) REVERT: H 532 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6893 (mm-30) REVERT: J 66 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.8203 (p0) REVERT: J 67 LEU cc_start: 0.6981 (mp) cc_final: 0.6775 (mp) REVERT: K 463 GLN cc_start: 0.8565 (tp40) cc_final: 0.8231 (tp-100) REVERT: K 483 ASP cc_start: 0.8084 (t0) cc_final: 0.7733 (t0) REVERT: L 463 GLN cc_start: 0.8077 (pt0) cc_final: 0.7854 (pt0) REVERT: L 489 MET cc_start: 0.7613 (ttm) cc_final: 0.7259 (tpp) REVERT: L 521 LEU cc_start: 0.7549 (tp) cc_final: 0.6535 (mt) REVERT: R 36 LYS cc_start: 0.7179 (tptt) cc_final: 0.6829 (tppt) REVERT: R 52 MET cc_start: 0.8415 (tpt) cc_final: 0.8153 (tpp) REVERT: S 51 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6480 (mp0) REVERT: U 22 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7410 (tm-30) REVERT: U 26 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7647 (tm-30) REVERT: U 42 MET cc_start: 0.6914 (tpp) cc_final: 0.6712 (tpp) REVERT: U 66 ASN cc_start: 0.8134 (p0) cc_final: 0.7741 (t0) REVERT: U 87 PHE cc_start: 0.7982 (t80) cc_final: 0.7772 (t80) REVERT: U 120 LEU cc_start: 0.8807 (pp) cc_final: 0.8437 (pp) REVERT: V 87 PHE cc_start: 0.7934 (t80) cc_final: 0.7423 (t80) outliers start: 94 outliers final: 54 residues processed: 386 average time/residue: 0.3097 time to fit residues: 188.9096 Evaluate side-chains 343 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 281 time to evaluate : 2.667 ------------------------------------------------------------------------------- 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 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 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 415 GLU 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 551 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 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 G residue 510 GLN Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 532 GLU 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 528 TRP Chi-restraints excluded: chain K residue 567 VAL 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 108 MET 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 122 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 79 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 GLN F 419 ASN ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 463 GLN ** 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 = 0.4228 r_free = 0.4228 target = 0.115512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.074537 restraints weight = 76732.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.076862 restraints weight = 41379.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.078266 restraints weight = 29353.315| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 22242 Z= 0.255 Angle : 0.775 14.844 30412 Z= 0.383 Chirality : 0.050 0.625 3600 Planarity : 0.005 0.084 3863 Dihedral : 7.427 89.889 3249 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 4.33 % Allowed : 15.94 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.16), residues: 2737 helix: -0.88 (0.33), residues: 221 sheet: -0.95 (0.16), residues: 1051 loop : -1.48 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 528 HIS 0.007 0.001 HIS H 540 PHE 0.025 0.002 PHE H 516 TYR 0.023 0.002 TYR E 455 ARG 0.012 0.001 ARG J 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00783 ( 10) link_NAG-ASN : angle 5.35473 ( 30) hydrogen bonds : bond 0.03952 ( 647) hydrogen bonds : angle 6.14248 ( 1941) SS BOND : bond 0.00609 ( 34) SS BOND : angle 1.49801 ( 68) covalent geometry : bond 0.00575 (22196) covalent geometry : angle 0.75397 (30314) Misc. bond : bond 0.00166 ( 2) *********************** 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 377 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 270 time to evaluate : 2.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 ASP cc_start: 0.6621 (t0) cc_final: 0.6140 (p0) REVERT: A 461 ARG cc_start: 0.8205 (tpm170) cc_final: 0.7963 (tpm170) REVERT: A 462 GLU cc_start: 0.8810 (pp20) cc_final: 0.8529 (pp20) REVERT: A 521 LEU cc_start: 0.8793 (tp) cc_final: 0.8574 (tt) REVERT: A 550 ARG cc_start: 0.8144 (mmm160) cc_final: 0.7827 (mmm160) REVERT: B 415 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8309 (mp0) REVERT: C 395 ASN cc_start: 0.5252 (t0) cc_final: 0.4905 (t0) REVERT: C 430 HIS cc_start: 0.4610 (OUTLIER) cc_final: 0.4395 (t70) REVERT: D 489 MET cc_start: 0.8497 (tpp) cc_final: 0.8285 (mmt) REVERT: D 510 GLN cc_start: 0.8439 (pp30) cc_final: 0.8192 (pp30) REVERT: E 461 ARG cc_start: 0.8222 (mmm160) cc_final: 0.7873 (mmm160) REVERT: E 465 ASN cc_start: 0.8573 (m-40) cc_final: 0.7618 (m-40) REVERT: E 568 MET cc_start: 0.6743 (tmm) cc_final: 0.6401 (ppp) REVERT: K 463 GLN cc_start: 0.8696 (tp40) cc_final: 0.8422 (tp-100) REVERT: K 483 ASP cc_start: 0.8184 (t0) cc_final: 0.7857 (t0) REVERT: L 489 MET cc_start: 0.7567 (ttm) cc_final: 0.7236 (tpp) REVERT: R 36 LYS cc_start: 0.7155 (tptt) cc_final: 0.6811 (tppt) REVERT: R 52 MET cc_start: 0.8364 (tpt) cc_final: 0.8114 (tpp) REVERT: S 51 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6619 (mp0) REVERT: S 52 MET cc_start: 0.8218 (ptt) cc_final: 0.7595 (ppp) REVERT: S 114 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7318 (ptpt) REVERT: U 26 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7724 (tm-30) REVERT: U 42 MET cc_start: 0.6978 (tpp) cc_final: 0.6762 (tpt) REVERT: U 66 ASN cc_start: 0.8247 (p0) cc_final: 0.8036 (p0) REVERT: U 87 PHE cc_start: 0.7987 (t80) cc_final: 0.7750 (t80) REVERT: U 121 ASN cc_start: 0.8487 (p0) cc_final: 0.8226 (p0) REVERT: V 52 MET cc_start: 0.7589 (tpp) cc_final: 0.7350 (tpp) REVERT: V 87 PHE cc_start: 0.7871 (t80) cc_final: 0.7481 (t80) outliers start: 107 outliers final: 77 residues processed: 356 average time/residue: 0.3124 time to fit residues: 176.7372 Evaluate side-chains 332 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 250 time to evaluate : 2.433 ------------------------------------------------------------------------------- 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 549 GLU 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 566 LEU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 430 HIS 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 569 SER Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 568 MET Chi-restraints excluded: chain E residue 350 ILE 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 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 510 GLN Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain H residue 417 ASP 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 58 THR 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 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 L residue 476 VAL 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 108 MET 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 122 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 114 optimal weight: 9.9990 chunk 166 optimal weight: 3.9990 chunk 238 optimal weight: 10.0000 chunk 28 optimal weight: 40.0000 chunk 50 optimal weight: 0.0770 chunk 255 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 200 optimal weight: 9.9990 chunk 139 optimal weight: 6.9990 chunk 184 optimal weight: 20.0000 chunk 75 optimal weight: 30.0000 overall best weight: 3.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 400 HIS S 93 GLN ** 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 = 0.4241 r_free = 0.4241 target = 0.116326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.075540 restraints weight = 75921.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.077947 restraints weight = 40241.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.079415 restraints weight = 28355.007| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22242 Z= 0.184 Angle : 0.727 14.468 30412 Z= 0.358 Chirality : 0.049 0.646 3600 Planarity : 0.005 0.084 3863 Dihedral : 7.016 75.237 3238 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 4.05 % Allowed : 17.64 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.16), residues: 2737 helix: -1.10 (0.33), residues: 220 sheet: -0.86 (0.16), residues: 1056 loop : -1.42 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 528 HIS 0.009 0.001 HIS E 450 PHE 0.021 0.002 PHE H 516 TYR 0.022 0.002 TYR K 455 ARG 0.004 0.000 ARG D 461 Details of bonding type rmsd link_NAG-ASN : bond 0.00684 ( 10) link_NAG-ASN : angle 5.30702 ( 30) hydrogen bonds : bond 0.03673 ( 647) hydrogen bonds : angle 5.87523 ( 1941) SS BOND : bond 0.00523 ( 34) SS BOND : angle 1.26515 ( 68) covalent geometry : bond 0.00420 (22196) covalent geometry : angle 0.70586 (30314) Misc. bond : bond 0.00047 ( 2) *********************** 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 375 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 275 time to evaluate : 2.846 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: symmetry clash revert: symmetry clash REVERT: A 376 ASP cc_start: 0.6662 (t0) cc_final: 0.6184 (p0) REVERT: A 455 TYR cc_start: 0.8028 (m-10) cc_final: 0.7648 (m-10) REVERT: A 461 ARG cc_start: 0.8170 (tpm170) cc_final: 0.7916 (tpm170) REVERT: A 462 GLU cc_start: 0.8891 (pp20) cc_final: 0.8509 (pp20) REVERT: A 550 ARG cc_start: 0.8315 (mmm160) cc_final: 0.7893 (mmm160) REVERT: B 415 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8325 (mp0) REVERT: C 395 ASN cc_start: 0.4970 (t0) cc_final: 0.4593 (t0) REVERT: C 430 HIS cc_start: 0.4509 (OUTLIER) cc_final: 0.4305 (t70) REVERT: D 510 GLN cc_start: 0.8455 (pp30) cc_final: 0.8196 (pp30) REVERT: E 461 ARG cc_start: 0.8220 (mmm160) cc_final: 0.7860 (mmm160) REVERT: E 465 ASN cc_start: 0.8584 (m-40) cc_final: 0.7609 (m-40) REVERT: E 483 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.7788 (t0) REVERT: F 461 ARG cc_start: 0.8167 (mmm160) cc_final: 0.7723 (mmm160) REVERT: F 463 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8406 (mm-40) REVERT: J 19 SER cc_start: 0.8553 (OUTLIER) cc_final: 0.8131 (p) REVERT: K 347 VAL cc_start: 0.0270 (OUTLIER) cc_final: -0.0074 (m) REVERT: K 463 GLN cc_start: 0.8706 (tp40) cc_final: 0.8472 (tp-100) REVERT: K 483 ASP cc_start: 0.8180 (t0) cc_final: 0.7823 (t0) REVERT: L 489 MET cc_start: 0.7408 (ttm) cc_final: 0.7132 (tpp) REVERT: L 568 MET cc_start: 0.5375 (mtt) cc_final: 0.5172 (mtm) REVERT: R 36 LYS cc_start: 0.7262 (tptt) cc_final: 0.6869 (tppt) REVERT: R 52 MET cc_start: 0.8333 (tpt) cc_final: 0.8093 (tpp) REVERT: S 51 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6377 (mp0) REVERT: S 69 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8070 (tptp) REVERT: S 114 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7501 (ptpt) REVERT: U 42 MET cc_start: 0.6945 (tpp) cc_final: 0.6675 (tpp) REVERT: U 66 ASN cc_start: 0.8207 (p0) cc_final: 0.7729 (t0) REVERT: U 87 PHE cc_start: 0.7963 (t80) cc_final: 0.7690 (t80) REVERT: V 52 MET cc_start: 0.7640 (tpp) cc_final: 0.7391 (tpp) REVERT: V 83 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.6791 (ptt-90) REVERT: V 87 PHE cc_start: 0.7884 (t80) cc_final: 0.7476 (t80) outliers start: 100 outliers final: 70 residues processed: 358 average time/residue: 0.3089 time to fit residues: 175.9767 Evaluate side-chains 329 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 250 time to evaluate : 2.450 ------------------------------------------------------------------------------- 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 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 430 HIS Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 533 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 514 ARG 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 518 HIS Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 363 THR 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 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 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 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 475 LEU Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 528 TRP Chi-restraints excluded: chain L residue 476 VAL 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 69 LYS Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 108 MET 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 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 28 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 57 optimal weight: 0.4980 chunk 128 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 52 optimal weight: 40.0000 chunk 32 optimal weight: 8.9990 chunk 249 optimal weight: 6.9990 chunk 145 optimal weight: 0.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 GLN ** E 450 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.116308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.076374 restraints weight = 76223.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.079449 restraints weight = 42638.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.079648 restraints weight = 26816.430| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22242 Z= 0.172 Angle : 0.717 15.010 30412 Z= 0.351 Chirality : 0.049 0.699 3600 Planarity : 0.005 0.083 3863 Dihedral : 6.696 59.018 3230 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 4.73 % Allowed : 18.69 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.16), residues: 2737 helix: -1.01 (0.33), residues: 219 sheet: -0.73 (0.16), residues: 1030 loop : -1.40 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 528 HIS 0.007 0.001 HIS A 518 PHE 0.022 0.002 PHE K 358 TYR 0.026 0.002 TYR B 455 ARG 0.004 0.000 ARG D 461 Details of bonding type rmsd link_NAG-ASN : bond 0.00809 ( 10) link_NAG-ASN : angle 5.25101 ( 30) hydrogen bonds : bond 0.03572 ( 647) hydrogen bonds : angle 5.76327 ( 1941) SS BOND : bond 0.00547 ( 34) SS BOND : angle 1.26236 ( 68) covalent geometry : bond 0.00393 (22196) covalent geometry : angle 0.69591 (30314) Misc. bond : bond 0.00030 ( 2) *********************** 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 389 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 272 time to evaluate : 2.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 PHE cc_start: 0.7536 (OUTLIER) cc_final: 0.7015 (p90) REVERT: A 376 ASP cc_start: 0.6448 (t0) cc_final: 0.6004 (p0) REVERT: A 455 TYR cc_start: 0.8024 (m-10) cc_final: 0.7590 (m-10) REVERT: A 462 GLU cc_start: 0.8880 (pp20) cc_final: 0.8426 (pp20) REVERT: A 550 ARG cc_start: 0.8394 (mmm160) cc_final: 0.7866 (mmm160) REVERT: B 415 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8329 (mp0) REVERT: B 515 TYR cc_start: 0.7694 (m-80) cc_final: 0.7433 (t80) REVERT: C 395 ASN cc_start: 0.4954 (t0) cc_final: 0.4533 (t0) REVERT: D 429 THR cc_start: 0.4425 (OUTLIER) cc_final: 0.4202 (m) REVERT: D 489 MET cc_start: 0.8363 (tpp) cc_final: 0.8101 (mmt) REVERT: D 510 GLN cc_start: 0.8436 (pp30) cc_final: 0.8159 (pp30) REVERT: E 461 ARG cc_start: 0.8239 (mmm160) cc_final: 0.8001 (mmm160) REVERT: E 465 ASN cc_start: 0.8589 (m-40) cc_final: 0.7603 (m-40) REVERT: E 483 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.7895 (t0) REVERT: F 366 THR cc_start: 0.8133 (OUTLIER) cc_final: 0.7930 (p) REVERT: F 430 HIS cc_start: 0.1584 (OUTLIER) cc_final: 0.1331 (m-70) REVERT: F 461 ARG cc_start: 0.8141 (mmm160) cc_final: 0.7890 (mmm160) REVERT: H 527 GLU cc_start: 0.8570 (tp30) cc_final: 0.8270 (tp30) REVERT: J 19 SER cc_start: 0.8372 (OUTLIER) cc_final: 0.7962 (p) REVERT: K 463 GLN cc_start: 0.8807 (tp40) cc_final: 0.8558 (tp-100) REVERT: K 483 ASP cc_start: 0.8207 (t0) cc_final: 0.7850 (t0) REVERT: L 489 MET cc_start: 0.7460 (ttm) cc_final: 0.7248 (tpp) REVERT: R 36 LYS cc_start: 0.7224 (tptt) cc_final: 0.6873 (tptt) REVERT: R 52 MET cc_start: 0.8478 (tpt) cc_final: 0.8129 (tpp) REVERT: R 69 LYS cc_start: 0.8693 (mmmm) cc_final: 0.8464 (mmmm) REVERT: R 73 LYS cc_start: 0.8239 (mttt) cc_final: 0.7899 (mttm) REVERT: S 69 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.8007 (tptp) REVERT: S 87 PHE cc_start: 0.8088 (m-80) cc_final: 0.7446 (m-80) REVERT: U 66 ASN cc_start: 0.8219 (p0) cc_final: 0.7730 (t0) REVERT: U 87 PHE cc_start: 0.8170 (t80) cc_final: 0.7837 (t80) REVERT: V 52 MET cc_start: 0.7581 (tpp) cc_final: 0.7331 (tpp) REVERT: V 83 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.6779 (ptt-90) REVERT: V 87 PHE cc_start: 0.8157 (t80) cc_final: 0.7699 (t80) outliers start: 117 outliers final: 87 residues processed: 369 average time/residue: 0.3085 time to fit residues: 179.3803 Evaluate side-chains 356 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 260 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 476 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 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 400 HIS 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 433 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain E residue 514 ARG 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 366 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 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 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 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 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 58 THR 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 475 LEU 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 567 VAL Chi-restraints excluded: chain L residue 476 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 46 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 69 LYS Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 108 MET 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 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 160 optimal weight: 50.0000 chunk 173 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 chunk 172 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 114 optimal weight: 0.0870 chunk 215 optimal weight: 30.0000 chunk 14 optimal weight: 7.9990 chunk 163 optimal weight: 40.0000 chunk 183 optimal weight: 1.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 HIS ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4269 r_free = 0.4269 target = 0.117976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.077639 restraints weight = 75704.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.080212 restraints weight = 39131.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.081771 restraints weight = 27099.616| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22242 Z= 0.125 Angle : 0.703 14.196 30412 Z= 0.343 Chirality : 0.048 0.649 3600 Planarity : 0.004 0.083 3863 Dihedral : 6.420 59.001 3226 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.92 % Allowed : 19.86 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.16), residues: 2737 helix: -1.04 (0.32), residues: 227 sheet: -0.63 (0.16), residues: 1042 loop : -1.41 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 528 HIS 0.005 0.001 HIS C 430 PHE 0.016 0.001 PHE F 516 TYR 0.023 0.002 TYR K 455 ARG 0.005 0.000 ARG D 461 Details of bonding type rmsd link_NAG-ASN : bond 0.00981 ( 10) link_NAG-ASN : angle 5.14127 ( 30) hydrogen bonds : bond 0.03390 ( 647) hydrogen bonds : angle 5.51578 ( 1941) SS BOND : bond 0.00411 ( 34) SS BOND : angle 1.01003 ( 68) covalent geometry : bond 0.00285 (22196) covalent geometry : angle 0.68372 (30314) Misc. bond : bond 0.00037 ( 2) *********************** 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 390 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 293 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 PHE cc_start: 0.7544 (OUTLIER) cc_final: 0.7016 (p90) REVERT: A 376 ASP cc_start: 0.6544 (t0) cc_final: 0.6091 (p0) REVERT: A 455 TYR cc_start: 0.8088 (m-10) cc_final: 0.7747 (m-10) REVERT: A 461 ARG cc_start: 0.8135 (tpm170) cc_final: 0.7903 (tpm170) REVERT: A 462 GLU cc_start: 0.8881 (pp20) cc_final: 0.8400 (pp20) REVERT: A 550 ARG cc_start: 0.8275 (mmm160) cc_final: 0.7784 (mmm160) REVERT: B 415 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8207 (mp0) REVERT: C 395 ASN cc_start: 0.4917 (t0) cc_final: 0.4572 (m-40) REVERT: D 429 THR cc_start: 0.4421 (OUTLIER) cc_final: 0.4208 (m) REVERT: D 510 GLN cc_start: 0.8374 (pp30) cc_final: 0.8131 (pp30) REVERT: E 354 PHE cc_start: 0.8683 (t80) cc_final: 0.8373 (t80) REVERT: E 461 ARG cc_start: 0.8138 (mmm160) cc_final: 0.7777 (mmm160) REVERT: E 465 ASN cc_start: 0.8589 (m-40) cc_final: 0.7670 (m-40) REVERT: E 483 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7674 (t0) REVERT: F 366 THR cc_start: 0.8271 (OUTLIER) cc_final: 0.8041 (p) REVERT: F 461 ARG cc_start: 0.8171 (mmm160) cc_final: 0.7706 (mmm160) REVERT: F 463 GLN cc_start: 0.8993 (mm-40) cc_final: 0.8330 (mm-40) REVERT: J 103 TYR cc_start: 0.8965 (m-10) cc_final: 0.8726 (m-10) REVERT: K 347 VAL cc_start: 0.0134 (OUTLIER) cc_final: -0.0208 (m) REVERT: K 463 GLN cc_start: 0.8682 (tp40) cc_final: 0.8459 (tp-100) REVERT: K 483 ASP cc_start: 0.8128 (t0) cc_final: 0.7856 (t0) REVERT: K 506 MET cc_start: 0.7679 (mpp) cc_final: 0.7392 (mpp) REVERT: L 452 PRO cc_start: 0.9025 (Cg_endo) cc_final: 0.8670 (Cg_exo) REVERT: R 52 MET cc_start: 0.8253 (tpt) cc_final: 0.7982 (tpp) REVERT: R 69 LYS cc_start: 0.8526 (mmmm) cc_final: 0.8279 (mmmm) REVERT: R 73 LYS cc_start: 0.8232 (mttt) cc_final: 0.7917 (mttm) REVERT: S 69 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7866 (tptp) REVERT: S 87 PHE cc_start: 0.7757 (m-80) cc_final: 0.7231 (m-80) REVERT: U 66 ASN cc_start: 0.8035 (p0) cc_final: 0.7635 (t0) REVERT: V 83 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.6715 (ptt-90) REVERT: V 87 PHE cc_start: 0.7795 (t80) cc_final: 0.7359 (t80) outliers start: 97 outliers final: 73 residues processed: 367 average time/residue: 0.3179 time to fit residues: 186.6455 Evaluate side-chains 351 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 270 time to evaluate : 2.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 B residue 415 GLU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 537 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 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain D residue 348 PHE Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 538 VAL 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 366 THR Chi-restraints excluded: chain F residue 454 VAL 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 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 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 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 567 VAL Chi-restraints excluded: chain L residue 476 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 55 SER 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 69 LYS Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 108 MET 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 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 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 81 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 161 optimal weight: 0.4980 chunk 262 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 234 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 193 optimal weight: 0.0970 chunk 60 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 ASN ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 63 HIS ** 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 = 0.4245 r_free = 0.4245 target = 0.116453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.076607 restraints weight = 76447.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.079835 restraints weight = 42805.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.079982 restraints weight = 26061.432| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22242 Z= 0.177 Angle : 0.726 15.641 30412 Z= 0.354 Chirality : 0.048 0.433 3600 Planarity : 0.005 0.083 3863 Dihedral : 6.375 58.978 3223 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 4.25 % Allowed : 20.27 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.16), residues: 2737 helix: -0.83 (0.32), residues: 234 sheet: -0.67 (0.16), residues: 1046 loop : -1.38 (0.16), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 528 HIS 0.004 0.001 HIS F 430 PHE 0.027 0.002 PHE H 516 TYR 0.023 0.002 TYR K 455 ARG 0.004 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 10) link_NAG-ASN : angle 5.11846 ( 30) hydrogen bonds : bond 0.03475 ( 647) hydrogen bonds : angle 5.60802 ( 1941) SS BOND : bond 0.00510 ( 34) SS BOND : angle 1.18291 ( 68) covalent geometry : bond 0.00406 (22196) covalent geometry : angle 0.70676 (30314) Misc. bond : bond 0.00022 ( 2) *********************** 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 374 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 269 time to evaluate : 2.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 PHE cc_start: 0.7546 (OUTLIER) cc_final: 0.7012 (p90) REVERT: A 376 ASP cc_start: 0.6453 (t0) cc_final: 0.5977 (p0) REVERT: A 455 TYR cc_start: 0.8118 (m-10) cc_final: 0.7775 (m-10) REVERT: A 461 ARG cc_start: 0.8230 (tpm170) cc_final: 0.7948 (tpm170) REVERT: A 462 GLU cc_start: 0.8920 (pp20) cc_final: 0.8392 (pp20) REVERT: A 550 ARG cc_start: 0.8409 (mmm160) cc_final: 0.7820 (mmm160) REVERT: B 415 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8361 (mp0) REVERT: B 515 TYR cc_start: 0.7656 (m-80) cc_final: 0.7441 (t80) REVERT: C 395 ASN cc_start: 0.4843 (t0) cc_final: 0.4569 (t0) REVERT: D 429 THR cc_start: 0.4365 (OUTLIER) cc_final: 0.4146 (m) REVERT: D 489 MET cc_start: 0.8334 (tpp) cc_final: 0.8122 (mmt) REVERT: D 510 GLN cc_start: 0.8407 (pp30) cc_final: 0.8136 (pp30) REVERT: E 461 ARG cc_start: 0.8292 (mmm160) cc_final: 0.7916 (mmm160) REVERT: E 465 ASN cc_start: 0.8667 (m-40) cc_final: 0.7753 (m-40) REVERT: E 483 ASP cc_start: 0.8358 (t0) cc_final: 0.7784 (t0) REVERT: F 365 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7024 (mm) REVERT: F 366 THR cc_start: 0.8127 (OUTLIER) cc_final: 0.7890 (p) REVERT: F 461 ARG cc_start: 0.8177 (mmm160) cc_final: 0.7887 (mmm160) REVERT: J 19 SER cc_start: 0.8370 (OUTLIER) cc_final: 0.7966 (p) REVERT: J 63 HIS cc_start: 0.7214 (OUTLIER) cc_final: 0.6836 (m-70) REVERT: K 347 VAL cc_start: -0.0003 (OUTLIER) cc_final: -0.0374 (m) REVERT: K 463 GLN cc_start: 0.8871 (tp40) cc_final: 0.8661 (tp-100) REVERT: K 483 ASP cc_start: 0.8215 (t0) cc_final: 0.7909 (t0) REVERT: K 506 MET cc_start: 0.7818 (mpp) cc_final: 0.7603 (mpp) REVERT: R 36 LYS cc_start: 0.7350 (tptt) cc_final: 0.6978 (tptt) REVERT: R 52 MET cc_start: 0.8529 (tpt) cc_final: 0.8142 (tpp) REVERT: S 69 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.8005 (tptp) REVERT: S 87 PHE cc_start: 0.8120 (m-80) cc_final: 0.7483 (m-80) REVERT: U 42 MET cc_start: 0.6952 (tpp) cc_final: 0.6721 (tpp) REVERT: V 83 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.6787 (ptt-90) REVERT: V 87 PHE cc_start: 0.8107 (t80) cc_final: 0.7658 (t80) outliers start: 105 outliers final: 88 residues processed: 356 average time/residue: 0.3134 time to fit residues: 177.8759 Evaluate side-chains 359 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 261 time to evaluate : 2.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 B residue 415 GLU 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 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 400 HIS Chi-restraints excluded: chain D residue 416 ASP 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 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 514 ARG 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 365 LEU Chi-restraints excluded: chain F residue 366 THR 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 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 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 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 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 567 VAL Chi-restraints excluded: chain L residue 476 VAL Chi-restraints excluded: chain L residue 506 MET 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 55 SER 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 69 LYS Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 108 MET 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 22 GLU Chi-restraints excluded: chain U residue 101 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 62 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 229 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 133 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 256 optimal weight: 8.9990 chunk 66 optimal weight: 30.0000 chunk 170 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.116821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.076325 restraints weight = 75448.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.078780 restraints weight = 39589.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.080241 restraints weight = 27616.433| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22242 Z= 0.140 Angle : 0.723 13.319 30412 Z= 0.351 Chirality : 0.048 0.470 3600 Planarity : 0.005 0.083 3863 Dihedral : 6.176 58.410 3223 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 4.09 % Allowed : 21.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.16), residues: 2737 helix: -0.82 (0.32), residues: 240 sheet: -0.60 (0.16), residues: 1046 loop : -1.36 (0.16), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 528 HIS 0.012 0.001 HIS J 63 PHE 0.027 0.001 PHE H 516 TYR 0.019 0.002 TYR C 375 ARG 0.005 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00546 ( 10) link_NAG-ASN : angle 4.80660 ( 30) hydrogen bonds : bond 0.03372 ( 647) hydrogen bonds : angle 5.50120 ( 1941) SS BOND : bond 0.00435 ( 34) SS BOND : angle 1.07827 ( 68) covalent geometry : bond 0.00324 (22196) covalent geometry : angle 0.70654 (30314) Misc. bond : bond 0.00021 ( 2) *********************** 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 383 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 282 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.7077 (p90) REVERT: A 376 ASP cc_start: 0.6750 (t0) cc_final: 0.6256 (p0) REVERT: A 455 TYR cc_start: 0.8139 (m-10) cc_final: 0.7806 (m-10) REVERT: A 461 ARG cc_start: 0.8213 (tpm170) cc_final: 0.7909 (tpm170) REVERT: A 462 GLU cc_start: 0.8891 (pp20) cc_final: 0.8351 (pp20) REVERT: A 550 ARG cc_start: 0.8407 (mmm160) cc_final: 0.7832 (mmm160) REVERT: B 415 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8280 (mp0) REVERT: B 515 TYR cc_start: 0.7740 (m-80) cc_final: 0.7425 (t80) REVERT: C 395 ASN cc_start: 0.4859 (t0) cc_final: 0.4456 (m-40) REVERT: D 370 THR cc_start: 0.2359 (OUTLIER) cc_final: 0.2007 (m) REVERT: D 429 THR cc_start: 0.4387 (OUTLIER) cc_final: 0.4169 (m) REVERT: D 510 GLN cc_start: 0.8471 (pp30) cc_final: 0.8192 (pp30) REVERT: E 461 ARG cc_start: 0.8313 (mmm160) cc_final: 0.7899 (mmm160) REVERT: E 465 ASN cc_start: 0.8686 (m-40) cc_final: 0.7808 (m-40) REVERT: E 483 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7674 (t0) REVERT: E 508 GLU cc_start: 0.8029 (tp30) cc_final: 0.7738 (tp30) REVERT: F 366 THR cc_start: 0.8217 (OUTLIER) cc_final: 0.8014 (p) REVERT: F 461 ARG cc_start: 0.8269 (mmm160) cc_final: 0.7736 (mmm160) REVERT: F 463 GLN cc_start: 0.9078 (mm-40) cc_final: 0.8458 (mm-40) REVERT: J 19 SER cc_start: 0.8497 (OUTLIER) cc_final: 0.8129 (p) REVERT: J 63 HIS cc_start: 0.7088 (m-70) cc_final: 0.6887 (m-70) REVERT: K 347 VAL cc_start: 0.0031 (OUTLIER) cc_final: -0.0359 (m) REVERT: K 453 ASP cc_start: 0.8487 (m-30) cc_final: 0.7517 (p0) REVERT: K 463 GLN cc_start: 0.8835 (tp40) cc_final: 0.8618 (tp-100) REVERT: K 483 ASP cc_start: 0.8197 (t0) cc_final: 0.7882 (t0) REVERT: K 506 MET cc_start: 0.7790 (mpp) cc_final: 0.7588 (mpp) REVERT: R 36 LYS cc_start: 0.7309 (tptt) cc_final: 0.6957 (tptt) REVERT: R 52 MET cc_start: 0.8340 (tpt) cc_final: 0.8023 (tpp) REVERT: S 69 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.8050 (tptp) REVERT: S 87 PHE cc_start: 0.7910 (m-80) cc_final: 0.7295 (m-80) REVERT: U 42 MET cc_start: 0.6974 (tpp) cc_final: 0.6712 (tpp) REVERT: V 83 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.6826 (ptt-90) REVERT: V 87 PHE cc_start: 0.7852 (t80) cc_final: 0.7426 (t80) outliers start: 101 outliers final: 84 residues processed: 362 average time/residue: 0.3281 time to fit residues: 191.2228 Evaluate side-chains 358 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 264 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 400 HIS Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 538 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 483 ASP Chi-restraints excluded: chain E residue 514 ARG 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 366 THR 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 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 462 GLU 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 58 THR 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 567 VAL Chi-restraints excluded: chain L residue 476 VAL Chi-restraints excluded: chain L residue 506 MET 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 55 SER 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 69 LYS Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 108 MET Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 19 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 61 optimal weight: 4.9990 chunk 214 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 98 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 450 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** J 63 HIS ** 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 = 0.4222 r_free = 0.4222 target = 0.115695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.075602 restraints weight = 73798.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.078026 restraints weight = 38125.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.079487 restraints weight = 26344.016| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22242 Z= 0.182 Angle : 0.750 13.105 30412 Z= 0.366 Chirality : 0.048 0.489 3600 Planarity : 0.005 0.083 3863 Dihedral : 6.170 57.702 3222 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 4.00 % Allowed : 21.40 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.16), residues: 2737 helix: -0.65 (0.33), residues: 226 sheet: -0.63 (0.16), residues: 1039 loop : -1.33 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 528 HIS 0.005 0.001 HIS C 430 PHE 0.027 0.002 PHE H 516 TYR 0.029 0.002 TYR H 375 ARG 0.005 0.000 ARG D 461 Details of bonding type rmsd link_NAG-ASN : bond 0.00575 ( 10) link_NAG-ASN : angle 4.67157 ( 30) hydrogen bonds : bond 0.03469 ( 647) hydrogen bonds : angle 5.59457 ( 1941) SS BOND : bond 0.00470 ( 34) SS BOND : angle 1.20234 ( 68) covalent geometry : bond 0.00420 (22196) covalent geometry : angle 0.73472 (30314) Misc. bond : bond 0.00033 ( 2) ********************** 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 361 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 262 time to evaluate : 3.115 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: A 358 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7158 (p90) REVERT: A 376 ASP cc_start: 0.6722 (t0) cc_final: 0.6231 (p0) REVERT: A 461 ARG cc_start: 0.8225 (tpm170) cc_final: 0.7935 (tpm170) REVERT: A 462 GLU cc_start: 0.8901 (pp20) cc_final: 0.8328 (pp20) REVERT: A 550 ARG cc_start: 0.8421 (mmm160) cc_final: 0.7857 (mmm160) REVERT: B 415 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8275 (mp0) REVERT: B 515 TYR cc_start: 0.7699 (m-80) cc_final: 0.7476 (t80) REVERT: C 395 ASN cc_start: 0.5039 (t0) cc_final: 0.4534 (m-40) REVERT: D 370 THR cc_start: 0.2314 (OUTLIER) cc_final: 0.1969 (m) REVERT: D 429 THR cc_start: 0.4343 (OUTLIER) cc_final: 0.4123 (m) REVERT: D 510 GLN cc_start: 0.8491 (pp30) cc_final: 0.8188 (pp30) REVERT: E 461 ARG cc_start: 0.8295 (mmm160) cc_final: 0.7914 (mmm160) REVERT: E 465 ASN cc_start: 0.8676 (m-40) cc_final: 0.7749 (m-40) REVERT: E 483 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7803 (t0) REVERT: E 508 GLU cc_start: 0.8056 (tp30) cc_final: 0.7710 (tp30) REVERT: F 366 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.8119 (p) REVERT: F 461 ARG cc_start: 0.8172 (mmm160) cc_final: 0.7887 (mmm160) REVERT: J 19 SER cc_start: 0.8544 (OUTLIER) cc_final: 0.8197 (p) REVERT: J 46 ARG cc_start: 0.7928 (mmt180) cc_final: 0.7148 (mmm160) REVERT: K 347 VAL cc_start: 0.0125 (OUTLIER) cc_final: -0.0282 (m) REVERT: K 453 ASP cc_start: 0.8452 (m-30) cc_final: 0.7581 (p0) REVERT: K 483 ASP cc_start: 0.8225 (t0) cc_final: 0.7928 (t0) REVERT: K 506 MET cc_start: 0.7728 (mpp) cc_final: 0.7394 (mpp) REVERT: R 36 LYS cc_start: 0.7203 (tptt) cc_final: 0.6880 (tptt) REVERT: R 52 MET cc_start: 0.8224 (tpt) cc_final: 0.7937 (tpp) REVERT: R 73 LYS cc_start: 0.8228 (mttt) cc_final: 0.7820 (mmtm) REVERT: S 69 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.8074 (tptp) REVERT: S 87 PHE cc_start: 0.7975 (m-80) cc_final: 0.7432 (m-80) REVERT: V 83 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.6833 (ptt-90) REVERT: V 87 PHE cc_start: 0.7796 (t80) cc_final: 0.7366 (t80) outliers start: 99 outliers final: 84 residues processed: 340 average time/residue: 0.3446 time to fit residues: 186.0133 Evaluate side-chains 351 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 257 time to evaluate : 2.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 400 HIS Chi-restraints excluded: chain D residue 416 ASP 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 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 514 ARG 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 366 THR 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 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 462 GLU 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 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 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 567 VAL Chi-restraints excluded: chain L residue 476 VAL Chi-restraints excluded: chain L residue 506 MET Chi-restraints excluded: chain L residue 521 LEU Chi-restraints excluded: chain L residue 522 THR 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 55 SER 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 69 LYS Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain U residue 19 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 142 optimal weight: 0.7980 chunk 220 optimal weight: 0.8980 chunk 138 optimal weight: 0.0010 chunk 181 optimal weight: 6.9990 chunk 88 optimal weight: 30.0000 chunk 246 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 221 optimal weight: 8.9990 chunk 233 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 overall best weight: 2.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.116350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.076559 restraints weight = 74069.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.078937 restraints weight = 38484.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.080378 restraints weight = 26691.277| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22242 Z= 0.152 Angle : 0.738 12.580 30412 Z= 0.361 Chirality : 0.048 0.475 3600 Planarity : 0.005 0.083 3863 Dihedral : 6.049 56.744 3222 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 4.00 % Allowed : 21.60 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.16), residues: 2737 helix: -0.77 (0.32), residues: 238 sheet: -0.50 (0.16), residues: 1019 loop : -1.33 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 528 HIS 0.004 0.001 HIS L 518 PHE 0.027 0.002 PHE H 516 TYR 0.030 0.002 TYR H 375 ARG 0.005 0.000 ARG D 461 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 10) link_NAG-ASN : angle 4.58044 ( 30) hydrogen bonds : bond 0.03384 ( 647) hydrogen bonds : angle 5.50796 ( 1941) SS BOND : bond 0.00430 ( 34) SS BOND : angle 1.11188 ( 68) covalent geometry : bond 0.00352 (22196) covalent geometry : angle 0.72264 (30314) Misc. bond : bond 0.00020 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10714.90 seconds wall clock time: 188 minutes 33.31 seconds (11313.31 seconds total)