Starting phenix.real_space_refine on Tue Mar 19 06:32:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kge_22867/03_2024/7kge_22867_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kge_22867/03_2024/7kge_22867.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kge_22867/03_2024/7kge_22867.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kge_22867/03_2024/7kge_22867.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kge_22867/03_2024/7kge_22867_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kge_22867/03_2024/7kge_22867_updated.pdb" } resolution = 3.21 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= 0.189 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 135 5.16 5 C 15213 2.51 5 N 3795 2.21 5 O 4332 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 66": "OE1" <-> "OE2" Residue "A ARG 123": "NH1" <-> "NH2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A ARG 160": "NH1" <-> "NH2" Residue "A ARG 168": "NH1" <-> "NH2" 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 319": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A GLU 525": "OE1" <-> "OE2" Residue "A GLU 563": "OE1" <-> "OE2" Residue "A PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A ARG 585": "NH1" <-> "NH2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "A ARG 632": "NH1" <-> "NH2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A GLU 693": "OE1" <-> "OE2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A ARG 771": "NH1" <-> "NH2" Residue "A ARG 809": "NH1" <-> "NH2" Residue "A GLU 849": "OE1" <-> "OE2" Residue "A GLU 861": "OE1" <-> "OE2" Residue "A ARG 910": "NH1" <-> "NH2" Residue "A GLU 938": "OE1" <-> "OE2" Residue "A ARG 961": "NH1" <-> "NH2" Residue "A ARG 963": "NH1" <-> "NH2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "B ARG 7": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B GLU 66": "OE1" <-> "OE2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B ARG 160": "NH1" <-> "NH2" Residue "B GLU 164": "OE1" <-> "OE2" Residue "B ARG 168": "NH1" <-> "NH2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B ARG 218": "NH1" <-> "NH2" Residue "B GLU 244": "OE1" <-> "OE2" 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 312": "OE1" <-> "OE2" Residue "B GLU 322": "OE1" <-> "OE2" Residue "B TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 346": "OE1" <-> "OE2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B ARG 418": "NH1" <-> "NH2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B GLU 564": "OE1" <-> "OE2" Residue "B GLU 582": "OE1" <-> "OE2" Residue "B ARG 583": "NH1" <-> "NH2" Residue "B ARG 585": "NH1" <-> "NH2" Residue "B ARG 632": "NH1" <-> "NH2" Residue "B GLU 665": "OE1" <-> "OE2" Residue "B ARG 675": "NH1" <-> "NH2" Residue "B GLU 710": "OE1" <-> "OE2" Residue "B ARG 758": "NH1" <-> "NH2" Residue "B ARG 771": "NH1" <-> "NH2" Residue "B ARG 813": "NH1" <-> "NH2" Residue "B ARG 833": "NH1" <-> "NH2" Residue "B GLU 834": "OE1" <-> "OE2" Residue "B GLU 836": "OE1" <-> "OE2" Residue "B ARG 910": "NH1" <-> "NH2" Residue "B GLU 946": "OE1" <-> "OE2" Residue "B ARG 961": "NH1" <-> "NH2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "C ARG 7": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C GLU 66": "OE1" <-> "OE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 101": "OE1" <-> "OE2" Residue "C ARG 123": "NH1" <-> "NH2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "C ARG 160": "NH1" <-> "NH2" Residue "C GLU 164": "OE1" <-> "OE2" Residue "C ARG 168": "NH1" <-> "NH2" Residue "C ARG 185": "NH1" <-> "NH2" Residue "C ARG 208": "NH1" <-> "NH2" 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 322": "OE1" <-> "OE2" Residue "C GLU 346": "OE1" <-> "OE2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 418": "NH1" <-> "NH2" Residue "C GLU 423": "OE1" <-> "OE2" Residue "C ARG 583": "NH1" <-> "NH2" Residue "C ARG 585": "NH1" <-> "NH2" Residue "C GLU 631": "OE1" <-> "OE2" Residue "C ARG 632": "NH1" <-> "NH2" 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 710": "OE1" <-> "OE2" Residue "C ARG 724": "NH1" <-> "NH2" Residue "C ARG 758": "NH1" <-> "NH2" Residue "C ARG 771": "NH1" <-> "NH2" Residue "C GLU 794": "OE1" <-> "OE2" Residue "C ARG 809": "NH1" <-> "NH2" Residue "C GLU 830": "OE1" <-> "OE2" Residue "C ARG 833": "NH1" <-> "NH2" Residue "C GLU 945": "OE1" <-> "OE2" Residue "C GLU 952": "OE1" <-> "OE2" Residue "C ARG 961": "NH1" <-> "NH2" Residue "C ARG 963": "NH1" <-> "NH2" Residue "C PHE 1016": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23478 Number of models: 1 Model: "" Number of chains: 5 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 Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 73 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 27 Time building chain proxies: 12.69, per 1000 atoms: 0.54 Number of scatterers: 23478 At special positions: 0 Unit cell: (124.2, 117.72, 141.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 135 16.00 P 3 15.00 O 4332 8.00 N 3795 7.00 C 15213 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: 9.34 Conformation dependent library (CDL) restraints added in 4.3 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... running ksdssp... Secondary structure from input PDB file: 116 helices and 25 sheets defined 55.4% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.49 Creating SS restraints... Processing helix chain 'A' and resid 4 through 7 No H-bonds generated for 'chain 'A' and resid 4 through 7' Processing helix chain 'A' and resid 9 through 29 Proline residue: A 28 - end of helix Processing helix chain 'A' and resid 54 through 60 Processing helix chain 'A' and resid 62 through 71 removed outlier: 3.647A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLY A 71 " --> pdb=" O ARG A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 115 removed outlier: 4.009A pdb=" N ALA A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 299 through 316 removed outlier: 4.104A pdb=" N LEU A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASN A 316 " --> pdb=" O GLU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 359 removed outlier: 4.054A pdb=" N LYS A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 386 removed outlier: 3.758A pdb=" N ILE A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Proline residue: A 368 - end of helix removed outlier: 4.333A pdb=" N VAL A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 4.326A 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 392 through 405 removed outlier: 4.323A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 423 Processing helix chain 'A' and resid 427 through 458 removed outlier: 5.479A pdb=" N SER A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) Proline residue: A 441 - end of helix removed outlier: 3.965A pdb=" N PHE A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Proline residue: A 455 - end of helix removed outlier: 4.234A pdb=" N PHE A 458 " --> pdb=" O LEU A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 496 removed outlier: 3.688A pdb=" N GLN A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 4.209A 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 533 removed outlier: 3.888A pdb=" N LYS A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 555 Processing helix chain 'A' and resid 581 through 596 Processing helix chain 'A' and resid 629 through 631 No H-bonds generated for 'chain 'A' and resid 629 through 631' Processing helix chain 'A' and resid 636 through 650 removed outlier: 3.866A pdb=" N ASN A 649 " --> pdb=" O SER A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 700 removed outlier: 3.658A pdb=" N LYS A 700 " --> pdb=" O ALA A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 730 Processing helix chain 'A' and resid 734 through 745 removed outlier: 4.434A pdb=" N MET A 745 " --> pdb=" O ILE A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 774 through 777 No H-bonds generated for 'chain 'A' and resid 774 through 777' Processing helix chain 'A' and resid 792 through 795 Processing helix chain 'A' and resid 828 through 841 removed outlier: 3.656A pdb=" N LYS A 841 " --> pdb=" O GLN A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 862 Processing helix chain 'A' and resid 864 through 883 Processing helix chain 'A' and resid 888 through 894 Processing helix chain 'A' and resid 896 through 910 Processing helix chain 'A' and resid 916 through 946 removed outlier: 3.679A pdb=" N ASN A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 935 " --> pdb=" O LYS A 931 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE A 936 " --> pdb=" O ASN A 932 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 980 removed outlier: 4.969A 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 987 through 1026 removed outlier: 3.994A pdb=" N LEU A 993 " --> pdb=" O THR A 989 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY A 996 " --> pdb=" O ALA A 992 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL A 997 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE A1009 " --> pdb=" O THR A1005 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE A1010 " --> pdb=" O ILE A1006 " (cutoff:3.500A) Proline residue: A1013 - end of helix Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 9 through 29 Proline residue: B 28 - end of helix Processing helix chain 'B' and resid 62 through 71 removed outlier: 4.052A pdb=" N GLY B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 117 removed outlier: 3.680A pdb=" N VAL B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ALA B 116 " --> pdb=" O LYS B 112 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ARG B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 151 through 160 Processing helix chain 'B' and resid 162 through 168 removed outlier: 3.731A pdb=" N ARG B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 195 Processing helix chain 'B' and resid 200 through 210 Processing helix chain 'B' and resid 243 through 247 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 299 through 316 removed outlier: 3.917A pdb=" N LEU B 315 " --> pdb=" O GLU B 311 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASN B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 359 Processing helix chain 'B' and resid 362 through 386 Proline residue: B 368 - end of helix removed outlier: 4.424A pdb=" N VAL B 371 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 4.075A 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 392 through 423 removed outlier: 4.498A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASP B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ASP B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ALA B 409 " --> pdb=" O ILE B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 451 removed outlier: 5.639A pdb=" N SER B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Proline residue: B 441 - end of helix Processing helix chain 'B' and resid 454 through 458 removed outlier: 4.138A pdb=" N PHE B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 454 through 458' Processing helix chain 'B' and resid 462 through 495 removed outlier: 3.709A pdb=" N GLN B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 4.034A 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 533 removed outlier: 4.048A pdb=" N LYS B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 555 Processing helix chain 'B' and resid 581 through 594 Processing helix chain 'B' and resid 629 through 631 No H-bonds generated for 'chain 'B' and resid 629 through 631' Processing helix chain 'B' and resid 636 through 650 removed outlier: 4.903A pdb=" N ASN B 649 " --> pdb=" O SER B 645 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER B 650 " --> pdb=" O SER B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 700 Processing helix chain 'B' and resid 724 through 730 Processing helix chain 'B' and resid 734 through 744 Processing helix chain 'B' and resid 768 through 770 No H-bonds generated for 'chain 'B' and resid 768 through 770' Processing helix chain 'B' and resid 774 through 778 Processing helix chain 'B' and resid 785 through 787 No H-bonds generated for 'chain 'B' and resid 785 through 787' Processing helix chain 'B' and resid 792 through 795 No H-bonds generated for 'chain 'B' and resid 792 through 795' Processing helix chain 'B' and resid 828 through 841 removed outlier: 3.669A pdb=" N LYS B 841 " --> pdb=" O GLN B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 862 Processing helix chain 'B' and resid 864 through 882 Processing helix chain 'B' and resid 887 through 910 removed outlier: 3.758A pdb=" N VAL B 895 " --> pdb=" O SER B 891 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL B 896 " --> pdb=" O VAL B 892 " (cutoff:3.500A) Proline residue: B 897 - end of helix removed outlier: 3.551A pdb=" N GLY B 902 " --> pdb=" O LEU B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 946 removed outlier: 3.941A pdb=" N ILE B 936 " --> pdb=" O ASN B 932 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE B 939 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 960 Processing helix chain 'B' and resid 962 through 975 removed outlier: 3.718A pdb=" N PHE B 972 " --> pdb=" O THR B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 980 No H-bonds generated for 'chain 'B' and resid 977 through 980' Processing helix chain 'B' and resid 987 through 1008 removed outlier: 4.323A pdb=" N GLY B 996 " --> pdb=" O ALA B 992 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL B 997 " --> pdb=" O LEU B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1026 Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 9 through 27 Processing helix chain 'C' and resid 54 through 60 Processing helix chain 'C' and resid 62 through 71 removed outlier: 3.716A pdb=" N GLU C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLY C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 113 Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 151 through 160 Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 200 through 210 Processing helix chain 'C' and resid 243 through 247 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 299 through 314 Processing helix chain 'C' and resid 330 through 359 removed outlier: 3.943A pdb=" N LYS C 334 " --> pdb=" O ALA C 330 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE C 335 " --> pdb=" O PRO C 331 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER C 336 " --> pdb=" O PHE C 332 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE C 337 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU C 357 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE C 358 " --> pdb=" O VAL C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 386 Proline residue: C 368 - end of helix removed outlier: 4.586A pdb=" N VAL C 371 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 4.356A 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 392 through 403 removed outlier: 4.469A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 422 Processing helix chain 'C' and resid 427 through 452 removed outlier: 3.555A pdb=" N THR C 431 " --> pdb=" O PRO C 427 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER C 432 " --> pdb=" O LYS C 428 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N SER C 440 " --> pdb=" O LYS C 436 " (cutoff:3.500A) Proline residue: C 441 - end of helix Processing helix chain 'C' and resid 455 through 458 Processing helix chain 'C' and resid 462 through 495 removed outlier: 3.631A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR C 473 " --> pdb=" O GLN C 469 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C 477 " --> pdb=" O THR C 473 " (cutoff:3.500A) removed outlier: 4.380A 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 533 Processing helix chain 'C' and resid 535 through 555 Processing helix chain 'C' and resid 581 through 596 Processing helix chain 'C' and resid 636 through 648 Processing helix chain 'C' and resid 684 through 700 Processing helix chain 'C' and resid 724 through 730 Processing helix chain 'C' and resid 734 through 744 removed outlier: 3.583A pdb=" N SER C 744 " --> pdb=" O ILE C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 770 No H-bonds generated for 'chain 'C' and resid 768 through 770' Processing helix chain 'C' and resid 774 through 779 Processing helix chain 'C' and resid 792 through 795 No H-bonds generated for 'chain 'C' and resid 792 through 795' Processing helix chain 'C' and resid 828 through 841 removed outlier: 3.635A pdb=" N LYS C 841 " --> pdb=" O GLN C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 862 Processing helix chain 'C' and resid 864 through 883 Processing helix chain 'C' and resid 886 through 909 removed outlier: 3.951A pdb=" N VAL C 895 " --> pdb=" O SER C 891 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL C 896 " --> pdb=" O VAL C 892 " (cutoff:3.500A) Proline residue: C 897 - end of helix Processing helix chain 'C' and resid 916 through 945 removed outlier: 4.949A pdb=" N PHE C 939 " --> pdb=" O LEU C 935 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N MET C 942 " --> pdb=" O GLU C 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 950 through 980 removed outlier: 3.608A pdb=" N ALA C 958 " --> pdb=" O THR C 954 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 5.413A 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 987 through 1006 removed outlier: 4.627A pdb=" N GLY C 996 " --> pdb=" O ALA C 992 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL C 997 " --> pdb=" O LEU C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1008 through 1026 Proline residue: C1013 - end of helix removed outlier: 4.459A pdb=" N PHE C1018 " --> pdb=" O VAL C1014 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C1020 " --> pdb=" O PHE C1016 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLY C1021 " --> pdb=" O ILE C1017 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 128 through 130 Processing sheet with id= B, first strand: chain 'A' and resid 322 through 324 Processing sheet with id= C, first strand: chain 'A' and resid 266 through 272 removed outlier: 8.304A pdb=" N LYS A 182 " --> pdb=" O MET A 759 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLN A 761 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN A 751 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL A 764 " --> pdb=" O TYR A 749 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N TYR A 749 " --> pdb=" O VAL A 764 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 217 through 219 Processing sheet with id= E, first strand: chain 'A' and resid 250 through 252 Processing sheet with id= F, first strand: chain 'A' and resid 278 through 280 removed outlier: 7.053A pdb=" N THR A 625 " --> pdb=" O LYS A 602 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASN A 604 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N PHE A 623 " --> pdb=" O ASN A 604 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ALA A 606 " --> pdb=" O VAL A 621 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL A 621 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU A 608 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL A 619 " --> pdb=" O LEU A 608 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 846 through 850 removed outlier: 3.876A pdb=" N MET A 706 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 715 through 722 Processing sheet with id= I, first strand: chain 'B' and resid 127 through 131 Processing sheet with id= J, first strand: chain 'B' and resid 322 through 324 Processing sheet with id= K, first strand: chain 'B' and resid 266 through 272 removed outlier: 8.122A pdb=" N LYS B 182 " --> pdb=" O MET B 759 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLN B 761 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN B 751 " --> pdb=" O VAL B 762 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL B 764 " --> pdb=" O TYR B 749 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N TYR B 749 " --> pdb=" O VAL B 764 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 217 through 219 Processing sheet with id= M, first strand: chain 'B' and resid 250 through 252 Processing sheet with id= N, first strand: chain 'B' and resid 278 through 280 removed outlier: 6.906A pdb=" N THR B 625 " --> pdb=" O LYS B 602 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN B 604 " --> pdb=" O PHE B 623 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE B 623 " --> pdb=" O ASN B 604 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ALA B 606 " --> pdb=" O VAL B 621 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL B 621 " --> pdb=" O ALA B 606 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU B 608 " --> pdb=" O VAL B 619 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL B 619 " --> pdb=" O LEU B 608 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 846 through 850 removed outlier: 4.055A pdb=" N MET B 706 " --> pdb=" O ILE B 821 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 715 through 722 removed outlier: 3.548A pdb=" N GLY B 715 " --> pdb=" O ALA B 803 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 781 through 783 Processing sheet with id= R, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.224A pdb=" N ASN C 808 " --> pdb=" O SER C 815 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N SER C 673 " --> pdb=" O THR C 851 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 322 through 324 Processing sheet with id= T, first strand: chain 'C' and resid 266 through 272 removed outlier: 7.867A pdb=" N LYS C 182 " --> pdb=" O MET C 759 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLN C 761 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN C 751 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL C 764 " --> pdb=" O TYR C 749 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N TYR C 749 " --> pdb=" O VAL C 764 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 217 through 219 Processing sheet with id= V, first strand: chain 'C' and resid 250 through 252 Processing sheet with id= W, first strand: chain 'C' and resid 278 through 280 removed outlier: 6.888A pdb=" N THR C 625 " --> pdb=" O LYS C 602 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASN C 604 " --> pdb=" O PHE C 623 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE C 623 " --> pdb=" O ASN C 604 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ALA C 606 " --> pdb=" O VAL C 621 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL C 621 " --> pdb=" O ALA C 606 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU C 608 " --> pdb=" O VAL C 619 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N VAL C 619 " --> pdb=" O LEU C 608 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 715 through 722 Processing sheet with id= Y, first strand: chain 'C' and resid 704 through 709 removed outlier: 7.256A pdb=" N ILE C 821 " --> pdb=" O TYR C 705 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VAL C 707 " --> pdb=" O ALA C 819 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA C 819 " --> pdb=" O VAL C 707 " (cutoff:3.500A) 1363 hydrogen bonds defined for protein. 3960 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: 9.47 Time building geometry restraints manager: 10.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 3843 1.26 - 1.39: 5194 1.39 - 1.53: 13776 1.53 - 1.67: 824 1.67 - 1.81: 264 Bond restraints: 23901 Sorted by residual: bond pdb=" C LYS C 931 " pdb=" O LYS C 931 " ideal model delta sigma weight residual 1.237 1.116 0.120 1.19e-02 7.06e+03 1.02e+02 bond pdb=" C MET A 539 " pdb=" O MET A 539 " ideal model delta sigma weight residual 1.237 1.120 0.116 1.19e-02 7.06e+03 9.58e+01 bond pdb=" C SER A 828 " pdb=" O SER A 828 " ideal model delta sigma weight residual 1.237 1.128 0.108 1.19e-02 7.06e+03 8.30e+01 bond pdb=" C LYS B 931 " pdb=" O LYS B 931 " ideal model delta sigma weight residual 1.237 1.134 0.102 1.19e-02 7.06e+03 7.38e+01 bond pdb=" C PHE A 998 " pdb=" O PHE A 998 " ideal model delta sigma weight residual 1.237 1.141 0.096 1.19e-02 7.06e+03 6.46e+01 ... (remaining 23896 not shown) Histogram of bond angle deviations from ideal: 97.96 - 105.23: 536 105.23 - 112.50: 12643 112.50 - 119.77: 7813 119.77 - 127.04: 11196 127.04 - 134.31: 197 Bond angle restraints: 32385 Sorted by residual: angle pdb=" CA MET A 539 " pdb=" C MET A 539 " pdb=" O MET A 539 " ideal model delta sigma weight residual 120.42 111.54 8.88 1.06e+00 8.90e-01 7.03e+01 angle pdb=" CA SER A 828 " pdb=" C SER A 828 " pdb=" O SER A 828 " ideal model delta sigma weight residual 120.42 111.54 8.88 1.06e+00 8.90e-01 7.02e+01 angle pdb=" CA MET A 539 " pdb=" C MET A 539 " pdb=" N VAL A 540 " ideal model delta sigma weight residual 117.39 127.76 -10.37 1.24e+00 6.50e-01 6.99e+01 angle pdb=" CA ILE B 21 " pdb=" C ILE B 21 " pdb=" O ILE B 21 " ideal model delta sigma weight residual 120.47 111.79 8.68 1.08e+00 8.57e-01 6.46e+01 angle pdb=" CA PHE B 11 " pdb=" C PHE B 11 " pdb=" N ALA B 12 " ideal model delta sigma weight residual 117.30 125.82 -8.52 1.16e+00 7.43e-01 5.39e+01 ... (remaining 32380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 14208 35.29 - 70.57: 271 70.57 - 105.86: 24 105.86 - 141.14: 0 141.14 - 176.43: 5 Dihedral angle restraints: 14508 sinusoidal: 5691 harmonic: 8817 Sorted by residual: dihedral pdb=" N1 PTY B1102 " pdb=" C2 PTY B1102 " pdb=" C3 PTY B1102 " pdb=" O11 PTY B1102 " ideal model delta sinusoidal sigma weight residual 65.33 -118.24 -176.43 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 PTY B1101 " pdb=" O11 PTY B1101 " pdb=" P1 PTY B1101 " pdb=" O12 PTY B1101 " ideal model delta sinusoidal sigma weight residual -59.77 102.66 -162.43 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C ASN C 932 " pdb=" N ASN C 932 " pdb=" CA ASN C 932 " pdb=" CB ASN C 932 " ideal model delta harmonic sigma weight residual -122.60 -111.35 -11.25 0 2.50e+00 1.60e-01 2.03e+01 ... (remaining 14505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.306: 3871 0.306 - 0.613: 1 0.613 - 0.919: 0 0.919 - 1.226: 0 1.226 - 1.532: 1 Chirality restraints: 3873 Sorted by residual: chirality pdb=" CB VAL A1014 " pdb=" CA VAL A1014 " pdb=" CG1 VAL A1014 " pdb=" CG2 VAL A1014 " both_signs ideal model delta sigma weight residual False -2.63 -1.10 -1.53 2.00e-01 2.50e+01 5.87e+01 chirality pdb=" CB ILE B 21 " pdb=" CA ILE B 21 " pdb=" CG1 ILE B 21 " pdb=" CG2 ILE B 21 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" CA ARG B 363 " pdb=" N ARG B 363 " pdb=" C ARG B 363 " pdb=" CB ARG B 363 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 3870 not shown) Planarity restraints: 4062 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 704 " 0.023 2.00e-02 2.50e+03 4.34e-02 1.88e+01 pdb=" C PHE C 704 " -0.075 2.00e-02 2.50e+03 pdb=" O PHE C 704 " 0.027 2.00e-02 2.50e+03 pdb=" N TYR C 705 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 573 " 0.018 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C PHE B 573 " -0.064 2.00e-02 2.50e+03 pdb=" O PHE B 573 " 0.024 2.00e-02 2.50e+03 pdb=" N GLN B 574 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 930 " -0.015 2.00e-02 2.50e+03 3.15e-02 9.93e+00 pdb=" C ALA A 930 " 0.054 2.00e-02 2.50e+03 pdb=" O ALA A 930 " -0.021 2.00e-02 2.50e+03 pdb=" N LYS A 931 " -0.018 2.00e-02 2.50e+03 ... (remaining 4059 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 243 2.66 - 3.22: 23032 3.22 - 3.78: 35872 3.78 - 4.34: 50394 4.34 - 4.90: 83422 Nonbonded interactions: 192963 Sorted by model distance: nonbonded pdb=" O THR A 546 " pdb=" OG1 THR A 549 " model vdw 2.101 2.440 nonbonded pdb=" O VAL C 38 " pdb=" OG SER C 462 " model vdw 2.124 2.440 nonbonded pdb=" O ALA B 52 " pdb=" OG1 THR B 53 " model vdw 2.190 2.440 nonbonded pdb=" O ASN A 161 " pdb=" OE1 GLU A 165 " model vdw 2.197 3.040 nonbonded pdb=" O VAL C 362 " pdb=" OG1 THR C 365 " model vdw 2.209 2.440 ... (remaining 192958 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' and resid 1 through 1027) selection = (chain 'B' and resid 1 through 1027) 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: 0.090 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: 2.110 Check model and map are aligned: 0.370 Set scattering table: 0.240 Process input model: 64.610 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 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 : 0.004 0.123 23901 Z= 0.285 Angle : 0.768 17.200 32385 Z= 0.477 Chirality : 0.051 1.532 3873 Planarity : 0.006 0.075 4062 Dihedral : 14.747 176.425 8802 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.90 % Allowed : 0.70 % Favored : 98.40 % Cbeta Deviations : 0.07 % 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: 1.64 (0.16), residues: 3048 helix: 1.85 (0.13), residues: 1683 sheet: 0.53 (0.22), residues: 454 loop : 0.05 (0.22), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 556 HIS 0.004 0.001 HIS B 360 PHE 0.029 0.001 PHE A 569 TYR 0.024 0.001 TYR A 749 ARG 0.008 0.001 ARG A 585 *********************** 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 581 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 558 time to evaluate : 2.523 Fit side-chains revert: symmetry clash REVERT: A 241 SER cc_start: 0.8128 (p) cc_final: 0.7812 (p) REVERT: A 483 LEU cc_start: 0.8336 (tp) cc_final: 0.8040 (tp) REVERT: A 849 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7738 (mt-10) REVERT: A 923 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7239 (mt) REVERT: A 931 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7387 (ttpt) REVERT: A 948 MET cc_start: 0.7445 (ttm) cc_final: 0.6979 (ttp) REVERT: B 252 LYS cc_start: 0.7823 (mtmm) cc_final: 0.7583 (mtmt) REVERT: B 264 ASP cc_start: 0.6878 (m-30) cc_final: 0.6634 (m-30) REVERT: B 385 LEU cc_start: 0.8136 (mt) cc_final: 0.7843 (mt) REVERT: B 570 MET cc_start: 0.8025 (ttm) cc_final: 0.7721 (ttm) REVERT: B 656 MET cc_start: 0.8921 (tpt) cc_final: 0.8596 (tpp) REVERT: B 931 LYS cc_start: 0.7152 (OUTLIER) cc_final: 0.5174 (pttp) REVERT: B 932 ASN cc_start: 0.8104 (t0) cc_final: 0.7850 (t0) REVERT: B 959 LYS cc_start: 0.6982 (ttpt) cc_final: 0.6597 (tptp) REVERT: B 963 ARG cc_start: 0.7693 (ttp-170) cc_final: 0.7454 (ttp80) REVERT: C 151 GLU cc_start: 0.6361 (pt0) cc_final: 0.6111 (pt0) REVERT: C 570 MET cc_start: 0.8628 (ttp) cc_final: 0.8376 (ttm) REVERT: C 681 ASN cc_start: 0.7280 (t0) cc_final: 0.6892 (t0) REVERT: C 684 MET cc_start: 0.8521 (mmm) cc_final: 0.8077 (mmm) REVERT: C 893 MET cc_start: 0.6519 (mmp) cc_final: 0.6246 (mmm) REVERT: C 931 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.6704 (ttpt) outliers start: 23 outliers final: 9 residues processed: 577 average time/residue: 0.3229 time to fit residues: 295.2775 Evaluate side-chains 506 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 492 time to evaluate : 2.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 TYR Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 884 GLU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 931 LYS Chi-restraints excluded: chain C residue 931 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 4.9990 chunk 231 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 79 optimal weight: 0.0020 chunk 156 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 239 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 178 optimal weight: 8.9990 chunk 277 optimal weight: 4.9990 overall best weight: 4.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN A 161 ASN A 799 GLN A 859 GLN B 574 GLN B 594 ASN B 691 GLN B 859 GLN B 863 GLN C 176 GLN C 691 GLN C 714 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 23901 Z= 0.272 Angle : 0.591 9.521 32385 Z= 0.306 Chirality : 0.043 0.272 3873 Planarity : 0.005 0.062 4062 Dihedral : 9.333 175.038 3335 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.95 % Allowed : 8.65 % Favored : 89.40 % 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: 1.51 (0.15), residues: 3048 helix: 1.76 (0.13), residues: 1686 sheet: 0.57 (0.22), residues: 447 loop : -0.11 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 187 HIS 0.004 0.001 HIS A 991 PHE 0.019 0.002 PHE B 998 TYR 0.022 0.002 TYR B 49 ARG 0.007 0.000 ARG C 185 *********************** 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 571 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 521 time to evaluate : 2.715 Fit side-chains revert: symmetry clash REVERT: A 241 SER cc_start: 0.8153 (p) cc_final: 0.7826 (p) REVERT: A 435 MET cc_start: 0.7428 (mmm) cc_final: 0.7031 (mmm) REVERT: A 593 ASN cc_start: 0.7759 (m-40) cc_final: 0.7376 (m-40) REVERT: A 834 GLU cc_start: 0.7867 (tp30) cc_final: 0.7565 (tp30) REVERT: A 931 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7622 (pptt) REVERT: A 932 ASN cc_start: 0.8275 (OUTLIER) cc_final: 0.8030 (m-40) REVERT: A 948 MET cc_start: 0.7464 (ttm) cc_final: 0.6895 (ttp) REVERT: B 110 LYS cc_start: 0.7669 (mttp) cc_final: 0.7156 (mmtp) REVERT: B 252 LYS cc_start: 0.7838 (mtmm) cc_final: 0.7629 (mtmt) REVERT: B 385 LEU cc_start: 0.8263 (mt) cc_final: 0.7977 (mt) REVERT: B 398 MET cc_start: 0.8022 (mtt) cc_final: 0.7818 (mtt) REVERT: B 627 LYS cc_start: 0.6625 (mttt) cc_final: 0.6320 (mttt) REVERT: B 691 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7868 (tt0) REVERT: B 695 MET cc_start: 0.8317 (mmp) cc_final: 0.7999 (mmp) REVERT: B 748 MET cc_start: 0.8570 (mtt) cc_final: 0.8307 (mtp) REVERT: B 931 LYS cc_start: 0.7152 (OUTLIER) cc_final: 0.5445 (pttp) REVERT: B 959 LYS cc_start: 0.7114 (ttpt) cc_final: 0.6635 (tptp) REVERT: B 963 ARG cc_start: 0.7752 (ttp-170) cc_final: 0.7543 (ttp80) REVERT: B 1011 PHE cc_start: 0.7764 (m-80) cc_final: 0.7461 (m-80) REVERT: C 69 LEU cc_start: 0.7397 (tp) cc_final: 0.7192 (tp) REVERT: C 402 ILE cc_start: 0.8407 (mm) cc_final: 0.8157 (tp) REVERT: C 474 MET cc_start: 0.8181 (mtp) cc_final: 0.7914 (mtp) REVERT: C 684 MET cc_start: 0.8653 (mmm) cc_final: 0.8016 (mmt) REVERT: C 758 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.6904 (ttp80) REVERT: C 935 LEU cc_start: 0.7817 (mt) cc_final: 0.7615 (mt) REVERT: C 942 MET cc_start: 0.7099 (OUTLIER) cc_final: 0.6851 (ttp) outliers start: 50 outliers final: 31 residues processed: 549 average time/residue: 0.3259 time to fit residues: 285.1394 Evaluate side-chains 533 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 496 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 931 LYS Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 942 MET Chi-restraints excluded: chain C residue 948 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 40.0000 chunk 86 optimal weight: 3.9990 chunk 231 optimal weight: 9.9990 chunk 189 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 278 optimal weight: 3.9990 chunk 300 optimal weight: 0.9990 chunk 247 optimal weight: 20.0000 chunk 276 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 chunk 223 optimal weight: 0.2980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN A 799 GLN B 691 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23901 Z= 0.174 Angle : 0.519 9.967 32385 Z= 0.269 Chirality : 0.040 0.208 3873 Planarity : 0.005 0.056 4062 Dihedral : 8.197 178.030 3314 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.03 % Allowed : 11.19 % Favored : 86.78 % 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: 1.63 (0.15), residues: 3048 helix: 1.91 (0.13), residues: 1680 sheet: 0.50 (0.21), residues: 481 loop : -0.10 (0.22), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 800 HIS 0.002 0.000 HIS A 991 PHE 0.017 0.001 PHE B 824 TYR 0.015 0.001 TYR B 49 ARG 0.003 0.000 ARG C 185 *********************** 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 544 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 492 time to evaluate : 2.740 Fit side-chains revert: symmetry clash REVERT: A 241 SER cc_start: 0.8082 (p) cc_final: 0.7771 (p) REVERT: A 435 MET cc_start: 0.7375 (mmm) cc_final: 0.7041 (mmm) REVERT: A 456 MET cc_start: 0.8928 (ptt) cc_final: 0.8672 (ptm) REVERT: A 527 MET cc_start: 0.7643 (mmm) cc_final: 0.7253 (tpp) REVERT: A 593 ASN cc_start: 0.7699 (m-40) cc_final: 0.7328 (m-40) REVERT: A 834 GLU cc_start: 0.7872 (tp30) cc_final: 0.7573 (tp30) REVERT: A 931 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7416 (pptt) REVERT: A 942 MET cc_start: 0.6856 (mtp) cc_final: 0.6457 (ttp) REVERT: A 948 MET cc_start: 0.7395 (ttm) cc_final: 0.6834 (ttp) REVERT: B 110 LYS cc_start: 0.7698 (mttp) cc_final: 0.7176 (mmtp) REVERT: B 252 LYS cc_start: 0.7824 (mtmm) cc_final: 0.7600 (mtmt) REVERT: B 385 LEU cc_start: 0.8292 (mt) cc_final: 0.8025 (mt) REVERT: B 398 MET cc_start: 0.7936 (mtt) cc_final: 0.7417 (mtt) REVERT: B 627 LYS cc_start: 0.6638 (mttt) cc_final: 0.6433 (mttt) REVERT: B 931 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.5486 (pttp) REVERT: B 959 LYS cc_start: 0.7126 (ttpt) cc_final: 0.6682 (tptp) REVERT: B 963 ARG cc_start: 0.7849 (ttp-170) cc_final: 0.7634 (ttp80) REVERT: B 1011 PHE cc_start: 0.7813 (m-80) cc_final: 0.7492 (m-80) REVERT: C 69 LEU cc_start: 0.7322 (tp) cc_final: 0.7097 (tp) REVERT: C 110 LYS cc_start: 0.7654 (mmtm) cc_final: 0.7081 (mmtm) REVERT: C 334 LYS cc_start: 0.7733 (ttmm) cc_final: 0.7379 (mtpt) REVERT: C 474 MET cc_start: 0.8144 (mtp) cc_final: 0.7862 (mtp) REVERT: C 639 MET cc_start: 0.8501 (mmm) cc_final: 0.8033 (mtp) REVERT: C 684 MET cc_start: 0.8640 (mmm) cc_final: 0.8142 (mmt) REVERT: C 758 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.6962 (ttp80) REVERT: C 965 ILE cc_start: 0.6250 (OUTLIER) cc_final: 0.5982 (mp) outliers start: 52 outliers final: 33 residues processed: 524 average time/residue: 0.3347 time to fit residues: 279.6791 Evaluate side-chains 514 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 477 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 931 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 316 ASN Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 777 ILE Chi-restraints excluded: chain C residue 965 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 20.0000 chunk 209 optimal weight: 3.9990 chunk 144 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 186 optimal weight: 20.0000 chunk 279 optimal weight: 9.9990 chunk 295 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 264 optimal weight: 5.9990 chunk 79 optimal weight: 0.0370 overall best weight: 3.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN A 799 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 23901 Z= 0.253 Angle : 0.552 10.653 32385 Z= 0.284 Chirality : 0.042 0.216 3873 Planarity : 0.005 0.060 4062 Dihedral : 7.889 174.631 3314 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.53 % Allowed : 12.44 % Favored : 85.03 % 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: 1.46 (0.15), residues: 3048 helix: 1.79 (0.13), residues: 1689 sheet: 0.32 (0.22), residues: 471 loop : -0.15 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 556 HIS 0.001 0.000 HIS B 360 PHE 0.026 0.001 PHE B 998 TYR 0.015 0.001 TYR B 49 ARG 0.004 0.000 ARG A 515 *********************** 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 558 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 493 time to evaluate : 2.700 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7785 (mt) cc_final: 0.7410 (mt) REVERT: A 22 PHE cc_start: 0.7229 (OUTLIER) cc_final: 0.6300 (t80) REVERT: A 241 SER cc_start: 0.8150 (p) cc_final: 0.7839 (p) REVERT: A 454 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8397 (mp) REVERT: A 527 MET cc_start: 0.7697 (mmm) cc_final: 0.7328 (tpp) REVERT: A 593 ASN cc_start: 0.7719 (m-40) cc_final: 0.7312 (m-40) REVERT: A 931 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7600 (pptt) REVERT: A 932 ASN cc_start: 0.8560 (OUTLIER) cc_final: 0.8053 (m-40) REVERT: A 942 MET cc_start: 0.6968 (mtp) cc_final: 0.6595 (ttp) REVERT: A 948 MET cc_start: 0.7481 (ttm) cc_final: 0.6858 (ttp) REVERT: B 110 LYS cc_start: 0.7753 (mttp) cc_final: 0.7283 (mmtp) REVERT: B 252 LYS cc_start: 0.7791 (mtmm) cc_final: 0.7572 (mtmt) REVERT: B 385 LEU cc_start: 0.8316 (mt) cc_final: 0.8077 (mt) REVERT: B 398 MET cc_start: 0.8008 (mtt) cc_final: 0.7512 (mtt) REVERT: B 627 LYS cc_start: 0.6894 (mttt) cc_final: 0.6646 (mttt) REVERT: B 695 MET cc_start: 0.8227 (mmp) cc_final: 0.8014 (mmp) REVERT: B 801 ASN cc_start: 0.7781 (p0) cc_final: 0.7564 (p0) REVERT: B 893 MET cc_start: 0.8292 (mmp) cc_final: 0.7875 (mmp) REVERT: B 931 LYS cc_start: 0.7240 (OUTLIER) cc_final: 0.5798 (pttp) REVERT: B 959 LYS cc_start: 0.7147 (ttpt) cc_final: 0.6706 (tptp) REVERT: B 963 ARG cc_start: 0.7773 (ttp-170) cc_final: 0.7463 (ttp-170) REVERT: B 1011 PHE cc_start: 0.7802 (m-80) cc_final: 0.7467 (m-80) REVERT: C 69 LEU cc_start: 0.7417 (tp) cc_final: 0.7161 (tp) REVERT: C 334 LYS cc_start: 0.7737 (ttmm) cc_final: 0.7395 (mtpt) REVERT: C 681 ASN cc_start: 0.7353 (t0) cc_final: 0.7091 (t0) REVERT: C 684 MET cc_start: 0.8659 (mmm) cc_final: 0.8216 (mmt) REVERT: C 758 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.6859 (ttp80) REVERT: C 905 ILE cc_start: 0.7918 (pt) cc_final: 0.7699 (mt) REVERT: C 935 LEU cc_start: 0.7888 (mt) cc_final: 0.7432 (tp) outliers start: 65 outliers final: 47 residues processed: 532 average time/residue: 0.3296 time to fit residues: 277.4782 Evaluate side-chains 529 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 476 time to evaluate : 2.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 267 ASN Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 931 LYS Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 348 MET Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 777 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: 4.9990 chunk 4 optimal weight: 2.9990 chunk 220 optimal weight: 8.9990 chunk 122 optimal weight: 0.7980 chunk 252 optimal weight: 9.9990 chunk 204 optimal weight: 30.0000 chunk 0 optimal weight: 50.0000 chunk 151 optimal weight: 5.9990 chunk 265 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 799 GLN C 128 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 23901 Z= 0.274 Angle : 0.565 12.667 32385 Z= 0.290 Chirality : 0.042 0.192 3873 Planarity : 0.005 0.060 4062 Dihedral : 7.654 168.415 3314 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.81 % Allowed : 13.45 % Favored : 83.74 % 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: 1.32 (0.15), residues: 3048 helix: 1.73 (0.13), residues: 1684 sheet: 0.15 (0.21), residues: 484 loop : -0.26 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 610 HIS 0.002 0.000 HIS B 360 PHE 0.023 0.001 PHE B 998 TYR 0.018 0.001 TYR C 157 ARG 0.005 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 572 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 500 time to evaluate : 2.776 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7805 (mt) cc_final: 0.7442 (mt) REVERT: A 22 PHE cc_start: 0.7312 (OUTLIER) cc_final: 0.6287 (t80) REVERT: A 241 SER cc_start: 0.8274 (p) cc_final: 0.7974 (p) REVERT: A 352 PHE cc_start: 0.7910 (t80) cc_final: 0.7627 (t80) REVERT: A 355 MET cc_start: 0.7438 (mtt) cc_final: 0.7175 (mtp) REVERT: A 435 MET cc_start: 0.7418 (mmm) cc_final: 0.7209 (mmm) REVERT: A 454 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8468 (mp) REVERT: A 527 MET cc_start: 0.7715 (mmm) cc_final: 0.7353 (tpp) REVERT: A 593 ASN cc_start: 0.7717 (m-40) cc_final: 0.7305 (m-40) REVERT: A 692 ASP cc_start: 0.7502 (m-30) cc_final: 0.7120 (m-30) REVERT: A 931 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7684 (tmmt) REVERT: A 932 ASN cc_start: 0.8663 (OUTLIER) cc_final: 0.7993 (m-40) REVERT: B 110 LYS cc_start: 0.7764 (mttp) cc_final: 0.7355 (mmtp) REVERT: B 252 LYS cc_start: 0.7741 (mtmm) cc_final: 0.7533 (mtmt) REVERT: B 385 LEU cc_start: 0.8344 (mt) cc_final: 0.8115 (mt) REVERT: B 398 MET cc_start: 0.7984 (mtt) cc_final: 0.7455 (mtt) REVERT: B 695 MET cc_start: 0.8315 (mmp) cc_final: 0.8077 (mmp) REVERT: B 801 ASN cc_start: 0.7762 (p0) cc_final: 0.7539 (p0) REVERT: B 931 LYS cc_start: 0.7312 (OUTLIER) cc_final: 0.5771 (pttp) REVERT: B 963 ARG cc_start: 0.7840 (ttp-170) cc_final: 0.7458 (ttp-170) REVERT: C 69 LEU cc_start: 0.7444 (tp) cc_final: 0.7163 (tp) REVERT: C 110 LYS cc_start: 0.7589 (mmtm) cc_final: 0.7075 (mmtm) REVERT: C 334 LYS cc_start: 0.7706 (ttmm) cc_final: 0.7380 (mtpt) REVERT: C 402 ILE cc_start: 0.8498 (mm) cc_final: 0.8277 (tp) REVERT: C 639 MET cc_start: 0.8546 (mmm) cc_final: 0.8047 (mtp) REVERT: C 681 ASN cc_start: 0.7381 (t0) cc_final: 0.7178 (t0) REVERT: C 758 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.6738 (ttp80) REVERT: C 935 LEU cc_start: 0.7780 (mt) cc_final: 0.7481 (tp) outliers start: 72 outliers final: 51 residues processed: 540 average time/residue: 0.3339 time to fit residues: 287.8982 Evaluate side-chains 540 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 483 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 267 ASN Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 931 LYS Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 777 ILE Chi-restraints excluded: chain C residue 929 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 2.9990 chunk 266 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 296 optimal weight: 7.9990 chunk 245 optimal weight: 10.0000 chunk 137 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN A 248 ASN A 799 GLN B 717 ASN B 863 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 23901 Z= 0.331 Angle : 0.591 12.169 32385 Z= 0.305 Chirality : 0.043 0.156 3873 Planarity : 0.005 0.062 4062 Dihedral : 7.554 166.811 3313 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.04 % Allowed : 14.66 % Favored : 82.30 % 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: 1.07 (0.15), residues: 3048 helix: 1.57 (0.12), residues: 1682 sheet: -0.12 (0.21), residues: 499 loop : -0.33 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 556 HIS 0.006 0.001 HIS B 360 PHE 0.022 0.002 PHE B 998 TYR 0.020 0.002 TYR C 157 ARG 0.005 0.000 ARG A 515 *********************** 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 569 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 491 time to evaluate : 2.229 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7885 (mt) cc_final: 0.7496 (mt) REVERT: A 22 PHE cc_start: 0.7317 (OUTLIER) cc_final: 0.6238 (t80) REVERT: A 241 SER cc_start: 0.8334 (p) cc_final: 0.8033 (p) REVERT: A 352 PHE cc_start: 0.7925 (t80) cc_final: 0.7671 (t80) REVERT: A 435 MET cc_start: 0.7453 (mmm) cc_final: 0.7163 (mmm) REVERT: A 527 MET cc_start: 0.7735 (mmm) cc_final: 0.7391 (tpp) REVERT: A 593 ASN cc_start: 0.7784 (m-40) cc_final: 0.7380 (m-40) REVERT: A 931 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7795 (tmmt) REVERT: A 932 ASN cc_start: 0.8768 (OUTLIER) cc_final: 0.8132 (m-40) REVERT: B 110 LYS cc_start: 0.7780 (mttp) cc_final: 0.7410 (mttp) REVERT: B 252 LYS cc_start: 0.7736 (mtmm) cc_final: 0.7529 (mtmt) REVERT: B 385 LEU cc_start: 0.8360 (mt) cc_final: 0.8140 (mt) REVERT: B 642 ASP cc_start: 0.7295 (m-30) cc_final: 0.7055 (m-30) REVERT: B 665 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.7046 (mt-10) REVERT: B 801 ASN cc_start: 0.7780 (p0) cc_final: 0.7563 (p0) REVERT: B 931 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.5923 (pttm) REVERT: B 1007 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7862 (tt) REVERT: C 69 LEU cc_start: 0.7456 (tp) cc_final: 0.7170 (tp) REVERT: C 110 LYS cc_start: 0.7557 (mmtm) cc_final: 0.7048 (mmtm) REVERT: C 334 LYS cc_start: 0.7682 (ttmm) cc_final: 0.7359 (mtpt) REVERT: C 402 ILE cc_start: 0.8465 (mm) cc_final: 0.8257 (tp) REVERT: C 639 MET cc_start: 0.8545 (mmm) cc_final: 0.8111 (mtp) REVERT: C 681 ASN cc_start: 0.7432 (t0) cc_final: 0.7219 (t0) REVERT: C 758 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.6916 (ttp80) REVERT: C 935 LEU cc_start: 0.7810 (mt) cc_final: 0.7477 (tp) outliers start: 78 outliers final: 55 residues processed: 537 average time/residue: 0.3329 time to fit residues: 286.2035 Evaluate side-chains 545 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 483 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 267 ASN Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 665 GLU Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 931 LYS Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 348 MET Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 777 ILE Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 929 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 216 optimal weight: 0.9980 chunk 167 optimal weight: 0.2980 chunk 249 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 chunk 294 optimal weight: 8.9990 chunk 184 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 799 GLN B 598 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23901 Z= 0.195 Angle : 0.530 12.636 32385 Z= 0.272 Chirality : 0.040 0.187 3873 Planarity : 0.005 0.058 4062 Dihedral : 7.248 170.381 3311 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.50 % Allowed : 16.10 % Favored : 81.40 % 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: 1.78 (0.13), residues: 1685 sheet: -0.07 (0.22), residues: 489 loop : -0.25 (0.22), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 610 HIS 0.004 0.001 HIS B 360 PHE 0.030 0.001 PHE C 939 TYR 0.024 0.001 TYR C 157 ARG 0.006 0.000 ARG A 515 *********************** 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 561 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 497 time to evaluate : 2.799 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7761 (mt) cc_final: 0.7401 (mt) REVERT: A 22 PHE cc_start: 0.7194 (OUTLIER) cc_final: 0.6094 (t80) REVERT: A 241 SER cc_start: 0.8150 (p) cc_final: 0.7864 (p) REVERT: A 352 PHE cc_start: 0.7901 (t80) cc_final: 0.7647 (t80) REVERT: A 435 MET cc_start: 0.7378 (mmm) cc_final: 0.7143 (mmm) REVERT: A 527 MET cc_start: 0.7705 (mmm) cc_final: 0.7396 (tpp) REVERT: A 593 ASN cc_start: 0.7668 (m-40) cc_final: 0.7274 (m-40) REVERT: A 684 MET cc_start: 0.8370 (mmm) cc_final: 0.8053 (mmm) REVERT: A 931 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7679 (tmmt) REVERT: A 932 ASN cc_start: 0.8568 (OUTLIER) cc_final: 0.7884 (m-40) REVERT: B 110 LYS cc_start: 0.7783 (mttp) cc_final: 0.7406 (mttp) REVERT: B 252 LYS cc_start: 0.7720 (mtmm) cc_final: 0.7513 (mtmt) REVERT: B 385 LEU cc_start: 0.8353 (mt) cc_final: 0.8114 (mt) REVERT: B 398 MET cc_start: 0.7969 (mtt) cc_final: 0.7625 (mtt) REVERT: B 642 ASP cc_start: 0.7231 (m-30) cc_final: 0.6972 (m-30) REVERT: B 665 GLU cc_start: 0.7239 (mp0) cc_final: 0.6986 (mt-10) REVERT: B 801 ASN cc_start: 0.7714 (p0) cc_final: 0.7496 (p0) REVERT: B 859 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7849 (mt0) REVERT: B 893 MET cc_start: 0.8387 (mmp) cc_final: 0.8046 (mmp) REVERT: B 931 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.5884 (pttp) REVERT: C 69 LEU cc_start: 0.7383 (tp) cc_final: 0.7118 (tp) REVERT: C 110 LYS cc_start: 0.7597 (mmtm) cc_final: 0.7063 (mmtm) REVERT: C 334 LYS cc_start: 0.7539 (ttmm) cc_final: 0.7217 (mtpt) REVERT: C 402 ILE cc_start: 0.8475 (mm) cc_final: 0.8271 (tp) REVERT: C 639 MET cc_start: 0.8507 (mmm) cc_final: 0.8100 (mtp) REVERT: C 758 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.6692 (ttp80) REVERT: C 809 ARG cc_start: 0.8514 (ttm-80) cc_final: 0.8175 (ttm-80) REVERT: C 965 ILE cc_start: 0.6658 (OUTLIER) cc_final: 0.6288 (mp) outliers start: 64 outliers final: 43 residues processed: 533 average time/residue: 0.3280 time to fit residues: 280.2395 Evaluate side-chains 536 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 486 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 859 GLN Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 931 LYS Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 348 MET Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 777 ILE Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 965 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 176 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 187 optimal weight: 10.0000 chunk 200 optimal weight: 5.9990 chunk 145 optimal weight: 0.1980 chunk 27 optimal weight: 9.9990 chunk 231 optimal weight: 9.9990 chunk 268 optimal weight: 5.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN A 799 GLN B 204 ASN C 128 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 23901 Z= 0.274 Angle : 0.572 13.054 32385 Z= 0.293 Chirality : 0.042 0.222 3873 Planarity : 0.005 0.060 4062 Dihedral : 7.184 177.446 3311 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.57 % Allowed : 16.84 % Favored : 80.58 % 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: 1.17 (0.15), residues: 3048 helix: 1.68 (0.13), residues: 1684 sheet: -0.11 (0.21), residues: 489 loop : -0.37 (0.21), residues: 875 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 0.031 0.001 PHE C 939 TYR 0.023 0.001 TYR C 157 ARG 0.007 0.000 ARG A 515 *********************** 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 559 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 493 time to evaluate : 3.003 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7789 (mt) cc_final: 0.7414 (mt) REVERT: A 22 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.6154 (t80) REVERT: A 241 SER cc_start: 0.8314 (p) cc_final: 0.8009 (p) REVERT: A 352 PHE cc_start: 0.7905 (t80) cc_final: 0.7646 (t80) REVERT: A 435 MET cc_start: 0.7444 (mmm) cc_final: 0.7174 (mmm) REVERT: A 527 MET cc_start: 0.7712 (mmm) cc_final: 0.7409 (tpp) REVERT: A 593 ASN cc_start: 0.7699 (m-40) cc_final: 0.7308 (m-40) REVERT: A 692 ASP cc_start: 0.7245 (m-30) cc_final: 0.6712 (m-30) REVERT: A 931 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7479 (ttpp) REVERT: A 932 ASN cc_start: 0.8727 (OUTLIER) cc_final: 0.8112 (m-40) REVERT: B 110 LYS cc_start: 0.7786 (mttp) cc_final: 0.7401 (mttp) REVERT: B 385 LEU cc_start: 0.8330 (mt) cc_final: 0.8123 (mt) REVERT: B 398 MET cc_start: 0.8003 (mtt) cc_final: 0.7669 (mtt) REVERT: B 665 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.7038 (mt-10) REVERT: B 801 ASN cc_start: 0.7751 (p0) cc_final: 0.7533 (p0) REVERT: B 859 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7910 (mt0) REVERT: B 893 MET cc_start: 0.8397 (mmp) cc_final: 0.8041 (mmp) REVERT: C 69 LEU cc_start: 0.7423 (tp) cc_final: 0.7121 (tp) REVERT: C 110 LYS cc_start: 0.7602 (mmtm) cc_final: 0.7083 (mmtm) REVERT: C 334 LYS cc_start: 0.7635 (ttmm) cc_final: 0.7317 (mtpt) REVERT: C 639 MET cc_start: 0.8539 (mmm) cc_final: 0.8128 (mtp) REVERT: C 758 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.6715 (ttp80) REVERT: C 794 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6884 (mp0) REVERT: C 809 ARG cc_start: 0.8481 (ttm-80) cc_final: 0.8173 (ttm-80) REVERT: C 965 ILE cc_start: 0.6692 (OUTLIER) cc_final: 0.6291 (mp) outliers start: 66 outliers final: 53 residues processed: 536 average time/residue: 0.3324 time to fit residues: 285.8283 Evaluate side-chains 544 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 483 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 665 GLU Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 859 GLN Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 348 MET Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 777 ILE Chi-restraints excluded: chain C residue 794 GLU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 965 ILE Chi-restraints excluded: chain C residue 986 SER Chi-restraints excluded: chain C residue 1020 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 0.4980 chunk 257 optimal weight: 8.9990 chunk 274 optimal weight: 9.9990 chunk 165 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 259 optimal weight: 0.6980 chunk 273 optimal weight: 9.9990 chunk 180 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 799 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23901 Z= 0.185 Angle : 0.534 13.442 32385 Z= 0.273 Chirality : 0.040 0.212 3873 Planarity : 0.005 0.059 4062 Dihedral : 6.899 178.555 3307 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.26 % Allowed : 17.31 % Favored : 80.43 % 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: 1.82 (0.13), residues: 1686 sheet: -0.02 (0.22), residues: 489 loop : -0.29 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 610 HIS 0.004 0.001 HIS B 360 PHE 0.030 0.001 PHE C 939 TYR 0.022 0.001 TYR C 157 ARG 0.008 0.000 ARG A 515 *********************** 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 551 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 493 time to evaluate : 2.727 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7724 (mt) cc_final: 0.7363 (mt) REVERT: A 22 PHE cc_start: 0.7196 (OUTLIER) cc_final: 0.6082 (t80) REVERT: A 241 SER cc_start: 0.8146 (p) cc_final: 0.7848 (p) REVERT: A 435 MET cc_start: 0.7369 (mmm) cc_final: 0.7139 (mmm) REVERT: A 527 MET cc_start: 0.7681 (mmm) cc_final: 0.7395 (tpp) REVERT: A 593 ASN cc_start: 0.7666 (m-40) cc_final: 0.7263 (m-40) REVERT: A 692 ASP cc_start: 0.7245 (m-30) cc_final: 0.6717 (m-30) REVERT: A 834 GLU cc_start: 0.7921 (tp30) cc_final: 0.7637 (tp30) REVERT: A 931 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7694 (tmmt) REVERT: A 932 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.7856 (m-40) REVERT: B 110 LYS cc_start: 0.7729 (mttp) cc_final: 0.7457 (mttp) REVERT: B 385 LEU cc_start: 0.8327 (mt) cc_final: 0.8096 (mt) REVERT: B 398 MET cc_start: 0.7962 (mtt) cc_final: 0.7649 (mtt) REVERT: B 642 ASP cc_start: 0.7181 (m-30) cc_final: 0.6920 (m-30) REVERT: B 665 GLU cc_start: 0.7253 (mp0) cc_final: 0.7011 (mt-10) REVERT: B 695 MET cc_start: 0.8184 (mmt) cc_final: 0.7974 (mmp) REVERT: B 801 ASN cc_start: 0.7734 (p0) cc_final: 0.7507 (p0) REVERT: B 859 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7847 (mt0) REVERT: B 893 MET cc_start: 0.8309 (mmp) cc_final: 0.7930 (mmp) REVERT: B 963 ARG cc_start: 0.7818 (ttp-170) cc_final: 0.7456 (ttp-170) REVERT: C 69 LEU cc_start: 0.7378 (tp) cc_final: 0.7086 (tp) REVERT: C 110 LYS cc_start: 0.7615 (mmtm) cc_final: 0.7071 (mmtm) REVERT: C 334 LYS cc_start: 0.7540 (ttmm) cc_final: 0.7233 (mtpt) REVERT: C 639 MET cc_start: 0.8498 (mmm) cc_final: 0.8147 (mtp) REVERT: C 758 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8555 (ttt-90) REVERT: C 794 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7052 (mp0) REVERT: C 965 ILE cc_start: 0.6582 (OUTLIER) cc_final: 0.6216 (mp) outliers start: 58 outliers final: 49 residues processed: 531 average time/residue: 0.3312 time to fit residues: 281.2535 Evaluate side-chains 540 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 484 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 859 GLN Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 348 MET Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 777 ILE Chi-restraints excluded: chain C residue 794 GLU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 965 ILE Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1020 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 10.0000 chunk 177 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 202 optimal weight: 0.9990 chunk 304 optimal weight: 10.0000 chunk 280 optimal weight: 8.9990 chunk 242 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 187 optimal weight: 9.9990 chunk 148 optimal weight: 6.9990 chunk 192 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 799 GLN C 128 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 23901 Z= 0.269 Angle : 0.575 13.596 32385 Z= 0.293 Chirality : 0.042 0.227 3873 Planarity : 0.005 0.061 4062 Dihedral : 6.896 178.284 3307 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.34 % Allowed : 17.54 % Favored : 80.12 % 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: 1.20 (0.15), residues: 3048 helix: 1.70 (0.13), residues: 1685 sheet: -0.05 (0.21), residues: 495 loop : -0.36 (0.22), residues: 868 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 0.032 0.001 PHE C 939 TYR 0.021 0.001 TYR C 157 ARG 0.008 0.000 ARG A 515 ********************** 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 551 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 491 time to evaluate : 2.610 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7772 (mt) cc_final: 0.7448 (mt) REVERT: A 22 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.6094 (t80) REVERT: A 241 SER cc_start: 0.8222 (p) cc_final: 0.7897 (p) REVERT: A 352 PHE cc_start: 0.7894 (t80) cc_final: 0.7613 (t80) REVERT: A 435 MET cc_start: 0.7396 (mmm) cc_final: 0.7118 (mmm) REVERT: A 527 MET cc_start: 0.7695 (mmm) cc_final: 0.7400 (tpp) REVERT: A 593 ASN cc_start: 0.7697 (m-40) cc_final: 0.7273 (m-40) REVERT: A 692 ASP cc_start: 0.7265 (m-30) cc_final: 0.6742 (m-30) REVERT: A 931 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7718 (tmmt) REVERT: A 932 ASN cc_start: 0.8703 (OUTLIER) cc_final: 0.8105 (m-40) REVERT: A 942 MET cc_start: 0.6863 (mtp) cc_final: 0.6596 (ttp) REVERT: B 110 LYS cc_start: 0.7736 (mttp) cc_final: 0.7336 (mttp) REVERT: B 385 LEU cc_start: 0.8330 (mt) cc_final: 0.8129 (mt) REVERT: B 398 MET cc_start: 0.8004 (mtt) cc_final: 0.7684 (mtt) REVERT: B 665 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.7074 (mt-10) REVERT: B 801 ASN cc_start: 0.7776 (p0) cc_final: 0.7553 (p0) REVERT: B 859 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7905 (mt0) REVERT: B 893 MET cc_start: 0.8318 (mmp) cc_final: 0.7918 (mmp) REVERT: B 963 ARG cc_start: 0.7873 (ttp-170) cc_final: 0.7615 (ttp-170) REVERT: C 69 LEU cc_start: 0.7435 (tp) cc_final: 0.7141 (tp) REVERT: C 334 LYS cc_start: 0.7587 (ttmm) cc_final: 0.7271 (mtpt) REVERT: C 639 MET cc_start: 0.8532 (mmm) cc_final: 0.8136 (mtp) REVERT: C 758 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.6665 (ttp80) REVERT: C 794 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7061 (mp0) REVERT: C 965 ILE cc_start: 0.6659 (OUTLIER) cc_final: 0.6239 (mp) outliers start: 60 outliers final: 49 residues processed: 530 average time/residue: 0.3206 time to fit residues: 272.9339 Evaluate side-chains 546 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 489 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 665 GLU Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 859 GLN Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 348 MET Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 777 ILE Chi-restraints excluded: chain C residue 794 GLU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 965 ILE Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1020 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 223 optimal weight: 0.0170 chunk 35 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 243 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 249 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 799 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.151995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.122748 restraints weight = 26315.594| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.67 r_work: 0.3005 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23901 Z= 0.199 Angle : 0.544 13.717 32385 Z= 0.276 Chirality : 0.040 0.208 3873 Planarity : 0.005 0.059 4062 Dihedral : 6.687 175.110 3307 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.34 % Allowed : 17.50 % Favored : 80.16 % 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: 1.81 (0.13), residues: 1685 sheet: 0.04 (0.22), residues: 495 loop : -0.29 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 610 HIS 0.003 0.001 HIS B 360 PHE 0.030 0.001 PHE C 939 TYR 0.020 0.001 TYR C 157 ARG 0.008 0.000 ARG A 515 =============================================================================== Job complete usr+sys time: 5801.41 seconds wall clock time: 104 minutes 42.17 seconds (6282.17 seconds total)