Starting phenix.real_space_refine on Mon Feb 19 02:52:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgi_22871/02_2024/7kgi_22871_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgi_22871/02_2024/7kgi_22871.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgi_22871/02_2024/7kgi_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_2024/7kgi_22871_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgi_22871/02_2024/7kgi_22871_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgi_22871/02_2024/7kgi_22871.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgi_22871/02_2024/7kgi_22871.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgi_22871/02_2024/7kgi_22871_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgi_22871/02_2024/7kgi_22871_updated.pdb" } resolution = 3.34 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 15259 2.51 5 N 3804 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 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 12.56, per 1000 atoms: 0.53 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: 9.67 Conformation dependent library (CDL) restraints added in 4.4 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: 6.00 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: 9.23 Time building geometry restraints manager: 10.09 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: 13988 29.60 - 59.19: 457 59.19 - 88.79: 45 88.79 - 118.39: 3 118.39 - 147.99: 1 Dihedral angle restraints: 14494 sinusoidal: 5677 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 14491 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 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: 0.140 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: 0.080 Extract box with map and model: 2.210 Check model and map are aligned: 0.400 Set scattering table: 0.260 Process input model: 64.880 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 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 : 14.417 147.987 8788 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 % Allowed : 1.17 % Favored : 98.01 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 512 HIS 0.002 0.000 HIS C 991 PHE 0.032 0.001 PHE A 972 TYR 0.015 0.001 TYR B 77 ARG 0.006 0.000 ARG A 34 *********************** 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 : 2.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7379 (mm-30) REVERT: A 245 GLN cc_start: 0.8074 (mt0) cc_final: 0.7829 (mt0) REVERT: A 328 ASP cc_start: 0.8552 (t0) cc_final: 0.8206 (t0) REVERT: A 468 LYS cc_start: 0.7333 (tptt) cc_final: 0.7092 (tptt) REVERT: A 553 MET cc_start: 0.6402 (tmm) cc_final: 0.6078 (tmm) REVERT: A 570 MET cc_start: 0.7720 (ptt) cc_final: 0.7517 (ptt) REVERT: A 747 SER cc_start: 0.7681 (m) cc_final: 0.7450 (t) REVERT: A 769 LYS cc_start: 0.7831 (ptpt) cc_final: 0.7409 (mtmm) REVERT: A 772 MET cc_start: 0.8069 (tpp) cc_final: 0.7712 (tpt) REVERT: A 810 TYR cc_start: 0.8624 (t80) cc_final: 0.8213 (t80) REVERT: A 885 SER cc_start: 0.7647 (m) cc_final: 0.7257 (p) REVERT: A 908 MET cc_start: 0.8298 (mmp) cc_final: 0.8055 (mmm) REVERT: A 931 LYS cc_start: 0.7072 (OUTLIER) cc_final: 0.6681 (tptp) REVERT: A 965 ILE cc_start: 0.6967 (mm) cc_final: 0.6746 (mm) REVERT: B 101 GLU cc_start: 0.7610 (mp0) cc_final: 0.7217 (mt-10) REVERT: B 310 ILE cc_start: 0.7988 (mt) cc_final: 0.7715 (mt) REVERT: B 836 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7366 (mt-10) REVERT: C 1 MET cc_start: 0.4966 (mmt) cc_final: 0.4355 (tpt) REVERT: C 66 GLU cc_start: 0.7396 (tt0) cc_final: 0.7086 (tt0) REVERT: C 205 ASN cc_start: 0.7296 (m-40) cc_final: 0.6994 (m-40) REVERT: C 214 ILE cc_start: 0.9005 (mt) cc_final: 0.8727 (mt) REVERT: C 837 GLN cc_start: 0.7479 (mt0) cc_final: 0.7161 (mt0) REVERT: C 967 MET cc_start: 0.8802 (mtp) cc_final: 0.8573 (mtm) REVERT: C 1015 PHE cc_start: 0.7861 (m-80) cc_final: 0.7579 (m-80) outliers start: 21 outliers final: 6 residues processed: 575 average time/residue: 0.3408 time to fit residues: 311.9915 Evaluate side-chains 504 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 496 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 TYR Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 440 SER 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: 9.9990 chunk 239 optimal weight: 9.9990 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 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** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23965 Z= 0.257 Angle : 0.590 10.404 32485 Z= 0.303 Chirality : 0.043 0.235 3873 Planarity : 0.004 0.063 4068 Dihedral : 7.383 173.373 3301 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.87 % Allowed : 8.73 % 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: 1.47 (0.15), residues: 3048 helix: 1.91 (0.13), residues: 1684 sheet: -0.13 (0.23), residues: 487 loop : -0.09 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 800 HIS 0.003 0.001 HIS C 534 PHE 0.028 0.002 PHE A1015 TYR 0.015 0.001 TYR A 327 ARG 0.004 0.000 ARG B 8 *********************** 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 565 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 517 time to evaluate : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8165 (mmmm) cc_final: 0.7798 (mtmm) REVERT: A 165 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7050 (mm-30) REVERT: A 245 GLN cc_start: 0.8071 (mt0) cc_final: 0.7854 (mt0) REVERT: A 474 MET cc_start: 0.7806 (tpt) cc_final: 0.6064 (tpt) REVERT: A 553 MET cc_start: 0.6668 (tmm) cc_final: 0.6217 (tmm) REVERT: A 565 ASP cc_start: 0.6315 (t0) cc_final: 0.5248 (p0) REVERT: A 639 MET cc_start: 0.6712 (mmt) cc_final: 0.6470 (mmt) REVERT: A 706 MET cc_start: 0.3685 (mtp) cc_final: 0.3163 (mpp) REVERT: A 772 MET cc_start: 0.8402 (tpp) cc_final: 0.7792 (tpt) REVERT: A 908 MET cc_start: 0.8453 (mmp) cc_final: 0.8103 (mmm) REVERT: A 931 LYS cc_start: 0.6756 (OUTLIER) cc_final: 0.6381 (tptp) REVERT: A 965 ILE cc_start: 0.6920 (mm) cc_final: 0.6626 (mm) REVERT: B 7 ARG cc_start: 0.6732 (ttm110) cc_final: 0.6489 (ttm110) REVERT: B 104 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7876 (tm130) REVERT: B 310 ILE cc_start: 0.8038 (mt) cc_final: 0.7745 (mt) REVERT: B 346 GLU cc_start: 0.7216 (tt0) cc_final: 0.6859 (tt0) REVERT: B 358 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.6840 (t80) REVERT: B 600 ASP cc_start: 0.6499 (m-30) cc_final: 0.6259 (m-30) REVERT: B 678 ASP cc_start: 0.8203 (t0) cc_final: 0.7905 (t70) REVERT: B 681 ASN cc_start: 0.7694 (m110) cc_final: 0.7424 (m-40) REVERT: B 836 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7413 (mt-10) REVERT: B 849 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7859 (mt-10) REVERT: B 868 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8419 (mp) REVERT: C 29 LYS cc_start: 0.8060 (mtmm) cc_final: 0.7646 (mttt) REVERT: C 205 ASN cc_start: 0.7613 (m-40) cc_final: 0.7098 (m-40) REVERT: C 733 LYS cc_start: 0.7804 (mttp) cc_final: 0.7595 (mmtp) REVERT: C 799 GLN cc_start: 0.7682 (pt0) cc_final: 0.7444 (pt0) REVERT: C 837 GLN cc_start: 0.7590 (mt0) cc_final: 0.7256 (mt0) REVERT: C 967 MET cc_start: 0.8968 (mtp) cc_final: 0.8604 (mtm) outliers start: 48 outliers final: 34 residues processed: 534 average time/residue: 0.3390 time to fit residues: 286.7131 Evaluate side-chains 519 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 479 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 415 ASN Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 868 LEU Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 750 ILE 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: 3.9990 chunk 231 optimal weight: 9.9990 chunk 189 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 chunk 278 optimal weight: 7.9990 chunk 300 optimal weight: 6.9990 chunk 247 optimal weight: 7.9990 chunk 276 optimal weight: 8.9990 chunk 94 optimal weight: 40.0000 chunk 223 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 282 ASN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 23965 Z= 0.340 Angle : 0.612 13.477 32485 Z= 0.315 Chirality : 0.044 0.230 3873 Planarity : 0.005 0.062 4068 Dihedral : 7.149 173.515 3299 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.73 % Allowed : 11.81 % Favored : 85.46 % 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: 1.67 (0.12), residues: 1677 sheet: -0.18 (0.23), residues: 468 loop : -0.19 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 800 HIS 0.002 0.001 HIS A 534 PHE 0.026 0.002 PHE A1015 TYR 0.015 0.002 TYR A 275 ARG 0.004 0.001 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 577 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 507 time to evaluate : 2.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8257 (mmmm) cc_final: 0.7913 (mtmm) REVERT: A 165 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7369 (mm-30) REVERT: A 358 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.7464 (t80) REVERT: A 553 MET cc_start: 0.6710 (tmm) cc_final: 0.6203 (tmm) REVERT: A 565 ASP cc_start: 0.6329 (t0) cc_final: 0.5620 (p0) REVERT: A 714 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.6912 (tm-30) REVERT: A 749 TYR cc_start: 0.8466 (t80) cc_final: 0.8171 (t80) REVERT: A 772 MET cc_start: 0.8204 (tpp) cc_final: 0.7731 (tpt) REVERT: A 908 MET cc_start: 0.8536 (mmp) cc_final: 0.8094 (mmm) REVERT: A 931 LYS cc_start: 0.6824 (OUTLIER) cc_final: 0.6434 (tptt) REVERT: A 942 MET cc_start: 0.6561 (tmm) cc_final: 0.6049 (tmm) REVERT: A 965 ILE cc_start: 0.6834 (mm) cc_final: 0.6571 (mm) REVERT: B 7 ARG cc_start: 0.6785 (ttm110) cc_final: 0.6474 (ttm110) REVERT: B 310 ILE cc_start: 0.8016 (mt) cc_final: 0.7733 (mt) REVERT: B 346 GLU cc_start: 0.7285 (tt0) cc_final: 0.6928 (tt0) REVERT: B 681 ASN cc_start: 0.7783 (m110) cc_final: 0.7548 (m-40) REVERT: B 836 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7338 (mt-10) REVERT: B 849 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8199 (mt-10) REVERT: B 942 MET cc_start: 0.6508 (mmm) cc_final: 0.6203 (tpt) REVERT: C 205 ASN cc_start: 0.7732 (m-40) cc_final: 0.7085 (m-40) REVERT: C 526 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8209 (tp) REVERT: C 733 LYS cc_start: 0.7873 (mttp) cc_final: 0.7627 (mmtp) REVERT: C 837 GLN cc_start: 0.7648 (mt0) cc_final: 0.7307 (mt0) REVERT: C 967 MET cc_start: 0.9097 (mtp) cc_final: 0.8642 (mtm) REVERT: C 1015 PHE cc_start: 0.7966 (m-10) cc_final: 0.7588 (m-80) REVERT: C 1019 ILE cc_start: 0.8362 (mm) cc_final: 0.8131 (mm) outliers start: 70 outliers final: 48 residues processed: 541 average time/residue: 0.3467 time to fit residues: 298.2427 Evaluate side-chains 537 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 483 time to evaluate : 2.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 415 ASN Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 891 SER Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 1003 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 9.9990 chunk 209 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 186 optimal weight: 5.9990 chunk 279 optimal weight: 5.9990 chunk 295 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 264 optimal weight: 0.2980 chunk 79 optimal weight: 8.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 701 ASN A 779 ASN ** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN B 108 GLN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23965 Z= 0.265 Angle : 0.571 11.183 32485 Z= 0.293 Chirality : 0.042 0.231 3873 Planarity : 0.004 0.057 4068 Dihedral : 6.736 162.028 3297 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.35 % Allowed : 14.00 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.15), residues: 3048 helix: 1.71 (0.13), residues: 1684 sheet: -0.27 (0.23), residues: 476 loop : -0.19 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 850 HIS 0.002 0.001 HIS B 534 PHE 0.023 0.002 PHE A1015 TYR 0.014 0.001 TYR B 883 ARG 0.003 0.000 ARG B 632 *********************** 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 590 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 504 time to evaluate : 2.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8161 (m-80) cc_final: 0.7901 (m-80) REVERT: A 73 LYS cc_start: 0.8240 (mmmm) cc_final: 0.7899 (mtmm) REVERT: A 165 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7550 (mm-30) REVERT: A 184 MET cc_start: 0.6796 (tpp) cc_final: 0.6591 (tpp) REVERT: A 358 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.6468 (t80) REVERT: A 553 MET cc_start: 0.6736 (tmm) cc_final: 0.6218 (tmm) REVERT: A 565 ASP cc_start: 0.6530 (t0) cc_final: 0.5828 (p0) REVERT: A 706 MET cc_start: 0.3630 (mtp) cc_final: 0.3107 (mpp) REVERT: A 714 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7002 (tm-30) REVERT: A 749 TYR cc_start: 0.8393 (t80) cc_final: 0.8189 (t80) REVERT: A 772 MET cc_start: 0.8192 (tpp) cc_final: 0.7888 (tpt) REVERT: A 792 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7629 (mp) REVERT: A 813 ARG cc_start: 0.7385 (mpt-90) cc_final: 0.6593 (mpt-90) REVERT: A 931 LYS cc_start: 0.6799 (OUTLIER) cc_final: 0.6374 (tptt) REVERT: A 965 ILE cc_start: 0.6809 (mm) cc_final: 0.6598 (mm) REVERT: B 7 ARG cc_start: 0.6896 (ttm110) cc_final: 0.6581 (ttm110) REVERT: B 73 LYS cc_start: 0.7911 (ptpt) cc_final: 0.7496 (ptmm) REVERT: B 112 LYS cc_start: 0.7813 (mttt) cc_final: 0.7381 (mtpt) REVERT: B 310 ILE cc_start: 0.8015 (mt) cc_final: 0.7723 (mt) REVERT: B 346 GLU cc_start: 0.7194 (tt0) cc_final: 0.6810 (tt0) REVERT: B 415 ASN cc_start: 0.7841 (OUTLIER) cc_final: 0.7560 (m-40) REVERT: B 656 MET cc_start: 0.7366 (tpp) cc_final: 0.6954 (mmt) REVERT: B 681 ASN cc_start: 0.7784 (m110) cc_final: 0.7557 (m-40) REVERT: B 836 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7332 (mt-10) REVERT: B 849 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8168 (mt-10) REVERT: B 942 MET cc_start: 0.6485 (mmm) cc_final: 0.6166 (tpt) REVERT: B 967 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8180 (mtm) REVERT: C 66 GLU cc_start: 0.7649 (tt0) cc_final: 0.7155 (tt0) REVERT: C 112 LYS cc_start: 0.8170 (mtpp) cc_final: 0.7854 (mttt) REVERT: C 205 ASN cc_start: 0.7902 (m-40) cc_final: 0.7248 (m-40) REVERT: C 526 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8223 (tp) REVERT: C 585 ARG cc_start: 0.7673 (tmt-80) cc_final: 0.7258 (tmt170) REVERT: C 837 GLN cc_start: 0.7653 (mt0) cc_final: 0.7251 (mt0) REVERT: C 967 MET cc_start: 0.8999 (mtp) cc_final: 0.8606 (mtm) REVERT: C 1015 PHE cc_start: 0.7898 (m-10) cc_final: 0.7554 (m-80) REVERT: C 1019 ILE cc_start: 0.8371 (mm) cc_final: 0.8103 (mm) outliers start: 86 outliers final: 55 residues processed: 550 average time/residue: 0.3386 time to fit residues: 292.8301 Evaluate side-chains 546 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 482 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 415 ASN Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 776 ASP Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 891 SER Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 1003 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 220 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 252 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 151 optimal weight: 6.9990 chunk 265 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 44 ASN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN C 146 ASN C 161 ASN C 604 ASN ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23965 Z= 0.205 Angle : 0.545 10.999 32485 Z= 0.279 Chirality : 0.041 0.234 3873 Planarity : 0.004 0.058 4068 Dihedral : 6.500 155.207 3295 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.35 % Allowed : 14.78 % Favored : 81.87 % 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: 1.83 (0.13), residues: 1679 sheet: -0.35 (0.23), residues: 495 loop : -0.15 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 556 HIS 0.001 0.000 HIS B 534 PHE 0.020 0.001 PHE A 918 TYR 0.016 0.001 TYR B 883 ARG 0.003 0.000 ARG A 34 *********************** 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 591 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 505 time to evaluate : 2.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8088 (m-80) cc_final: 0.7762 (m-80) REVERT: A 73 LYS cc_start: 0.8216 (mmmm) cc_final: 0.7873 (mtmm) REVERT: A 165 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7597 (mm-30) REVERT: A 184 MET cc_start: 0.6756 (tpp) cc_final: 0.6534 (tpp) REVERT: A 358 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.7532 (t80) REVERT: A 553 MET cc_start: 0.6775 (tmm) cc_final: 0.6255 (tmm) REVERT: A 714 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.6978 (tm-30) REVERT: A 743 THR cc_start: 0.8050 (p) cc_final: 0.7558 (t) REVERT: A 772 MET cc_start: 0.8143 (tpp) cc_final: 0.7909 (tpt) REVERT: A 908 MET cc_start: 0.8350 (mmm) cc_final: 0.8037 (mmm) REVERT: A 931 LYS cc_start: 0.6781 (OUTLIER) cc_final: 0.6391 (tptp) REVERT: A 965 ILE cc_start: 0.6827 (mm) cc_final: 0.6566 (mm) REVERT: B 7 ARG cc_start: 0.6910 (ttm110) cc_final: 0.6586 (ttm110) REVERT: B 73 LYS cc_start: 0.7909 (ptpt) cc_final: 0.7502 (ptmm) REVERT: B 101 GLU cc_start: 0.7881 (mp0) cc_final: 0.7595 (mt-10) REVERT: B 112 LYS cc_start: 0.7703 (mttt) cc_final: 0.7347 (ttmt) REVERT: B 310 ILE cc_start: 0.8007 (mt) cc_final: 0.7722 (mt) REVERT: B 525 GLU cc_start: 0.6491 (tt0) cc_final: 0.6224 (tt0) REVERT: B 681 ASN cc_start: 0.7735 (m110) cc_final: 0.7527 (m-40) REVERT: B 836 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7331 (mt-10) REVERT: B 849 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8115 (mt-10) REVERT: B 868 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8389 (mp) REVERT: B 942 MET cc_start: 0.6536 (mmm) cc_final: 0.6193 (tpt) REVERT: C 66 GLU cc_start: 0.7526 (tt0) cc_final: 0.6995 (tt0) REVERT: C 112 LYS cc_start: 0.8177 (mtpp) cc_final: 0.7876 (mttt) REVERT: C 205 ASN cc_start: 0.7820 (m-40) cc_final: 0.7155 (m-40) REVERT: C 526 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8200 (tp) REVERT: C 550 PHE cc_start: 0.6877 (t80) cc_final: 0.6523 (t80) REVERT: C 585 ARG cc_start: 0.7642 (tmt-80) cc_final: 0.7280 (tmt170) REVERT: C 837 GLN cc_start: 0.7600 (mt0) cc_final: 0.7195 (mt0) REVERT: C 1015 PHE cc_start: 0.7827 (m-10) cc_final: 0.7542 (m-80) REVERT: C 1019 ILE cc_start: 0.8356 (mm) cc_final: 0.8089 (mm) outliers start: 86 outliers final: 59 residues processed: 550 average time/residue: 0.3367 time to fit residues: 292.1602 Evaluate side-chains 554 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 488 time to evaluate : 2.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 415 ASN Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 828 SER Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 868 LEU Chi-restraints excluded: chain B residue 891 SER Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 799 GLN Chi-restraints excluded: chain C residue 801 ASN Chi-restraints excluded: chain C residue 928 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 10.0000 chunk 266 optimal weight: 50.0000 chunk 58 optimal weight: 0.9990 chunk 173 optimal weight: 20.0000 chunk 73 optimal weight: 5.9990 chunk 296 optimal weight: 7.9990 chunk 245 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 97 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 44 ASN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23965 Z= 0.282 Angle : 0.575 11.352 32485 Z= 0.294 Chirality : 0.042 0.253 3873 Planarity : 0.004 0.058 4068 Dihedral : 6.455 149.839 3295 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.82 % Allowed : 15.09 % Favored : 81.09 % 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: 1.19 (0.15), residues: 3048 helix: 1.70 (0.13), residues: 1680 sheet: -0.31 (0.23), residues: 496 loop : -0.19 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 800 HIS 0.003 0.001 HIS A 534 PHE 0.019 0.002 PHE C 352 TYR 0.015 0.001 TYR B 883 ARG 0.006 0.000 ARG B 8 *********************** 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 602 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 504 time to evaluate : 2.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8149 (m-80) cc_final: 0.7834 (m-80) REVERT: A 73 LYS cc_start: 0.8195 (mmmm) cc_final: 0.7879 (mtmm) REVERT: A 102 MET cc_start: 0.8611 (mmm) cc_final: 0.8091 (mmm) REVERT: A 165 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7636 (mm-30) REVERT: A 358 PHE cc_start: 0.7936 (OUTLIER) cc_final: 0.7547 (t80) REVERT: A 474 MET cc_start: 0.7473 (tpt) cc_final: 0.5970 (tpt) REVERT: A 553 MET cc_start: 0.6785 (tmm) cc_final: 0.6266 (tmm) REVERT: A 649 ASN cc_start: 0.6518 (OUTLIER) cc_final: 0.6005 (p0) REVERT: A 714 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7025 (tm-30) REVERT: A 743 THR cc_start: 0.8089 (p) cc_final: 0.7681 (t) REVERT: A 908 MET cc_start: 0.8348 (mmm) cc_final: 0.8077 (mmm) REVERT: A 965 ILE cc_start: 0.6815 (mm) cc_final: 0.6557 (mm) REVERT: B 7 ARG cc_start: 0.6919 (ttm110) cc_final: 0.6615 (ttm110) REVERT: B 73 LYS cc_start: 0.7844 (ptpt) cc_final: 0.7437 (ptmm) REVERT: B 101 GLU cc_start: 0.7885 (mp0) cc_final: 0.7640 (mt-10) REVERT: B 284 LYS cc_start: 0.7134 (tppt) cc_final: 0.6753 (mmmt) REVERT: B 310 ILE cc_start: 0.8027 (mt) cc_final: 0.7742 (mt) REVERT: B 358 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.7180 (t80) REVERT: B 415 ASN cc_start: 0.7781 (OUTLIER) cc_final: 0.7530 (m-40) REVERT: B 525 GLU cc_start: 0.6511 (tt0) cc_final: 0.6228 (tt0) REVERT: B 681 ASN cc_start: 0.7741 (m110) cc_final: 0.7535 (m-40) REVERT: B 836 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7342 (mt-10) REVERT: B 849 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8348 (mt-10) REVERT: B 863 GLN cc_start: 0.8832 (pm20) cc_final: 0.8589 (pm20) REVERT: B 883 TYR cc_start: 0.8356 (m-80) cc_final: 0.8110 (m-80) REVERT: B 942 MET cc_start: 0.6481 (mmm) cc_final: 0.6200 (tpt) REVERT: C 8 ARG cc_start: 0.7701 (mtt-85) cc_final: 0.7499 (mtp85) REVERT: C 66 GLU cc_start: 0.7515 (tt0) cc_final: 0.6969 (tt0) REVERT: C 112 LYS cc_start: 0.8222 (mtpp) cc_final: 0.7878 (mttt) REVERT: C 138 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7599 (ptm) REVERT: C 205 ASN cc_start: 0.7883 (m-40) cc_final: 0.7213 (m-40) REVERT: C 526 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8252 (tp) REVERT: C 550 PHE cc_start: 0.6890 (t80) cc_final: 0.6536 (t80) REVERT: C 585 ARG cc_start: 0.7676 (tmt-80) cc_final: 0.7218 (tmt170) REVERT: C 837 GLN cc_start: 0.7639 (mt0) cc_final: 0.7250 (mt0) REVERT: C 1015 PHE cc_start: 0.7935 (m-10) cc_final: 0.7659 (m-80) REVERT: C 1019 ILE cc_start: 0.8352 (mm) cc_final: 0.8097 (mm) outliers start: 98 outliers final: 73 residues processed: 556 average time/residue: 0.3345 time to fit residues: 291.7537 Evaluate side-chains 568 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 486 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 415 ASN Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 776 ASP Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 828 SER Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 891 SER Chi-restraints excluded: chain B residue 905 ILE Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 706 MET Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 723 ASP Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 776 ASP Chi-restraints excluded: chain C residue 799 GLN Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 1003 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 168 optimal weight: 8.9990 chunk 216 optimal weight: 6.9990 chunk 167 optimal weight: 9.9990 chunk 249 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 chunk 294 optimal weight: 0.9980 chunk 184 optimal weight: 0.9990 chunk 179 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN 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 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2352 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= 0.257 Angle : 0.566 11.219 32485 Z= 0.290 Chirality : 0.042 0.251 3873 Planarity : 0.004 0.058 4068 Dihedral : 6.340 144.301 3295 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.02 % Allowed : 15.71 % Favored : 80.27 % 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: 1.23 (0.15), residues: 3048 helix: 1.76 (0.13), residues: 1666 sheet: -0.31 (0.23), residues: 496 loop : -0.21 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 800 HIS 0.001 0.000 HIS C 342 PHE 0.020 0.002 PHE C 352 TYR 0.012 0.001 TYR B 883 ARG 0.006 0.000 ARG B 8 *********************** 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 602 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 499 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8150 (m-80) cc_final: 0.7863 (m-80) REVERT: A 73 LYS cc_start: 0.8201 (mmmm) cc_final: 0.7882 (mtmm) REVERT: A 165 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7576 (mm-30) REVERT: A 358 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.7554 (t80) REVERT: A 553 MET cc_start: 0.6796 (tmm) cc_final: 0.6275 (tmm) REVERT: A 593 ASN cc_start: 0.7664 (m-40) cc_final: 0.7424 (m-40) REVERT: A 714 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7124 (tm-30) REVERT: A 743 THR cc_start: 0.8098 (p) cc_final: 0.7699 (t) REVERT: A 908 MET cc_start: 0.8360 (mmm) cc_final: 0.8154 (mmm) REVERT: A 965 ILE cc_start: 0.6790 (mm) cc_final: 0.6534 (mm) REVERT: A 972 PHE cc_start: 0.7169 (t80) cc_final: 0.6828 (t80) REVERT: B 7 ARG cc_start: 0.6937 (ttm110) cc_final: 0.6709 (ttm110) REVERT: B 101 GLU cc_start: 0.7902 (mp0) cc_final: 0.7655 (mt-10) REVERT: B 284 LYS cc_start: 0.7225 (tppt) cc_final: 0.6832 (mmmt) REVERT: B 310 ILE cc_start: 0.8027 (mt) cc_final: 0.7738 (mt) REVERT: B 358 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.7207 (t80) REVERT: B 478 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8440 (mp) REVERT: B 525 GLU cc_start: 0.6514 (tt0) cc_final: 0.6225 (tt0) REVERT: B 681 ASN cc_start: 0.7726 (m110) cc_final: 0.7516 (m-40) REVERT: B 695 MET cc_start: 0.8785 (mmt) cc_final: 0.8498 (mmt) REVERT: B 836 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7315 (mt-10) REVERT: B 868 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8483 (mp) REVERT: B 883 TYR cc_start: 0.8362 (m-80) cc_final: 0.8080 (m-80) REVERT: B 942 MET cc_start: 0.6571 (mmm) cc_final: 0.6204 (tpt) REVERT: C 66 GLU cc_start: 0.7531 (tt0) cc_final: 0.6965 (tt0) REVERT: C 112 LYS cc_start: 0.8203 (mtpp) cc_final: 0.7895 (mttt) REVERT: C 138 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7563 (ptm) REVERT: C 205 ASN cc_start: 0.7888 (m-40) cc_final: 0.7214 (m-40) REVERT: C 230 ILE cc_start: 0.8410 (pt) cc_final: 0.8180 (pt) REVERT: C 307 ARG cc_start: 0.7721 (mtp85) cc_final: 0.7463 (mtp85) REVERT: C 436 LYS cc_start: 0.7601 (mtpp) cc_final: 0.7058 (mtpp) REVERT: C 526 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8269 (tp) REVERT: C 550 PHE cc_start: 0.6908 (t80) cc_final: 0.6532 (t80) REVERT: C 837 GLN cc_start: 0.7637 (mt0) cc_final: 0.7242 (mt0) REVERT: C 1015 PHE cc_start: 0.7963 (m-10) cc_final: 0.7702 (m-80) REVERT: C 1019 ILE cc_start: 0.8346 (mm) cc_final: 0.8102 (mm) outliers start: 103 outliers final: 76 residues processed: 558 average time/residue: 0.3504 time to fit residues: 307.8161 Evaluate side-chains 571 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 487 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 415 ASN Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 776 ASP Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 828 SER Chi-restraints excluded: chain B residue 868 LEU Chi-restraints excluded: chain B residue 891 SER Chi-restraints excluded: chain B residue 905 ILE Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 723 ASP Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 776 ASP Chi-restraints excluded: chain C residue 799 GLN Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 1003 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 176 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 chunk 200 optimal weight: 20.0000 chunk 145 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 231 optimal weight: 4.9990 chunk 268 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2416 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= 0.244 Angle : 0.563 11.160 32485 Z= 0.288 Chirality : 0.042 0.273 3873 Planarity : 0.004 0.058 4068 Dihedral : 6.276 140.379 3295 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.86 % Allowed : 15.83 % Favored : 80.31 % 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: 1.25 (0.15), residues: 3048 helix: 1.78 (0.13), residues: 1665 sheet: -0.30 (0.23), residues: 496 loop : -0.20 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 800 HIS 0.001 0.000 HIS C 342 PHE 0.020 0.001 PHE C 352 TYR 0.012 0.001 TYR B 883 ARG 0.006 0.000 ARG B 8 *********************** 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 603 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 504 time to evaluate : 2.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8155 (m-80) cc_final: 0.7865 (m-80) REVERT: A 73 LYS cc_start: 0.8213 (mmmm) cc_final: 0.7902 (mtmm) REVERT: A 165 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7633 (mm-30) REVERT: A 358 PHE cc_start: 0.7925 (OUTLIER) cc_final: 0.7523 (t80) REVERT: A 474 MET cc_start: 0.7454 (tpt) cc_final: 0.5869 (tpt) REVERT: A 553 MET cc_start: 0.6832 (tmm) cc_final: 0.6320 (tmm) REVERT: A 593 ASN cc_start: 0.7663 (m-40) cc_final: 0.7440 (m-40) REVERT: A 669 PHE cc_start: 0.6225 (OUTLIER) cc_final: 0.5295 (m-80) REVERT: A 714 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7131 (tm-30) REVERT: A 743 THR cc_start: 0.8119 (p) cc_final: 0.7698 (t) REVERT: A 772 MET cc_start: 0.8054 (mmp) cc_final: 0.7680 (tpt) REVERT: A 779 ASN cc_start: 0.7699 (m-40) cc_final: 0.7470 (m110) REVERT: A 965 ILE cc_start: 0.6752 (mm) cc_final: 0.6466 (mm) REVERT: A 972 PHE cc_start: 0.7235 (t80) cc_final: 0.6765 (t80) REVERT: B 7 ARG cc_start: 0.6945 (ttm110) cc_final: 0.6726 (ttm110) REVERT: B 101 GLU cc_start: 0.7874 (mp0) cc_final: 0.7638 (mt-10) REVERT: B 211 ASN cc_start: 0.8066 (t0) cc_final: 0.7728 (t0) REVERT: B 284 LYS cc_start: 0.7250 (tppt) cc_final: 0.6772 (mmmt) REVERT: B 310 ILE cc_start: 0.7990 (mt) cc_final: 0.7712 (mt) REVERT: B 415 ASN cc_start: 0.7767 (OUTLIER) cc_final: 0.7476 (m-40) REVERT: B 478 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8413 (mp) REVERT: B 525 GLU cc_start: 0.6506 (tt0) cc_final: 0.6221 (tt0) REVERT: B 695 MET cc_start: 0.8768 (mmt) cc_final: 0.8490 (mmt) REVERT: B 710 GLU cc_start: 0.8000 (pt0) cc_final: 0.7135 (mm-30) REVERT: B 836 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7321 (mt-10) REVERT: B 883 TYR cc_start: 0.8284 (m-80) cc_final: 0.8018 (m-80) REVERT: B 942 MET cc_start: 0.6632 (mmm) cc_final: 0.6281 (tpt) REVERT: C 66 GLU cc_start: 0.7392 (tt0) cc_final: 0.6758 (tt0) REVERT: C 112 LYS cc_start: 0.8214 (mtpp) cc_final: 0.7876 (mttt) REVERT: C 205 ASN cc_start: 0.7878 (m-40) cc_final: 0.7202 (m-40) REVERT: C 230 ILE cc_start: 0.8420 (pt) cc_final: 0.8188 (pt) REVERT: C 307 ARG cc_start: 0.7716 (mtp85) cc_final: 0.7441 (mtp85) REVERT: C 526 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8278 (tp) REVERT: C 550 PHE cc_start: 0.6919 (t80) cc_final: 0.6538 (t80) REVERT: C 834 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7171 (tt0) REVERT: C 837 GLN cc_start: 0.7647 (mt0) cc_final: 0.7257 (mt0) REVERT: C 1015 PHE cc_start: 0.7956 (m-10) cc_final: 0.7694 (m-80) REVERT: C 1019 ILE cc_start: 0.8347 (mm) cc_final: 0.8103 (mm) outliers start: 99 outliers final: 77 residues processed: 562 average time/residue: 0.3418 time to fit residues: 302.5984 Evaluate side-chains 582 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 497 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 415 ASN Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 776 ASP Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 828 SER Chi-restraints excluded: chain B residue 891 SER Chi-restraints excluded: chain B residue 905 ILE Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 776 ASP Chi-restraints excluded: chain C residue 799 GLN Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 834 GLU Chi-restraints excluded: chain C residue 928 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 1.9990 chunk 257 optimal weight: 0.9990 chunk 274 optimal weight: 9.9990 chunk 165 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 248 optimal weight: 5.9990 chunk 259 optimal weight: 0.0770 chunk 273 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 overall best weight: 1.4146 ------------------------------------------------------------------------------- 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 44 ASN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN C 701 ASN ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 23965 Z= 0.158 Angle : 0.538 10.588 32485 Z= 0.273 Chirality : 0.041 0.263 3873 Planarity : 0.004 0.056 4068 Dihedral : 6.021 133.419 3295 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.14 % Allowed : 17.86 % Favored : 80.00 % 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: 1.48 (0.16), residues: 3048 helix: 1.98 (0.13), residues: 1666 sheet: -0.17 (0.23), residues: 488 loop : -0.16 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 556 HIS 0.002 0.000 HIS C 991 PHE 0.021 0.001 PHE C 352 TYR 0.007 0.001 TYR C 883 ARG 0.006 0.000 ARG B 8 *********************** 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 571 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 516 time to evaluate : 2.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8103 (m-80) cc_final: 0.7811 (m-80) REVERT: A 73 LYS cc_start: 0.8202 (mmmm) cc_final: 0.7889 (mtmm) REVERT: A 165 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7660 (mm-30) REVERT: A 358 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7450 (t80) REVERT: A 474 MET cc_start: 0.7343 (tpt) cc_final: 0.5715 (tpt) REVERT: A 553 MET cc_start: 0.6879 (tmm) cc_final: 0.6376 (tmm) REVERT: A 570 MET cc_start: 0.7386 (ptt) cc_final: 0.7117 (ptm) REVERT: A 593 ASN cc_start: 0.7643 (m-40) cc_final: 0.7421 (m-40) REVERT: A 743 THR cc_start: 0.8068 (p) cc_final: 0.7666 (t) REVERT: A 763 ILE cc_start: 0.8204 (mt) cc_final: 0.7986 (mt) REVERT: A 772 MET cc_start: 0.8109 (mmp) cc_final: 0.7731 (tpt) REVERT: A 779 ASN cc_start: 0.7724 (m-40) cc_final: 0.7363 (m110) REVERT: A 965 ILE cc_start: 0.6742 (mm) cc_final: 0.6456 (mm) REVERT: A 972 PHE cc_start: 0.7003 (t80) cc_final: 0.6491 (t80) REVERT: B 7 ARG cc_start: 0.6951 (ttm110) cc_final: 0.6640 (ttp-110) REVERT: B 101 GLU cc_start: 0.7889 (mp0) cc_final: 0.7639 (mt-10) REVERT: B 211 ASN cc_start: 0.8036 (t0) cc_final: 0.7730 (t0) REVERT: B 284 LYS cc_start: 0.7151 (tppt) cc_final: 0.6702 (mmmt) REVERT: B 310 ILE cc_start: 0.7899 (mt) cc_final: 0.7638 (mt) REVERT: B 358 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.7148 (t80) REVERT: B 478 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8468 (mp) REVERT: B 525 GLU cc_start: 0.6482 (tt0) cc_final: 0.6197 (tt0) REVERT: B 695 MET cc_start: 0.8792 (mmt) cc_final: 0.8526 (mmt) REVERT: B 836 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7361 (mt-10) REVERT: B 883 TYR cc_start: 0.8082 (m-80) cc_final: 0.7815 (m-80) REVERT: B 942 MET cc_start: 0.6686 (mmm) cc_final: 0.6291 (tpt) REVERT: C 66 GLU cc_start: 0.7366 (tt0) cc_final: 0.6704 (tt0) REVERT: C 112 LYS cc_start: 0.8177 (mtpp) cc_final: 0.7882 (mttt) REVERT: C 138 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7571 (ptm) REVERT: C 181 GLU cc_start: 0.6612 (mm-30) cc_final: 0.6384 (mt-10) REVERT: C 205 ASN cc_start: 0.7805 (m-40) cc_final: 0.7144 (m-40) REVERT: C 307 ARG cc_start: 0.7687 (mtp85) cc_final: 0.7473 (mtp85) REVERT: C 436 LYS cc_start: 0.7527 (mtpp) cc_final: 0.7078 (mtpp) REVERT: C 585 ARG cc_start: 0.7593 (tmt-80) cc_final: 0.7195 (tmt170) REVERT: C 837 GLN cc_start: 0.7634 (mt0) cc_final: 0.7217 (mt0) REVERT: C 1015 PHE cc_start: 0.7982 (m-10) cc_final: 0.7737 (m-80) REVERT: C 1019 ILE cc_start: 0.8327 (mm) cc_final: 0.8099 (mm) outliers start: 55 outliers final: 42 residues processed: 549 average time/residue: 0.3316 time to fit residues: 287.5459 Evaluate side-chains 549 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 502 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 799 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 202 optimal weight: 1.9990 chunk 304 optimal weight: 2.9990 chunk 280 optimal weight: 5.9990 chunk 242 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 187 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 192 optimal weight: 8.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 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: 0.7585 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 23965 Z= 0.159 Angle : 0.540 11.668 32485 Z= 0.272 Chirality : 0.041 0.245 3873 Planarity : 0.004 0.056 4068 Dihedral : 5.862 127.051 3295 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.99 % Allowed : 18.09 % Favored : 79.92 % 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: 1.58 (0.16), residues: 3048 helix: 2.04 (0.13), residues: 1676 sheet: -0.04 (0.23), residues: 499 loop : -0.14 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 886 HIS 0.002 0.000 HIS C 991 PHE 0.026 0.001 PHE C 550 TYR 0.008 0.001 TYR B 883 ARG 0.006 0.000 ARG B 8 ********************** 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 566 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 515 time to evaluate : 2.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8098 (m-80) cc_final: 0.7801 (m-80) REVERT: A 73 LYS cc_start: 0.8188 (mmmm) cc_final: 0.7882 (mtmm) REVERT: A 102 MET cc_start: 0.8467 (mmm) cc_final: 0.8065 (mmm) REVERT: A 165 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7556 (mm-30) REVERT: A 358 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7358 (t80) REVERT: A 474 MET cc_start: 0.7336 (tpt) cc_final: 0.5646 (tpt) REVERT: A 570 MET cc_start: 0.7364 (ptt) cc_final: 0.7133 (ptm) REVERT: A 592 GLU cc_start: 0.7489 (tp30) cc_final: 0.7269 (tp30) REVERT: A 714 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7109 (tm-30) REVERT: A 743 THR cc_start: 0.8071 (p) cc_final: 0.7648 (t) REVERT: A 763 ILE cc_start: 0.8178 (mt) cc_final: 0.7941 (mt) REVERT: A 772 MET cc_start: 0.8049 (mmp) cc_final: 0.7664 (tpt) REVERT: A 965 ILE cc_start: 0.6759 (mm) cc_final: 0.6471 (mm) REVERT: A 972 PHE cc_start: 0.6967 (t80) cc_final: 0.6479 (t80) REVERT: B 7 ARG cc_start: 0.6915 (ttm110) cc_final: 0.6655 (ttp-110) REVERT: B 73 LYS cc_start: 0.7835 (pttt) cc_final: 0.7590 (ptmm) REVERT: B 101 GLU cc_start: 0.7875 (mp0) cc_final: 0.7613 (mt-10) REVERT: B 211 ASN cc_start: 0.8013 (t0) cc_final: 0.7713 (t0) REVERT: B 284 LYS cc_start: 0.7105 (tppt) cc_final: 0.6657 (mmmt) REVERT: B 310 ILE cc_start: 0.7891 (mt) cc_final: 0.7646 (mt) REVERT: B 358 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7186 (t80) REVERT: B 478 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8450 (mp) REVERT: B 525 GLU cc_start: 0.6484 (tt0) cc_final: 0.6201 (tt0) REVERT: B 695 MET cc_start: 0.8776 (mmt) cc_final: 0.8520 (mmt) REVERT: B 714 GLN cc_start: 0.8113 (tt0) cc_final: 0.7896 (tt0) REVERT: B 836 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7406 (mt-10) REVERT: B 883 TYR cc_start: 0.8076 (m-80) cc_final: 0.7787 (m-80) REVERT: B 942 MET cc_start: 0.6654 (mmm) cc_final: 0.6217 (tpt) REVERT: C 66 GLU cc_start: 0.7423 (tt0) cc_final: 0.6727 (tt0) REVERT: C 138 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7544 (ptm) REVERT: C 205 ASN cc_start: 0.7824 (m-40) cc_final: 0.7149 (m-40) REVERT: C 307 ARG cc_start: 0.7675 (mtp85) cc_final: 0.7454 (mtp85) REVERT: C 436 LYS cc_start: 0.7478 (mtpp) cc_final: 0.7048 (mtpp) REVERT: C 498 LYS cc_start: 0.7820 (mttt) cc_final: 0.7382 (ptpt) REVERT: C 550 PHE cc_start: 0.6901 (t80) cc_final: 0.6541 (t80) REVERT: C 585 ARG cc_start: 0.7603 (tmt-80) cc_final: 0.7205 (tmt170) REVERT: C 834 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7045 (tt0) REVERT: C 837 GLN cc_start: 0.7632 (mt0) cc_final: 0.7222 (mt0) REVERT: C 1001 MET cc_start: 0.7550 (tpt) cc_final: 0.7011 (mmm) REVERT: C 1015 PHE cc_start: 0.7967 (m-10) cc_final: 0.7757 (m-80) REVERT: C 1019 ILE cc_start: 0.8313 (mm) cc_final: 0.8072 (mm) outliers start: 51 outliers final: 41 residues processed: 543 average time/residue: 0.3353 time to fit residues: 286.3918 Evaluate side-chains 557 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 509 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 828 SER Chi-restraints excluded: chain B residue 905 ILE Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 722 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 799 GLN Chi-restraints excluded: chain C residue 834 GLU 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: 3.9990 chunk 223 optimal weight: 4.9990 chunk 35 optimal weight: 20.0000 chunk 67 optimal weight: 10.0000 chunk 243 optimal weight: 10.0000 chunk 101 optimal weight: 50.0000 chunk 249 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 213 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.156059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.122417 restraints weight = 26767.038| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.79 r_work: 0.3038 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2595 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= 0.266 Angle : 0.582 11.095 32485 Z= 0.296 Chirality : 0.042 0.255 3873 Planarity : 0.004 0.058 4068 Dihedral : 5.999 124.357 3295 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.34 % Allowed : 18.21 % Favored : 79.45 % 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 (0.15), residues: 3048 helix: 1.88 (0.13), residues: 1674 sheet: -0.15 (0.23), residues: 493 loop : -0.16 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 800 HIS 0.002 0.000 HIS C 360 PHE 0.022 0.002 PHE C 550 TYR 0.012 0.001 TYR B 883 ARG 0.005 0.000 ARG A 34 =============================================================================== Job complete usr+sys time: 5753.43 seconds wall clock time: 104 minutes 37.95 seconds (6277.95 seconds total)