Starting phenix.real_space_refine on Tue Mar 19 05:46:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgf_22868/03_2024/7kgf_22868.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgf_22868/03_2024/7kgf_22868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgf_22868/03_2024/7kgf_22868.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgf_22868/03_2024/7kgf_22868.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgf_22868/03_2024/7kgf_22868.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgf_22868/03_2024/7kgf_22868.pdb" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.139 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 135 5.16 5 C 15120 2.51 5 N 3792 2.21 5 O 4308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 7": "NH1" <-> "NH2" Residue "A ARG 8": "NH1" <-> "NH2" Residue "A ARG 34": "NH1" <-> "NH2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A ARG 123": "NH1" <-> "NH2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A ARG 160": "NH1" <-> "NH2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A GLU 269": "OE1" <-> "OE2" Residue "A GLU 304": "OE1" <-> "OE2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A GLU 563": "OE1" <-> "OE2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A ARG 585": "NH1" <-> "NH2" Residue "A ARG 632": "NH1" <-> "NH2" Residue "A GLU 652": "OE1" <-> "OE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 665": "OE1" <-> "OE2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A GLU 693": "OE1" <-> "OE2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "A ARG 771": "NH1" <-> "NH2" Residue "A ARG 809": "NH1" <-> "NH2" Residue "A ARG 813": "NH1" <-> "NH2" Residue "A GLU 830": "OE1" <-> "OE2" Residue "A ARG 833": "NH1" <-> "NH2" Residue "A GLU 849": "OE1" <-> "OE2" Residue "A GLU 884": "OE1" <-> "OE2" Residue "A ARG 910": "NH1" <-> "NH2" Residue "A ARG 961": "NH1" <-> "NH2" Residue "A ARG 963": "NH1" <-> "NH2" Residue "B ARG 7": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ARG 160": "NH1" <-> "NH2" Residue "B ARG 168": "NH1" <-> "NH2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B ARG 185": "NH1" <-> "NH2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B ARG 218": "NH1" <-> "NH2" Residue "B GLU 269": "OE1" <-> "OE2" Residue "B GLU 304": "OE1" <-> "OE2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B GLU 322": "OE1" <-> "OE2" Residue "B GLU 414": "OE1" <-> "OE2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B ARG 418": "NH1" <-> "NH2" Residue "B GLU 563": "OE1" <-> "OE2" Residue "B ARG 583": "NH1" <-> "NH2" Residue "B ARG 585": "NH1" <-> "NH2" Residue "B ARG 632": "NH1" <-> "NH2" Residue "B GLU 652": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 665": "OE1" <-> "OE2" Residue "B ARG 675": "NH1" <-> "NH2" Residue "B ARG 679": "NH1" <-> "NH2" Residue "B GLU 693": "OE1" <-> "OE2" Residue "B ARG 758": "NH1" <-> "NH2" Residue "B ARG 771": "NH1" <-> "NH2" Residue "B ARG 809": "NH1" <-> "NH2" Residue "B ARG 813": "NH1" <-> "NH2" Residue "B GLU 830": "OE1" <-> "OE2" Residue "B ARG 833": "NH1" <-> "NH2" Residue "B GLU 849": "OE1" <-> "OE2" Residue "B GLU 884": "OE1" <-> "OE2" Residue "B ARG 910": "NH1" <-> "NH2" Residue "B ARG 961": "NH1" <-> "NH2" Residue "B ARG 963": "NH1" <-> "NH2" Residue "C ARG 7": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C ARG 123": "NH1" <-> "NH2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C ARG 160": "NH1" <-> "NH2" Residue "C ARG 168": "NH1" <-> "NH2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C ARG 185": "NH1" <-> "NH2" Residue "C ARG 208": "NH1" <-> "NH2" Residue "C GLU 209": "OE1" <-> "OE2" Residue "C ARG 218": "NH1" <-> "NH2" Residue "C GLU 269": "OE1" <-> "OE2" Residue "C GLU 304": "OE1" <-> "OE2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C GLU 311": "OE1" <-> "OE2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "C GLU 414": "OE1" <-> "OE2" Residue "C GLU 417": "OE1" <-> "OE2" Residue "C ARG 418": "NH1" <-> "NH2" Residue "C GLU 563": "OE1" <-> "OE2" Residue "C ARG 583": "NH1" <-> "NH2" Residue "C ARG 585": "NH1" <-> "NH2" Residue "C ARG 632": "NH1" <-> "NH2" Residue "C GLU 652": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 665": "OE1" <-> "OE2" Residue "C ARG 675": "NH1" <-> "NH2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C GLU 693": "OE1" <-> "OE2" Residue "C ARG 758": "NH1" <-> "NH2" Residue "C ARG 771": "NH1" <-> "NH2" Residue "C ARG 809": "NH1" <-> "NH2" Residue "C ARG 813": "NH1" <-> "NH2" Residue "C GLU 830": "OE1" <-> "OE2" Residue "C ARG 833": "NH1" <-> "NH2" Residue "C GLU 849": "OE1" <-> "OE2" Residue "C GLU 884": "OE1" <-> "OE2" Residue "C ARG 910": "NH1" <-> "NH2" Residue "C ARG 961": "NH1" <-> "NH2" Residue "C ARG 963": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23355 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7785 Classifications: {'peptide': 1020} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 973} Chain breaks: 1 Chain: "B" Number of atoms: 7785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7785 Classifications: {'peptide': 1020} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 973} Chain breaks: 1 Chain: "C" Number of atoms: 7785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7785 Classifications: {'peptide': 1020} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 973} Chain breaks: 1 Time building chain proxies: 13.31, per 1000 atoms: 0.57 Number of scatterers: 23355 At special positions: 0 Unit cell: (119.88, 123.12, 140.4, 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 135 16.00 O 4308 8.00 N 3792 7.00 C 15120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=0, symmetry=0 Time building additional restraints: 10.20 Conformation dependent library (CDL) restraints added in 4.0 seconds 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5706 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 24 sheets defined 61.6% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.74 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 8 through 30 removed outlier: 4.289A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) Proline residue: A 28 - end of helix Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 70 removed outlier: 3.777A pdb=" N ARG A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 116 removed outlier: 4.290A pdb=" N ALA A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 removed outlier: 3.626A pdb=" N GLN A 125 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 161 through 169 removed outlier: 3.545A pdb=" N ARG A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A 169 " --> pdb=" O GLU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 197 removed outlier: 3.652A pdb=" N LEU A 193 " --> pdb=" O ASP A 189 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 194 " --> pdb=" O PRO A 190 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.615A pdb=" N PHE A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 298 through 314 Processing helix chain 'A' and resid 329 through 360 removed outlier: 3.915A pdb=" N VAL A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE A 335 " --> pdb=" O PRO A 331 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET A 355 " --> pdb=" O VAL A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 387 removed outlier: 4.064A pdb=" N ILE A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Proline residue: A 368 - end of helix removed outlier: 3.852A pdb=" N VAL A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 391 through 406 removed outlier: 4.498A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 424 Processing helix chain 'A' and resid 426 through 453 removed outlier: 5.326A pdb=" N SER A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) Proline residue: A 441 - end of helix removed outlier: 4.319A pdb=" N PHE A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 458 removed outlier: 3.630A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE A 458 " --> pdb=" O LEU A 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 453 through 458' Processing helix chain 'A' and resid 460 through 497 removed outlier: 3.571A pdb=" N GLY A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR A 473 " --> pdb=" O GLN A 469 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 509 through 534 Processing helix chain 'A' and resid 535 through 556 Processing helix chain 'A' and resid 580 through 597 removed outlier: 3.609A pdb=" N THR A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP A 597 " --> pdb=" O ASN A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 632 Processing helix chain 'A' and resid 635 through 650 Processing helix chain 'A' and resid 683 through 701 removed outlier: 3.681A pdb=" N LYS A 700 " --> pdb=" O ALA A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 730 Processing helix chain 'A' and resid 733 through 743 removed outlier: 3.651A pdb=" N VAL A 737 " --> pdb=" O LYS A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 771 removed outlier: 3.567A pdb=" N ARG A 771 " --> pdb=" O ALA A 768 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 768 through 771' Processing helix chain 'A' and resid 773 through 779 removed outlier: 3.879A pdb=" N ILE A 777 " --> pdb=" O GLN A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 841 removed outlier: 3.783A pdb=" N LYS A 841 " --> pdb=" O GLN A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 862 Processing helix chain 'A' and resid 863 through 884 Processing helix chain 'A' and resid 886 through 894 Processing helix chain 'A' and resid 895 through 911 Processing helix chain 'A' and resid 915 through 947 removed outlier: 3.807A pdb=" N ILE A 936 " --> pdb=" O ASN A 932 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 981 removed outlier: 5.016A pdb=" N ARG A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Proline residue: A 964 - end of helix Proline residue: A 978 - end of helix Processing helix chain 'A' and resid 986 through 1027 removed outlier: 4.802A pdb=" N GLY A 996 " --> pdb=" O ALA A 992 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL A 997 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE A1010 " --> pdb=" O ILE A1006 " (cutoff:3.500A) Proline residue: A1013 - end of helix Processing helix chain 'B' and resid 3 through 8 Processing helix chain 'B' and resid 8 through 30 removed outlier: 4.289A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Proline residue: B 28 - end of helix Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 70 removed outlier: 3.777A pdb=" N ARG B 67 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 116 removed outlier: 4.291A pdb=" N ALA B 116 " --> pdb=" O LYS B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 removed outlier: 3.626A pdb=" N GLN B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 161 through 169 removed outlier: 3.546A pdb=" N ARG B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 197 removed outlier: 3.651A pdb=" N LEU B 193 " --> pdb=" O ASP B 189 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 194 " --> pdb=" O PRO B 190 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B 195 " --> pdb=" O ASN B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.614A pdb=" N PHE B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 298 through 314 Processing helix chain 'B' and resid 329 through 360 removed outlier: 3.914A pdb=" N VAL B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE B 335 " --> pdb=" O PRO B 331 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET B 355 " --> pdb=" O VAL B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 387 removed outlier: 4.064A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix removed outlier: 3.851A pdb=" N VAL B 371 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA B 372 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 391 through 406 removed outlier: 4.498A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 424 Processing helix chain 'B' and resid 426 through 453 removed outlier: 5.325A pdb=" N SER B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Proline residue: B 441 - end of helix removed outlier: 4.319A pdb=" N PHE B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.629A pdb=" N ALA B 457 " --> pdb=" O PHE B 453 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 453 through 458' Processing helix chain 'B' and resid 460 through 497 removed outlier: 3.572A pdb=" N GLY B 464 " --> pdb=" O SER B 460 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR B 473 " --> pdb=" O GLN B 469 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Proline residue: B 490 - end of helix Processing helix chain 'B' and resid 509 through 534 Processing helix chain 'B' and resid 535 through 556 Processing helix chain 'B' and resid 580 through 597 removed outlier: 3.609A pdb=" N THR B 584 " --> pdb=" O THR B 580 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP B 597 " --> pdb=" O ASN B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 635 through 650 Processing helix chain 'B' and resid 683 through 701 removed outlier: 3.683A pdb=" N LYS B 700 " --> pdb=" O ALA B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 730 Processing helix chain 'B' and resid 733 through 743 removed outlier: 3.652A pdb=" N VAL B 737 " --> pdb=" O LYS B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 771 removed outlier: 3.567A pdb=" N ARG B 771 " --> pdb=" O ALA B 768 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 768 through 771' Processing helix chain 'B' and resid 773 through 779 removed outlier: 3.880A pdb=" N ILE B 777 " --> pdb=" O GLN B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 841 removed outlier: 3.782A pdb=" N LYS B 841 " --> pdb=" O GLN B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 862 Processing helix chain 'B' and resid 863 through 884 Processing helix chain 'B' and resid 886 through 894 Processing helix chain 'B' and resid 895 through 911 Processing helix chain 'B' and resid 915 through 947 removed outlier: 3.807A pdb=" N ILE B 936 " --> pdb=" O ASN B 932 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE B 939 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 981 removed outlier: 5.016A pdb=" N ARG B 963 " --> pdb=" O LYS B 959 " (cutoff:3.500A) Proline residue: B 964 - end of helix Proline residue: B 978 - end of helix Processing helix chain 'B' and resid 986 through 1027 removed outlier: 4.802A pdb=" N GLY B 996 " --> pdb=" O ALA B 992 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL B 997 " --> pdb=" O LEU B 993 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE B1010 " --> pdb=" O ILE B1006 " (cutoff:3.500A) Proline residue: B1013 - end of helix Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 8 through 30 removed outlier: 4.288A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Proline residue: C 28 - end of helix Processing helix chain 'C' and resid 53 through 61 Processing helix chain 'C' and resid 61 through 70 removed outlier: 3.777A pdb=" N ARG C 67 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 116 removed outlier: 4.291A pdb=" N ALA C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 removed outlier: 3.627A pdb=" N GLN C 125 " --> pdb=" O VAL C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 161 Processing helix chain 'C' and resid 161 through 169 removed outlier: 3.546A pdb=" N ARG C 168 " --> pdb=" O GLU C 164 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL C 169 " --> pdb=" O GLU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 197 removed outlier: 3.652A pdb=" N LEU C 193 " --> pdb=" O ASP C 189 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C 194 " --> pdb=" O PRO C 190 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER C 195 " --> pdb=" O ASN C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 211 Processing helix chain 'C' and resid 242 through 248 removed outlier: 3.614A pdb=" N PHE C 246 " --> pdb=" O SER C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 265 No H-bonds generated for 'chain 'C' and resid 262 through 265' Processing helix chain 'C' and resid 298 through 314 Processing helix chain 'C' and resid 329 through 360 removed outlier: 3.914A pdb=" N VAL C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS C 334 " --> pdb=" O ALA C 330 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE C 335 " --> pdb=" O PRO C 331 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET C 355 " --> pdb=" O VAL C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 387 removed outlier: 4.063A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix removed outlier: 3.850A pdb=" N VAL C 371 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) Proline residue: C 373 - end of helix Processing helix chain 'C' and resid 391 through 406 removed outlier: 4.498A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 424 Processing helix chain 'C' and resid 426 through 453 removed outlier: 5.326A pdb=" N SER C 440 " --> pdb=" O LYS C 436 " (cutoff:3.500A) Proline residue: C 441 - end of helix removed outlier: 4.319A pdb=" N PHE C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 458 removed outlier: 3.629A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE C 458 " --> pdb=" O LEU C 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 453 through 458' Processing helix chain 'C' and resid 460 through 497 removed outlier: 3.571A pdb=" N GLY C 464 " --> pdb=" O SER C 460 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR C 473 " --> pdb=" O GLN C 469 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) Proline residue: C 490 - end of helix Processing helix chain 'C' and resid 509 through 534 Processing helix chain 'C' and resid 535 through 556 Processing helix chain 'C' and resid 580 through 597 removed outlier: 3.609A pdb=" N THR C 584 " --> pdb=" O THR C 580 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP C 597 " --> pdb=" O ASN C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 632 Processing helix chain 'C' and resid 635 through 650 Processing helix chain 'C' and resid 683 through 701 removed outlier: 3.681A pdb=" N LYS C 700 " --> pdb=" O ALA C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 730 Processing helix chain 'C' and resid 733 through 743 removed outlier: 3.651A pdb=" N VAL C 737 " --> pdb=" O LYS C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 771 removed outlier: 3.568A pdb=" N ARG C 771 " --> pdb=" O ALA C 768 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 768 through 771' Processing helix chain 'C' and resid 773 through 779 removed outlier: 3.879A pdb=" N ILE C 777 " --> pdb=" O GLN C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 841 removed outlier: 3.782A pdb=" N LYS C 841 " --> pdb=" O GLN C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 862 Processing helix chain 'C' and resid 863 through 884 Processing helix chain 'C' and resid 886 through 894 Processing helix chain 'C' and resid 895 through 911 Processing helix chain 'C' and resid 915 through 946 removed outlier: 3.807A pdb=" N ILE C 936 " --> pdb=" O ASN C 932 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE C 939 " --> pdb=" O LEU C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 949 through 981 removed outlier: 5.017A pdb=" N ARG C 963 " --> pdb=" O LYS C 959 " (cutoff:3.500A) Proline residue: C 964 - end of helix Proline residue: C 978 - end of helix Processing helix chain 'C' and resid 986 through 1027 removed outlier: 4.803A pdb=" N GLY C 996 " --> pdb=" O ALA C 992 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL C 997 " --> pdb=" O LEU C 993 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE C1010 " --> pdb=" O ILE C1006 " (cutoff:3.500A) Proline residue: C1013 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 127 through 132 removed outlier: 3.715A pdb=" N SER A 132 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLN A 42 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N THR A 87 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N THR A 82 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU A 89 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA A 80 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR A 91 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR A 78 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR A 93 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN A 808 " --> pdb=" O SER A 815 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N MET A 706 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 132 removed outlier: 3.715A pdb=" N SER A 132 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLN A 42 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N THR A 87 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N THR A 82 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU A 89 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA A 80 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR A 91 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR A 78 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR A 93 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN A 808 " --> pdb=" O SER A 815 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.603A pdb=" N LYS A 174 " --> pdb=" O GLN A 292 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A 287 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET A 138 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU A 139 " --> pdb=" O PRO A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.603A pdb=" N LYS A 174 " --> pdb=" O GLN A 292 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 286 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER A 603 " --> pdb=" O THR A 625 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU A 654 " --> pdb=" O GLN A 574 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 272 removed outlier: 7.656A pdb=" N LYS A 182 " --> pdb=" O GLN A 761 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ILE A 763 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N MET A 184 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N GLN A 765 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE A 186 " --> pdb=" O GLN A 765 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ARG A 758 " --> pdb=" O PRO A 754 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLN A 760 " --> pdb=" O ASP A 752 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASP A 752 " --> pdb=" O GLN A 760 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL A 762 " --> pdb=" O ILE A 750 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 217 through 218 removed outlier: 4.073A pdb=" N ILE C 722 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS C 721 " --> pdb=" O THR C 797 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 250 through 252 Processing sheet with id=AA8, first strand: chain 'A' and resid 796 through 803 removed outlier: 3.692A pdb=" N LYS A 721 " --> pdb=" O THR A 797 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASP A 716 " --> pdb=" O PRO B 233 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N SER B 235 " --> pdb=" O ASP A 716 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE A 718 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N GLN B 237 " --> pdb=" O ILE A 718 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU A 720 " --> pdb=" O GLN B 237 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 781 through 783 Processing sheet with id=AB1, first strand: chain 'B' and resid 127 through 132 removed outlier: 3.714A pdb=" N SER B 132 " --> pdb=" O GLN B 42 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLN B 42 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N THR B 87 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N THR B 82 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU B 89 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA B 80 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR B 91 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR B 78 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR B 93 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN B 808 " --> pdb=" O SER B 815 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N MET B 706 " --> pdb=" O ILE B 821 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 127 through 132 removed outlier: 3.714A pdb=" N SER B 132 " --> pdb=" O GLN B 42 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLN B 42 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N THR B 87 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N THR B 82 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU B 89 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA B 80 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR B 91 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR B 78 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR B 93 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN B 808 " --> pdb=" O SER B 815 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.604A pdb=" N LYS B 174 " --> pdb=" O GLN B 292 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR B 287 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET B 138 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LEU B 139 " --> pdb=" O PRO B 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.604A pdb=" N LYS B 174 " --> pdb=" O GLN B 292 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 286 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER B 603 " --> pdb=" O THR B 625 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU B 654 " --> pdb=" O GLN B 574 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 266 through 272 removed outlier: 7.656A pdb=" N LYS B 182 " --> pdb=" O GLN B 761 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N ILE B 763 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N MET B 184 " --> pdb=" O ILE B 763 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLN B 765 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE B 186 " --> pdb=" O GLN B 765 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ARG B 758 " --> pdb=" O PRO B 754 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLN B 760 " --> pdb=" O ASP B 752 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP B 752 " --> pdb=" O GLN B 760 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL B 762 " --> pdb=" O ILE B 750 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 250 through 252 Processing sheet with id=AB7, first strand: chain 'B' and resid 796 through 803 removed outlier: 3.693A pdb=" N LYS B 721 " --> pdb=" O THR B 797 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ASP B 716 " --> pdb=" O PRO C 233 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N SER C 235 " --> pdb=" O ASP B 716 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE B 718 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N GLN C 237 " --> pdb=" O ILE B 718 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU B 720 " --> pdb=" O GLN C 237 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 781 through 783 Processing sheet with id=AB9, first strand: chain 'C' and resid 127 through 132 removed outlier: 3.715A pdb=" N SER C 132 " --> pdb=" O GLN C 42 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLN C 42 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N THR C 87 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N THR C 82 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU C 89 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA C 80 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR C 91 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR C 78 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR C 93 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN C 808 " --> pdb=" O SER C 815 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N MET C 706 " --> pdb=" O ILE C 821 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 127 through 132 removed outlier: 3.715A pdb=" N SER C 132 " --> pdb=" O GLN C 42 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLN C 42 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N THR C 87 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N THR C 82 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU C 89 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA C 80 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR C 91 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR C 78 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR C 93 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN C 808 " --> pdb=" O SER C 815 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 172 through 177 removed outlier: 3.603A pdb=" N LYS C 174 " --> pdb=" O GLN C 292 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR C 287 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET C 138 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU C 139 " --> pdb=" O PRO C 326 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 172 through 177 removed outlier: 3.603A pdb=" N LYS C 174 " --> pdb=" O GLN C 292 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C 286 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER C 603 " --> pdb=" O THR C 625 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU C 654 " --> pdb=" O GLN C 574 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 266 through 272 removed outlier: 7.656A pdb=" N LYS C 182 " --> pdb=" O GLN C 761 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N ILE C 763 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N MET C 184 " --> pdb=" O ILE C 763 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLN C 765 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE C 186 " --> pdb=" O GLN C 765 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ARG C 758 " --> pdb=" O PRO C 754 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLN C 760 " --> pdb=" O ASP C 752 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASP C 752 " --> pdb=" O GLN C 760 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL C 762 " --> pdb=" O ILE C 750 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 250 through 252 Processing sheet with id=AC6, first strand: chain 'C' and resid 781 through 783 1563 hydrogen bonds defined for protein. 4581 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: 10.92 Time building geometry restraints manager: 10.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.21: 33 1.21 - 1.36: 7431 1.36 - 1.52: 7083 1.52 - 1.67: 8970 1.67 - 1.82: 264 Bond restraints: 23781 Sorted by residual: bond pdb=" C SER A 817 " pdb=" O SER A 817 " ideal model delta sigma weight residual 1.236 1.062 0.173 1.22e-02 6.72e+03 2.02e+02 bond pdb=" C SER B 817 " pdb=" O SER B 817 " ideal model delta sigma weight residual 1.236 1.063 0.173 1.22e-02 6.72e+03 2.02e+02 bond pdb=" C SER C 817 " pdb=" O SER C 817 " ideal model delta sigma weight residual 1.236 1.063 0.173 1.22e-02 6.72e+03 2.01e+02 bond pdb=" C ILE C 57 " pdb=" O ILE C 57 " ideal model delta sigma weight residual 1.237 1.124 0.113 1.29e-02 6.01e+03 7.65e+01 bond pdb=" C ILE A 57 " pdb=" O ILE A 57 " ideal model delta sigma weight residual 1.237 1.124 0.113 1.29e-02 6.01e+03 7.64e+01 ... (remaining 23776 not shown) Histogram of bond angle deviations from ideal: 99.42 - 106.33: 684 106.33 - 113.24: 13261 113.24 - 120.15: 8240 120.15 - 127.06: 9866 127.06 - 133.97: 199 Bond angle restraints: 32250 Sorted by residual: angle pdb=" CA SER B 817 " pdb=" C SER B 817 " pdb=" O SER B 817 " ideal model delta sigma weight residual 120.36 107.26 13.10 1.07e+00 8.73e-01 1.50e+02 angle pdb=" CA SER C 817 " pdb=" C SER C 817 " pdb=" O SER C 817 " ideal model delta sigma weight residual 120.36 107.30 13.06 1.07e+00 8.73e-01 1.49e+02 angle pdb=" CA SER A 817 " pdb=" C SER A 817 " pdb=" O SER A 817 " ideal model delta sigma weight residual 120.36 107.34 13.02 1.07e+00 8.73e-01 1.48e+02 angle pdb=" CA MET A 835 " pdb=" C MET A 835 " pdb=" O MET A 835 " ideal model delta sigma weight residual 120.42 112.80 7.62 1.06e+00 8.90e-01 5.17e+01 angle pdb=" CA MET B 835 " pdb=" C MET B 835 " pdb=" O MET B 835 " ideal model delta sigma weight residual 120.42 112.80 7.62 1.06e+00 8.90e-01 5.16e+01 ... (remaining 32245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 13020 18.00 - 35.99: 1083 35.99 - 53.99: 234 53.99 - 71.98: 42 71.98 - 89.98: 30 Dihedral angle restraints: 14409 sinusoidal: 5592 harmonic: 8817 Sorted by residual: dihedral pdb=" CA ASN A 161 " pdb=" C ASN A 161 " pdb=" N VAL A 162 " pdb=" CA VAL A 162 " ideal model delta harmonic sigma weight residual -180.00 -161.62 -18.38 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA ASN B 161 " pdb=" C ASN B 161 " pdb=" N VAL B 162 " pdb=" CA VAL B 162 " ideal model delta harmonic sigma weight residual -180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA ASN C 161 " pdb=" C ASN C 161 " pdb=" N VAL C 162 " pdb=" CA VAL C 162 " ideal model delta harmonic sigma weight residual -180.00 -161.69 -18.31 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 14406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.341: 3864 0.341 - 0.682: 0 0.682 - 1.024: 0 1.024 - 1.365: 0 1.365 - 1.706: 6 Chirality restraints: 3870 Sorted by residual: chirality pdb=" CG LEU B 962 " pdb=" CB LEU B 962 " pdb=" CD1 LEU B 962 " pdb=" CD2 LEU B 962 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.28e+01 chirality pdb=" CG LEU C 962 " pdb=" CB LEU C 962 " pdb=" CD1 LEU C 962 " pdb=" CD2 LEU C 962 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.24e+01 chirality pdb=" CG LEU A 962 " pdb=" CB LEU A 962 " pdb=" CD1 LEU A 962 " pdb=" CD2 LEU A 962 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.24e+01 ... (remaining 3867 not shown) Planarity restraints: 4056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 656 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C MET C 656 " 0.056 2.00e-02 2.50e+03 pdb=" O MET C 656 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA C 657 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 338 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C GLU C 338 " 0.056 2.00e-02 2.50e+03 pdb=" O GLU C 338 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS C 339 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 656 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C MET A 656 " 0.056 2.00e-02 2.50e+03 pdb=" O MET A 656 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA A 657 " -0.020 2.00e-02 2.50e+03 ... (remaining 4053 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 132 2.55 - 3.14: 19551 3.14 - 3.73: 36108 3.73 - 4.31: 50279 4.31 - 4.90: 84808 Nonbonded interactions: 190878 Sorted by model distance: nonbonded pdb=" O ARG B 67 " pdb=" OG SER B 70 " model vdw 1.967 2.440 nonbonded pdb=" O ARG C 67 " pdb=" OG SER C 70 " model vdw 1.968 2.440 nonbonded pdb=" O ARG A 67 " pdb=" OG SER A 70 " model vdw 1.968 2.440 nonbonded pdb=" OD1 ASN B 143 " pdb=" N SER B 144 " model vdw 2.099 2.520 nonbonded pdb=" OD1 ASN A 143 " pdb=" N SER A 144 " model vdw 2.099 2.520 ... (remaining 190873 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.330 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 66.640 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 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 : 0.005 0.173 23781 Z= 0.347 Angle : 0.801 13.102 32250 Z= 0.517 Chirality : 0.080 1.706 3870 Planarity : 0.005 0.061 4056 Dihedral : 14.605 89.978 8703 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.94 % Allowed : 1.33 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.15), residues: 3048 helix: 1.76 (0.13), residues: 1647 sheet: 0.30 (0.24), residues: 429 loop : 0.05 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 187 HIS 0.003 0.001 HIS C 360 PHE 0.018 0.001 PHE C 569 TYR 0.009 0.001 TYR C 705 ARG 0.005 0.001 ARG B 724 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 514 time to evaluate : 2.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 LYS cc_start: 0.5992 (OUTLIER) cc_final: 0.5779 (mttm) REVERT: A 322 GLU cc_start: 0.7114 (tt0) cc_final: 0.6676 (tp30) REVERT: A 335 ILE cc_start: 0.8231 (tp) cc_final: 0.8028 (tp) REVERT: A 578 ASP cc_start: 0.7145 (OUTLIER) cc_final: 0.6887 (p0) REVERT: A 632 ARG cc_start: 0.6560 (mtm-85) cc_final: 0.5875 (mtm-85) REVERT: A 740 ILE cc_start: 0.6898 (tt) cc_final: 0.6630 (tt) REVERT: A 759 MET cc_start: 0.7595 (mmm) cc_final: 0.7267 (mmp) REVERT: A 783 MET cc_start: 0.6422 (tpp) cc_final: 0.6168 (tpt) REVERT: A 967 MET cc_start: 0.6128 (mtp) cc_final: 0.5904 (mmt) REVERT: B 192 LYS cc_start: 0.6015 (OUTLIER) cc_final: 0.5705 (mttm) REVERT: B 304 GLU cc_start: 0.5796 (mm-30) cc_final: 0.5543 (mm-30) REVERT: B 322 GLU cc_start: 0.6987 (tt0) cc_final: 0.6555 (tp30) REVERT: B 578 ASP cc_start: 0.7373 (OUTLIER) cc_final: 0.7075 (p0) REVERT: B 638 LYS cc_start: 0.7299 (mtpp) cc_final: 0.6681 (mtpp) REVERT: B 759 MET cc_start: 0.7508 (mmm) cc_final: 0.7225 (mmp) REVERT: C 35 PHE cc_start: 0.8568 (m-80) cc_final: 0.8244 (m-10) REVERT: C 192 LYS cc_start: 0.6286 (OUTLIER) cc_final: 0.5934 (mttm) REVERT: C 226 LYS cc_start: 0.7268 (mtpp) cc_final: 0.7011 (ttmm) REVERT: C 322 GLU cc_start: 0.7157 (tt0) cc_final: 0.6854 (tp30) REVERT: C 481 SER cc_start: 0.7568 (t) cc_final: 0.7294 (t) REVERT: C 578 ASP cc_start: 0.7179 (OUTLIER) cc_final: 0.6905 (p0) REVERT: C 632 ARG cc_start: 0.6569 (mtm-85) cc_final: 0.6073 (mtm-85) REVERT: C 638 LYS cc_start: 0.7412 (mtpp) cc_final: 0.6988 (mtpp) REVERT: C 656 MET cc_start: 0.7616 (mmm) cc_final: 0.7367 (tpt) REVERT: C 844 LYS cc_start: 0.7738 (ptmm) cc_final: 0.7359 (tmtt) REVERT: C 857 GLU cc_start: 0.8262 (tt0) cc_final: 0.7964 (tt0) REVERT: C 908 MET cc_start: 0.7204 (mtm) cc_final: 0.6915 (mtp) REVERT: C 942 MET cc_start: 0.5588 (mtp) cc_final: 0.5349 (mtt) REVERT: C 967 MET cc_start: 0.6163 (mtp) cc_final: 0.5962 (mmt) outliers start: 24 outliers final: 0 residues processed: 532 average time/residue: 0.3298 time to fit residues: 275.7177 Evaluate side-chains 439 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 433 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain C residue 192 LYS Chi-restraints excluded: chain C residue 578 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 9.9990 chunk 231 optimal weight: 7.9990 chunk 128 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 chunk 123 optimal weight: 8.9990 chunk 239 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 145 optimal weight: 20.0000 chunk 178 optimal weight: 9.9990 chunk 277 optimal weight: 8.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN ** A 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 ASN B 256 ASN ** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 ASN ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 23781 Z= 0.477 Angle : 0.772 10.302 32250 Z= 0.403 Chirality : 0.049 0.196 3870 Planarity : 0.006 0.068 4056 Dihedral : 5.246 51.115 3216 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.08 % Allowed : 11.35 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.15), residues: 3048 helix: 1.35 (0.12), residues: 1695 sheet: -0.09 (0.22), residues: 483 loop : -0.20 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 568 HIS 0.008 0.003 HIS B 360 PHE 0.025 0.002 PHE B 824 TYR 0.033 0.003 TYR C 77 ARG 0.009 0.001 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 477 time to evaluate : 2.473 Fit side-chains revert: symmetry clash REVERT: A 192 LYS cc_start: 0.6178 (OUTLIER) cc_final: 0.5819 (mttm) REVERT: A 269 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7004 (mt-10) REVERT: A 304 GLU cc_start: 0.6213 (mm-30) cc_final: 0.6013 (mm-30) REVERT: A 592 GLU cc_start: 0.7122 (pt0) cc_final: 0.6910 (pt0) REVERT: A 631 GLU cc_start: 0.6191 (mm-30) cc_final: 0.5396 (mm-30) REVERT: A 656 MET cc_start: 0.7804 (mmm) cc_final: 0.7494 (tpt) REVERT: A 723 ASP cc_start: 0.7301 (t0) cc_final: 0.7008 (t70) REVERT: A 832 MET cc_start: 0.8070 (mtp) cc_final: 0.7748 (mtp) REVERT: A 834 GLU cc_start: 0.6683 (mt-10) cc_final: 0.6328 (mm-30) REVERT: A 849 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7688 (mt-10) REVERT: A 893 MET cc_start: 0.6897 (mmt) cc_final: 0.6597 (mmt) REVERT: B 192 LYS cc_start: 0.6142 (OUTLIER) cc_final: 0.5797 (mttp) REVERT: B 213 GLU cc_start: 0.7439 (tp30) cc_final: 0.6998 (tt0) REVERT: B 334 LYS cc_start: 0.7916 (mmmm) cc_final: 0.7590 (mmmm) REVERT: B 435 MET cc_start: 0.7233 (mmm) cc_final: 0.6806 (mtt) REVERT: B 638 LYS cc_start: 0.7557 (mtpp) cc_final: 0.7265 (mtpp) REVERT: B 700 LYS cc_start: 0.7594 (ptpt) cc_final: 0.7329 (ptpt) REVERT: C 29 LYS cc_start: 0.6648 (mttt) cc_final: 0.6340 (mmmm) REVERT: C 68 GLU cc_start: 0.6701 (mm-30) cc_final: 0.6468 (tp30) REVERT: C 192 LYS cc_start: 0.6236 (OUTLIER) cc_final: 0.5866 (mttm) REVERT: C 226 LYS cc_start: 0.7402 (mtpp) cc_final: 0.7179 (ttmm) REVERT: C 269 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6799 (mt-10) REVERT: C 301 LYS cc_start: 0.7667 (mtpp) cc_final: 0.7315 (mttm) REVERT: C 322 GLU cc_start: 0.7307 (tt0) cc_final: 0.6959 (tp30) REVERT: C 561 MET cc_start: 0.6930 (mmm) cc_final: 0.6576 (mmm) REVERT: C 632 ARG cc_start: 0.6843 (mtm-85) cc_final: 0.6263 (mtm-85) REVERT: C 832 MET cc_start: 0.8039 (mtp) cc_final: 0.7783 (mtp) REVERT: C 849 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7549 (tp30) REVERT: C 905 ILE cc_start: 0.7557 (pt) cc_final: 0.7304 (mt) REVERT: C 967 MET cc_start: 0.6404 (mtp) cc_final: 0.6132 (mmt) outliers start: 79 outliers final: 57 residues processed: 520 average time/residue: 0.3336 time to fit residues: 272.6034 Evaluate side-chains 511 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 448 time to evaluate : 2.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 678 ASP Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 ASN Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 681 ASN Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 936 ILE Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 192 LYS Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 827 SER Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1024 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 20.0000 chunk 86 optimal weight: 7.9990 chunk 231 optimal weight: 6.9990 chunk 189 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 278 optimal weight: 0.6980 chunk 300 optimal weight: 5.9990 chunk 247 optimal weight: 9.9990 chunk 276 optimal weight: 3.9990 chunk 94 optimal weight: 40.0000 chunk 223 optimal weight: 5.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN A 714 GLN A 799 GLN ** A 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 ASN ** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN C 391 ASN ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 714 GLN ** C 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 23781 Z= 0.335 Angle : 0.651 11.128 32250 Z= 0.343 Chirality : 0.044 0.172 3870 Planarity : 0.005 0.059 4056 Dihedral : 5.108 56.182 3216 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.82 % Allowed : 15.52 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.15), residues: 3048 helix: 1.45 (0.12), residues: 1710 sheet: -0.19 (0.22), residues: 471 loop : -0.40 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 556 HIS 0.005 0.001 HIS B 360 PHE 0.022 0.002 PHE B 901 TYR 0.019 0.002 TYR C 77 ARG 0.004 0.001 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 465 time to evaluate : 2.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 LYS cc_start: 0.6022 (OUTLIER) cc_final: 0.5658 (mttm) REVERT: A 269 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7035 (mt-10) REVERT: A 656 MET cc_start: 0.7719 (mmm) cc_final: 0.7444 (tpt) REVERT: A 723 ASP cc_start: 0.7319 (t0) cc_final: 0.6993 (t70) REVERT: A 832 MET cc_start: 0.7933 (mtp) cc_final: 0.7642 (mtp) REVERT: A 834 GLU cc_start: 0.6767 (mt-10) cc_final: 0.6552 (mm-30) REVERT: A 893 MET cc_start: 0.6920 (mmt) cc_final: 0.6644 (mmt) REVERT: B 158 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8147 (tt) REVERT: B 192 LYS cc_start: 0.5977 (OUTLIER) cc_final: 0.5669 (mttm) REVERT: B 213 GLU cc_start: 0.7398 (tp30) cc_final: 0.6890 (tt0) REVERT: B 334 LYS cc_start: 0.7904 (mmmm) cc_final: 0.7623 (mmmm) REVERT: B 339 LYS cc_start: 0.7587 (tptp) cc_final: 0.7295 (tptp) REVERT: B 435 MET cc_start: 0.7146 (mmm) cc_final: 0.6858 (mmm) REVERT: B 700 LYS cc_start: 0.7625 (ptpt) cc_final: 0.7225 (ptpt) REVERT: C 192 LYS cc_start: 0.6220 (OUTLIER) cc_final: 0.5879 (mttp) REVERT: C 226 LYS cc_start: 0.7371 (mtpp) cc_final: 0.7169 (ttmm) REVERT: C 269 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6914 (mt-10) REVERT: C 304 GLU cc_start: 0.6161 (mm-30) cc_final: 0.5933 (mm-30) REVERT: C 322 GLU cc_start: 0.7359 (tt0) cc_final: 0.7008 (tp30) REVERT: C 334 LYS cc_start: 0.8116 (mmmm) cc_final: 0.7887 (mmmm) REVERT: C 420 MET cc_start: 0.6479 (tpp) cc_final: 0.6254 (tpp) REVERT: C 561 MET cc_start: 0.6669 (mmm) cc_final: 0.6279 (mmm) REVERT: C 578 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7327 (p0) REVERT: C 632 ARG cc_start: 0.6819 (mtm-85) cc_final: 0.6283 (mtm-85) REVERT: C 684 MET cc_start: 0.7063 (mmm) cc_final: 0.6843 (mmm) REVERT: C 687 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7939 (tp) REVERT: C 857 GLU cc_start: 0.8324 (tt0) cc_final: 0.8108 (tt0) REVERT: C 872 MET cc_start: 0.6976 (mtm) cc_final: 0.6673 (mtm) REVERT: C 967 MET cc_start: 0.6285 (mtp) cc_final: 0.5979 (mmt) outliers start: 98 outliers final: 65 residues processed: 524 average time/residue: 0.3324 time to fit residues: 275.0508 Evaluate side-chains 515 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 443 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 678 ASP Chi-restraints excluded: chain A residue 681 ASN Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 267 ASN Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 681 ASN Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 896 VAL Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 192 LYS Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 827 SER Chi-restraints excluded: chain C residue 896 VAL Chi-restraints excluded: chain C residue 908 MET Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 912 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 4.9990 chunk 209 optimal weight: 0.0060 chunk 144 optimal weight: 50.0000 chunk 30 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 186 optimal weight: 5.9990 chunk 279 optimal weight: 2.9990 chunk 295 optimal weight: 0.7980 chunk 145 optimal weight: 30.0000 chunk 264 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 overall best weight: 2.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 GLN A 805 GLN A 837 GLN ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN B 837 GLN ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 594 ASN C 691 GLN ** C 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23781 Z= 0.241 Angle : 0.601 8.131 32250 Z= 0.312 Chirality : 0.042 0.238 3870 Planarity : 0.004 0.052 4056 Dihedral : 4.941 59.379 3216 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.05 % Allowed : 18.05 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.15), residues: 3048 helix: 1.64 (0.12), residues: 1716 sheet: -0.16 (0.23), residues: 471 loop : -0.34 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 556 HIS 0.004 0.001 HIS C 360 PHE 0.038 0.001 PHE B 824 TYR 0.012 0.001 TYR A 848 ARG 0.002 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 462 time to evaluate : 2.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 LYS cc_start: 0.5938 (OUTLIER) cc_final: 0.5632 (mttm) REVERT: A 656 MET cc_start: 0.7786 (mmm) cc_final: 0.7547 (tpt) REVERT: A 723 ASP cc_start: 0.7225 (t0) cc_final: 0.6913 (t70) REVERT: A 834 GLU cc_start: 0.6816 (mt-10) cc_final: 0.6569 (mm-30) REVERT: A 893 MET cc_start: 0.6990 (mmt) cc_final: 0.6688 (mmt) REVERT: B 29 LYS cc_start: 0.6745 (mttt) cc_final: 0.6126 (mmmm) REVERT: B 192 LYS cc_start: 0.6009 (OUTLIER) cc_final: 0.5765 (mttm) REVERT: B 213 GLU cc_start: 0.7433 (tp30) cc_final: 0.6902 (tt0) REVERT: B 334 LYS cc_start: 0.7885 (mmmm) cc_final: 0.7485 (mmmm) REVERT: B 339 LYS cc_start: 0.7622 (tptp) cc_final: 0.7358 (tptp) REVERT: B 435 MET cc_start: 0.6997 (mmm) cc_final: 0.6769 (mmm) REVERT: B 656 MET cc_start: 0.7510 (tpt) cc_final: 0.7094 (tpt) REVERT: B 700 LYS cc_start: 0.7542 (ptpt) cc_final: 0.7180 (ptpt) REVERT: B 833 ARG cc_start: 0.6377 (ttm110) cc_final: 0.6069 (ttm110) REVERT: B 893 MET cc_start: 0.6593 (mpp) cc_final: 0.6241 (mpp) REVERT: C 68 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6632 (tp30) REVERT: C 192 LYS cc_start: 0.6009 (OUTLIER) cc_final: 0.5706 (mttm) REVERT: C 226 LYS cc_start: 0.7370 (mtpp) cc_final: 0.7156 (ttmm) REVERT: C 269 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6924 (mt-10) REVERT: C 322 GLU cc_start: 0.7449 (tt0) cc_final: 0.7104 (tp30) REVERT: C 334 LYS cc_start: 0.8088 (mmmm) cc_final: 0.7864 (mmmm) REVERT: C 339 LYS cc_start: 0.7787 (tptp) cc_final: 0.7474 (tptp) REVERT: C 578 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7332 (p0) REVERT: C 632 ARG cc_start: 0.6859 (mtm-85) cc_final: 0.6256 (mtm-85) REVERT: C 684 MET cc_start: 0.7021 (mmm) cc_final: 0.6788 (mmm) REVERT: C 834 GLU cc_start: 0.6804 (mt-10) cc_final: 0.6261 (mm-30) REVERT: C 837 GLN cc_start: 0.7093 (OUTLIER) cc_final: 0.6587 (mp10) REVERT: C 896 VAL cc_start: 0.7934 (OUTLIER) cc_final: 0.7431 (t) REVERT: C 967 MET cc_start: 0.6278 (mtp) cc_final: 0.5892 (mmt) outliers start: 104 outliers final: 67 residues processed: 521 average time/residue: 0.3306 time to fit residues: 271.5215 Evaluate side-chains 519 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 446 time to evaluate : 2.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 678 ASP Chi-restraints excluded: chain A residue 681 ASN Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 805 GLN Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 267 ASN Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 681 ASN Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 896 VAL Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 936 ILE Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 192 LYS Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 827 SER Chi-restraints excluded: chain C residue 837 GLN Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 896 VAL Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 912 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 50.0000 chunk 167 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 220 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 252 optimal weight: 10.0000 chunk 204 optimal weight: 50.0000 chunk 0 optimal weight: 50.0000 chunk 151 optimal weight: 3.9990 chunk 265 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN A 799 GLN ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 837 GLN ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23781 Z= 0.271 Angle : 0.624 13.895 32250 Z= 0.319 Chirality : 0.043 0.282 3870 Planarity : 0.004 0.051 4056 Dihedral : 4.892 57.057 3216 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.86 % Allowed : 19.77 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.15), residues: 3048 helix: 1.66 (0.12), residues: 1713 sheet: -0.28 (0.23), residues: 465 loop : -0.42 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 556 HIS 0.004 0.001 HIS C 360 PHE 0.033 0.001 PHE B 824 TYR 0.016 0.002 TYR C 77 ARG 0.003 0.000 ARG C 185 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 442 time to evaluate : 2.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.7665 (mm-40) cc_final: 0.7447 (mm-40) REVERT: A 192 LYS cc_start: 0.5933 (OUTLIER) cc_final: 0.5685 (mttm) REVERT: A 656 MET cc_start: 0.7765 (mmm) cc_final: 0.7512 (tpt) REVERT: A 723 ASP cc_start: 0.7202 (t0) cc_final: 0.6901 (t70) REVERT: B 29 LYS cc_start: 0.6787 (mttt) cc_final: 0.6196 (mmmm) REVERT: B 186 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7645 (mm) REVERT: B 192 LYS cc_start: 0.5985 (OUTLIER) cc_final: 0.5689 (mttm) REVERT: B 213 GLU cc_start: 0.7415 (tp30) cc_final: 0.6888 (tt0) REVERT: B 334 LYS cc_start: 0.7873 (mmmm) cc_final: 0.7478 (mmmm) REVERT: B 339 LYS cc_start: 0.7592 (tptp) cc_final: 0.7329 (tptp) REVERT: B 435 MET cc_start: 0.7037 (mmm) cc_final: 0.6790 (mmm) REVERT: B 656 MET cc_start: 0.7538 (tpt) cc_final: 0.6385 (tpt) REVERT: B 700 LYS cc_start: 0.7703 (ptpt) cc_final: 0.7327 (ptpt) REVERT: B 833 ARG cc_start: 0.6362 (ttm110) cc_final: 0.6078 (ttm110) REVERT: C 68 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6583 (tp30) REVERT: C 192 LYS cc_start: 0.6095 (OUTLIER) cc_final: 0.5783 (mttm) REVERT: C 226 LYS cc_start: 0.7428 (mtpp) cc_final: 0.7183 (ttmm) REVERT: C 322 GLU cc_start: 0.7519 (tt0) cc_final: 0.7104 (tp30) REVERT: C 578 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7329 (p0) REVERT: C 632 ARG cc_start: 0.6887 (mtm-85) cc_final: 0.6314 (mtm-85) REVERT: C 834 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6291 (mm-30) REVERT: C 837 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.6541 (mp10) REVERT: C 849 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7633 (tp30) REVERT: C 896 VAL cc_start: 0.7962 (OUTLIER) cc_final: 0.7489 (t) REVERT: C 967 MET cc_start: 0.6382 (mtp) cc_final: 0.6025 (mmt) outliers start: 99 outliers final: 78 residues processed: 495 average time/residue: 0.3370 time to fit residues: 261.9979 Evaluate side-chains 524 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 438 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 681 ASN Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 267 ASN Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 681 ASN Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 896 VAL Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 912 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 192 LYS Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 827 SER Chi-restraints excluded: chain C residue 837 GLN Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 896 VAL Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 912 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1005 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 4.9990 chunk 266 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 73 optimal weight: 0.0270 chunk 296 optimal weight: 9.9990 chunk 245 optimal weight: 6.9990 chunk 137 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 overall best weight: 1.7444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 ASN ** B 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 837 GLN B 859 GLN ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23781 Z= 0.199 Angle : 0.568 9.759 32250 Z= 0.294 Chirality : 0.041 0.191 3870 Planarity : 0.004 0.044 4056 Dihedral : 4.695 58.614 3216 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.82 % Allowed : 20.51 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.15), residues: 3048 helix: 1.77 (0.12), residues: 1719 sheet: 0.04 (0.24), residues: 444 loop : -0.38 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 556 HIS 0.005 0.001 HIS C 360 PHE 0.029 0.001 PHE B 824 TYR 0.010 0.001 TYR A 77 ARG 0.012 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 457 time to evaluate : 2.143 Fit side-chains revert: symmetry clash REVERT: A 32 ILE cc_start: 0.7592 (pt) cc_final: 0.7370 (pt) REVERT: A 192 LYS cc_start: 0.5722 (OUTLIER) cc_final: 0.5458 (mttt) REVERT: A 656 MET cc_start: 0.7717 (mmm) cc_final: 0.7460 (tpt) REVERT: A 723 ASP cc_start: 0.7167 (t0) cc_final: 0.6847 (t70) REVERT: A 853 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.8077 (tp) REVERT: A 893 MET cc_start: 0.7171 (mmt) cc_final: 0.6928 (mpp) REVERT: A 938 GLU cc_start: 0.6422 (mm-30) cc_final: 0.6100 (mm-30) REVERT: B 29 LYS cc_start: 0.6774 (mttt) cc_final: 0.6231 (mmmm) REVERT: B 186 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7664 (mm) REVERT: B 192 LYS cc_start: 0.5993 (OUTLIER) cc_final: 0.5742 (mttm) REVERT: B 334 LYS cc_start: 0.7848 (mmmm) cc_final: 0.7449 (mmmm) REVERT: B 339 LYS cc_start: 0.7636 (tptp) cc_final: 0.7354 (tptp) REVERT: B 435 MET cc_start: 0.7007 (mmm) cc_final: 0.6788 (mmm) REVERT: B 656 MET cc_start: 0.7486 (tpt) cc_final: 0.6394 (tpt) REVERT: B 833 ARG cc_start: 0.6377 (ttm110) cc_final: 0.6094 (ttm110) REVERT: B 857 GLU cc_start: 0.8208 (tt0) cc_final: 0.7832 (tt0) REVERT: B 872 MET cc_start: 0.7211 (mmm) cc_final: 0.6878 (mmm) REVERT: C 35 PHE cc_start: 0.8533 (m-80) cc_final: 0.8295 (m-10) REVERT: C 68 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6550 (tp30) REVERT: C 192 LYS cc_start: 0.6012 (OUTLIER) cc_final: 0.5751 (mttm) REVERT: C 226 LYS cc_start: 0.7392 (mtpp) cc_final: 0.6851 (tppt) REVERT: C 322 GLU cc_start: 0.7507 (tt0) cc_final: 0.7141 (tp30) REVERT: C 339 LYS cc_start: 0.7769 (tptp) cc_final: 0.7401 (tptp) REVERT: C 578 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7239 (p0) REVERT: C 632 ARG cc_start: 0.6903 (mtm-85) cc_final: 0.6237 (mtm-85) REVERT: C 834 GLU cc_start: 0.6770 (mt-10) cc_final: 0.6277 (mm-30) REVERT: C 837 GLN cc_start: 0.7175 (OUTLIER) cc_final: 0.6583 (mp10) REVERT: C 872 MET cc_start: 0.7101 (mtm) cc_final: 0.6679 (mpp) REVERT: C 896 VAL cc_start: 0.7933 (OUTLIER) cc_final: 0.7506 (t) REVERT: C 967 MET cc_start: 0.6322 (mtp) cc_final: 0.6027 (mmt) outliers start: 98 outliers final: 67 residues processed: 512 average time/residue: 0.3535 time to fit residues: 287.1830 Evaluate side-chains 517 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 442 time to evaluate : 2.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 681 ASN Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 267 ASN Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 681 ASN Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 813 ARG Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 896 VAL Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 936 ILE Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 192 LYS Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 748 MET Chi-restraints excluded: chain C residue 827 SER Chi-restraints excluded: chain C residue 837 GLN Chi-restraints excluded: chain C residue 896 VAL Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 912 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 168 optimal weight: 4.9990 chunk 216 optimal weight: 5.9990 chunk 167 optimal weight: 0.8980 chunk 249 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 294 optimal weight: 8.9990 chunk 184 optimal weight: 9.9990 chunk 179 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN ** A 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN B 837 GLN ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23781 Z= 0.262 Angle : 0.606 8.438 32250 Z= 0.315 Chirality : 0.042 0.206 3870 Planarity : 0.004 0.045 4056 Dihedral : 4.757 59.320 3216 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.13 % Allowed : 20.90 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.15), residues: 3048 helix: 1.69 (0.12), residues: 1719 sheet: 0.00 (0.24), residues: 444 loop : -0.44 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 556 HIS 0.005 0.001 HIS C 360 PHE 0.029 0.001 PHE B 824 TYR 0.015 0.001 TYR C 77 ARG 0.008 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 445 time to evaluate : 2.603 Fit side-chains revert: symmetry clash REVERT: A 32 ILE cc_start: 0.7615 (pt) cc_final: 0.7396 (pt) REVERT: A 230 ILE cc_start: 0.7660 (OUTLIER) cc_final: 0.7434 (mp) REVERT: A 656 MET cc_start: 0.7741 (mmm) cc_final: 0.7456 (tpt) REVERT: A 723 ASP cc_start: 0.7194 (t0) cc_final: 0.6870 (t70) REVERT: A 838 LEU cc_start: 0.8623 (mm) cc_final: 0.8369 (mt) REVERT: A 853 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.8081 (tp) REVERT: A 893 MET cc_start: 0.7291 (mmt) cc_final: 0.6971 (mpp) REVERT: A 938 GLU cc_start: 0.6528 (mm-30) cc_final: 0.6224 (mm-30) REVERT: A 1001 MET cc_start: 0.7367 (tpt) cc_final: 0.7044 (tpt) REVERT: B 29 LYS cc_start: 0.6768 (mttt) cc_final: 0.6239 (mmmm) REVERT: B 186 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7687 (mm) REVERT: B 192 LYS cc_start: 0.6084 (OUTLIER) cc_final: 0.5809 (mttm) REVERT: B 334 LYS cc_start: 0.7880 (mmmm) cc_final: 0.7498 (mmmm) REVERT: B 339 LYS cc_start: 0.7609 (tptp) cc_final: 0.7336 (tptp) REVERT: B 435 MET cc_start: 0.7009 (mmm) cc_final: 0.6788 (mmm) REVERT: B 656 MET cc_start: 0.7536 (tpt) cc_final: 0.6535 (tpt) REVERT: B 833 ARG cc_start: 0.6387 (ttm110) cc_final: 0.6118 (ttm110) REVERT: B 857 GLU cc_start: 0.8266 (tt0) cc_final: 0.7848 (tt0) REVERT: C 35 PHE cc_start: 0.8541 (m-80) cc_final: 0.8184 (m-10) REVERT: C 68 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6552 (tp30) REVERT: C 192 LYS cc_start: 0.6050 (OUTLIER) cc_final: 0.5777 (mttm) REVERT: C 226 LYS cc_start: 0.7435 (mtpp) cc_final: 0.6921 (tppt) REVERT: C 322 GLU cc_start: 0.7527 (tt0) cc_final: 0.7121 (tp30) REVERT: C 339 LYS cc_start: 0.7797 (tptp) cc_final: 0.7486 (tptp) REVERT: C 376 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7439 (mp) REVERT: C 578 ASP cc_start: 0.7545 (OUTLIER) cc_final: 0.7245 (p0) REVERT: C 632 ARG cc_start: 0.6946 (mtm-85) cc_final: 0.6263 (mtm-85) REVERT: C 834 GLU cc_start: 0.6889 (mt-10) cc_final: 0.6369 (mm-30) REVERT: C 835 MET cc_start: 0.8897 (tpt) cc_final: 0.8468 (tpt) REVERT: C 837 GLN cc_start: 0.7265 (OUTLIER) cc_final: 0.6589 (mp10) REVERT: C 849 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7642 (tp30) REVERT: C 872 MET cc_start: 0.7218 (mtm) cc_final: 0.6882 (mpp) REVERT: C 896 VAL cc_start: 0.7973 (OUTLIER) cc_final: 0.7505 (t) REVERT: C 967 MET cc_start: 0.6382 (mtp) cc_final: 0.6060 (mmt) outliers start: 106 outliers final: 79 residues processed: 509 average time/residue: 0.3289 time to fit residues: 264.5744 Evaluate side-chains 526 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 437 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 681 ASN Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 267 ASN Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 681 ASN Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 813 ARG Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 896 VAL Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 912 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 192 LYS Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 748 MET Chi-restraints excluded: chain C residue 813 ARG Chi-restraints excluded: chain C residue 827 SER Chi-restraints excluded: chain C residue 837 GLN Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 896 VAL Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 912 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 187 optimal weight: 4.9990 chunk 200 optimal weight: 6.9990 chunk 145 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 231 optimal weight: 9.9990 chunk 268 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN A 799 GLN ** A 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 GLN B 248 ASN B 837 GLN ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN C 859 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23781 Z= 0.260 Angle : 0.602 12.484 32250 Z= 0.313 Chirality : 0.042 0.199 3870 Planarity : 0.004 0.045 4056 Dihedral : 4.647 59.534 3212 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.94 % Allowed : 21.56 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.15), residues: 3048 helix: 1.67 (0.12), residues: 1710 sheet: -0.05 (0.24), residues: 444 loop : -0.46 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 556 HIS 0.005 0.001 HIS B 360 PHE 0.028 0.001 PHE B 824 TYR 0.015 0.001 TYR C 77 ARG 0.008 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 440 time to evaluate : 2.811 Fit side-chains revert: symmetry clash REVERT: A 32 ILE cc_start: 0.7630 (pt) cc_final: 0.7420 (pt) REVERT: A 435 MET cc_start: 0.6759 (mtp) cc_final: 0.6521 (mtp) REVERT: A 647 MET cc_start: 0.6002 (mmm) cc_final: 0.4363 (mmm) REVERT: A 656 MET cc_start: 0.7743 (mmm) cc_final: 0.7470 (tpt) REVERT: A 723 ASP cc_start: 0.7199 (t0) cc_final: 0.6859 (t70) REVERT: A 832 MET cc_start: 0.8684 (mtm) cc_final: 0.8410 (mtp) REVERT: A 834 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6815 (mm-30) REVERT: A 838 LEU cc_start: 0.8602 (mm) cc_final: 0.8380 (mt) REVERT: A 893 MET cc_start: 0.7134 (mmt) cc_final: 0.6912 (mpp) REVERT: A 938 GLU cc_start: 0.6542 (mm-30) cc_final: 0.6255 (mm-30) REVERT: A 1001 MET cc_start: 0.7388 (tpt) cc_final: 0.7029 (tpt) REVERT: B 29 LYS cc_start: 0.6747 (mttt) cc_final: 0.6229 (mmmm) REVERT: B 158 LEU cc_start: 0.8493 (tt) cc_final: 0.8233 (tt) REVERT: B 186 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7692 (mm) REVERT: B 192 LYS cc_start: 0.6120 (OUTLIER) cc_final: 0.5832 (mttm) REVERT: B 334 LYS cc_start: 0.7886 (mmmm) cc_final: 0.7511 (mmmm) REVERT: B 339 LYS cc_start: 0.7552 (tptp) cc_final: 0.7290 (tptp) REVERT: B 435 MET cc_start: 0.6993 (mmm) cc_final: 0.6766 (mmm) REVERT: B 656 MET cc_start: 0.7506 (tpt) cc_final: 0.6514 (tpt) REVERT: B 833 ARG cc_start: 0.6389 (ttm110) cc_final: 0.5915 (ttm170) REVERT: B 837 GLN cc_start: 0.7217 (mm110) cc_final: 0.6977 (mm110) REVERT: B 857 GLU cc_start: 0.8278 (tt0) cc_final: 0.7853 (tt0) REVERT: B 872 MET cc_start: 0.7341 (mmm) cc_final: 0.6965 (mmm) REVERT: B 967 MET cc_start: 0.6650 (mmp) cc_final: 0.6426 (mmt) REVERT: C 68 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6592 (tp30) REVERT: C 192 LYS cc_start: 0.5996 (OUTLIER) cc_final: 0.5730 (mttm) REVERT: C 226 LYS cc_start: 0.7432 (mtpp) cc_final: 0.6924 (tppt) REVERT: C 322 GLU cc_start: 0.7533 (tt0) cc_final: 0.7121 (tp30) REVERT: C 339 LYS cc_start: 0.7776 (tptp) cc_final: 0.7440 (tptp) REVERT: C 376 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7398 (mp) REVERT: C 578 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7260 (p0) REVERT: C 632 ARG cc_start: 0.7007 (mtm-85) cc_final: 0.6285 (mtm-85) REVERT: C 834 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6507 (mm-30) REVERT: C 837 GLN cc_start: 0.7282 (OUTLIER) cc_final: 0.6691 (mp10) REVERT: C 849 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7634 (tp30) REVERT: C 872 MET cc_start: 0.7197 (mtm) cc_final: 0.6975 (mtm) REVERT: C 896 VAL cc_start: 0.7872 (OUTLIER) cc_final: 0.7403 (t) REVERT: C 967 MET cc_start: 0.6375 (mtp) cc_final: 0.6026 (mmt) outliers start: 101 outliers final: 81 residues processed: 505 average time/residue: 0.3564 time to fit residues: 285.4896 Evaluate side-chains 529 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 440 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 681 ASN Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 813 ARG Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 267 ASN Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 681 ASN Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 813 ARG Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 844 LYS Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 896 VAL Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 912 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 192 LYS Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 597 ASP Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 748 MET Chi-restraints excluded: chain C residue 813 ARG Chi-restraints excluded: chain C residue 827 SER Chi-restraints excluded: chain C residue 837 GLN Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 896 VAL Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 912 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 10.0000 chunk 257 optimal weight: 5.9990 chunk 274 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 chunk 119 optimal weight: 0.0470 chunk 215 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 248 optimal weight: 5.9990 chunk 259 optimal weight: 0.8980 chunk 273 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN ** A 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN ** B 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 837 GLN ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23781 Z= 0.170 Angle : 0.560 12.027 32250 Z= 0.292 Chirality : 0.040 0.200 3870 Planarity : 0.004 0.041 4056 Dihedral : 4.404 59.995 3212 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.38 % Allowed : 23.16 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.15), residues: 3048 helix: 1.82 (0.12), residues: 1710 sheet: 0.10 (0.24), residues: 444 loop : -0.32 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 556 HIS 0.004 0.001 HIS B 360 PHE 0.025 0.001 PHE B 824 TYR 0.007 0.001 TYR A 848 ARG 0.009 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 445 time to evaluate : 2.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ILE cc_start: 0.7528 (pt) cc_final: 0.7223 (pt) REVERT: A 68 GLU cc_start: 0.6723 (mm-30) cc_final: 0.6356 (tp30) REVERT: A 230 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7360 (mp) REVERT: A 647 MET cc_start: 0.6083 (mmm) cc_final: 0.4717 (mmm) REVERT: A 656 MET cc_start: 0.7645 (mmm) cc_final: 0.7381 (tpt) REVERT: A 723 ASP cc_start: 0.7130 (t0) cc_final: 0.6800 (t70) REVERT: A 838 LEU cc_start: 0.8580 (mm) cc_final: 0.8376 (mt) REVERT: A 893 MET cc_start: 0.6999 (mmt) cc_final: 0.6771 (mpp) REVERT: A 1001 MET cc_start: 0.7390 (tpt) cc_final: 0.6931 (tpt) REVERT: B 29 LYS cc_start: 0.6716 (mttt) cc_final: 0.6211 (mmmm) REVERT: B 158 LEU cc_start: 0.8317 (tt) cc_final: 0.7981 (tt) REVERT: B 186 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7727 (mm) REVERT: B 192 LYS cc_start: 0.5999 (OUTLIER) cc_final: 0.5770 (mttm) REVERT: B 334 LYS cc_start: 0.7802 (mmmm) cc_final: 0.7435 (mmmm) REVERT: B 339 LYS cc_start: 0.7605 (tptp) cc_final: 0.7350 (tptp) REVERT: B 656 MET cc_start: 0.7382 (tpt) cc_final: 0.6446 (tpt) REVERT: B 705 TYR cc_start: 0.8201 (t80) cc_final: 0.7896 (t80) REVERT: B 833 ARG cc_start: 0.6372 (ttm110) cc_final: 0.5926 (ttm170) REVERT: B 872 MET cc_start: 0.7318 (mmm) cc_final: 0.7033 (mmm) REVERT: B 967 MET cc_start: 0.6555 (mmp) cc_final: 0.6316 (mmt) REVERT: C 32 ILE cc_start: 0.7480 (pt) cc_final: 0.7137 (pt) REVERT: C 68 GLU cc_start: 0.6908 (mm-30) cc_final: 0.6506 (tp30) REVERT: C 226 LYS cc_start: 0.7241 (mtpp) cc_final: 0.6699 (tppt) REVERT: C 322 GLU cc_start: 0.7493 (tt0) cc_final: 0.7112 (tp30) REVERT: C 339 LYS cc_start: 0.7785 (tptp) cc_final: 0.7543 (tptp) REVERT: C 376 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7298 (mp) REVERT: C 578 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.7257 (p0) REVERT: C 632 ARG cc_start: 0.6945 (mtm-85) cc_final: 0.6251 (mtm-85) REVERT: C 834 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6508 (mm-30) REVERT: C 835 MET cc_start: 0.8864 (tpt) cc_final: 0.8476 (tpt) REVERT: C 837 GLN cc_start: 0.7268 (OUTLIER) cc_final: 0.6605 (mp10) REVERT: C 896 VAL cc_start: 0.7814 (OUTLIER) cc_final: 0.7220 (t) REVERT: C 967 MET cc_start: 0.6292 (mtp) cc_final: 0.6036 (mmt) outliers start: 61 outliers final: 43 residues processed: 480 average time/residue: 0.3322 time to fit residues: 250.7685 Evaluate side-chains 486 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 436 time to evaluate : 3.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 681 ASN Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 681 ASN Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 896 VAL Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 936 ILE Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 748 MET Chi-restraints excluded: chain C residue 813 ARG Chi-restraints excluded: chain C residue 827 SER Chi-restraints excluded: chain C residue 837 GLN Chi-restraints excluded: chain C residue 896 VAL Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 chunk 202 optimal weight: 5.9990 chunk 304 optimal weight: 4.9990 chunk 280 optimal weight: 0.5980 chunk 242 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 192 optimal weight: 6.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 GLN ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN C 267 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23781 Z= 0.300 Angle : 0.625 10.999 32250 Z= 0.324 Chirality : 0.043 0.199 3870 Planarity : 0.004 0.045 4056 Dihedral : 4.460 55.939 3206 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.65 % Allowed : 22.73 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.15), residues: 3048 helix: 1.64 (0.12), residues: 1716 sheet: 0.02 (0.24), residues: 441 loop : -0.47 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 556 HIS 0.004 0.001 HIS B 360 PHE 0.029 0.002 PHE B 824 TYR 0.019 0.002 TYR C 77 ARG 0.007 0.000 ARG C 168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 439 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ILE cc_start: 0.7614 (pt) cc_final: 0.7398 (pt) REVERT: A 68 GLU cc_start: 0.6754 (mm-30) cc_final: 0.6348 (tp30) REVERT: A 230 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7416 (mp) REVERT: A 647 MET cc_start: 0.6227 (mmm) cc_final: 0.4461 (mmm) REVERT: A 656 MET cc_start: 0.7745 (mmm) cc_final: 0.7455 (tpt) REVERT: A 723 ASP cc_start: 0.7199 (t0) cc_final: 0.6855 (t70) REVERT: A 838 LEU cc_start: 0.8617 (mm) cc_final: 0.8383 (mt) REVERT: A 893 MET cc_start: 0.7152 (mmt) cc_final: 0.6928 (mpp) REVERT: A 1001 MET cc_start: 0.7416 (tpt) cc_final: 0.6991 (tpt) REVERT: B 29 LYS cc_start: 0.6778 (mttt) cc_final: 0.6390 (mmmm) REVERT: B 158 LEU cc_start: 0.8492 (tt) cc_final: 0.8244 (tt) REVERT: B 186 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7753 (mm) REVERT: B 192 LYS cc_start: 0.6154 (OUTLIER) cc_final: 0.5872 (mttm) REVERT: B 334 LYS cc_start: 0.7878 (mmmm) cc_final: 0.7503 (mmmm) REVERT: B 339 LYS cc_start: 0.7554 (tptp) cc_final: 0.7296 (tptp) REVERT: B 656 MET cc_start: 0.7528 (tpt) cc_final: 0.7093 (tpt) REVERT: B 833 ARG cc_start: 0.6297 (ttm110) cc_final: 0.6030 (ttm170) REVERT: B 872 MET cc_start: 0.7324 (mmm) cc_final: 0.6957 (mmm) REVERT: B 967 MET cc_start: 0.6655 (mmp) cc_final: 0.6447 (mmt) REVERT: C 68 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6588 (tp30) REVERT: C 226 LYS cc_start: 0.7428 (mtpp) cc_final: 0.6922 (tppt) REVERT: C 322 GLU cc_start: 0.7567 (tt0) cc_final: 0.7114 (tp30) REVERT: C 339 LYS cc_start: 0.7802 (tptp) cc_final: 0.7577 (tptp) REVERT: C 376 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7397 (mp) REVERT: C 578 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.7311 (p0) REVERT: C 632 ARG cc_start: 0.7001 (mtm-85) cc_final: 0.6306 (mtm-85) REVERT: C 834 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6454 (mm-30) REVERT: C 837 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6592 (mp10) REVERT: C 849 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7667 (tp30) REVERT: C 896 VAL cc_start: 0.7809 (OUTLIER) cc_final: 0.7278 (t) outliers start: 68 outliers final: 48 residues processed: 482 average time/residue: 0.3256 time to fit residues: 248.0622 Evaluate side-chains 491 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 435 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 681 ASN Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 681 ASN Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 896 VAL Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 912 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 813 ARG Chi-restraints excluded: chain C residue 827 SER Chi-restraints excluded: chain C residue 837 GLN Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 896 VAL Chi-restraints excluded: chain C residue 912 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 20.0000 chunk 74 optimal weight: 0.5980 chunk 223 optimal weight: 0.0670 chunk 35 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 249 optimal weight: 0.0970 chunk 30 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 overall best weight: 1.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN ** A 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 GLN B 248 ASN ** C 210 ASN ** 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 = 0.3859 r_free = 0.3859 target = 0.184095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.149354 restraints weight = 25342.380| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.61 r_work: 0.3209 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23781 Z= 0.182 Angle : 0.574 11.312 32250 Z= 0.297 Chirality : 0.041 0.196 3870 Planarity : 0.004 0.042 4056 Dihedral : 4.277 58.996 3206 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.38 % Allowed : 23.27 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.15), residues: 3048 helix: 1.79 (0.12), residues: 1716 sheet: 0.10 (0.24), residues: 441 loop : -0.34 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 556 HIS 0.004 0.001 HIS B 360 PHE 0.026 0.001 PHE A 824 TYR 0.008 0.001 TYR A 77 ARG 0.008 0.000 ARG C 168 =============================================================================== Job complete usr+sys time: 5305.78 seconds wall clock time: 96 minutes 19.66 seconds (5779.66 seconds total)