Starting phenix.real_space_refine (version: dev) on Fri Feb 24 17:57:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgi_22871/02_2023/7kgi_22871_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgi_22871/02_2023/7kgi_22871.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgi_22871/02_2023/7kgi_22871_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgi_22871/02_2023/7kgi_22871_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgi_22871/02_2023/7kgi_22871_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgi_22871/02_2023/7kgi_22871.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgi_22871/02_2023/7kgi_22871.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgi_22871/02_2023/7kgi_22871_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgi_22871/02_2023/7kgi_22871_updated.pdb" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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 ARG 160": "NH1" <-> "NH2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A GLU 269": "OE1" <-> "OE2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A GLU 563": "OE1" <-> "OE2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A ARG 585": "NH1" <-> "NH2" Residue "A ARG 632": "NH1" <-> "NH2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "A ARG 771": "NH1" <-> "NH2" Residue "A ARG 809": "NH1" <-> "NH2" Residue "A ARG 813": "NH1" <-> "NH2" Residue "A GLU 830": "OE1" <-> "OE2" Residue "A ARG 833": "NH1" <-> "NH2" Residue "A GLU 834": "OE1" <-> "OE2" Residue "A GLU 836": "OE1" <-> "OE2" Residue "A GLU 857": "OE1" <-> "OE2" Residue "A GLU 884": "OE1" <-> "OE2" Residue "A ARG 910": "NH1" <-> "NH2" Residue "A GLU 946": "OE1" <-> "OE2" Residue "A ARG 961": "NH1" <-> "NH2" Residue "A ARG 963": "NH1" <-> "NH2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 1024": "OE1" <-> "OE2" Residue "B ARG 7": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B GLU 164": "OE1" <-> "OE2" Residue "B ARG 168": "NH1" <-> "NH2" Residue "B ARG 185": "NH1" <-> "NH2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B GLU 213": "OE1" <-> "OE2" Residue "B ARG 218": "NH1" <-> "NH2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B GLU 414": "OE1" <-> "OE2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B ARG 418": "NH1" <-> "NH2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B ARG 583": "NH1" <-> "NH2" Residue "B ARG 585": "NH1" <-> "NH2" Residue "B ARG 632": "NH1" <-> "NH2" Residue "B ARG 675": "NH1" <-> "NH2" Residue "B ARG 679": "NH1" <-> "NH2" Residue "B ARG 724": "NH1" <-> "NH2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B ARG 758": "NH1" <-> "NH2" Residue "B GLU 767": "OE1" <-> "OE2" Residue "B ARG 771": "NH1" <-> "NH2" Residue "B GLU 794": "OE1" <-> "OE2" Residue "B ARG 809": "NH1" <-> "NH2" Residue "B ARG 813": "NH1" <-> "NH2" Residue "B ARG 833": "NH1" <-> "NH2" Residue "B GLU 834": "OE1" <-> "OE2" Residue "B GLU 857": "OE1" <-> "OE2" Residue "B GLU 884": "OE1" <-> "OE2" Residue "B ARG 910": "NH1" <-> "NH2" Residue "B GLU 952": "OE1" <-> "OE2" Residue "B ARG 961": "NH1" <-> "NH2" Residue "B ARG 963": "NH1" <-> "NH2" Residue "B GLU 1024": "OE1" <-> "OE2" Residue "C ARG 7": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C GLU 101": "OE1" <-> "OE2" Residue "C ARG 123": "NH1" <-> "NH2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "C ARG 160": "NH1" <-> "NH2" Residue "C ARG 168": "NH1" <-> "NH2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C ARG 185": "NH1" <-> "NH2" Residue "C ARG 208": "NH1" <-> "NH2" Residue "C GLU 209": "OE1" <-> "OE2" Residue "C ARG 218": "NH1" <-> "NH2" Residue "C GLU 244": "OE1" <-> "OE2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C GLU 346": "OE1" <-> "OE2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 418": "NH1" <-> "NH2" Residue "C GLU 525": "OE1" <-> "OE2" Residue "C ARG 583": "NH1" <-> "NH2" Residue "C ARG 585": "NH1" <-> "NH2" Residue "C GLU 592": "OE1" <-> "OE2" Residue "C ARG 632": "NH1" <-> "NH2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C ARG 675": "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 ARG 809": "NH1" <-> "NH2" Residue "C ARG 813": "NH1" <-> "NH2" Residue "C GLU 834": "OE1" <-> "OE2" Residue "C GLU 849": "OE1" <-> "OE2" Residue "C GLU 857": "OE1" <-> "OE2" Residue "C ARG 910": "NH1" <-> "NH2" Residue "C GLU 938": "OE1" <-> "OE2" Residue "C GLU 946": "OE1" <-> "OE2" Residue "C ARG 961": "NH1" <-> "NH2" Residue "C ARG 963": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 23533 Number of models: 1 Model: "" Number of chains: 6 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {' ET': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "C" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {' ET': 2, 'PTY': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Time building chain proxies: 13.77, per 1000 atoms: 0.59 Number of scatterers: 23533 At special positions: 0 Unit cell: (118.8, 114.48, 143.64, 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 3804 7.00 C 15259 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: 12.33 Conformation dependent library (CDL) restraints added in 3.7 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: 115 helices and 23 sheets defined 54.9% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.87 Creating SS restraints... Processing helix chain 'A' and resid 2 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 69 removed outlier: 3.783A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 114 removed outlier: 4.105A pdb=" N ALA A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 4.255A 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 161 Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 190 through 196 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 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 299 through 315 removed outlier: 3.910A pdb=" N LEU A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 359 Processing helix chain 'A' and resid 362 through 386 removed outlier: 3.942A pdb=" N ILE A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Proline residue: A 368 - end of helix Proline residue: A 373 - end of helix removed outlier: 3.618A pdb=" N LEU A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 422 removed outlier: 4.515A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA A 409 " --> pdb=" O ILE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 437 Processing helix chain 'A' and resid 439 through 456 removed outlier: 3.717A pdb=" N PHE A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 461 through 495 removed outlier: 3.526A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A 473 " --> pdb=" O GLN A 469 " (cutoff:3.500A) removed outlier: 4.127A 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 Processing helix chain 'A' and resid 536 through 555 Processing helix chain 'A' and resid 581 through 597 removed outlier: 3.990A pdb=" N ASP A 597 " --> pdb=" O ASN A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 648 removed outlier: 3.690A pdb=" N ALA A 648 " --> pdb=" O ASN A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 700 Processing helix chain 'A' and resid 724 through 730 Processing helix chain 'A' and resid 734 through 744 Processing helix chain 'A' and resid 768 through 771 Processing helix chain 'A' and resid 774 through 779 removed outlier: 3.506A pdb=" N ASN A 779 " --> pdb=" O LYS A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 795 No H-bonds generated for 'chain 'A' and resid 792 through 795' Processing helix chain 'A' and resid 828 through 840 Processing helix chain 'A' and resid 853 through 858 Processing helix chain 'A' and resid 861 through 883 removed outlier: 4.674A pdb=" N ALA A 865 " --> pdb=" O GLU A 861 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE A 866 " --> pdb=" O SER A 862 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL A 875 " --> pdb=" O SER A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 910 removed outlier: 3.977A pdb=" N VAL A 892 " --> pdb=" O ILE A 888 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL A 896 " --> pdb=" O VAL A 892 " (cutoff:3.500A) Proline residue: A 897 - end of helix removed outlier: 3.873A pdb=" N GLY A 902 " --> pdb=" O LEU A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 945 removed outlier: 3.594A pdb=" N ALA A 930 " --> pdb=" O ILE A 926 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A 935 " --> pdb=" O LYS A 931 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE A 936 " --> pdb=" O ASN A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 975 removed outlier: 4.818A pdb=" N ARG A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Proline residue: A 964 - end of helix Processing helix chain 'A' and resid 977 through 981 Processing helix chain 'A' and resid 987 through 1026 removed outlier: 4.059A pdb=" N GLY A 996 " --> pdb=" O ALA A 992 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 997 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 4.268A 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 7 Processing helix chain 'B' and resid 9 through 29 Proline residue: B 28 - end of helix Processing helix chain 'B' and resid 54 through 60 Processing helix chain 'B' and resid 62 through 70 removed outlier: 3.576A pdb=" N ARG B 67 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU B 69 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N SER B 70 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 114 removed outlier: 3.705A pdb=" N LYS B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS B 112 " --> pdb=" O GLN B 108 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VAL B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 removed outlier: 3.803A pdb=" N GLN B 124 " --> pdb=" O GLN B 120 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 120 through 125' Processing helix chain 'B' and resid 151 through 161 Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 190 through 195 Processing helix chain 'B' and resid 200 through 210 removed outlier: 3.669A pdb=" N ASN B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 248 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: 4.383A pdb=" N LEU B 315 " --> pdb=" O GLU B 311 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASN B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 359 removed outlier: 3.706A pdb=" N LYS B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 386 removed outlier: 3.859A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix removed outlier: 4.149A pdb=" N VAL B 371 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 3.970A 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 402 Processing helix chain 'B' and resid 407 through 422 Processing helix chain 'B' and resid 427 through 437 Processing helix chain 'B' and resid 439 through 458 removed outlier: 3.807A pdb=" N PHE B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Proline residue: B 455 - end of helix removed outlier: 4.004A pdb=" N PHE B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 485 removed outlier: 3.552A pdb=" N GLN B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 495 Processing helix chain 'B' and resid 509 through 533 removed outlier: 3.940A 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 596 Processing helix chain 'B' and resid 637 through 649 removed outlier: 3.760A pdb=" N ASN B 649 " --> pdb=" O SER B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 700 removed outlier: 3.754A pdb=" N LYS B 700 " --> pdb=" O ALA B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 729 Processing helix chain 'B' and resid 734 through 745 removed outlier: 4.405A pdb=" N MET B 745 " --> pdb=" O ILE B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 771 removed outlier: 3.565A pdb=" N ARG B 771 " --> pdb=" O ALA B 768 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 768 through 771' Processing helix chain 'B' and resid 774 through 778 Processing helix chain 'B' and resid 792 through 794 No H-bonds generated for 'chain 'B' and resid 792 through 794' Processing helix chain 'B' and resid 828 through 841 removed outlier: 3.712A 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 883 removed outlier: 3.704A pdb=" N MET B 872 " --> pdb=" O LEU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 894 Processing helix chain 'B' and resid 896 through 910 removed outlier: 4.493A pdb=" N GLY B 902 " --> pdb=" O LEU B 898 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA B 903 " --> pdb=" O GLY B 899 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE B 905 " --> pdb=" O PHE B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 945 removed outlier: 3.709A pdb=" N ILE B 936 " --> pdb=" O ASN B 932 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE B 939 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 975 removed outlier: 5.021A pdb=" N ARG B 963 " --> pdb=" O LYS B 959 " (cutoff:3.500A) Proline residue: B 964 - end of helix 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 1026 removed outlier: 4.420A pdb=" N GLY B 996 " --> pdb=" O ALA B 992 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL B 997 " --> pdb=" O LEU B 993 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE B1010 " --> pdb=" O ILE B1006 " (cutoff:3.500A) Proline residue: B1013 - end of helix Processing helix chain 'C' and resid 2 through 7 removed outlier: 3.596A pdb=" N ARG C 7 " --> pdb=" O PHE C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 29 Proline residue: C 28 - end of helix Processing helix chain 'C' and resid 54 through 60 Processing helix chain 'C' and resid 62 through 70 removed outlier: 3.594A pdb=" N GLU C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 111 Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 151 through 161 Processing helix chain 'C' and resid 163 through 168 removed outlier: 3.843A pdb=" N ARG C 168 " --> pdb=" O GLU C 164 " (cutoff:3.500A) 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 316 removed outlier: 3.935A pdb=" N LEU C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN C 316 " --> pdb=" O GLU C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 358 removed outlier: 3.560A pdb=" N LEU C 345 " --> pdb=" O ILE C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 386 removed outlier: 4.089A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix Proline residue: C 373 - end of helix Processing helix chain 'C' and resid 392 through 423 removed outlier: 4.498A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA C 409 " --> pdb=" O ILE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 452 removed outlier: 5.531A 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 454 through 457 No H-bonds generated for 'chain 'C' and resid 454 through 457' Processing helix chain 'C' and resid 461 through 485 removed outlier: 3.733A pdb=" N THR C 473 " --> pdb=" O GLN C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 496 Processing helix chain 'C' and resid 509 through 533 removed outlier: 3.840A pdb=" N LYS C 533 " --> pdb=" O LEU C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 555 Processing helix chain 'C' and resid 581 through 597 removed outlier: 3.691A pdb=" N ASP C 597 " --> pdb=" O ASN C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 646 Processing helix chain 'C' and resid 684 through 700 removed outlier: 3.862A pdb=" N LYS C 700 " --> pdb=" O ALA C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 730 Processing helix chain 'C' and resid 734 through 744 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 794 No H-bonds generated for 'chain 'C' and resid 792 through 794' Processing helix chain 'C' and resid 828 through 841 removed outlier: 3.577A pdb=" N LYS C 841 " --> pdb=" O GLN C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 859 Processing helix chain 'C' and resid 863 through 883 Processing helix chain 'C' and resid 888 through 910 removed outlier: 3.894A pdb=" N VAL C 892 " --> pdb=" O ILE C 888 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL C 895 " --> pdb=" O SER C 891 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL C 896 " --> pdb=" O VAL C 892 " (cutoff:3.500A) Proline residue: C 897 - end of helix removed outlier: 3.609A pdb=" N ILE C 900 " --> pdb=" O VAL C 896 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY C 902 " --> pdb=" O LEU C 898 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA C 903 " --> pdb=" O GLY C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 945 Processing helix chain 'C' and resid 950 through 975 removed outlier: 4.599A pdb=" N ARG C 963 " --> pdb=" O LYS C 959 " (cutoff:3.500A) Proline residue: C 964 - end of helix Processing helix chain 'C' and resid 977 through 980 No H-bonds generated for 'chain 'C' and resid 977 through 980' Processing helix chain 'C' and resid 987 through 1026 removed outlier: 4.042A pdb=" N GLY C 996 " --> pdb=" O ALA C 992 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 997 " --> pdb=" O LEU C 993 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE C1009 " --> pdb=" O THR C1005 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE C1010 " --> pdb=" O ILE C1006 " (cutoff:3.500A) Proline residue: C1013 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 128 through 131 Processing sheet with id= B, first strand: chain 'A' and resid 322 through 324 removed outlier: 3.865A pdb=" N MET A 138 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 266 through 272 removed outlier: 8.316A pdb=" N LYS A 182 " --> pdb=" O MET A 759 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLN A 761 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN A 751 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL A 764 " --> pdb=" O TYR A 749 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N TYR A 749 " --> pdb=" O VAL A 764 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 250 through 253 Processing sheet with id= E, first strand: chain 'A' and resid 278 through 280 removed outlier: 6.977A pdb=" N THR A 625 " --> pdb=" O LYS A 602 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASN A 604 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N PHE A 623 " --> pdb=" O ASN A 604 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ALA A 606 " --> pdb=" O VAL A 621 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL A 621 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LEU A 608 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL A 619 " --> pdb=" O LEU A 608 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET A 570 " --> pdb=" O VAL A 658 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 672 through 677 removed outlier: 3.591A pdb=" N PHE A 672 " --> pdb=" O GLY A 820 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 820 " --> pdb=" O PHE A 672 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER A 817 " --> pdb=" O GLU A 710 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 819 " --> pdb=" O TRP A 708 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP A 708 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET A 706 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 715 through 722 Processing sheet with id= H, first strand: chain 'A' and resid 781 through 783 Processing sheet with id= I, first strand: chain 'B' and resid 127 through 132 removed outlier: 4.164A pdb=" N GLN B 42 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP B 83 " --> pdb=" O THR B 87 " (cutoff:3.500A) 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: 8.373A pdb=" N LYS B 182 " --> pdb=" O MET B 759 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLN B 761 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASN B 751 " --> pdb=" O VAL B 762 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 764 " --> pdb=" O TYR B 749 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N TYR B 749 " --> pdb=" O VAL B 764 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 250 through 252 removed outlier: 3.581A pdb=" N LEU B 251 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE B 260 " --> pdb=" O LEU B 251 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'B' and resid 278 through 280 removed outlier: 6.733A pdb=" N THR B 625 " --> pdb=" O LYS B 602 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASN B 604 " --> pdb=" O PHE B 623 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N PHE B 623 " --> pdb=" O ASN B 604 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ALA B 606 " --> pdb=" O VAL B 621 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL B 621 " --> pdb=" O ALA B 606 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU B 608 " --> pdb=" O VAL B 619 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N VAL B 619 " --> pdb=" O LEU B 608 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 846 through 851 removed outlier: 4.678A pdb=" N SER B 673 " --> pdb=" O THR B 851 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET B 706 " --> pdb=" O ILE B 821 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 714 through 718 Processing sheet with id= P, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.720A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP C 83 " --> pdb=" O THR C 87 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 322 through 324 removed outlier: 3.942A pdb=" N GLN C 292 " --> pdb=" O LYS C 174 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LYS C 174 " --> pdb=" O GLN C 292 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 266 through 272 removed outlier: 8.079A pdb=" N LYS C 182 " --> pdb=" O MET C 759 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLN C 761 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN C 751 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL C 764 " --> pdb=" O TYR C 749 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N TYR C 749 " --> pdb=" O VAL C 764 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 217 through 219 Processing sheet with id= T, first strand: chain 'C' and resid 250 through 252 Processing sheet with id= U, first strand: chain 'C' and resid 278 through 281 removed outlier: 6.625A pdb=" N THR C 625 " --> pdb=" O LYS C 602 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASN C 604 " --> pdb=" O PHE C 623 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N PHE C 623 " --> pdb=" O ASN C 604 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ALA C 606 " --> pdb=" O VAL C 621 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 621 " --> pdb=" O ALA C 606 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU C 608 " --> pdb=" O VAL C 619 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL C 619 " --> pdb=" O LEU C 608 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 846 through 850 removed outlier: 3.997A pdb=" N SER C 817 " --> pdb=" O GLU C 710 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET C 706 " --> pdb=" O ILE C 821 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 715 through 719 1333 hydrogen bonds defined for protein. 3885 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: 9.95 Time building geometry restraints manager: 12.70 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: 3842 1.26 - 1.40: 5228 1.40 - 1.54: 13984 1.54 - 1.68: 647 1.68 - 1.81: 264 Bond restraints: 23965 Sorted by residual: bond pdb=" C SER A 969 " pdb=" O SER A 969 " ideal model delta sigma weight residual 1.236 1.116 0.120 1.15e-02 7.56e+03 1.09e+02 bond pdb=" C GLN B 691 " pdb=" O GLN B 691 " ideal model delta sigma weight residual 1.237 1.137 0.100 1.19e-02 7.06e+03 7.06e+01 bond pdb=" C ASP C 407 " pdb=" O ASP C 407 " ideal model delta sigma weight residual 1.236 1.152 0.084 1.25e-02 6.40e+03 4.56e+01 bond pdb=" C PHE C 939 " pdb=" O PHE C 939 " ideal model delta sigma weight residual 1.236 1.155 0.081 1.26e-02 6.30e+03 4.18e+01 bond pdb=" C GLN B 863 " pdb=" O GLN B 863 " ideal model delta sigma weight residual 1.235 1.150 0.085 1.33e-02 5.65e+03 4.11e+01 ... (remaining 23960 not shown) Histogram of bond angle deviations from ideal: 97.28 - 104.62: 484 104.62 - 111.96: 12101 111.96 - 119.30: 7826 119.30 - 126.64: 11805 126.64 - 133.98: 269 Bond angle restraints: 32485 Sorted by residual: angle pdb=" CA PHE A 11 " pdb=" C PHE A 11 " pdb=" O PHE A 11 " ideal model delta sigma weight residual 120.55 110.34 10.21 1.06e+00 8.90e-01 9.27e+01 angle pdb=" CA PHE B 824 " pdb=" C PHE B 824 " pdb=" O PHE B 824 " ideal model delta sigma weight residual 121.19 111.76 9.43 1.10e+00 8.26e-01 7.36e+01 angle pdb=" CA SER A 969 " pdb=" C SER A 969 " pdb=" O SER A 969 " ideal model delta sigma weight residual 121.00 112.00 9.00 1.05e+00 9.07e-01 7.35e+01 angle pdb=" CA PHE C 11 " pdb=" C PHE C 11 " pdb=" O PHE C 11 " ideal model delta sigma weight residual 119.97 111.11 8.86 1.15e+00 7.56e-01 5.93e+01 angle pdb=" CA PHE C 939 " pdb=" C PHE C 939 " pdb=" O PHE C 939 " ideal model delta sigma weight residual 119.97 111.75 8.22 1.15e+00 7.56e-01 5.11e+01 ... (remaining 32480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.60: 13976 29.60 - 59.19: 451 59.19 - 88.79: 45 88.79 - 118.39: 3 118.39 - 147.99: 1 Dihedral angle restraints: 14476 sinusoidal: 5659 harmonic: 8817 Sorted by residual: dihedral pdb=" C ASP B 106 " pdb=" N ASP B 106 " pdb=" CA ASP B 106 " pdb=" CB ASP B 106 " ideal model delta harmonic sigma weight residual -122.60 -136.40 13.80 0 2.50e+00 1.60e-01 3.05e+01 dihedral pdb=" C GLU C 592 " pdb=" N GLU C 592 " pdb=" CA GLU C 592 " pdb=" CB GLU C 592 " ideal model delta harmonic sigma weight residual -122.60 -111.12 -11.48 0 2.50e+00 1.60e-01 2.11e+01 dihedral pdb=" C3 PTY C1102 " pdb=" O11 PTY C1102 " pdb=" P1 PTY C1102 " pdb=" O12 PTY C1102 " ideal model delta sinusoidal sigma weight residual -59.77 88.22 -147.99 1 3.00e+01 1.11e-03 1.97e+01 ... (remaining 14473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 3613 0.083 - 0.167: 230 0.167 - 0.250: 25 0.250 - 0.333: 2 0.333 - 0.417: 3 Chirality restraints: 3873 Sorted by residual: chirality pdb=" CA GLU C 592 " pdb=" N GLU C 592 " pdb=" C GLU C 592 " pdb=" CB GLU C 592 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CA ASP B 106 " pdb=" N ASP B 106 " pdb=" C ASP B 106 " pdb=" CB ASP B 106 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CA ILE C 186 " pdb=" N ILE C 186 " pdb=" C ILE C 186 " pdb=" CB ILE C 186 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 3870 not shown) Planarity restraints: 4068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 174 " -0.025 2.00e-02 2.50e+03 5.18e-02 2.68e+01 pdb=" C LYS A 174 " 0.090 2.00e-02 2.50e+03 pdb=" O LYS A 174 " -0.033 2.00e-02 2.50e+03 pdb=" N VAL A 175 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 573 " 0.023 2.00e-02 2.50e+03 4.66e-02 2.17e+01 pdb=" C PHE C 573 " -0.081 2.00e-02 2.50e+03 pdb=" O PHE C 573 " 0.029 2.00e-02 2.50e+03 pdb=" N GLN C 574 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 969 " -0.022 2.00e-02 2.50e+03 4.59e-02 2.11e+01 pdb=" C SER A 969 " 0.079 2.00e-02 2.50e+03 pdb=" O SER A 969 " -0.030 2.00e-02 2.50e+03 pdb=" N LEU A 970 " -0.028 2.00e-02 2.50e+03 ... (remaining 4065 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 178 2.60 - 3.17: 20983 3.17 - 3.75: 36381 3.75 - 4.32: 50695 4.32 - 4.90: 84927 Nonbonded interactions: 193164 Sorted by model distance: nonbonded pdb=" O MET B 647 " pdb=" OG1 THR B 651 " model vdw 2.021 2.440 nonbonded pdb=" OE2 GLU C 281 " pdb=" OG1 THR C 605 " model vdw 2.121 2.440 nonbonded pdb=" O MET A 435 " pdb=" OG1 THR A 439 " model vdw 2.127 2.440 nonbonded pdb=" OD1 ASP A 739 " pdb=" N ILE A 740 " model vdw 2.149 2.520 nonbonded pdb=" NH2 ARG A 363 " pdb=" O ILE A 496 " model vdw 2.157 2.520 ... (remaining 193159 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' and resid 1 through 1027) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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 15259 2.51 5 N 3804 2.21 5 O 4332 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.010 Extract box with map and model: 2.810 Check model and map are aligned: 0.350 Process input model: 67.560 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.250 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.120 23965 Z= 0.310 Angle : 0.811 17.882 32485 Z= 0.502 Chirality : 0.045 0.417 3873 Planarity : 0.005 0.088 4068 Dihedral : 14.358 147.987 8770 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 0.82 % 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: 1.36 (0.16), residues: 3048 helix: 1.86 (0.13), residues: 1670 sheet: -0.11 (0.24), residues: 453 loop : -0.24 (0.20), residues: 925 *********************** 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 587 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 566 time to evaluate : 3.085 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 6 residues processed: 575 average time/residue: 0.3475 time to fit residues: 316.5883 Evaluate side-chains 497 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 491 time to evaluate : 2.922 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2310 time to fit residues: 6.6773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 20.0000 chunk 231 optimal weight: 7.9990 chunk 128 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 239 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 145 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 277 optimal weight: 0.0010 overall best weight: 3.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN A 574 GLN A 779 ASN ** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 GLN B 44 ASN B 104 GLN B 282 ASN B 859 GLN C 120 GLN C 128 GLN C 161 ASN C 604 ASN C 677 GLN ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 837 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 23965 Z= 0.264 Angle : 0.593 10.345 32485 Z= 0.304 Chirality : 0.043 0.239 3873 Planarity : 0.005 0.060 4068 Dihedral : 6.787 171.447 3265 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 1.75 % 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: 1.49 (0.15), residues: 3048 helix: 1.93 (0.13), residues: 1685 sheet: -0.13 (0.23), residues: 487 loop : -0.11 (0.21), residues: 876 *********************** 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 560 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 515 time to evaluate : 2.592 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 30 residues processed: 530 average time/residue: 0.3547 time to fit residues: 296.7568 Evaluate side-chains 504 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 474 time to evaluate : 2.928 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2304 time to fit residues: 16.9482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 20.0000 chunk 86 optimal weight: 2.9990 chunk 231 optimal weight: 9.9990 chunk 189 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 278 optimal weight: 6.9990 chunk 300 optimal weight: 5.9990 chunk 247 optimal weight: 4.9990 chunk 276 optimal weight: 20.0000 chunk 94 optimal weight: 40.0000 chunk 223 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 ASN ** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN B 282 ASN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 ASN ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 837 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 23965 Z= 0.302 Angle : 0.598 12.839 32485 Z= 0.307 Chirality : 0.044 0.232 3873 Planarity : 0.005 0.063 4068 Dihedral : 6.589 174.917 3265 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 1.48 % 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: 1.26 (0.15), residues: 3048 helix: 1.71 (0.13), residues: 1686 sheet: -0.16 (0.24), residues: 458 loop : -0.18 (0.21), residues: 904 *********************** 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 550 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 512 time to evaluate : 2.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 19 residues processed: 532 average time/residue: 0.3600 time to fit residues: 303.4566 Evaluate side-chains 500 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 481 time to evaluate : 2.883 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2257 time to fit residues: 12.2713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 7.9990 chunk 209 optimal weight: 10.0000 chunk 144 optimal weight: 0.0060 chunk 30 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 chunk 279 optimal weight: 6.9990 chunk 295 optimal weight: 1.9990 chunk 145 optimal weight: 8.9990 chunk 264 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 overall best weight: 4.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 ASN ** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 ASN ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 837 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 23965 Z= 0.261 Angle : 0.577 11.094 32485 Z= 0.295 Chirality : 0.042 0.228 3873 Planarity : 0.004 0.059 4068 Dihedral : 6.292 165.868 3265 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 1.83 % 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: 1.27 (0.15), residues: 3048 helix: 1.74 (0.13), residues: 1685 sheet: -0.20 (0.23), residues: 482 loop : -0.17 (0.21), residues: 881 *********************** 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 550 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 503 time to evaluate : 3.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 29 residues processed: 521 average time/residue: 0.3632 time to fit residues: 298.2937 Evaluate side-chains 511 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 482 time to evaluate : 2.635 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2564 time to fit residues: 17.3994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 0.0470 chunk 167 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 220 optimal weight: 0.9980 chunk 122 optimal weight: 8.9990 chunk 252 optimal weight: 3.9990 chunk 204 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 151 optimal weight: 4.9990 chunk 265 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 overall best weight: 2.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 701 ASN A 779 ASN ** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN C 146 ASN C 161 ASN C 604 ASN C 837 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 23965 Z= 0.196 Angle : 0.544 10.926 32485 Z= 0.278 Chirality : 0.041 0.236 3873 Planarity : 0.004 0.058 4068 Dihedral : 5.964 155.498 3265 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer Outliers : 1.44 % 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: 1.39 (0.15), residues: 3048 helix: 1.86 (0.13), residues: 1683 sheet: -0.21 (0.23), residues: 500 loop : -0.11 (0.21), residues: 865 *********************** 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 540 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 503 time to evaluate : 2.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 24 residues processed: 525 average time/residue: 0.3614 time to fit residues: 298.9076 Evaluate side-chains 507 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 483 time to evaluate : 2.734 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2170 time to fit residues: 13.6498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 7.9990 chunk 266 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 173 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 296 optimal weight: 6.9990 chunk 245 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 ASN ** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN C 146 ASN C 837 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 23965 Z= 0.327 Angle : 0.607 11.616 32485 Z= 0.310 Chirality : 0.044 0.252 3873 Planarity : 0.005 0.060 4068 Dihedral : 5.986 149.534 3265 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 1.44 % 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: 1.12 (0.15), residues: 3048 helix: 1.62 (0.13), residues: 1684 sheet: -0.20 (0.24), residues: 477 loop : -0.28 (0.21), residues: 887 *********************** 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 535 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 498 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 21 residues processed: 513 average time/residue: 0.3736 time to fit residues: 300.1413 Evaluate side-chains 502 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 481 time to evaluate : 2.613 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2215 time to fit residues: 12.4483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 167 optimal weight: 7.9990 chunk 249 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 294 optimal weight: 9.9990 chunk 184 optimal weight: 5.9990 chunk 179 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 ASN ** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN ** C 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 837 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 23965 Z= 0.243 Angle : 0.567 11.066 32485 Z= 0.290 Chirality : 0.042 0.258 3873 Planarity : 0.004 0.058 4068 Dihedral : 5.820 142.945 3265 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 1.40 % 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: 1.23 (0.15), residues: 3048 helix: 1.73 (0.13), residues: 1679 sheet: -0.23 (0.24), residues: 479 loop : -0.24 (0.21), residues: 890 *********************** 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 535 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 499 time to evaluate : 4.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 15 residues processed: 518 average time/residue: 0.3767 time to fit residues: 307.5466 Evaluate side-chains 500 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 485 time to evaluate : 2.742 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2632 time to fit residues: 11.1543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 7.9990 chunk 117 optimal weight: 9.9990 chunk 176 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 231 optimal weight: 8.9990 chunk 268 optimal weight: 5.9990 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 779 ASN ** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN ** C 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 837 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 23965 Z= 0.255 Angle : 0.580 11.202 32485 Z= 0.296 Chirality : 0.042 0.275 3873 Planarity : 0.004 0.058 4068 Dihedral : 5.758 137.894 3265 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 1.01 % 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: 1.24 (0.15), residues: 3048 helix: 1.75 (0.13), residues: 1674 sheet: -0.19 (0.23), residues: 491 loop : -0.24 (0.21), residues: 883 *********************** 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 512 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 486 time to evaluate : 2.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 502 average time/residue: 0.3683 time to fit residues: 290.9587 Evaluate side-chains 494 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 484 time to evaluate : 2.713 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2447 time to fit residues: 8.7615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 8.9990 chunk 257 optimal weight: 0.9990 chunk 274 optimal weight: 30.0000 chunk 165 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 215 optimal weight: 0.0270 chunk 84 optimal weight: 8.9990 chunk 248 optimal weight: 3.9990 chunk 259 optimal weight: 0.0060 chunk 273 optimal weight: 4.9990 chunk 180 optimal weight: 9.9990 overall best weight: 2.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 ASN ** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 23965 Z= 0.179 Angle : 0.554 10.760 32485 Z= 0.281 Chirality : 0.041 0.265 3873 Planarity : 0.004 0.097 4068 Dihedral : 5.573 131.014 3265 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer Outliers : 0.39 % 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: 1.40 (0.16), residues: 3048 helix: 1.88 (0.13), residues: 1675 sheet: -0.13 (0.23), residues: 506 loop : -0.19 (0.21), residues: 867 *********************** 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 515 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 505 time to evaluate : 2.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 508 average time/residue: 0.3690 time to fit residues: 295.8102 Evaluate side-chains 496 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 490 time to evaluate : 2.677 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2462 time to fit residues: 6.5546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 202 optimal weight: 0.9980 chunk 304 optimal weight: 4.9990 chunk 280 optimal weight: 5.9990 chunk 242 optimal weight: 9.9990 chunk 25 optimal weight: 0.0070 chunk 187 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 overall best weight: 3.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 23965 Z= 0.215 Angle : 0.577 12.358 32485 Z= 0.292 Chirality : 0.042 0.332 3873 Planarity : 0.004 0.079 4068 Dihedral : 5.548 127.123 3265 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 0.27 % 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: 1.84 (0.13), residues: 1681 sheet: -0.14 (0.23), residues: 503 loop : -0.23 (0.21), residues: 864 ********************** 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 497 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 490 time to evaluate : 2.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 493 average time/residue: 0.3701 time to fit residues: 285.8033 Evaluate side-chains 490 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 485 time to evaluate : 2.892 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2554 time to fit residues: 6.6520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 223 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 243 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 249 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 213 optimal weight: 7.9990 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 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 ASN ** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN C 837 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.154912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.121281 restraints weight = 26827.236| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.78 r_work: 0.3024 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 23965 Z= 0.318 Angle : 0.618 11.297 32485 Z= 0.315 Chirality : 0.044 0.269 3873 Planarity : 0.005 0.098 4068 Dihedral : 5.676 124.374 3265 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer Outliers : 0.51 % 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: 1.66 (0.13), residues: 1667 sheet: -0.12 (0.23), residues: 488 loop : -0.25 (0.21), residues: 893 =============================================================================== Job complete usr+sys time: 5703.68 seconds wall clock time: 104 minutes 22.71 seconds (6262.71 seconds total)