Starting phenix.real_space_refine on Sun Aug 24 17:54:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ytd_34086/08_2025/7ytd_34086.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ytd_34086/08_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_34086/08_2025/7ytd_34086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ytd_34086/08_2025/7ytd_34086.map" model { file = "/net/cci-nas-00/data/ceres_data/7ytd_34086/08_2025/7ytd_34086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ytd_34086/08_2025/7ytd_34086.cif" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 116 5.16 5 C 13645 2.51 5 N 3696 2.21 5 O 4236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21693 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1773 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 18, 'TRANS': 210} Chain: "B" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1749 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 18, 'TRANS': 206} Chain: "C" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1748 Classifications: {'peptide': 225} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 206} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1749 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 18, 'TRANS': 206} Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "F" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1723 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 18, 'TRANS': 202} Chain breaks: 1 Chain: "G" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1742 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1730 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 18, 'TRANS': 203} Chain breaks: 1 Chain: "J" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 834 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 7, 'TRANS': 96} Chain breaks: 1 Chain: "K" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1737 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 18, 'TRANS': 204} Chain breaks: 1 Chain: "L" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1761 Classifications: {'peptide': 227} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 208} Chain breaks: 1 Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "S" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "U" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "V" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen 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: 5.48, per 1000 atoms: 0.25 Number of scatterers: 21693 At special positions: 0 Unit cell: (121.716, 187.128, 164.772, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 116 16.00 O 4236 8.00 N 3696 7.00 C 13645 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 536 " distance=2.04 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 414 " - pdb=" SG CYS C 414 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 536 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 426 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 536 " distance=2.03 Simple disulfide: pdb=" SG CYS D 367 " - pdb=" SG CYS D 426 " distance=2.04 Simple disulfide: pdb=" SG CYS D 414 " - pdb=" SG CYS E 414 " distance=2.03 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 536 " distance=2.04 Simple disulfide: pdb=" SG CYS E 367 " - pdb=" SG CYS E 426 " distance=2.03 Simple disulfide: pdb=" SG CYS E 474 " - pdb=" SG CYS E 536 " distance=2.04 Simple disulfide: pdb=" SG CYS F 367 " - pdb=" SG CYS F 426 " distance=2.03 Simple disulfide: pdb=" SG CYS F 414 " - pdb=" SG CYS G 414 " distance=2.03 Simple disulfide: pdb=" SG CYS F 474 " - pdb=" SG CYS F 536 " distance=2.04 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 426 " distance=2.03 Simple disulfide: pdb=" SG CYS G 474 " - pdb=" SG CYS G 536 " distance=2.03 Simple disulfide: pdb=" SG CYS H 367 " - pdb=" SG CYS H 426 " distance=2.04 Simple disulfide: pdb=" SG CYS H 474 " - pdb=" SG CYS H 536 " distance=2.05 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 100 " distance=1.99 Simple disulfide: pdb=" SG CYS J 14 " - pdb=" SG CYS L 575 " distance=1.88 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 133 " distance=2.03 Simple disulfide: pdb=" SG CYS K 367 " - pdb=" SG CYS K 426 " distance=2.03 Simple disulfide: pdb=" SG CYS K 474 " - pdb=" SG CYS K 536 " distance=2.04 Simple disulfide: pdb=" SG CYS L 367 " - pdb=" SG CYS L 426 " distance=2.03 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 536 " distance=2.04 Simple disulfide: pdb=" SG CYS R 37 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 49 " - pdb=" SG CYS R 58 " distance=2.03 Simple disulfide: pdb=" SG CYS S 37 " - pdb=" SG CYS S 104 " distance=2.03 Simple disulfide: pdb=" SG CYS S 49 " - pdb=" SG CYS S 58 " distance=2.02 Simple disulfide: pdb=" SG CYS U 37 " - pdb=" SG CYS U 104 " distance=2.03 Simple disulfide: pdb=" SG CYS U 49 " - pdb=" SG CYS U 58 " distance=2.03 Simple disulfide: pdb=" SG CYS V 37 " - pdb=" SG CYS V 104 " distance=2.03 Simple disulfide: pdb=" SG CYS V 49 " - pdb=" SG CYS V 58 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 563 " " NAG B 601 " - " ASN B 563 " " NAG C 601 " - " ASN C 563 " " NAG D 601 " - " ASN D 563 " " NAG E 601 " - " ASN E 563 " " NAG F 601 " - " ASN F 563 " " NAG G 601 " - " ASN G 563 " " NAG H 601 " - " ASN H 563 " " NAG K 601 " - " ASN K 563 " " NAG L 601 " - " ASN L 563 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 950.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.06 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: 4.50 Time building geometry restraints manager: 2.53 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 601)) selection = (chain 'F' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 601)) selection = (chain 'G' and (resid 345 through 444 or resid 449 through 512 or (resid 513 and \ (name N or name CA or name C )) or resid 514 through 601)) selection = (chain 'H' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 601)) selection = (chain 'K' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'L' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 512 or (resid 513 and (name N \ or name CA or name C )) or resid 514 through 568 or resid 601)) } ncs_group { reference = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.870 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.670 ------------------------------------------------------------------------------- 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 : 29.55 Ramachandran Plot: Outliers : 0.91 % Allowed : 8.59 % Favored : 90.50 % Rotamer: Outliers : 4.37 % Allowed : 2.63 % Favored : 93.00 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.16), residues: 2737 helix: -0.88 (0.37), residues: 180 sheet: -0.96 (0.16), residues: 1037 loop : -1.52 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG U 112 TYR 0.027 0.002 TYR B 455 PHE 0.019 0.002 PHE H 516 TRP 0.025 0.002 TRP K 528 HIS 0.009 0.001 HIS F 518 Details of bonding type rmsd covalent geometry : bond 0.00516 (22196) covalent geometry : angle 0.96340 (30314) SS BOND : bond 0.02779 ( 34) SS BOND : angle 4.52527 ( 68) hydrogen bonds : bond 0.18078 ( 647) hydrogen bonds : angle 8.26643 ( 1941) Misc. bond : bond 0.17356 ( 2) link_NAG-ASN : bond 0.16107 ( 10) link_NAG-ASN : angle 16.02283 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 388 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 529 ASN cc_start: 0.9264 (m110) cc_final: 0.9026 (m110) REVERT: C 395 ASN cc_start: 0.5687 (t0) cc_final: 0.5278 (t0) REVERT: C 561 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8741 (mm) REVERT: D 424 PHE cc_start: 0.8586 (m-80) cc_final: 0.8245 (m-80) REVERT: D 510 GLN cc_start: 0.8305 (pp30) cc_final: 0.8071 (pp30) REVERT: D 534 TYR cc_start: 0.8559 (m-80) cc_final: 0.7940 (m-80) REVERT: E 461 ARG cc_start: 0.8015 (mmm160) cc_final: 0.7737 (mmm160) REVERT: F 493 GLN cc_start: 0.8285 (pp30) cc_final: 0.7886 (pp30) REVERT: H 506 MET cc_start: 0.7857 (mmp) cc_final: 0.7603 (mmm) REVERT: J 16 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.6523 (tmm160) REVERT: L 520 ILE cc_start: 0.9135 (pt) cc_final: 0.8931 (pt) REVERT: R 36 LYS cc_start: 0.7196 (tptt) cc_final: 0.6964 (tppt) REVERT: R 46 ILE cc_start: 0.9213 (tp) cc_final: 0.8860 (tp) REVERT: R 52 MET cc_start: 0.8274 (tpt) cc_final: 0.8046 (tpp) REVERT: S 46 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8698 (tp) REVERT: U 26 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7648 (tp30) REVERT: U 66 ASN cc_start: 0.8082 (p0) cc_final: 0.7512 (t0) REVERT: U 87 PHE cc_start: 0.8080 (t80) cc_final: 0.7711 (t80) REVERT: U 111 ASP cc_start: 0.7822 (p0) cc_final: 0.7598 (p0) REVERT: U 112 ARG cc_start: 0.8211 (mmp80) cc_final: 0.7988 (mmp80) REVERT: V 43 HIS cc_start: 0.6836 (m-70) cc_final: 0.6610 (m-70) REVERT: V 83 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6511 (ptt-90) REVERT: V 87 PHE cc_start: 0.8110 (t80) cc_final: 0.7529 (t80) outliers start: 108 outliers final: 73 residues processed: 472 average time/residue: 0.1423 time to fit residues: 103.1946 Evaluate side-chains 362 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 284 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 562 TYR Chi-restraints excluded: chain C residue 563 ASN Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 568 MET Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain E residue 485 PHE Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain E residue 514 ARG Chi-restraints excluded: chain E residue 561 LEU Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 510 GLN Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 16 ARG Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 66 ASP Chi-restraints excluded: chain J residue 68 CYS Chi-restraints excluded: chain J residue 134 TYR Chi-restraints excluded: chain K residue 490 GLN Chi-restraints excluded: chain K residue 493 GLN Chi-restraints excluded: chain K residue 567 VAL Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain R residue 95 THR Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 122 VAL Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 28 GLU Chi-restraints excluded: chain S residue 41 GLU Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 94 LEU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 98 ASP Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain S residue 114 LYS Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 22 GLU Chi-restraints excluded: chain U residue 26 GLU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 122 VAL Chi-restraints excluded: chain V residue 19 ILE Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 23 VAL Chi-restraints excluded: chain V residue 26 GLU Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 80 GLN Chi-restraints excluded: chain V residue 81 TYR Chi-restraints excluded: chain V residue 83 ARG Chi-restraints excluded: chain V residue 84 LYS Chi-restraints excluded: chain V residue 85 ASN Chi-restraints excluded: chain V residue 96 GLU Chi-restraints excluded: chain V residue 118 VAL Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 123 HIS Chi-restraints excluded: chain V residue 124 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.0050 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 HIS ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 GLN ** F 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 463 GLN ** H 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 529 ASN ** H 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 ASN L 400 HIS ** S 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 116 GLN U 121 ASN V 80 GLN V 123 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.117511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.076917 restraints weight = 75963.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.079419 restraints weight = 39873.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.080892 restraints weight = 27881.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.081467 restraints weight = 22986.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.082121 restraints weight = 20992.899| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22242 Z= 0.191 Angle : 0.794 17.375 30412 Z= 0.390 Chirality : 0.051 0.616 3600 Planarity : 0.005 0.082 3863 Dihedral : 9.540 104.369 3346 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.82 % Favored : 92.11 % Rotamer: Outliers : 3.60 % Allowed : 11.73 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.16), residues: 2737 helix: -1.31 (0.31), residues: 221 sheet: -0.90 (0.16), residues: 1060 loop : -1.52 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 514 TYR 0.021 0.002 TYR H 375 PHE 0.021 0.002 PHE B 354 TRP 0.021 0.002 TRP H 528 HIS 0.007 0.001 HIS C 430 Details of bonding type rmsd covalent geometry : bond 0.00427 (22196) covalent geometry : angle 0.76871 (30314) SS BOND : bond 0.00609 ( 34) SS BOND : angle 1.53682 ( 68) hydrogen bonds : bond 0.04321 ( 647) hydrogen bonds : angle 6.49479 ( 1941) Misc. bond : bond 0.00060 ( 2) link_NAG-ASN : bond 0.00807 ( 10) link_NAG-ASN : angle 6.04207 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 313 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7727 (tp) REVERT: B 489 MET cc_start: 0.8182 (mmt) cc_final: 0.7979 (mmt) REVERT: C 395 ASN cc_start: 0.5412 (t0) cc_final: 0.4972 (t0) REVERT: C 561 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7908 (mm) REVERT: D 424 PHE cc_start: 0.8454 (m-80) cc_final: 0.8210 (m-80) REVERT: D 510 GLN cc_start: 0.8270 (pp30) cc_final: 0.8056 (pp30) REVERT: D 534 TYR cc_start: 0.8814 (m-80) cc_final: 0.8103 (m-80) REVERT: E 461 ARG cc_start: 0.8103 (mmm160) cc_final: 0.7832 (mmm160) REVERT: E 483 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.7576 (t0) REVERT: F 493 GLN cc_start: 0.8280 (pp30) cc_final: 0.7995 (pp30) REVERT: J 8 VAL cc_start: 0.4444 (p) cc_final: 0.4126 (t) REVERT: J 37 ILE cc_start: 0.6975 (mm) cc_final: 0.6708 (mm) REVERT: J 66 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.8219 (p0) REVERT: K 463 GLN cc_start: 0.8401 (tp-100) cc_final: 0.8128 (tp-100) REVERT: K 475 LEU cc_start: 0.9071 (tp) cc_final: 0.8824 (tp) REVERT: K 483 ASP cc_start: 0.8147 (t0) cc_final: 0.7896 (t0) REVERT: L 489 MET cc_start: 0.7616 (ttm) cc_final: 0.7331 (tpp) REVERT: L 521 LEU cc_start: 0.7548 (tp) cc_final: 0.6756 (mt) REVERT: R 36 LYS cc_start: 0.7252 (tptt) cc_final: 0.6898 (tppt) REVERT: S 26 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7295 (tp30) REVERT: S 42 MET cc_start: 0.8329 (ptp) cc_final: 0.7023 (pmm) REVERT: S 51 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6526 (mp0) REVERT: S 94 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7524 (tp) REVERT: U 26 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7474 (tp30) REVERT: U 66 ASN cc_start: 0.8163 (p0) cc_final: 0.7641 (t0) REVERT: U 87 PHE cc_start: 0.7966 (t80) cc_final: 0.7763 (t80) REVERT: U 120 LEU cc_start: 0.8901 (pp) cc_final: 0.8700 (pp) REVERT: V 26 GLU cc_start: 0.6001 (OUTLIER) cc_final: 0.5635 (tt0) REVERT: V 81 TYR cc_start: 0.6932 (OUTLIER) cc_final: 0.5238 (m-80) REVERT: V 83 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.6617 (mtm180) REVERT: V 87 PHE cc_start: 0.7857 (t80) cc_final: 0.7410 (t80) outliers start: 89 outliers final: 56 residues processed: 380 average time/residue: 0.1293 time to fit residues: 77.2617 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 : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 561 LEU Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 510 GLN Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 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 118 VAL Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 123 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 155 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 52 optimal weight: 50.0000 chunk 177 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 194 optimal weight: 50.0000 chunk 80 optimal weight: 5.9990 chunk 96 optimal weight: 30.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 419 ASN D 450 HIS F 419 ASN F 545 ASN ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 529 ASN K 463 GLN L 463 GLN ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.114452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.073450 restraints weight = 76628.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.075739 restraints weight = 41491.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.077103 restraints weight = 29523.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.077739 restraints weight = 24605.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.078282 restraints weight = 22439.722| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 22242 Z= 0.302 Angle : 0.820 18.827 30412 Z= 0.408 Chirality : 0.051 0.562 3600 Planarity : 0.006 0.086 3863 Dihedral : 8.257 86.063 3271 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.44 % Favored : 91.52 % Rotamer: Outliers : 4.77 % Allowed : 14.72 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.16), residues: 2737 helix: -1.05 (0.32), residues: 223 sheet: -1.10 (0.16), residues: 1047 loop : -1.55 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 45 TYR 0.028 0.003 TYR E 455 PHE 0.024 0.002 PHE H 516 TRP 0.015 0.002 TRP G 488 HIS 0.013 0.002 HIS E 450 Details of bonding type rmsd covalent geometry : bond 0.00679 (22196) covalent geometry : angle 0.79570 (30314) SS BOND : bond 0.00650 ( 34) SS BOND : angle 1.74643 ( 68) hydrogen bonds : bond 0.04286 ( 647) hydrogen bonds : angle 6.43324 ( 1941) Misc. bond : bond 0.00091 ( 2) link_NAG-ASN : bond 0.00714 ( 10) link_NAG-ASN : angle 5.89487 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 275 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 550 ARG cc_start: 0.8089 (mmm160) cc_final: 0.7738 (mmm160) REVERT: B 415 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8318 (mp0) REVERT: B 489 MET cc_start: 0.8193 (mmt) cc_final: 0.7963 (mmt) REVERT: C 395 ASN cc_start: 0.5377 (t0) cc_final: 0.5052 (t0) REVERT: D 489 MET cc_start: 0.8471 (tpp) cc_final: 0.8263 (mmt) REVERT: D 510 GLN cc_start: 0.8294 (pp30) cc_final: 0.8045 (pp30) REVERT: E 568 MET cc_start: 0.6668 (tmm) cc_final: 0.6195 (ppp) REVERT: F 493 GLN cc_start: 0.8097 (pp30) cc_final: 0.7760 (pp30) REVERT: G 483 ASP cc_start: 0.7881 (t0) cc_final: 0.7625 (t0) REVERT: H 461 ARG cc_start: 0.8251 (mmm160) cc_final: 0.7895 (tpt90) REVERT: H 489 MET cc_start: 0.8514 (mmp) cc_final: 0.8283 (mmm) REVERT: J 66 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8224 (p0) REVERT: K 463 GLN cc_start: 0.8623 (tp40) cc_final: 0.8376 (tp-100) REVERT: K 483 ASP cc_start: 0.8167 (t0) cc_final: 0.7878 (t0) REVERT: L 489 MET cc_start: 0.7615 (ttm) cc_final: 0.7275 (tpp) REVERT: L 521 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7140 (tp) REVERT: U 26 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: U 87 PHE cc_start: 0.7933 (t80) cc_final: 0.7715 (t80) REVERT: V 52 MET cc_start: 0.7721 (tpp) cc_final: 0.7489 (tpp) REVERT: V 81 TYR cc_start: 0.7288 (OUTLIER) cc_final: 0.5988 (m-80) REVERT: V 83 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.6912 (mtm180) REVERT: V 87 PHE cc_start: 0.7852 (t80) cc_final: 0.7393 (t80) outliers start: 118 outliers final: 73 residues processed: 371 average time/residue: 0.1251 time to fit residues: 74.7684 Evaluate side-chains 327 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 248 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 568 MET Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 561 LEU Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 533 THR Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 486 VAL Chi-restraints excluded: chain G residue 510 GLN Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 63 HIS Chi-restraints excluded: chain J residue 66 ASP Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 528 TRP Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain L residue 521 LEU Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 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 114 LYS Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 22 GLU Chi-restraints excluded: chain U residue 26 GLU Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 122 VAL Chi-restraints excluded: chain V residue 81 TYR Chi-restraints excluded: chain V residue 83 ARG Chi-restraints excluded: chain V residue 85 ASN Chi-restraints excluded: chain V residue 118 VAL Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 123 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 222 optimal weight: 4.9990 chunk 160 optimal weight: 50.0000 chunk 31 optimal weight: 40.0000 chunk 170 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 145 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 GLN A 510 GLN ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 400 HIS ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 93 GLN ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.115515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.074623 restraints weight = 75859.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.077038 restraints weight = 40056.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.078488 restraints weight = 28085.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.079317 restraints weight = 23168.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.079609 restraints weight = 20909.117| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 22242 Z= 0.210 Angle : 0.754 14.885 30412 Z= 0.371 Chirality : 0.050 0.644 3600 Planarity : 0.005 0.089 3863 Dihedral : 7.605 84.356 3248 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.96 % Favored : 92.00 % Rotamer: Outliers : 4.41 % Allowed : 17.19 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.16), residues: 2737 helix: -1.11 (0.33), residues: 213 sheet: -1.03 (0.16), residues: 1055 loop : -1.47 (0.16), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 45 TYR 0.022 0.002 TYR B 455 PHE 0.025 0.002 PHE H 485 TRP 0.013 0.001 TRP A 488 HIS 0.006 0.001 HIS V 43 Details of bonding type rmsd covalent geometry : bond 0.00473 (22196) covalent geometry : angle 0.73243 (30314) SS BOND : bond 0.00555 ( 34) SS BOND : angle 1.40496 ( 68) hydrogen bonds : bond 0.03860 ( 647) hydrogen bonds : angle 6.13053 ( 1941) Misc. bond : bond 0.00082 ( 2) link_NAG-ASN : bond 0.00693 ( 10) link_NAG-ASN : angle 5.52673 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 269 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 ASP cc_start: 0.6491 (t0) cc_final: 0.6062 (p0) REVERT: A 455 TYR cc_start: 0.7973 (m-10) cc_final: 0.7622 (m-10) REVERT: A 550 ARG cc_start: 0.8171 (mmm160) cc_final: 0.7777 (mmm160) REVERT: B 415 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8254 (mp0) REVERT: B 489 MET cc_start: 0.8208 (mmt) cc_final: 0.8002 (mmt) REVERT: C 395 ASN cc_start: 0.5052 (t0) cc_final: 0.4687 (t0) REVERT: C 561 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8234 (mm) REVERT: D 510 GLN cc_start: 0.8356 (pp30) cc_final: 0.8105 (pp30) REVERT: E 483 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.7664 (t0) REVERT: H 461 ARG cc_start: 0.8178 (mmm160) cc_final: 0.7818 (tpt90) REVERT: K 463 GLN cc_start: 0.8679 (tp40) cc_final: 0.8473 (tp-100) REVERT: K 483 ASP cc_start: 0.8165 (t0) cc_final: 0.7867 (t0) REVERT: L 489 MET cc_start: 0.7436 (ttm) cc_final: 0.7144 (tpp) REVERT: L 521 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7125 (tp) REVERT: R 36 LYS cc_start: 0.7160 (tptt) cc_final: 0.6878 (tptt) REVERT: S 52 MET cc_start: 0.7407 (pmm) cc_final: 0.7090 (pmm) REVERT: S 114 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7165 (ptpt) REVERT: U 26 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7673 (tm-30) REVERT: U 123 HIS cc_start: 0.7168 (OUTLIER) cc_final: 0.6543 (t-170) REVERT: V 52 MET cc_start: 0.7788 (tpp) cc_final: 0.7569 (tpp) REVERT: V 81 TYR cc_start: 0.7455 (OUTLIER) cc_final: 0.7093 (m-80) REVERT: V 83 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.6912 (ptt-90) REVERT: V 87 PHE cc_start: 0.7783 (t80) cc_final: 0.7354 (t80) outliers start: 109 outliers final: 72 residues processed: 360 average time/residue: 0.1247 time to fit residues: 72.0490 Evaluate side-chains 326 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 245 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 569 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain C residue 358 PHE Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 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 483 ASP Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 510 GLN Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 522 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 63 HIS Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 375 TYR Chi-restraints excluded: chain K residue 474 CYS Chi-restraints excluded: chain K residue 528 TRP Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain L residue 521 LEU Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 114 LYS Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 22 GLU Chi-restraints excluded: chain U residue 26 GLU Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 122 VAL Chi-restraints excluded: chain U residue 123 HIS Chi-restraints excluded: chain V residue 81 TYR Chi-restraints excluded: chain V residue 83 ARG Chi-restraints excluded: chain V residue 118 VAL Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 123 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 166 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 188 optimal weight: 20.0000 chunk 142 optimal weight: 4.9990 chunk 216 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 47 optimal weight: 20.0000 chunk 217 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 529 ASN ** D 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 ASN K 518 HIS ** 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 = 0.4226 r_free = 0.4226 target = 0.115330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.075393 restraints weight = 77897.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.078511 restraints weight = 42200.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.078566 restraints weight = 27595.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.078903 restraints weight = 23712.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.079005 restraints weight = 23819.175| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 22242 Z= 0.225 Angle : 0.757 14.889 30412 Z= 0.375 Chirality : 0.050 0.696 3600 Planarity : 0.005 0.087 3863 Dihedral : 7.359 74.865 3237 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.55 % Favored : 91.41 % Rotamer: Outliers : 4.98 % Allowed : 17.60 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.16), residues: 2737 helix: -1.01 (0.33), residues: 214 sheet: -1.03 (0.15), residues: 1050 loop : -1.44 (0.16), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG S 45 TYR 0.022 0.002 TYR K 455 PHE 0.017 0.002 PHE K 358 TRP 0.013 0.002 TRP K 528 HIS 0.005 0.001 HIS L 450 Details of bonding type rmsd covalent geometry : bond 0.00510 (22196) covalent geometry : angle 0.73578 (30314) SS BOND : bond 0.00546 ( 34) SS BOND : angle 1.40233 ( 68) hydrogen bonds : bond 0.03825 ( 647) hydrogen bonds : angle 6.08459 ( 1941) Misc. bond : bond 0.00052 ( 2) link_NAG-ASN : bond 0.00832 ( 10) link_NAG-ASN : angle 5.42955 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 265 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 ASP cc_start: 0.6397 (t0) cc_final: 0.5938 (p0) REVERT: A 455 TYR cc_start: 0.7990 (m-10) cc_final: 0.7602 (m-10) REVERT: A 550 ARG cc_start: 0.8365 (mmm160) cc_final: 0.7905 (mmm160) REVERT: B 415 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8325 (mp0) REVERT: B 490 GLN cc_start: 0.9048 (tm-30) cc_final: 0.8309 (tm-30) REVERT: C 395 ASN cc_start: 0.5035 (t0) cc_final: 0.4620 (t0) REVERT: C 561 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8326 (mm) REVERT: D 510 GLN cc_start: 0.8382 (pp30) cc_final: 0.8112 (pp30) REVERT: E 483 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.7681 (t0) REVERT: E 568 MET cc_start: 0.6269 (ppp) cc_final: 0.5925 (ppp) REVERT: F 430 HIS cc_start: 0.1071 (OUTLIER) cc_final: 0.0671 (m-70) REVERT: F 461 ARG cc_start: 0.8415 (mmm-85) cc_final: 0.8163 (mmm160) REVERT: H 489 MET cc_start: 0.8456 (mmp) cc_final: 0.8121 (mmm) REVERT: J 19 SER cc_start: 0.8472 (OUTLIER) cc_final: 0.8018 (p) REVERT: K 347 VAL cc_start: 0.0169 (OUTLIER) cc_final: -0.0204 (m) REVERT: K 483 ASP cc_start: 0.8207 (t0) cc_final: 0.7869 (t0) REVERT: L 489 MET cc_start: 0.7440 (ttm) cc_final: 0.7008 (tpp) REVERT: L 521 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7253 (tp) REVERT: R 36 LYS cc_start: 0.7228 (tptt) cc_final: 0.6889 (tptt) REVERT: S 114 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7531 (ptpt) REVERT: V 52 MET cc_start: 0.7839 (tpp) cc_final: 0.7624 (tpp) REVERT: V 81 TYR cc_start: 0.7634 (OUTLIER) cc_final: 0.7323 (m-80) REVERT: V 83 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.6848 (ptt-90) REVERT: V 87 PHE cc_start: 0.8116 (t80) cc_final: 0.7640 (t80) outliers start: 123 outliers final: 92 residues processed: 368 average time/residue: 0.1205 time to fit residues: 71.4080 Evaluate side-chains 347 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 245 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain C residue 358 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 430 HIS Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 487 GLN Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 486 VAL Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 394 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 63 HIS Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 375 TYR Chi-restraints excluded: chain K residue 474 CYS Chi-restraints excluded: chain K residue 528 TRP Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain K residue 567 VAL Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 521 LEU Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 562 TYR Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 114 LYS Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 22 GLU Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 122 VAL Chi-restraints excluded: chain V residue 81 TYR Chi-restraints excluded: chain V residue 83 ARG Chi-restraints excluded: chain V residue 118 VAL Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 123 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 19 optimal weight: 9.9990 chunk 159 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 185 optimal weight: 9.9990 chunk 46 optimal weight: 50.0000 chunk 1 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 247 optimal weight: 9.9990 chunk 191 optimal weight: 50.0000 chunk 219 optimal weight: 0.0030 overall best weight: 4.5998 ------------------------------------------------------------------------------- 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 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 545 ASN ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 463 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 = 0.4216 r_free = 0.4216 target = 0.114618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.075702 restraints weight = 78138.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.076589 restraints weight = 48268.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.077195 restraints weight = 35348.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.077712 restraints weight = 28082.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.077912 restraints weight = 26172.480| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 22242 Z= 0.249 Angle : 0.769 16.192 30412 Z= 0.381 Chirality : 0.050 0.706 3600 Planarity : 0.005 0.087 3863 Dihedral : 7.178 59.950 3231 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 5.38 % Allowed : 18.69 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.16), residues: 2737 helix: -0.91 (0.33), residues: 221 sheet: -1.06 (0.16), residues: 1042 loop : -1.44 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 461 TYR 0.024 0.002 TYR K 455 PHE 0.015 0.002 PHE F 354 TRP 0.014 0.002 TRP K 528 HIS 0.007 0.001 HIS A 518 Details of bonding type rmsd covalent geometry : bond 0.00562 (22196) covalent geometry : angle 0.74642 (30314) SS BOND : bond 0.00610 ( 34) SS BOND : angle 1.56595 ( 68) hydrogen bonds : bond 0.03833 ( 647) hydrogen bonds : angle 6.04328 ( 1941) Misc. bond : bond 0.00480 ( 2) link_NAG-ASN : bond 0.00798 ( 10) link_NAG-ASN : angle 5.52040 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 257 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 358 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.7191 (p90) REVERT: A 506 MET cc_start: 0.8979 (mmm) cc_final: 0.8763 (mmm) REVERT: A 550 ARG cc_start: 0.8378 (mmm160) cc_final: 0.7866 (mmm160) REVERT: B 415 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8366 (mp0) REVERT: B 485 PHE cc_start: 0.8531 (t80) cc_final: 0.8189 (t80) REVERT: C 395 ASN cc_start: 0.4829 (t0) cc_final: 0.4560 (t0) REVERT: C 561 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8364 (mm) REVERT: D 510 GLN cc_start: 0.8438 (pp30) cc_final: 0.8142 (pp30) REVERT: D 534 TYR cc_start: 0.8897 (m-80) cc_final: 0.8290 (m-80) REVERT: E 483 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.7934 (t0) REVERT: F 358 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.7774 (t80) REVERT: F 365 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7166 (mm) REVERT: F 430 HIS cc_start: 0.1092 (OUTLIER) cc_final: 0.0832 (m-70) REVERT: F 461 ARG cc_start: 0.8389 (mmm-85) cc_final: 0.8022 (mmm-85) REVERT: G 483 ASP cc_start: 0.7867 (t0) cc_final: 0.7638 (t0) REVERT: H 461 ARG cc_start: 0.8195 (mmm160) cc_final: 0.7969 (tpt90) REVERT: H 527 GLU cc_start: 0.8512 (tp30) cc_final: 0.8216 (tp30) REVERT: J 19 SER cc_start: 0.8487 (OUTLIER) cc_final: 0.8050 (p) REVERT: K 347 VAL cc_start: 0.0007 (OUTLIER) cc_final: -0.0396 (m) REVERT: K 483 ASP cc_start: 0.8254 (t0) cc_final: 0.7929 (t0) REVERT: L 489 MET cc_start: 0.7439 (ttm) cc_final: 0.7009 (tpp) REVERT: L 521 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7286 (tp) REVERT: R 36 LYS cc_start: 0.7172 (tptt) cc_final: 0.6834 (tptt) REVERT: S 87 PHE cc_start: 0.8476 (m-80) cc_final: 0.8267 (m-80) REVERT: V 52 MET cc_start: 0.7898 (tpp) cc_final: 0.7688 (tpp) REVERT: V 81 TYR cc_start: 0.7726 (OUTLIER) cc_final: 0.7354 (m-80) REVERT: V 83 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.6913 (ptt-90) REVERT: V 87 PHE cc_start: 0.8152 (t80) cc_final: 0.7681 (t80) outliers start: 133 outliers final: 98 residues processed: 369 average time/residue: 0.1373 time to fit residues: 81.5578 Evaluate side-chains 355 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 245 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 552 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain C residue 358 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain 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 484 VAL Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 430 HIS Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 487 GLN Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 533 THR Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 553 ASP Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 486 VAL Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 522 THR Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 63 HIS Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 375 TYR Chi-restraints excluded: chain K residue 474 CYS Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 528 TRP Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 521 LEU Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 562 TYR Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain 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 81 TYR 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 55 optimal weight: 0.9990 chunk 220 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 66 optimal weight: 30.0000 chunk 77 optimal weight: 0.7980 chunk 227 optimal weight: 10.0000 chunk 206 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 0 optimal weight: 70.0000 chunk 30 optimal weight: 30.0000 chunk 135 optimal weight: 10.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 HIS D 463 GLN ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 465 ASN ** G 545 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.116658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.076588 restraints weight = 73956.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.079080 restraints weight = 37592.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.080615 restraints weight = 25861.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.081465 restraints weight = 21059.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.081779 restraints weight = 18946.262| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22242 Z= 0.128 Angle : 0.719 14.630 30412 Z= 0.353 Chirality : 0.049 0.713 3600 Planarity : 0.005 0.086 3863 Dihedral : 6.566 59.293 3225 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 4.13 % Allowed : 20.35 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.16), residues: 2737 helix: -1.07 (0.32), residues: 228 sheet: -0.80 (0.16), residues: 1036 loop : -1.37 (0.16), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 514 TYR 0.024 0.002 TYR K 455 PHE 0.025 0.002 PHE K 358 TRP 0.014 0.001 TRP A 488 HIS 0.006 0.001 HIS A 518 Details of bonding type rmsd covalent geometry : bond 0.00288 (22196) covalent geometry : angle 0.69860 (30314) SS BOND : bond 0.00611 ( 34) SS BOND : angle 1.03918 ( 68) hydrogen bonds : bond 0.03507 ( 647) hydrogen bonds : angle 5.63699 ( 1941) Misc. bond : bond 0.00538 ( 2) link_NAG-ASN : bond 0.00927 ( 10) link_NAG-ASN : angle 5.33202 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 288 time to evaluate : 0.760 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: 0.7555 (OUTLIER) cc_final: 0.7197 (p90) REVERT: A 368 LEU cc_start: 0.6739 (OUTLIER) cc_final: 0.6509 (tp) REVERT: A 376 ASP cc_start: 0.6548 (t0) cc_final: 0.6138 (p0) REVERT: A 455 TYR cc_start: 0.7983 (m-10) cc_final: 0.7622 (m-10) REVERT: A 550 ARG cc_start: 0.8292 (mmm160) cc_final: 0.7739 (mmm160) REVERT: B 415 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8244 (mp0) REVERT: C 395 ASN cc_start: 0.4782 (t0) cc_final: 0.4354 (m-40) REVERT: D 429 THR cc_start: 0.4484 (OUTLIER) cc_final: 0.4267 (m) REVERT: D 489 MET cc_start: 0.8350 (tpp) cc_final: 0.8148 (mmt) REVERT: D 510 GLN cc_start: 0.8411 (pp30) cc_final: 0.8135 (pp30) REVERT: D 534 TYR cc_start: 0.8605 (m-80) cc_final: 0.8238 (m-80) REVERT: E 465 ASN cc_start: 0.8575 (m-40) cc_final: 0.8342 (m-40) REVERT: E 483 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7597 (t0) REVERT: E 508 GLU cc_start: 0.7897 (tp30) cc_final: 0.7541 (tp30) REVERT: H 461 ARG cc_start: 0.8095 (mmm160) cc_final: 0.7869 (tpt90) REVERT: H 489 MET cc_start: 0.8332 (mmp) cc_final: 0.8066 (mmm) REVERT: H 532 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6716 (mm-30) REVERT: J 19 SER cc_start: 0.8601 (OUTLIER) cc_final: 0.8213 (p) REVERT: K 347 VAL cc_start: 0.0101 (OUTLIER) cc_final: -0.0272 (m) REVERT: K 483 ASP cc_start: 0.8187 (t0) cc_final: 0.7919 (t0) REVERT: K 568 MET cc_start: 0.5849 (pmm) cc_final: 0.5442 (pmm) REVERT: L 521 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7321 (tp) REVERT: R 36 LYS cc_start: 0.7214 (tptt) cc_final: 0.6887 (tptt) REVERT: U 66 ASN cc_start: 0.7840 (p0) cc_final: 0.7401 (t0) REVERT: V 81 TYR cc_start: 0.7624 (OUTLIER) cc_final: 0.7137 (m-80) REVERT: V 83 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.6920 (ptt-90) REVERT: V 87 PHE cc_start: 0.7788 (t80) cc_final: 0.7341 (t80) outliers start: 102 outliers final: 76 residues processed: 370 average time/residue: 0.1294 time to fit residues: 77.3531 Evaluate side-chains 344 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 257 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 368 LEU 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 515 TYR Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 358 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 475 LEU 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 551 THR Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 430 HIS Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 487 GLN Chi-restraints excluded: chain F residue 518 HIS 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 462 GLU Chi-restraints excluded: chain H residue 522 THR 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 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 521 LEU Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 562 TYR Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 22 GLU Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 122 VAL Chi-restraints excluded: chain V residue 81 TYR Chi-restraints excluded: chain V residue 83 ARG Chi-restraints excluded: chain V residue 118 VAL Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 123 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 239 optimal weight: 10.0000 chunk 254 optimal weight: 8.9990 chunk 145 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 30 optimal weight: 50.0000 chunk 62 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 47 optimal weight: 20.0000 chunk 55 optimal weight: 0.0570 chunk 195 optimal weight: 20.0000 overall best weight: 2.8102 ------------------------------------------------------------------------------- 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 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.115575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.075224 restraints weight = 73999.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.077632 restraints weight = 38283.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.079083 restraints weight = 26513.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.079912 restraints weight = 21684.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.080294 restraints weight = 19481.331| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3687 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= 0.176 Angle : 0.732 15.421 30412 Z= 0.359 Chirality : 0.049 0.478 3600 Planarity : 0.005 0.085 3863 Dihedral : 6.506 59.616 3224 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 4.69 % Allowed : 20.75 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.16), residues: 2737 helix: -0.88 (0.32), residues: 235 sheet: -0.82 (0.16), residues: 1048 loop : -1.37 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 461 TYR 0.024 0.002 TYR K 455 PHE 0.032 0.002 PHE H 516 TRP 0.014 0.001 TRP K 528 HIS 0.004 0.001 HIS E 430 Details of bonding type rmsd covalent geometry : bond 0.00405 (22196) covalent geometry : angle 0.71270 (30314) SS BOND : bond 0.00498 ( 34) SS BOND : angle 1.21470 ( 68) hydrogen bonds : bond 0.03534 ( 647) hydrogen bonds : angle 5.66293 ( 1941) Misc. bond : bond 0.00050 ( 2) link_NAG-ASN : bond 0.00579 ( 10) link_NAG-ASN : angle 5.20570 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 258 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 PHE cc_start: 0.5904 (t80) cc_final: 0.5702 (t80) REVERT: A 358 PHE cc_start: 0.7602 (OUTLIER) cc_final: 0.7082 (p90) REVERT: A 368 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6538 (tp) REVERT: A 376 ASP cc_start: 0.6429 (t0) cc_final: 0.6062 (p0) REVERT: A 455 TYR cc_start: 0.7997 (m-10) cc_final: 0.7606 (m-10) REVERT: A 550 ARG cc_start: 0.8314 (mmm160) cc_final: 0.7760 (mmm160) REVERT: B 415 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8249 (mp0) REVERT: C 395 ASN cc_start: 0.5024 (t0) cc_final: 0.4732 (t0) REVERT: C 561 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8261 (mm) REVERT: D 370 THR cc_start: 0.2289 (OUTLIER) cc_final: 0.2070 (m) REVERT: D 429 THR cc_start: 0.4532 (OUTLIER) cc_final: 0.4307 (m) REVERT: D 489 MET cc_start: 0.8427 (tpp) cc_final: 0.8142 (mmt) REVERT: D 510 GLN cc_start: 0.8415 (pp30) cc_final: 0.8110 (pp30) REVERT: D 534 TYR cc_start: 0.8654 (m-80) cc_final: 0.8353 (m-80) REVERT: E 483 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.7705 (t0) REVERT: F 365 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7184 (mm) REVERT: H 489 MET cc_start: 0.8511 (mmp) cc_final: 0.8219 (mmm) REVERT: H 532 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.7113 (tp30) REVERT: H 567 VAL cc_start: 0.6997 (OUTLIER) cc_final: 0.6782 (m) REVERT: J 19 SER cc_start: 0.8660 (OUTLIER) cc_final: 0.8288 (p) REVERT: K 347 VAL cc_start: -0.0012 (OUTLIER) cc_final: -0.0418 (m) REVERT: K 453 ASP cc_start: 0.8407 (m-30) cc_final: 0.7570 (p0) REVERT: K 483 ASP cc_start: 0.8202 (t0) cc_final: 0.7932 (t0) REVERT: K 487 GLN cc_start: 0.8269 (tm-30) cc_final: 0.7568 (tm-30) REVERT: K 506 MET cc_start: 0.7668 (mpp) cc_final: 0.7435 (mpp) REVERT: K 568 MET cc_start: 0.6032 (pmm) cc_final: 0.5681 (pmm) REVERT: L 521 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7098 (tp) REVERT: R 36 LYS cc_start: 0.7166 (tptt) cc_final: 0.6854 (tptt) REVERT: S 87 PHE cc_start: 0.7568 (m-80) cc_final: 0.7107 (m-80) REVERT: V 81 TYR cc_start: 0.7636 (OUTLIER) cc_final: 0.7152 (m-80) REVERT: V 83 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.6948 (ptt-90) REVERT: V 87 PHE cc_start: 0.7779 (t80) cc_final: 0.7337 (t80) outliers start: 116 outliers final: 86 residues processed: 354 average time/residue: 0.1262 time to fit residues: 71.7848 Evaluate side-chains 349 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 248 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 515 TYR Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 358 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 348 PHE Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 429 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 449 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain F residue 354 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 430 HIS Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 487 GLN Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 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 462 GLU Chi-restraints excluded: chain H residue 522 THR 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 567 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 63 HIS Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 375 TYR Chi-restraints excluded: chain K residue 474 CYS Chi-restraints excluded: chain K residue 475 LEU Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 528 TRP Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain K residue 567 VAL Chi-restraints excluded: chain L residue 475 LEU Chi-restraints excluded: chain L residue 521 LEU Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 562 TYR Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain U residue 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 81 TYR 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 267 optimal weight: 8.9990 chunk 110 optimal weight: 30.0000 chunk 163 optimal weight: 30.0000 chunk 154 optimal weight: 50.0000 chunk 134 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 180 optimal weight: 8.9990 chunk 157 optimal weight: 0.0870 chunk 146 optimal weight: 3.9990 chunk 222 optimal weight: 20.0000 overall best weight: 2.5562 ------------------------------------------------------------------------------- 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 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 393 HIS ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.115215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.074306 restraints weight = 74368.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.076800 restraints weight = 37580.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.078314 restraints weight = 25755.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.079170 restraints weight = 20979.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.079538 restraints weight = 18835.103| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3810 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= 0.166 Angle : 0.735 13.743 30412 Z= 0.360 Chirality : 0.048 0.503 3600 Planarity : 0.005 0.085 3863 Dihedral : 6.354 59.926 3224 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 4.41 % Allowed : 21.24 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.16), residues: 2737 helix: -0.91 (0.32), residues: 226 sheet: -0.74 (0.16), residues: 1029 loop : -1.31 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 346 TYR 0.023 0.002 TYR K 455 PHE 0.031 0.002 PHE H 516 TRP 0.014 0.001 TRP K 528 HIS 0.004 0.001 HIS L 450 Details of bonding type rmsd covalent geometry : bond 0.00383 (22196) covalent geometry : angle 0.71674 (30314) SS BOND : bond 0.00505 ( 34) SS BOND : angle 1.24702 ( 68) hydrogen bonds : bond 0.03499 ( 647) hydrogen bonds : angle 5.58850 ( 1941) Misc. bond : bond 0.00031 ( 2) link_NAG-ASN : bond 0.00594 ( 10) link_NAG-ASN : angle 4.93345 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 262 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 PHE cc_start: 0.5948 (t80) cc_final: 0.5699 (t80) REVERT: A 358 PHE cc_start: 0.7649 (OUTLIER) cc_final: 0.7135 (p90) REVERT: A 376 ASP cc_start: 0.6516 (t0) cc_final: 0.6132 (p0) REVERT: A 455 TYR cc_start: 0.8058 (m-10) cc_final: 0.7705 (m-10) REVERT: A 550 ARG cc_start: 0.8404 (mmm160) cc_final: 0.7797 (mmm160) REVERT: B 415 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8323 (mp0) REVERT: B 515 TYR cc_start: 0.7330 (OUTLIER) cc_final: 0.6640 (m-80) REVERT: C 395 ASN cc_start: 0.4921 (t0) cc_final: 0.4410 (m-40) REVERT: C 430 HIS cc_start: 0.3925 (OUTLIER) cc_final: 0.3692 (t70) REVERT: C 561 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8124 (mm) REVERT: D 370 THR cc_start: 0.2303 (OUTLIER) cc_final: 0.2088 (m) REVERT: D 429 THR cc_start: 0.4342 (OUTLIER) cc_final: 0.4110 (m) REVERT: D 489 MET cc_start: 0.8423 (tpp) cc_final: 0.8088 (mmt) REVERT: D 510 GLN cc_start: 0.8517 (pp30) cc_final: 0.8175 (pp30) REVERT: D 534 TYR cc_start: 0.8697 (m-80) cc_final: 0.8227 (m-80) REVERT: E 483 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.7696 (t0) REVERT: F 365 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7155 (mm) REVERT: G 483 ASP cc_start: 0.7853 (t0) cc_final: 0.7640 (t0) REVERT: H 567 VAL cc_start: 0.7035 (OUTLIER) cc_final: 0.6807 (m) REVERT: J 19 SER cc_start: 0.8649 (OUTLIER) cc_final: 0.8283 (p) REVERT: J 46 ARG cc_start: 0.7955 (mmt180) cc_final: 0.7163 (mmm160) REVERT: K 347 VAL cc_start: -0.0076 (OUTLIER) cc_final: -0.0489 (m) REVERT: K 453 ASP cc_start: 0.8512 (m-30) cc_final: 0.7570 (p0) REVERT: K 483 ASP cc_start: 0.8222 (t0) cc_final: 0.7903 (t0) REVERT: K 487 GLN cc_start: 0.8253 (tm-30) cc_final: 0.7485 (tm-30) REVERT: K 506 MET cc_start: 0.7824 (mpp) cc_final: 0.7564 (mpp) REVERT: K 568 MET cc_start: 0.6018 (pmm) cc_final: 0.5655 (pmm) REVERT: L 521 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7184 (tp) REVERT: R 36 LYS cc_start: 0.7199 (tptt) cc_final: 0.6840 (tppt) REVERT: S 87 PHE cc_start: 0.7772 (m-80) cc_final: 0.7183 (m-80) REVERT: U 42 MET cc_start: 0.6845 (tpp) cc_final: 0.6503 (tpp) REVERT: U 66 ASN cc_start: 0.8045 (p0) cc_final: 0.7517 (t0) REVERT: V 81 TYR cc_start: 0.7737 (OUTLIER) cc_final: 0.7195 (m-80) REVERT: V 83 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.6988 (ptt-90) REVERT: V 87 PHE cc_start: 0.7901 (t80) cc_final: 0.7384 (t80) outliers start: 109 outliers final: 82 residues processed: 353 average time/residue: 0.1205 time to fit residues: 69.0074 Evaluate side-chains 350 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 253 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 515 TYR Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 358 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain 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 429 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 449 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 430 HIS Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 487 GLN Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 533 THR Chi-restraints excluded: chain F residue 553 ASP Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 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 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 567 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 63 HIS Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 375 TYR Chi-restraints excluded: chain K residue 474 CYS Chi-restraints excluded: chain K residue 475 LEU Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 528 TRP Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain L residue 521 LEU Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 562 TYR Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain 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 81 TYR 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 171 optimal weight: 3.9990 chunk 190 optimal weight: 0.3980 chunk 26 optimal weight: 0.0670 chunk 235 optimal weight: 9.9990 chunk 91 optimal weight: 30.0000 chunk 121 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 chunk 137 optimal weight: 30.0000 chunk 43 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 overall best weight: 2.4924 ------------------------------------------------------------------------------- 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 529 ASN ** 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 63 HIS K 518 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 = 0.4189 r_free = 0.4189 target = 0.115269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.074317 restraints weight = 74615.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.076838 restraints weight = 37707.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.078333 restraints weight = 25791.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.079200 restraints weight = 21025.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.079547 restraints weight = 18827.572| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22242 Z= 0.164 Angle : 0.736 13.130 30412 Z= 0.360 Chirality : 0.048 0.492 3600 Planarity : 0.005 0.085 3863 Dihedral : 6.243 59.830 3223 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.88 % Allowed : 21.80 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.16), residues: 2737 helix: -0.77 (0.32), residues: 233 sheet: -0.67 (0.16), residues: 1025 loop : -1.31 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 461 TYR 0.019 0.002 TYR C 375 PHE 0.030 0.002 PHE H 516 TRP 0.015 0.001 TRP K 528 HIS 0.005 0.001 HIS D 450 Details of bonding type rmsd covalent geometry : bond 0.00379 (22196) covalent geometry : angle 0.71971 (30314) SS BOND : bond 0.00453 ( 34) SS BOND : angle 1.16194 ( 68) hydrogen bonds : bond 0.03476 ( 647) hydrogen bonds : angle 5.56189 ( 1941) Misc. bond : bond 0.00030 ( 2) link_NAG-ASN : bond 0.00586 ( 10) link_NAG-ASN : angle 4.76912 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 264 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 PHE cc_start: 0.5905 (t80) cc_final: 0.5618 (t80) REVERT: A 358 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.7158 (p90) REVERT: A 375 TYR cc_start: 0.8921 (m-10) cc_final: 0.8457 (p90) REVERT: A 376 ASP cc_start: 0.6523 (t0) cc_final: 0.6176 (p0) REVERT: A 455 TYR cc_start: 0.8035 (m-10) cc_final: 0.7682 (m-10) REVERT: A 550 ARG cc_start: 0.8420 (mmm160) cc_final: 0.7806 (mmm160) REVERT: B 415 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8312 (mp0) REVERT: B 515 TYR cc_start: 0.7282 (OUTLIER) cc_final: 0.6548 (m-80) REVERT: C 395 ASN cc_start: 0.4970 (t0) cc_final: 0.4428 (m-40) REVERT: C 430 HIS cc_start: 0.3670 (OUTLIER) cc_final: 0.3424 (t70) REVERT: C 561 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8127 (mm) REVERT: D 370 THR cc_start: 0.2269 (OUTLIER) cc_final: 0.2065 (m) REVERT: D 429 THR cc_start: 0.4338 (OUTLIER) cc_final: 0.4125 (m) REVERT: D 510 GLN cc_start: 0.8512 (pp30) cc_final: 0.8169 (pp30) REVERT: D 534 TYR cc_start: 0.8692 (m-80) cc_final: 0.8306 (m-80) REVERT: E 461 ARG cc_start: 0.8375 (mmm160) cc_final: 0.8148 (mmm160) REVERT: E 483 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.7744 (t0) REVERT: F 365 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7187 (mm) REVERT: G 483 ASP cc_start: 0.7830 (t0) cc_final: 0.7616 (t0) REVERT: J 19 SER cc_start: 0.8633 (OUTLIER) cc_final: 0.8281 (p) REVERT: J 46 ARG cc_start: 0.7927 (mmt180) cc_final: 0.7130 (mmm160) REVERT: K 347 VAL cc_start: -0.0002 (OUTLIER) cc_final: -0.0438 (m) REVERT: K 453 ASP cc_start: 0.8504 (m-30) cc_final: 0.7461 (p0) REVERT: K 483 ASP cc_start: 0.8205 (t0) cc_final: 0.7890 (t0) REVERT: K 487 GLN cc_start: 0.8247 (tm-30) cc_final: 0.7492 (tm-30) REVERT: K 506 MET cc_start: 0.7805 (mpp) cc_final: 0.7453 (mpp) REVERT: K 568 MET cc_start: 0.6048 (pmm) cc_final: 0.5734 (pmm) REVERT: L 521 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7409 (tp) REVERT: R 36 LYS cc_start: 0.7209 (tptt) cc_final: 0.6874 (tptt) REVERT: S 87 PHE cc_start: 0.7826 (m-80) cc_final: 0.7244 (m-80) REVERT: U 66 ASN cc_start: 0.8002 (p0) cc_final: 0.7482 (t0) REVERT: V 81 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.7266 (m-80) REVERT: V 83 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.6969 (ptt-90) REVERT: V 87 PHE cc_start: 0.7881 (t80) cc_final: 0.7352 (t80) outliers start: 96 outliers final: 76 residues processed: 343 average time/residue: 0.1211 time to fit residues: 67.2666 Evaluate side-chains 348 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 258 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 552 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 515 TYR Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 358 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 489 MET Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 348 PHE Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 429 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 449 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 487 GLN Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 533 THR Chi-restraints excluded: chain F residue 553 ASP Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 394 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 522 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 375 TYR Chi-restraints excluded: chain K residue 474 CYS Chi-restraints excluded: chain K residue 475 LEU Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 528 TRP Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 545 ASN Chi-restraints excluded: chain L residue 521 LEU Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 562 TYR Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 95 THR 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 81 TYR 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 80 optimal weight: 0.0370 chunk 2 optimal weight: 50.0000 chunk 51 optimal weight: 20.0000 chunk 110 optimal weight: 30.0000 chunk 67 optimal weight: 8.9990 chunk 245 optimal weight: 0.5980 chunk 161 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 193 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 overall best weight: 2.9264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 HIS ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.114844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.073955 restraints weight = 74490.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.076433 restraints weight = 37615.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.077929 restraints weight = 25798.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.078525 restraints weight = 21007.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.079170 restraints weight = 19080.128| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22242 Z= 0.180 Angle : 0.745 13.029 30412 Z= 0.365 Chirality : 0.048 0.494 3600 Planarity : 0.005 0.085 3863 Dihedral : 6.201 59.653 3221 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.92 % Allowed : 21.80 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.16), residues: 2737 helix: -0.69 (0.33), residues: 232 sheet: -0.69 (0.16), residues: 1017 loop : -1.34 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 461 TYR 0.022 0.002 TYR K 455 PHE 0.032 0.002 PHE H 516 TRP 0.015 0.001 TRP K 528 HIS 0.011 0.001 HIS K 518 Details of bonding type rmsd covalent geometry : bond 0.00416 (22196) covalent geometry : angle 0.72913 (30314) SS BOND : bond 0.00483 ( 34) SS BOND : angle 1.21202 ( 68) hydrogen bonds : bond 0.03512 ( 647) hydrogen bonds : angle 5.58558 ( 1941) Misc. bond : bond 0.00029 ( 2) link_NAG-ASN : bond 0.00578 ( 10) link_NAG-ASN : angle 4.70148 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4702.84 seconds wall clock time: 81 minutes 45.71 seconds (4905.71 seconds total)