Starting phenix.real_space_refine on Sun Mar 17 17:22:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5h_13199/03_2024/7p5h_13199_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5h_13199/03_2024/7p5h_13199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5h_13199/03_2024/7p5h_13199.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5h_13199/03_2024/7p5h_13199.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5h_13199/03_2024/7p5h_13199_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5h_13199/03_2024/7p5h_13199_trim_updated.pdb" } resolution = 2.3 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 8 Type Number sf(0) Gaussians Fe 104 7.16 5 Zn 4 6.06 5 P 4 5.49 5 S 392 5.16 5 C 25156 2.51 5 N 6688 2.21 5 O 8120 1.98 5 H 39924 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 9": "OE1" <-> "OE2" Residue "A GLU 21": "OE1" <-> "OE2" Residue "A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "A GLU 390": "OE1" <-> "OE2" Residue "A GLU 425": "OE1" <-> "OE2" Residue "A GLU 444": "OE1" <-> "OE2" Residue "A PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 399": "OE1" <-> "OE2" Residue "B GLU 420": "OE1" <-> "OE2" Residue "B GLU 436": "OE1" <-> "OE2" Residue "B GLU 557": "OE1" <-> "OE2" Residue "C GLU 10": "OE1" <-> "OE2" Residue "C GLU 20": "OE1" <-> "OE2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "D GLU 9": "OE1" <-> "OE2" Residue "D GLU 21": "OE1" <-> "OE2" Residue "D TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D GLU 246": "OE1" <-> "OE2" Residue "D GLU 277": "OE1" <-> "OE2" Residue "D GLU 360": "OE1" <-> "OE2" Residue "D GLU 390": "OE1" <-> "OE2" Residue "D GLU 425": "OE1" <-> "OE2" Residue "D GLU 444": "OE1" <-> "OE2" Residue "D GLU 502": "OE1" <-> "OE2" Residue "D PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 531": "OE1" <-> "OE2" Residue "E GLU 107": "OE1" <-> "OE2" Residue "E GLU 209": "OE1" <-> "OE2" Residue "E PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 399": "OE1" <-> "OE2" Residue "E GLU 420": "OE1" <-> "OE2" Residue "E GLU 436": "OE1" <-> "OE2" Residue "E GLU 557": "OE1" <-> "OE2" Residue "F GLU 10": "OE1" <-> "OE2" Residue "F GLU 20": "OE1" <-> "OE2" Residue "F GLU 28": "OE1" <-> "OE2" Residue "F GLU 31": "OE1" <-> "OE2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "F GLU 108": "OE1" <-> "OE2" Residue "F GLU 146": "OE1" <-> "OE2" Residue "a GLU 9": "OE1" <-> "OE2" Residue "a GLU 21": "OE1" <-> "OE2" Residue "a TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 155": "OE1" <-> "OE2" Residue "a GLU 183": "OE1" <-> "OE2" Residue "a GLU 277": "OE1" <-> "OE2" Residue "a GLU 360": "OE1" <-> "OE2" Residue "a GLU 390": "OE1" <-> "OE2" Residue "a GLU 425": "OE1" <-> "OE2" Residue "a GLU 444": "OE1" <-> "OE2" Residue "a PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 531": "OE1" <-> "OE2" Residue "b GLU 107": "OE1" <-> "OE2" Residue "b GLU 209": "OE1" <-> "OE2" Residue "b PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 399": "OE1" <-> "OE2" Residue "b GLU 420": "OE1" <-> "OE2" Residue "b GLU 436": "OE1" <-> "OE2" Residue "b GLU 557": "OE1" <-> "OE2" Residue "c GLU 10": "OE1" <-> "OE2" Residue "c GLU 20": "OE1" <-> "OE2" Residue "c GLU 28": "OE1" <-> "OE2" Residue "d GLU 9": "OE1" <-> "OE2" Residue "d GLU 21": "OE1" <-> "OE2" Residue "d TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d GLU 155": "OE1" <-> "OE2" Residue "d GLU 183": "OE1" <-> "OE2" Residue "d GLU 360": "OE1" <-> "OE2" Residue "d GLU 390": "OE1" <-> "OE2" Residue "d GLU 425": "OE1" <-> "OE2" Residue "d GLU 444": "OE1" <-> "OE2" Residue "d GLU 502": "OE1" <-> "OE2" Residue "d PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d GLU 531": "OE1" <-> "OE2" Residue "e GLU 107": "OE1" <-> "OE2" Residue "e PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e GLU 399": "OE1" <-> "OE2" Residue "e GLU 420": "OE1" <-> "OE2" Residue "e GLU 557": "OE1" <-> "OE2" Residue "f GLU 10": "OE1" <-> "OE2" Residue "f GLU 20": "OE1" <-> "OE2" Residue "f GLU 28": "OE1" <-> "OE2" Residue "f GLU 108": "OE1" <-> "OE2" Residue "f GLU 146": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 80392 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 8791 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 554, 8766 Classifications: {'peptide': 554} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 532} Conformer: "B" Number of residues, atoms: 554, 8766 Classifications: {'peptide': 554} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 532} bond proxies already assigned to first conformer: 8812 Chain: "B" Number of atoms: 8600 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 555, 8579 Classifications: {'peptide': 555} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 527} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 555, 8579 Classifications: {'peptide': 555} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 527} Chain breaks: 1 bond proxies already assigned to first conformer: 8637 Chain: "C" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2463 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 148} Chain: "D" Number of atoms: 8791 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 554, 8766 Classifications: {'peptide': 554} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 532} Conformer: "B" Number of residues, atoms: 554, 8766 Classifications: {'peptide': 554} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 532} bond proxies already assigned to first conformer: 8812 Chain: "E" Number of atoms: 8600 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 555, 8579 Classifications: {'peptide': 555} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 527} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 555, 8579 Classifications: {'peptide': 555} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 527} Chain breaks: 1 bond proxies already assigned to first conformer: 8637 Chain: "F" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2463 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 148} Chain: "a" Number of atoms: 8791 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 554, 8766 Classifications: {'peptide': 554} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 532} Conformer: "B" Number of residues, atoms: 554, 8766 Classifications: {'peptide': 554} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 532} bond proxies already assigned to first conformer: 8812 Chain: "b" Number of atoms: 8600 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 555, 8579 Classifications: {'peptide': 555} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 527} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 555, 8579 Classifications: {'peptide': 555} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 527} Chain breaks: 1 bond proxies already assigned to first conformer: 8637 Chain: "c" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2463 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 148} Chain: "d" Number of atoms: 8791 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 554, 8766 Classifications: {'peptide': 554} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 532} Conformer: "B" Number of residues, atoms: 554, 8766 Classifications: {'peptide': 554} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 532} bond proxies already assigned to first conformer: 8812 Chain: "e" Number of atoms: 8600 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 555, 8579 Classifications: {'peptide': 555} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 527} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 555, 8579 Classifications: {'peptide': 555} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 527} Chain breaks: 1 bond proxies already assigned to first conformer: 8637 Chain: "f" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2463 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 148} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Unusual residues: {'FES': 1, 'SF4': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {' ZN': 1, 'FES': 1, 'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Unusual residues: {'FES': 1, 'SF4': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {' ZN': 1, 'FES': 1, 'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Unusual residues: {'FES': 1, 'SF4': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "b" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {' ZN': 1, 'FES': 1, 'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "c" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Unusual residues: {'FES': 1, 'SF4': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "e" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {' ZN': 1, 'FES': 1, 'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "f" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 135 Classifications: {'water': 135} Link IDs: {None: 134} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 135 Classifications: {'water': 135} Link IDs: {None: 134} Chain: "E" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "a" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 135 Classifications: {'water': 135} Link IDs: {None: 134} Chain: "b" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "c" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "d" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 135 Classifications: {'water': 135} Link IDs: {None: 134} Chain: "e" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "f" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5529 SG CYS A 350 77.305 88.932 69.321 1.00 18.54 S ATOM 4630 SG CYS A 295 71.612 91.304 70.794 1.00 18.54 S ATOM 7644 SG CYS A 486 75.852 90.046 75.527 1.00 18.54 S ATOM 7592 SG CYS A 482 72.886 85.296 71.689 1.00 18.54 S ATOM 3034 SG CYS A 192 73.007 79.119 63.448 1.00 18.54 S ATOM 2955 SG CYS A 186 72.006 84.678 60.322 1.00 18.54 S ATOM 3000 SG CYS A 189 70.863 83.780 66.644 1.00 18.54 S ATOM 2458 SG CYS A 153 66.936 80.872 62.326 1.00 18.54 S ATOM 3091 SG CYS A 196 75.860 71.807 63.554 1.00 18.54 S ATOM 2392 SG CYS A 149 70.084 73.539 61.533 1.00 18.54 S ATOM 2363 SG CYS A 146 70.864 68.235 64.487 1.00 18.54 S ATOM 2315 SG CYS A 143 72.660 68.878 58.280 1.00 18.54 S ATOM 1534 SG CYS A 96 86.801 63.625 62.067 1.00 18.54 S ATOM 1650 SG CYS A 105 81.300 64.907 65.600 1.00 18.54 S ATOM 1572 SG CYS A 99 84.092 69.469 62.303 1.00 18.54 S ATOM 754 SG CYS A 48 65.876 54.531 69.679 1.00 18.54 S ATOM 929 SG CYS A 60 63.448 57.102 69.540 1.00 14.70 S ATOM 549 SG CYS A 34 67.008 60.642 67.057 1.00 18.54 S ATOM 703 SG CYS A 45 69.218 57.680 66.738 1.00 18.54 S ATOM 16131 SG CYS B 485 60.704 61.571 55.509 1.00 18.54 S ATOM 16210 SG CYS B 491 63.372 55.965 53.205 1.00 18.54 S ATOM 16853 SG CYS B 531 57.547 56.164 56.128 1.00 18.54 S ATOM 16170 SG CYS B 488 63.914 56.689 58.448 1.00 18.54 S ATOM 9319 SG CYS B 31 35.566 54.790 29.452 1.00 40.78 S ATOM 9373 SG CYS B 36 37.969 54.135 27.016 1.00 37.39 S ATOM 9859 SG CYS B 78 37.941 51.680 33.218 1.00 38.71 S ATOM 9911 SG CYS B 82 40.824 51.231 31.155 1.00 37.13 S ATOM 15846 SG CYS B 468 68.108 41.534 35.147 1.00 31.55 S ATOM 17304 SG CYS B 560 70.168 40.568 31.985 1.00 38.99 S ATOM 17363 SG CYS B 565 70.272 44.267 33.387 1.00 37.21 S ATOM 19222 SG CYS C 119 49.598 54.016 35.332 1.00 26.31 S ATOM 19268 SG CYS C 123 49.136 51.377 33.261 1.00 29.82 S ATOM 18653 SG CYS C 78 54.106 55.884 32.960 1.00 28.13 S ATOM 18706 SG CYS C 83 54.036 53.735 30.359 1.00 27.71 S ATOM 25383 SG CYS D 350 77.306 37.964 115.255 1.00 18.54 S ATOM 24484 SG CYS D 295 71.611 35.599 113.788 1.00 18.54 S ATOM 27498 SG CYS D 486 75.853 36.850 109.049 1.00 18.54 S ATOM 27446 SG CYS D 482 72.885 41.600 112.888 1.00 18.54 S ATOM 22888 SG CYS D 192 73.007 47.776 121.128 1.00 18.54 S ATOM 22809 SG CYS D 186 72.006 42.218 124.253 1.00 18.54 S ATOM 22854 SG CYS D 189 70.863 43.115 117.931 1.00 18.54 S ATOM 22312 SG CYS D 153 66.936 46.024 122.250 1.00 18.54 S ATOM 22945 SG CYS D 196 75.859 55.089 121.022 1.00 18.54 S ATOM 22246 SG CYS D 149 70.083 53.357 123.043 1.00 18.54 S ATOM 22217 SG CYS D 146 70.865 58.661 120.088 1.00 18.54 S ATOM 22169 SG CYS D 143 72.660 58.018 126.296 1.00 18.54 S ATOM 21388 SG CYS D 96 86.801 63.271 122.509 1.00 18.54 S ATOM 21504 SG CYS D 105 81.300 61.989 118.976 1.00 18.54 S ATOM 21426 SG CYS D 99 84.093 57.427 122.273 1.00 18.54 S ATOM 20608 SG CYS D 48 65.876 72.365 114.898 1.00 18.54 S ATOM 20783 SG CYS D 60 63.448 69.795 115.037 1.00 15.05 S ATOM 20403 SG CYS D 34 67.007 66.253 117.519 1.00 18.54 S ATOM 20557 SG CYS D 45 69.217 69.216 117.837 1.00 18.54 S ATOM 35985 SG CYS E 485 60.704 65.325 129.067 1.00 18.54 S ATOM 36064 SG CYS E 491 63.372 70.931 131.371 1.00 18.54 S ATOM 36707 SG CYS E 531 57.547 70.732 128.448 1.00 18.54 S ATOM 36024 SG CYS E 488 63.915 70.207 126.128 1.00 18.54 S ATOM 29173 SG CYS E 31 35.542 72.138 155.121 1.00 40.79 S ATOM 29227 SG CYS E 36 37.967 72.759 157.554 1.00 37.24 S ATOM 29713 SG CYS E 78 37.944 75.211 151.356 1.00 38.72 S ATOM 29765 SG CYS E 82 40.830 75.658 153.422 1.00 37.23 S ATOM 35700 SG CYS E 468 68.111 85.376 149.423 1.00 31.73 S ATOM 37158 SG CYS E 560 70.168 86.328 152.593 1.00 39.34 S ATOM 37217 SG CYS E 565 70.268 82.632 151.188 1.00 37.43 S ATOM 39076 SG CYS F 119 49.598 72.880 149.244 1.00 26.43 S ATOM 39122 SG CYS F 123 49.136 75.520 151.315 1.00 29.96 S ATOM 38507 SG CYS F 78 54.106 71.015 151.615 1.00 28.13 S ATOM 38560 SG CYS F 83 54.036 73.162 154.218 1.00 27.75 S ATOM 45237 SG CYS a 350 100.679 37.964 69.321 1.00 18.54 S ATOM 44338 SG CYS a 295 106.372 35.592 70.794 1.00 18.54 S ATOM 47352 SG CYS a 486 102.132 36.850 75.527 1.00 18.54 S ATOM 47300 SG CYS a 482 105.099 41.600 71.688 1.00 18.54 S ATOM 42742 SG CYS a 192 104.977 47.777 63.448 1.00 18.54 S ATOM 42663 SG CYS a 186 105.978 42.218 60.323 1.00 18.54 S ATOM 42708 SG CYS a 189 107.120 43.116 66.646 1.00 18.54 S ATOM 42166 SG CYS a 153 111.048 46.024 62.326 1.00 18.54 S ATOM 42799 SG CYS a 196 102.125 55.089 63.554 1.00 18.54 S ATOM 42100 SG CYS a 149 107.901 53.357 61.533 1.00 18.54 S ATOM 42071 SG CYS a 146 107.119 58.661 64.488 1.00 18.54 S ATOM 42023 SG CYS a 143 105.324 58.018 58.280 1.00 18.54 S ATOM 41242 SG CYS a 96 91.183 63.271 62.067 1.00 18.54 S ATOM 41358 SG CYS a 105 96.684 61.989 65.600 1.00 18.54 S ATOM 41280 SG CYS a 99 93.891 57.427 62.303 1.00 18.54 S ATOM 40462 SG CYS a 48 112.108 72.364 69.677 1.00 18.54 S ATOM 40637 SG CYS a 60 114.536 69.793 69.540 1.00 14.75 S ATOM 40257 SG CYS a 34 110.976 66.254 67.057 1.00 18.54 S ATOM 40411 SG CYS a 45 108.767 69.216 66.737 1.00 18.54 S ATOM 55839 SG CYS b 485 117.280 65.325 55.509 1.00 18.54 S ATOM 55918 SG CYS b 491 114.611 70.931 53.205 1.00 18.54 S ATOM 56561 SG CYS b 531 120.437 70.732 56.128 1.00 18.54 S ATOM 55878 SG CYS b 488 114.070 70.206 58.448 1.00 18.54 S ATOM 49027 SG CYS b 31 142.419 72.108 29.450 1.00 40.81 S ATOM 49081 SG CYS b 36 140.013 72.762 27.014 1.00 37.14 S ATOM 49567 SG CYS b 78 140.042 75.210 33.214 1.00 38.98 S ATOM 49619 SG CYS b 82 137.153 75.659 31.153 1.00 37.12 S ATOM 55554 SG CYS b 468 109.873 85.377 35.153 1.00 31.69 S ATOM 57012 SG CYS b 560 107.817 86.329 31.982 1.00 39.34 S ATOM 57071 SG CYS b 565 107.716 82.632 33.388 1.00 37.64 S ATOM 58930 SG CYS c 119 128.386 72.880 35.332 1.00 26.32 S ATOM 58976 SG CYS c 123 128.848 75.520 33.261 1.00 29.73 S ATOM 58361 SG CYS c 78 123.878 71.015 32.960 1.00 28.25 S ATOM 58414 SG CYS c 83 123.948 73.162 30.358 1.00 27.67 S ATOM 65091 SG CYS d 350 100.678 88.932 115.255 1.00 18.54 S ATOM 64192 SG CYS d 295 106.374 91.297 113.788 1.00 18.54 S ATOM 67206 SG CYS d 486 102.132 90.046 109.049 1.00 18.54 S ATOM 67154 SG CYS d 482 105.097 85.296 112.887 1.00 18.54 S ATOM 62596 SG CYS d 192 104.977 79.119 121.128 1.00 18.54 S ATOM 62517 SG CYS d 186 105.978 84.678 124.254 1.00 18.54 S ATOM 62562 SG CYS d 189 107.120 83.781 117.932 1.00 18.54 S ATOM 62020 SG CYS d 153 111.048 80.872 122.250 1.00 18.54 S ATOM 62653 SG CYS d 196 102.125 71.807 121.022 1.00 18.54 S ATOM 61954 SG CYS d 149 107.901 73.539 123.043 1.00 18.54 S ATOM 61925 SG CYS d 146 107.120 68.235 120.088 1.00 18.54 S ATOM 61877 SG CYS d 143 105.324 68.878 126.296 1.00 18.54 S ATOM 61096 SG CYS d 96 91.183 63.625 122.508 1.00 18.54 S ATOM 61212 SG CYS d 105 96.684 64.907 118.976 1.00 18.54 S ATOM 61134 SG CYS d 99 93.892 69.469 122.273 1.00 18.54 S ATOM 60316 SG CYS d 48 112.109 54.531 114.898 1.00 18.54 S ATOM 60491 SG CYS d 60 114.536 57.104 115.035 1.00 14.80 S ATOM 60111 SG CYS d 34 110.976 60.641 117.519 1.00 18.54 S ATOM 60265 SG CYS d 45 108.768 57.680 117.839 1.00 18.54 S ATOM 75693 SG CYS e 485 117.280 61.571 129.067 1.00 18.54 S ATOM 75772 SG CYS e 491 114.612 55.965 131.371 1.00 18.54 S ATOM 76415 SG CYS e 531 120.437 56.164 128.448 1.00 18.54 S ATOM 75732 SG CYS e 488 114.070 56.689 126.128 1.00 18.54 S ATOM 68881 SG CYS e 31 142.419 54.788 155.126 1.00 40.64 S ATOM 68935 SG CYS e 36 140.014 54.135 157.561 1.00 37.56 S ATOM 69421 SG CYS e 78 140.041 51.687 151.360 1.00 38.71 S ATOM 69473 SG CYS e 82 137.154 51.237 153.422 1.00 37.24 S ATOM 75408 SG CYS e 468 109.873 41.521 149.423 1.00 31.58 S ATOM 76866 SG CYS e 560 107.815 40.566 152.591 1.00 39.21 S ATOM 76925 SG CYS e 565 107.715 44.264 151.189 1.00 37.37 S ATOM 78784 SG CYS f 119 128.384 54.017 149.242 1.00 26.30 S ATOM 78830 SG CYS f 123 128.848 51.378 151.314 1.00 29.77 S ATOM 78215 SG CYS f 78 123.877 55.881 151.616 1.00 28.16 S ATOM 78268 SG CYS f 83 123.948 53.734 154.218 1.00 27.75 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AARG A 130 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG A 130 " occ=0.50 residue: pdb=" N AARG D 130 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG D 130 " occ=0.50 residue: pdb=" N AARG a 130 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG a 130 " occ=0.50 residue: pdb=" N AARG d 130 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG d 130 " occ=0.50 Time building chain proxies: 47.04, per 1000 atoms: 0.59 Number of scatterers: 80392 At special positions: 0 Unit cell: (178.808, 127.72, 185.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 Fe 104 26.01 S 392 16.00 P 4 15.00 O 8120 8.00 N 6688 7.00 C 25156 6.00 H 39924 1.00 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: 56.27 Conformation dependent library (CDL) restraints added in 11.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 705 " pdb="FE2 FES A 705 " - pdb=" SG CYS A 34 " pdb="FE2 FES A 705 " - pdb=" SG CYS A 45 " pdb="FE1 FES A 705 " - pdb=" SG CYS A 60 " pdb="FE1 FES A 705 " - pdb=" SG CYS A 48 " pdb=" FES B 703 " pdb="FE2 FES B 703 " - pdb=" SG CYS B 82 " pdb="FE1 FES B 703 " - pdb=" SG CYS B 31 " pdb="FE2 FES B 703 " - pdb=" SG CYS B 78 " pdb="FE1 FES B 703 " - pdb=" SG CYS B 36 " pdb=" FES C 201 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 83 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 78 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 119 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 123 " pdb=" FES D 705 " pdb="FE2 FES D 705 " - pdb=" SG CYS D 34 " pdb="FE2 FES D 705 " - pdb=" SG CYS D 45 " pdb="FE1 FES D 705 " - pdb=" SG CYS D 60 " pdb="FE1 FES D 705 " - pdb=" SG CYS D 48 " pdb=" FES E 703 " pdb="FE2 FES E 703 " - pdb=" SG CYS E 82 " pdb="FE1 FES E 703 " - pdb=" SG CYS E 31 " pdb="FE2 FES E 703 " - pdb=" SG CYS E 78 " pdb="FE1 FES E 703 " - pdb=" SG CYS E 36 " pdb=" FES F 201 " pdb="FE2 FES F 201 " - pdb=" SG CYS F 83 " pdb="FE2 FES F 201 " - pdb=" SG CYS F 78 " pdb="FE1 FES F 201 " - pdb=" SG CYS F 119 " pdb="FE1 FES F 201 " - pdb=" SG CYS F 123 " pdb=" FES a 705 " pdb="FE2 FES a 705 " - pdb=" SG CYS a 34 " pdb="FE2 FES a 705 " - pdb=" SG CYS a 45 " pdb="FE1 FES a 705 " - pdb=" SG CYS a 60 " pdb="FE1 FES a 705 " - pdb=" SG CYS a 48 " pdb=" FES b 703 " pdb="FE2 FES b 703 " - pdb=" SG CYS b 82 " pdb="FE1 FES b 703 " - pdb=" SG CYS b 31 " pdb="FE2 FES b 703 " - pdb=" SG CYS b 78 " pdb="FE1 FES b 703 " - pdb=" SG CYS b 36 " pdb=" FES c 201 " pdb="FE2 FES c 201 " - pdb=" SG CYS c 83 " pdb="FE1 FES c 201 " - pdb=" SG CYS c 119 " pdb="FE2 FES c 201 " - pdb=" SG CYS c 78 " pdb="FE1 FES c 201 " - pdb=" SG CYS c 123 " pdb=" FES d 705 " pdb="FE2 FES d 705 " - pdb=" SG CYS d 34 " pdb="FE2 FES d 705 " - pdb=" SG CYS d 45 " pdb="FE1 FES d 705 " - pdb=" SG CYS d 60 " pdb="FE1 FES d 705 " - pdb=" SG CYS d 48 " pdb=" FES e 703 " pdb="FE2 FES e 703 " - pdb=" SG CYS e 82 " pdb="FE1 FES e 703 " - pdb=" SG CYS e 31 " pdb="FE2 FES e 703 " - pdb=" SG CYS e 78 " pdb="FE1 FES e 703 " - pdb=" SG CYS e 36 " pdb=" FES f 201 " pdb="FE2 FES f 201 " - pdb=" SG CYS f 83 " pdb="FE1 FES f 201 " - pdb=" SG CYS f 119 " pdb="FE2 FES f 201 " - pdb=" SG CYS f 78 " pdb="FE1 FES f 201 " - pdb=" SG CYS f 123 " pdb=" SF4 A 701 " pdb="FE4 SF4 A 701 " - pdb=" SG CYS A 482 " pdb="FE2 SF4 A 701 " - pdb=" SG CYS A 295 " pdb="FE1 SF4 A 701 " - pdb=" SG CYS A 350 " pdb="FE3 SF4 A 701 " - pdb=" SG CYS A 486 " pdb=" SF4 A 702 " pdb="FE1 SF4 A 702 " - pdb=" SG CYS A 192 " pdb="FE2 SF4 A 702 " - pdb=" SG CYS A 186 " pdb="FE3 SF4 A 702 " - pdb=" SG CYS A 189 " pdb="FE4 SF4 A 702 " - pdb=" SG CYS A 153 " pdb=" SF4 A 703 " pdb="FE4 SF4 A 703 " - pdb=" SG CYS A 143 " pdb="FE3 SF4 A 703 " - pdb=" SG CYS A 146 " pdb="FE1 SF4 A 703 " - pdb=" SG CYS A 196 " pdb="FE2 SF4 A 703 " - pdb=" SG CYS A 149 " pdb=" SF4 A 704 " pdb="FE3 SF4 A 704 " - pdb=" NE2 HIS A 92 " pdb="FE2 SF4 A 704 " - pdb=" SG CYS A 105 " pdb="FE1 SF4 A 704 " - pdb=" SG CYS A 96 " pdb="FE4 SF4 A 704 " - pdb=" SG CYS A 99 " pdb=" SF4 B 701 " pdb="FE3 SF4 B 701 " - pdb=" SG CYS B 531 " pdb="FE1 SF4 B 701 " - pdb=" SG CYS B 485 " pdb="FE2 SF4 B 701 " - pdb=" SG CYS B 491 " pdb="FE4 SF4 B 701 " - pdb=" SG CYS B 488 " pdb=" SF4 D 701 " pdb="FE4 SF4 D 701 " - pdb=" SG CYS D 482 " pdb="FE2 SF4 D 701 " - pdb=" SG CYS D 295 " pdb="FE1 SF4 D 701 " - pdb=" SG CYS D 350 " pdb="FE3 SF4 D 701 " - pdb=" SG CYS D 486 " pdb=" SF4 D 702 " pdb="FE1 SF4 D 702 " - pdb=" SG CYS D 192 " pdb="FE2 SF4 D 702 " - pdb=" SG CYS D 186 " pdb="FE3 SF4 D 702 " - pdb=" SG CYS D 189 " pdb="FE4 SF4 D 702 " - pdb=" SG CYS D 153 " pdb=" SF4 D 703 " pdb="FE4 SF4 D 703 " - pdb=" SG CYS D 143 " pdb="FE3 SF4 D 703 " - pdb=" SG CYS D 146 " pdb="FE1 SF4 D 703 " - pdb=" SG CYS D 196 " pdb="FE2 SF4 D 703 " - pdb=" SG CYS D 149 " pdb=" SF4 D 704 " pdb="FE3 SF4 D 704 " - pdb=" NE2 HIS D 92 " pdb="FE2 SF4 D 704 " - pdb=" SG CYS D 105 " pdb="FE1 SF4 D 704 " - pdb=" SG CYS D 96 " pdb="FE4 SF4 D 704 " - pdb=" SG CYS D 99 " pdb=" SF4 E 701 " pdb="FE3 SF4 E 701 " - pdb=" SG CYS E 531 " pdb="FE1 SF4 E 701 " - pdb=" SG CYS E 485 " pdb="FE2 SF4 E 701 " - pdb=" SG CYS E 491 " pdb="FE4 SF4 E 701 " - pdb=" SG CYS E 488 " pdb=" SF4 a 701 " pdb="FE4 SF4 a 701 " - pdb=" SG CYS a 482 " pdb="FE2 SF4 a 701 " - pdb=" SG CYS a 295 " pdb="FE1 SF4 a 701 " - pdb=" SG CYS a 350 " pdb="FE3 SF4 a 701 " - pdb=" SG CYS a 486 " pdb=" SF4 a 702 " pdb="FE1 SF4 a 702 " - pdb=" SG CYS a 192 " pdb="FE2 SF4 a 702 " - pdb=" SG CYS a 186 " pdb="FE3 SF4 a 702 " - pdb=" SG CYS a 189 " pdb="FE4 SF4 a 702 " - pdb=" SG CYS a 153 " pdb=" SF4 a 703 " pdb="FE4 SF4 a 703 " - pdb=" SG CYS a 143 " pdb="FE3 SF4 a 703 " - pdb=" SG CYS a 146 " pdb="FE1 SF4 a 703 " - pdb=" SG CYS a 196 " pdb="FE2 SF4 a 703 " - pdb=" SG CYS a 149 " pdb=" SF4 a 704 " pdb="FE3 SF4 a 704 " - pdb=" NE2 HIS a 92 " pdb="FE2 SF4 a 704 " - pdb=" SG CYS a 105 " pdb="FE1 SF4 a 704 " - pdb=" SG CYS a 96 " pdb="FE4 SF4 a 704 " - pdb=" SG CYS a 99 " pdb=" SF4 b 701 " pdb="FE3 SF4 b 701 " - pdb=" SG CYS b 531 " pdb="FE1 SF4 b 701 " - pdb=" SG CYS b 485 " pdb="FE2 SF4 b 701 " - pdb=" SG CYS b 491 " pdb="FE4 SF4 b 701 " - pdb=" SG CYS b 488 " pdb=" SF4 d 701 " pdb="FE4 SF4 d 701 " - pdb=" SG CYS d 482 " pdb="FE2 SF4 d 701 " - pdb=" SG CYS d 295 " pdb="FE1 SF4 d 701 " - pdb=" SG CYS d 350 " pdb="FE3 SF4 d 701 " - pdb=" SG CYS d 486 " pdb=" SF4 d 702 " pdb="FE1 SF4 d 702 " - pdb=" SG CYS d 192 " pdb="FE2 SF4 d 702 " - pdb=" SG CYS d 186 " pdb="FE3 SF4 d 702 " - pdb=" SG CYS d 189 " pdb="FE4 SF4 d 702 " - pdb=" SG CYS d 153 " pdb=" SF4 d 703 " pdb="FE4 SF4 d 703 " - pdb=" SG CYS d 143 " pdb="FE3 SF4 d 703 " - pdb=" SG CYS d 146 " pdb="FE1 SF4 d 703 " - pdb=" SG CYS d 196 " pdb="FE2 SF4 d 703 " - pdb=" SG CYS d 149 " pdb=" SF4 d 704 " pdb="FE3 SF4 d 704 " - pdb=" NE2 HIS d 92 " pdb="FE2 SF4 d 704 " - pdb=" SG CYS d 105 " pdb="FE1 SF4 d 704 " - pdb=" SG CYS d 96 " pdb="FE4 SF4 d 704 " - pdb=" SG CYS d 99 " pdb=" SF4 e 701 " pdb="FE3 SF4 e 701 " - pdb=" SG CYS e 531 " pdb="FE1 SF4 e 701 " - pdb=" SG CYS e 485 " pdb="FE2 SF4 e 701 " - pdb=" SG CYS e 491 " pdb="FE4 SF4 e 701 " - pdb=" SG CYS e 488 " Number of angles added : 300 Zn2+ tetrahedral coordination pdb=" ZN B 704 " pdb="ZN ZN B 704 " - pdb=" NE2 HIS B 555 " pdb="ZN ZN B 704 " - pdb=" SG CYS B 565 " pdb="ZN ZN B 704 " - pdb=" SG CYS B 468 " pdb="ZN ZN B 704 " - pdb=" SG CYS B 560 " pdb=" ZN E 704 " pdb="ZN ZN E 704 " - pdb=" NE2 HIS E 555 " pdb="ZN ZN E 704 " - pdb=" SG CYS E 565 " pdb="ZN ZN E 704 " - pdb=" SG CYS E 468 " pdb="ZN ZN E 704 " - pdb=" SG CYS E 560 " pdb=" ZN b 704 " pdb="ZN ZN b 704 " - pdb=" NE2 HIS b 555 " pdb="ZN ZN b 704 " - pdb=" SG CYS b 565 " pdb="ZN ZN b 704 " - pdb=" SG CYS b 468 " pdb="ZN ZN b 704 " - pdb=" SG CYS b 560 " pdb=" ZN e 704 " pdb="ZN ZN e 704 " - pdb=" NE2 HIS e 555 " pdb="ZN ZN e 704 " - pdb=" SG CYS e 565 " pdb="ZN ZN e 704 " - pdb=" SG CYS e 468 " pdb="ZN ZN e 704 " - pdb=" SG CYS e 560 " Number of angles added : 12 10088 Ramachandran restraints generated. 5044 Oldfield, 0 Emsley, 5044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9256 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 272 helices and 40 sheets defined 44.5% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.83 Creating SS restraints... Processing helix chain 'A' and resid 19 through 26 Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 75 through 91 removed outlier: 3.951A pdb=" N THR A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 148 through 155 Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 176 through 178 No H-bonds generated for 'chain 'A' and resid 176 through 178' Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 207 through 215 Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 244 through 254 Processing helix chain 'A' and resid 263 through 284 removed outlier: 3.532A pdb=" N HIS A 276 " --> pdb=" O TYR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 319 through 329 Processing helix chain 'A' and resid 331 through 335 Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 372 through 382 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 403 through 409 removed outlier: 3.819A pdb=" N PHE A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLY A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 425 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 486 through 488 No H-bonds generated for 'chain 'A' and resid 486 through 488' Processing helix chain 'A' and resid 498 through 514 removed outlier: 3.624A pdb=" N ILE A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 522 No H-bonds generated for 'chain 'A' and resid 520 through 522' Processing helix chain 'A' and resid 524 through 533 Processing helix chain 'A' and resid 537 through 544 Processing helix chain 'B' and resid 5 through 24 Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 41 through 55 Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 140 through 144 Processing helix chain 'B' and resid 161 through 166 Processing helix chain 'B' and resid 171 through 178 Processing helix chain 'B' and resid 182 through 192 Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 234 through 241 Processing helix chain 'B' and resid 243 through 256 Processing helix chain 'B' and resid 271 through 286 Processing helix chain 'B' and resid 312 through 315 Processing helix chain 'B' and resid 317 through 324 Processing helix chain 'B' and resid 343 through 345 No H-bonds generated for 'chain 'B' and resid 343 through 345' Processing helix chain 'B' and resid 353 through 364 Proline residue: B 360 - end of helix Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.609A pdb=" N LYS B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 428 through 430 No H-bonds generated for 'chain 'B' and resid 428 through 430' Processing helix chain 'B' and resid 437 through 439 No H-bonds generated for 'chain 'B' and resid 437 through 439' Processing helix chain 'B' and resid 447 through 450 No H-bonds generated for 'chain 'B' and resid 447 through 450' Processing helix chain 'B' and resid 469 through 483 Processing helix chain 'B' and resid 489 through 506 removed outlier: 3.997A pdb=" N MET B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 528 Processing helix chain 'B' and resid 532 through 537 Processing helix chain 'B' and resid 539 through 547 Processing helix chain 'B' and resid 549 through 557 Processing helix chain 'C' and resid 6 through 15 Processing helix chain 'C' and resid 19 through 33 removed outlier: 5.032A pdb=" N ILE C 23 " --> pdb=" O GLU C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 48 Processing helix chain 'C' and resid 52 through 59 Processing helix chain 'C' and resid 81 through 86 Processing helix chain 'C' and resid 88 through 99 Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 141 through 156 Processing helix chain 'D' and resid 19 through 26 Processing helix chain 'D' and resid 59 through 61 No H-bonds generated for 'chain 'D' and resid 59 through 61' Processing helix chain 'D' and resid 75 through 91 removed outlier: 3.950A pdb=" N THR D 91 " --> pdb=" O LEU D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'D' and resid 106 through 113 Processing helix chain 'D' and resid 140 through 142 No H-bonds generated for 'chain 'D' and resid 140 through 142' Processing helix chain 'D' and resid 148 through 155 Processing helix chain 'D' and resid 168 through 170 No H-bonds generated for 'chain 'D' and resid 168 through 170' Processing helix chain 'D' and resid 176 through 178 No H-bonds generated for 'chain 'D' and resid 176 through 178' Processing helix chain 'D' and resid 181 through 183 No H-bonds generated for 'chain 'D' and resid 181 through 183' Processing helix chain 'D' and resid 191 through 195 Processing helix chain 'D' and resid 207 through 215 Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 244 through 254 Processing helix chain 'D' and resid 263 through 284 removed outlier: 3.532A pdb=" N HIS D 276 " --> pdb=" O TYR D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 305 Processing helix chain 'D' and resid 307 through 309 No H-bonds generated for 'chain 'D' and resid 307 through 309' Processing helix chain 'D' and resid 319 through 329 Processing helix chain 'D' and resid 331 through 335 Processing helix chain 'D' and resid 339 through 341 No H-bonds generated for 'chain 'D' and resid 339 through 341' Processing helix chain 'D' and resid 352 through 357 Processing helix chain 'D' and resid 360 through 362 No H-bonds generated for 'chain 'D' and resid 360 through 362' Processing helix chain 'D' and resid 372 through 382 Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 403 through 409 removed outlier: 3.819A pdb=" N PHE D 408 " --> pdb=" O ALA D 404 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLY D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 425 Processing helix chain 'D' and resid 463 through 468 Processing helix chain 'D' and resid 486 through 488 No H-bonds generated for 'chain 'D' and resid 486 through 488' Processing helix chain 'D' and resid 498 through 514 removed outlier: 3.571A pdb=" N ILE D 514 " --> pdb=" O ASP D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 522 No H-bonds generated for 'chain 'D' and resid 520 through 522' Processing helix chain 'D' and resid 524 through 533 Processing helix chain 'D' and resid 537 through 544 Processing helix chain 'E' and resid 5 through 24 Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 41 through 55 Processing helix chain 'E' and resid 82 through 84 No H-bonds generated for 'chain 'E' and resid 82 through 84' Processing helix chain 'E' and resid 105 through 112 Processing helix chain 'E' and resid 140 through 144 Processing helix chain 'E' and resid 161 through 166 Processing helix chain 'E' and resid 171 through 178 Processing helix chain 'E' and resid 182 through 192 Processing helix chain 'E' and resid 204 through 213 Processing helix chain 'E' and resid 234 through 241 Processing helix chain 'E' and resid 243 through 256 Processing helix chain 'E' and resid 271 through 286 Processing helix chain 'E' and resid 312 through 315 Processing helix chain 'E' and resid 317 through 324 Processing helix chain 'E' and resid 343 through 345 No H-bonds generated for 'chain 'E' and resid 343 through 345' Processing helix chain 'E' and resid 353 through 364 Proline residue: E 360 - end of helix Processing helix chain 'E' and resid 367 through 372 removed outlier: 3.609A pdb=" N LYS E 372 " --> pdb=" O GLU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 Processing helix chain 'E' and resid 428 through 430 No H-bonds generated for 'chain 'E' and resid 428 through 430' Processing helix chain 'E' and resid 437 through 439 No H-bonds generated for 'chain 'E' and resid 437 through 439' Processing helix chain 'E' and resid 447 through 450 No H-bonds generated for 'chain 'E' and resid 447 through 450' Processing helix chain 'E' and resid 469 through 483 Processing helix chain 'E' and resid 489 through 506 removed outlier: 3.996A pdb=" N MET E 496 " --> pdb=" O ARG E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 512 through 528 Processing helix chain 'E' and resid 532 through 537 Processing helix chain 'E' and resid 539 through 547 Processing helix chain 'E' and resid 549 through 557 Processing helix chain 'F' and resid 6 through 15 Processing helix chain 'F' and resid 19 through 33 removed outlier: 5.032A pdb=" N ILE F 23 " --> pdb=" O GLU F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 48 Processing helix chain 'F' and resid 52 through 59 Processing helix chain 'F' and resid 81 through 86 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'F' and resid 123 through 125 No H-bonds generated for 'chain 'F' and resid 123 through 125' Processing helix chain 'F' and resid 141 through 156 Processing helix chain 'a' and resid 19 through 26 Processing helix chain 'a' and resid 59 through 61 No H-bonds generated for 'chain 'a' and resid 59 through 61' Processing helix chain 'a' and resid 75 through 91 removed outlier: 3.950A pdb=" N THR a 91 " --> pdb=" O LEU a 87 " (cutoff:3.500A) Processing helix chain 'a' and resid 96 through 98 No H-bonds generated for 'chain 'a' and resid 96 through 98' Processing helix chain 'a' and resid 106 through 113 Processing helix chain 'a' and resid 140 through 142 No H-bonds generated for 'chain 'a' and resid 140 through 142' Processing helix chain 'a' and resid 148 through 155 Processing helix chain 'a' and resid 168 through 170 No H-bonds generated for 'chain 'a' and resid 168 through 170' Processing helix chain 'a' and resid 176 through 178 No H-bonds generated for 'chain 'a' and resid 176 through 178' Processing helix chain 'a' and resid 181 through 183 No H-bonds generated for 'chain 'a' and resid 181 through 183' Processing helix chain 'a' and resid 191 through 195 Processing helix chain 'a' and resid 207 through 215 Processing helix chain 'a' and resid 234 through 236 No H-bonds generated for 'chain 'a' and resid 234 through 236' Processing helix chain 'a' and resid 244 through 254 Processing helix chain 'a' and resid 263 through 284 removed outlier: 3.532A pdb=" N HIS a 276 " --> pdb=" O TYR a 272 " (cutoff:3.500A) Processing helix chain 'a' and resid 296 through 305 Processing helix chain 'a' and resid 307 through 309 No H-bonds generated for 'chain 'a' and resid 307 through 309' Processing helix chain 'a' and resid 319 through 329 Processing helix chain 'a' and resid 331 through 335 Processing helix chain 'a' and resid 339 through 341 No H-bonds generated for 'chain 'a' and resid 339 through 341' Processing helix chain 'a' and resid 352 through 357 Processing helix chain 'a' and resid 360 through 362 No H-bonds generated for 'chain 'a' and resid 360 through 362' Processing helix chain 'a' and resid 372 through 382 Processing helix chain 'a' and resid 386 through 388 No H-bonds generated for 'chain 'a' and resid 386 through 388' Processing helix chain 'a' and resid 403 through 409 removed outlier: 3.819A pdb=" N PHE a 408 " --> pdb=" O ALA a 404 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLY a 409 " --> pdb=" O GLY a 405 " (cutoff:3.500A) Processing helix chain 'a' and resid 413 through 425 Processing helix chain 'a' and resid 463 through 468 Processing helix chain 'a' and resid 486 through 488 No H-bonds generated for 'chain 'a' and resid 486 through 488' Processing helix chain 'a' and resid 498 through 514 removed outlier: 3.624A pdb=" N ILE a 514 " --> pdb=" O ASP a 510 " (cutoff:3.500A) Processing helix chain 'a' and resid 520 through 522 No H-bonds generated for 'chain 'a' and resid 520 through 522' Processing helix chain 'a' and resid 524 through 533 Processing helix chain 'a' and resid 537 through 544 Processing helix chain 'b' and resid 5 through 24 Processing helix chain 'b' and resid 37 through 39 No H-bonds generated for 'chain 'b' and resid 37 through 39' Processing helix chain 'b' and resid 41 through 55 Processing helix chain 'b' and resid 82 through 84 No H-bonds generated for 'chain 'b' and resid 82 through 84' Processing helix chain 'b' and resid 105 through 112 Processing helix chain 'b' and resid 140 through 144 Processing helix chain 'b' and resid 161 through 166 Processing helix chain 'b' and resid 171 through 178 Processing helix chain 'b' and resid 182 through 192 Processing helix chain 'b' and resid 204 through 213 Processing helix chain 'b' and resid 234 through 241 Processing helix chain 'b' and resid 243 through 256 Processing helix chain 'b' and resid 271 through 286 Processing helix chain 'b' and resid 312 through 315 Processing helix chain 'b' and resid 317 through 324 Processing helix chain 'b' and resid 343 through 345 No H-bonds generated for 'chain 'b' and resid 343 through 345' Processing helix chain 'b' and resid 353 through 364 Proline residue: b 360 - end of helix Processing helix chain 'b' and resid 367 through 372 removed outlier: 3.608A pdb=" N LYS b 372 " --> pdb=" O GLU b 368 " (cutoff:3.500A) Processing helix chain 'b' and resid 404 through 410 Processing helix chain 'b' and resid 428 through 430 No H-bonds generated for 'chain 'b' and resid 428 through 430' Processing helix chain 'b' and resid 437 through 439 No H-bonds generated for 'chain 'b' and resid 437 through 439' Processing helix chain 'b' and resid 447 through 450 No H-bonds generated for 'chain 'b' and resid 447 through 450' Processing helix chain 'b' and resid 469 through 483 Processing helix chain 'b' and resid 489 through 506 removed outlier: 3.996A pdb=" N MET b 496 " --> pdb=" O ARG b 492 " (cutoff:3.500A) Processing helix chain 'b' and resid 512 through 528 Processing helix chain 'b' and resid 532 through 537 Processing helix chain 'b' and resid 539 through 547 Processing helix chain 'b' and resid 549 through 557 Processing helix chain 'c' and resid 6 through 15 Processing helix chain 'c' and resid 19 through 33 removed outlier: 5.054A pdb=" N ILE c 23 " --> pdb=" O GLU c 20 " (cutoff:3.500A) Processing helix chain 'c' and resid 38 through 48 Processing helix chain 'c' and resid 52 through 59 Processing helix chain 'c' and resid 81 through 86 Processing helix chain 'c' and resid 88 through 99 Processing helix chain 'c' and resid 123 through 125 No H-bonds generated for 'chain 'c' and resid 123 through 125' Processing helix chain 'c' and resid 141 through 156 Processing helix chain 'd' and resid 19 through 26 Processing helix chain 'd' and resid 59 through 61 No H-bonds generated for 'chain 'd' and resid 59 through 61' Processing helix chain 'd' and resid 75 through 91 removed outlier: 3.950A pdb=" N THR d 91 " --> pdb=" O LEU d 87 " (cutoff:3.500A) Processing helix chain 'd' and resid 96 through 98 No H-bonds generated for 'chain 'd' and resid 96 through 98' Processing helix chain 'd' and resid 106 through 113 Processing helix chain 'd' and resid 140 through 142 No H-bonds generated for 'chain 'd' and resid 140 through 142' Processing helix chain 'd' and resid 148 through 155 Processing helix chain 'd' and resid 168 through 170 No H-bonds generated for 'chain 'd' and resid 168 through 170' Processing helix chain 'd' and resid 176 through 178 No H-bonds generated for 'chain 'd' and resid 176 through 178' Processing helix chain 'd' and resid 181 through 183 No H-bonds generated for 'chain 'd' and resid 181 through 183' Processing helix chain 'd' and resid 191 through 195 Processing helix chain 'd' and resid 207 through 215 Processing helix chain 'd' and resid 234 through 236 No H-bonds generated for 'chain 'd' and resid 234 through 236' Processing helix chain 'd' and resid 244 through 254 Processing helix chain 'd' and resid 263 through 284 removed outlier: 3.532A pdb=" N HIS d 276 " --> pdb=" O TYR d 272 " (cutoff:3.500A) Processing helix chain 'd' and resid 296 through 305 Processing helix chain 'd' and resid 307 through 309 No H-bonds generated for 'chain 'd' and resid 307 through 309' Processing helix chain 'd' and resid 319 through 329 Processing helix chain 'd' and resid 331 through 335 Processing helix chain 'd' and resid 339 through 341 No H-bonds generated for 'chain 'd' and resid 339 through 341' Processing helix chain 'd' and resid 352 through 357 Processing helix chain 'd' and resid 360 through 362 No H-bonds generated for 'chain 'd' and resid 360 through 362' Processing helix chain 'd' and resid 372 through 382 Processing helix chain 'd' and resid 386 through 388 No H-bonds generated for 'chain 'd' and resid 386 through 388' Processing helix chain 'd' and resid 403 through 409 removed outlier: 3.819A pdb=" N PHE d 408 " --> pdb=" O ALA d 404 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLY d 409 " --> pdb=" O GLY d 405 " (cutoff:3.500A) Processing helix chain 'd' and resid 413 through 425 Processing helix chain 'd' and resid 463 through 468 Processing helix chain 'd' and resid 486 through 488 No H-bonds generated for 'chain 'd' and resid 486 through 488' Processing helix chain 'd' and resid 498 through 514 removed outlier: 3.624A pdb=" N ILE d 514 " --> pdb=" O ASP d 510 " (cutoff:3.500A) Processing helix chain 'd' and resid 520 through 522 No H-bonds generated for 'chain 'd' and resid 520 through 522' Processing helix chain 'd' and resid 524 through 533 Processing helix chain 'd' and resid 537 through 544 Processing helix chain 'e' and resid 5 through 24 Processing helix chain 'e' and resid 37 through 39 No H-bonds generated for 'chain 'e' and resid 37 through 39' Processing helix chain 'e' and resid 41 through 55 Processing helix chain 'e' and resid 82 through 84 No H-bonds generated for 'chain 'e' and resid 82 through 84' Processing helix chain 'e' and resid 105 through 112 Processing helix chain 'e' and resid 140 through 144 Processing helix chain 'e' and resid 161 through 166 Processing helix chain 'e' and resid 171 through 178 Processing helix chain 'e' and resid 182 through 192 Processing helix chain 'e' and resid 204 through 213 Processing helix chain 'e' and resid 234 through 241 Processing helix chain 'e' and resid 243 through 256 Processing helix chain 'e' and resid 271 through 286 Processing helix chain 'e' and resid 312 through 315 Processing helix chain 'e' and resid 317 through 324 Processing helix chain 'e' and resid 343 through 345 No H-bonds generated for 'chain 'e' and resid 343 through 345' Processing helix chain 'e' and resid 353 through 364 Proline residue: e 360 - end of helix Processing helix chain 'e' and resid 367 through 372 removed outlier: 3.608A pdb=" N LYS e 372 " --> pdb=" O GLU e 368 " (cutoff:3.500A) Processing helix chain 'e' and resid 404 through 410 Processing helix chain 'e' and resid 428 through 430 No H-bonds generated for 'chain 'e' and resid 428 through 430' Processing helix chain 'e' and resid 437 through 439 No H-bonds generated for 'chain 'e' and resid 437 through 439' Processing helix chain 'e' and resid 447 through 450 No H-bonds generated for 'chain 'e' and resid 447 through 450' Processing helix chain 'e' and resid 469 through 483 Processing helix chain 'e' and resid 489 through 506 removed outlier: 3.996A pdb=" N MET e 496 " --> pdb=" O ARG e 492 " (cutoff:3.500A) Processing helix chain 'e' and resid 512 through 528 Processing helix chain 'e' and resid 532 through 537 Processing helix chain 'e' and resid 539 through 547 Processing helix chain 'e' and resid 549 through 557 Processing helix chain 'f' and resid 6 through 15 Processing helix chain 'f' and resid 19 through 33 removed outlier: 5.032A pdb=" N ILE f 23 " --> pdb=" O GLU f 20 " (cutoff:3.500A) Processing helix chain 'f' and resid 38 through 48 Processing helix chain 'f' and resid 52 through 59 Processing helix chain 'f' and resid 81 through 86 Processing helix chain 'f' and resid 88 through 99 Processing helix chain 'f' and resid 123 through 125 No H-bonds generated for 'chain 'f' and resid 123 through 125' Processing helix chain 'f' and resid 141 through 156 Processing sheet with id= A, first strand: chain 'A' and resid 2 through 4 Processing sheet with id= B, first strand: chain 'A' and resid 49 through 52 Processing sheet with id= C, first strand: chain 'A' and resid 136 through 138 Processing sheet with id= D, first strand: chain 'A' and resid 163 through 165 Processing sheet with id= E, first strand: chain 'A' and resid 259 through 262 removed outlier: 3.582A pdb=" N LYS A 259 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE A 368 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N MET A 348 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU A 370 " --> pdb=" O MET A 348 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 431 through 434 removed outlier: 6.642A pdb=" N ILE A 476 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE A 458 " --> pdb=" O ILE A 476 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU A 478 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 72 through 76 Processing sheet with id= H, first strand: chain 'B' and resid 347 through 352 removed outlier: 6.833A pdb=" N LYS B 261 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N CYS B 223 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TYR B 263 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASP B 302 " --> pdb=" O GLY B 262 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ALA B 264 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU B 304 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ILE B 266 " --> pdb=" O GLU B 304 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LYS B 306 " --> pdb=" O ILE B 266 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 394 through 399 Processing sheet with id= J, first strand: chain 'C' and resid 112 through 117 removed outlier: 6.739A pdb=" N TYR C 73 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N ASP C 115 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE C 75 " --> pdb=" O ASP C 115 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL C 117 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL C 77 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 2 through 4 Processing sheet with id= L, first strand: chain 'D' and resid 49 through 52 Processing sheet with id= M, first strand: chain 'D' and resid 136 through 138 Processing sheet with id= N, first strand: chain 'D' and resid 163 through 165 Processing sheet with id= O, first strand: chain 'D' and resid 259 through 262 removed outlier: 3.583A pdb=" N LYS D 259 " --> pdb=" O VAL D 220 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE D 368 " --> pdb=" O SER D 346 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N MET D 348 " --> pdb=" O ILE D 368 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU D 370 " --> pdb=" O MET D 348 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 431 through 434 removed outlier: 6.642A pdb=" N ILE D 476 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE D 458 " --> pdb=" O ILE D 476 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU D 478 " --> pdb=" O ILE D 458 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 72 through 76 Processing sheet with id= R, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.826A pdb=" N LYS E 261 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N CYS E 223 " --> pdb=" O LYS E 261 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR E 263 " --> pdb=" O CYS E 223 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASP E 302 " --> pdb=" O GLY E 262 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ALA E 264 " --> pdb=" O ASP E 302 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLU E 304 " --> pdb=" O ALA E 264 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ILE E 266 " --> pdb=" O GLU E 304 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LYS E 306 " --> pdb=" O ILE E 266 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 394 through 399 Processing sheet with id= T, first strand: chain 'F' and resid 112 through 117 removed outlier: 6.730A pdb=" N TYR F 73 " --> pdb=" O SER F 113 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ASP F 115 " --> pdb=" O TYR F 73 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE F 75 " --> pdb=" O ASP F 115 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL F 117 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL F 77 " --> pdb=" O VAL F 117 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'a' and resid 2 through 4 Processing sheet with id= V, first strand: chain 'a' and resid 49 through 52 Processing sheet with id= W, first strand: chain 'a' and resid 136 through 138 Processing sheet with id= X, first strand: chain 'a' and resid 163 through 165 Processing sheet with id= Y, first strand: chain 'a' and resid 259 through 262 removed outlier: 3.582A pdb=" N LYS a 259 " --> pdb=" O VAL a 220 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE a 368 " --> pdb=" O SER a 346 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N MET a 348 " --> pdb=" O ILE a 368 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU a 370 " --> pdb=" O MET a 348 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'a' and resid 431 through 434 removed outlier: 6.641A pdb=" N ILE a 476 " --> pdb=" O ALA a 456 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE a 458 " --> pdb=" O ILE a 476 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU a 478 " --> pdb=" O ILE a 458 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'b' and resid 72 through 76 Processing sheet with id= AB, first strand: chain 'b' and resid 347 through 352 removed outlier: 6.825A pdb=" N LYS b 261 " --> pdb=" O VAL b 221 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N CYS b 223 " --> pdb=" O LYS b 261 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR b 263 " --> pdb=" O CYS b 223 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASP b 302 " --> pdb=" O GLY b 262 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ALA b 264 " --> pdb=" O ASP b 302 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLU b 304 " --> pdb=" O ALA b 264 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ILE b 266 " --> pdb=" O GLU b 304 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LYS b 306 " --> pdb=" O ILE b 266 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'b' and resid 394 through 399 Processing sheet with id= AD, first strand: chain 'c' and resid 112 through 117 removed outlier: 6.729A pdb=" N TYR c 73 " --> pdb=" O SER c 113 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ASP c 115 " --> pdb=" O TYR c 73 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE c 75 " --> pdb=" O ASP c 115 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL c 117 " --> pdb=" O ILE c 75 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL c 77 " --> pdb=" O VAL c 117 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'd' and resid 2 through 4 Processing sheet with id= AF, first strand: chain 'd' and resid 49 through 52 Processing sheet with id= AG, first strand: chain 'd' and resid 136 through 138 Processing sheet with id= AH, first strand: chain 'd' and resid 163 through 165 Processing sheet with id= AI, first strand: chain 'd' and resid 259 through 262 removed outlier: 3.582A pdb=" N LYS d 259 " --> pdb=" O VAL d 220 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE d 368 " --> pdb=" O SER d 346 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N MET d 348 " --> pdb=" O ILE d 368 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU d 370 " --> pdb=" O MET d 348 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'd' and resid 431 through 434 removed outlier: 6.641A pdb=" N ILE d 476 " --> pdb=" O ALA d 456 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE d 458 " --> pdb=" O ILE d 476 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU d 478 " --> pdb=" O ILE d 458 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'e' and resid 72 through 76 Processing sheet with id= AL, first strand: chain 'e' and resid 347 through 352 removed outlier: 6.826A pdb=" N LYS e 261 " --> pdb=" O VAL e 221 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N CYS e 223 " --> pdb=" O LYS e 261 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR e 263 " --> pdb=" O CYS e 223 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASP e 302 " --> pdb=" O GLY e 262 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ALA e 264 " --> pdb=" O ASP e 302 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLU e 304 " --> pdb=" O ALA e 264 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ILE e 266 " --> pdb=" O GLU e 304 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LYS e 306 " --> pdb=" O ILE e 266 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'e' and resid 394 through 399 Processing sheet with id= AN, first strand: chain 'f' and resid 112 through 117 removed outlier: 6.728A pdb=" N TYR f 73 " --> pdb=" O SER f 113 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ASP f 115 " --> pdb=" O TYR f 73 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE f 75 " --> pdb=" O ASP f 115 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL f 117 " --> pdb=" O ILE f 75 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL f 77 " --> pdb=" O VAL f 117 " (cutoff:3.500A) 1428 hydrogen bonds defined for protein. 4080 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: 30.50 Time building geometry restraints manager: 58.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.13: 39892 1.13 - 1.42: 16208 1.42 - 1.71: 23740 1.71 - 2.00: 408 2.00 - 2.29: 288 Bond restraints: 80536 Sorted by residual: bond pdb=" C ASP D 208 " pdb=" O ASP D 208 " ideal model delta sigma weight residual 1.237 1.210 0.026 1.17e-02 7.31e+03 5.05e+00 bond pdb=" C ASP a 208 " pdb=" O ASP a 208 " ideal model delta sigma weight residual 1.237 1.210 0.026 1.17e-02 7.31e+03 5.02e+00 bond pdb=" C ASP d 208 " pdb=" O ASP d 208 " ideal model delta sigma weight residual 1.237 1.211 0.026 1.17e-02 7.31e+03 4.81e+00 bond pdb=" C ASP A 208 " pdb=" O ASP A 208 " ideal model delta sigma weight residual 1.236 1.211 0.026 1.26e-02 6.30e+03 4.15e+00 bond pdb=" CB PRO b 182 " pdb=" CG PRO b 182 " ideal model delta sigma weight residual 1.492 1.568 -0.076 5.00e-02 4.00e+02 2.33e+00 ... (remaining 80531 not shown) Histogram of bond angle deviations from ideal: 73.52 - 85.63: 264 85.63 - 97.74: 0 97.74 - 109.85: 64059 109.85 - 121.96: 69237 121.96 - 134.07: 12704 Bond angle restraints: 146264 Sorted by residual: angle pdb=" CA PRO E 182 " pdb=" N PRO E 182 " pdb=" CD PRO E 182 " ideal model delta sigma weight residual 112.00 106.83 5.17 1.40e+00 5.10e-01 1.36e+01 angle pdb=" CA PRO b 182 " pdb=" N PRO b 182 " pdb=" CD PRO b 182 " ideal model delta sigma weight residual 112.00 106.83 5.17 1.40e+00 5.10e-01 1.36e+01 angle pdb=" CA PRO e 182 " pdb=" N PRO e 182 " pdb=" CD PRO e 182 " ideal model delta sigma weight residual 112.00 106.87 5.13 1.40e+00 5.10e-01 1.34e+01 angle pdb=" CA PRO B 182 " pdb=" N PRO B 182 " pdb=" CD PRO B 182 " ideal model delta sigma weight residual 112.00 106.88 5.12 1.40e+00 5.10e-01 1.34e+01 angle pdb=" N TYR E 148 " pdb=" CA TYR E 148 " pdb=" C TYR E 148 " ideal model delta sigma weight residual 114.62 111.13 3.49 1.14e+00 7.69e-01 9.36e+00 ... (remaining 146259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.35: 35669 34.35 - 68.70: 1607 68.70 - 103.05: 108 103.05 - 137.40: 0 137.40 - 171.75: 4 Dihedral angle restraints: 37388 sinusoidal: 20808 harmonic: 16580 Sorted by residual: dihedral pdb=" C10 FMN e 702 " pdb=" C1' FMN e 702 " pdb=" N10 FMN e 702 " pdb=" C2' FMN e 702 " ideal model delta sinusoidal sigma weight residual 257.59 85.84 171.75 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C10 FMN B 702 " pdb=" C1' FMN B 702 " pdb=" N10 FMN B 702 " pdb=" C2' FMN B 702 " ideal model delta sinusoidal sigma weight residual 257.59 85.86 171.73 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C10 FMN E 702 " pdb=" C1' FMN E 702 " pdb=" N10 FMN E 702 " pdb=" C2' FMN E 702 " ideal model delta sinusoidal sigma weight residual 257.59 85.87 171.73 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 37385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 3261 0.028 - 0.056: 1805 0.056 - 0.084: 644 0.084 - 0.112: 344 0.112 - 0.139: 110 Chirality restraints: 6164 Sorted by residual: chirality pdb=" CA ILE F 50 " pdb=" N ILE F 50 " pdb=" C ILE F 50 " pdb=" CB ILE F 50 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 chirality pdb=" CA ILE C 50 " pdb=" N ILE C 50 " pdb=" C ILE C 50 " pdb=" CB ILE C 50 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA ILE f 50 " pdb=" N ILE f 50 " pdb=" C ILE f 50 " pdb=" CB ILE f 50 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 6161 not shown) Planarity restraints: 11828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR b 181 " -0.051 5.00e-02 4.00e+02 7.52e-02 9.05e+00 pdb=" N PRO b 182 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO b 182 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO b 182 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 181 " 0.051 5.00e-02 4.00e+02 7.52e-02 9.05e+00 pdb=" N PRO E 182 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO E 182 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 182 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR e 181 " 0.051 5.00e-02 4.00e+02 7.51e-02 9.01e+00 pdb=" N PRO e 182 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO e 182 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO e 182 " 0.041 5.00e-02 4.00e+02 ... (remaining 11825 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 1829 2.09 - 2.72: 138960 2.72 - 3.34: 246582 3.34 - 3.97: 323265 3.97 - 4.60: 502193 Nonbonded interactions: 1212829 Sorted by model distance: nonbonded pdb=" O ASN d 15 " pdb="HD21 ASN d 15 " model vdw 1.461 1.850 nonbonded pdb=" O ASN a 15 " pdb="HD21 ASN a 15 " model vdw 1.461 1.850 nonbonded pdb=" O ASN A 15 " pdb="HD21 ASN A 15 " model vdw 1.461 1.850 nonbonded pdb=" O ASN D 15 " pdb="HD21 ASN D 15 " model vdw 1.461 1.850 nonbonded pdb="HH12 ARG E 197 " pdb=" O THR E 381 " model vdw 1.610 1.850 ... (remaining 1212824 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 129 or resid 132 through 554 or resid 701 throug \ h 705)) selection = (chain 'D' and (resid 1 through 129 or resid 132 through 554 or resid 701 throug \ h 705)) selection = (chain 'a' and (resid 1 through 129 or resid 132 through 554 or resid 701 throug \ h 705)) selection = (chain 'd' and (resid 1 through 129 or resid 132 through 554 or resid 701 throug \ h 705)) } ncs_group { reference = (chain 'B' and (resid 1 through 235 or resid 237 through 567 or resid 701 throug \ h 704)) selection = (chain 'E' and (resid 1 through 235 or resid 237 through 567 or resid 701 throug \ h 704)) selection = (chain 'b' and (resid 1 through 235 or resid 237 through 567 or resid 701 throug \ h 704)) selection = (chain 'e' and (resid 1 through 235 or resid 237 through 567 or resid 701 throug \ h 704)) } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'c' selection = chain 'f' } 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=0.50 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: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.000 Extract box with map and model: 10.320 Check model and map are aligned: 0.940 Set scattering table: 0.580 Process input model: 278.490 Find NCS groups from input model: 3.500 Set up NCS constraints: 0.440 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: 0.020 Load rotamer database and sin/cos tables:10.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 308.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 40612 Z= 0.274 Angle : 0.618 6.434 54892 Z= 0.334 Chirality : 0.043 0.139 6164 Planarity : 0.005 0.075 6992 Dihedral : 18.384 171.750 15404 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.38 % Allowed : 21.92 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.12), residues: 5044 helix: 1.10 (0.11), residues: 2352 sheet: -0.25 (0.22), residues: 540 loop : -0.54 (0.14), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 344 HIS 0.004 0.001 HIS E 244 PHE 0.015 0.002 PHE B 96 TYR 0.021 0.002 TYR A 459 ARG 0.006 0.001 ARG D 551 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10088 Ramachandran restraints generated. 5044 Oldfield, 0 Emsley, 5044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10088 Ramachandran restraints generated. 5044 Oldfield, 0 Emsley, 5044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 4268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 628 time to evaluate : 4.995 Fit side-chains outliers start: 98 outliers final: 83 residues processed: 718 average time/residue: 3.0870 time to fit residues: 2671.9641 Evaluate side-chains 693 residues out of total 4268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 610 time to evaluate : 4.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 533 ASP Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 430 SER Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 503 GLU Chi-restraints excluded: chain F residue 30 GLN Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain a residue 15 ASN Chi-restraints excluded: chain a residue 26 VAL Chi-restraints excluded: chain a residue 419 LEU Chi-restraints excluded: chain a residue 435 SER Chi-restraints excluded: chain a residue 440 ILE Chi-restraints excluded: chain a residue 533 ASP Chi-restraints excluded: chain b residue 34 THR Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain b residue 172 SER Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 354 GLU Chi-restraints excluded: chain b residue 365 ASP Chi-restraints excluded: chain b residue 381 THR Chi-restraints excluded: chain b residue 430 SER Chi-restraints excluded: chain b residue 433 CYS Chi-restraints excluded: chain b residue 455 VAL Chi-restraints excluded: chain b residue 503 GLU Chi-restraints excluded: chain c residue 30 GLN Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain c residue 77 VAL Chi-restraints excluded: chain c residue 135 VAL Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 419 LEU Chi-restraints excluded: chain d residue 435 SER Chi-restraints excluded: chain d residue 440 ILE Chi-restraints excluded: chain d residue 533 ASP Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 349 LEU Chi-restraints excluded: chain e residue 354 GLU Chi-restraints excluded: chain e residue 365 ASP Chi-restraints excluded: chain e residue 381 THR Chi-restraints excluded: chain e residue 386 VAL Chi-restraints excluded: chain e residue 430 SER Chi-restraints excluded: chain e residue 433 CYS Chi-restraints excluded: chain e residue 455 VAL Chi-restraints excluded: chain e residue 503 GLU Chi-restraints excluded: chain f residue 30 GLN Chi-restraints excluded: chain f residue 45 SER Chi-restraints excluded: chain f residue 77 VAL Chi-restraints excluded: chain f residue 135 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 422 optimal weight: 8.9990 chunk 378 optimal weight: 2.9990 chunk 210 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 255 optimal weight: 4.9990 chunk 202 optimal weight: 8.9990 chunk 391 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 238 optimal weight: 5.9990 chunk 291 optimal weight: 5.9990 chunk 454 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 55 GLN B 4 ASN B 145 GLN D 15 ASN D 55 GLN E 4 ASN E 145 GLN a 55 GLN b 145 GLN d 15 ASN d 55 GLN e 145 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.0407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 40612 Z= 0.347 Angle : 0.639 5.363 54892 Z= 0.342 Chirality : 0.046 0.165 6164 Planarity : 0.006 0.062 6992 Dihedral : 8.550 170.089 5718 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.20 % Allowed : 19.89 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.12), residues: 5044 helix: 0.73 (0.10), residues: 2356 sheet: -0.32 (0.21), residues: 544 loop : -0.61 (0.14), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP b 344 HIS 0.005 0.001 HIS e 244 PHE 0.017 0.002 PHE D 408 TYR 0.025 0.003 TYR a 459 ARG 0.007 0.001 ARG D 549 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10088 Ramachandran restraints generated. 5044 Oldfield, 0 Emsley, 5044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10088 Ramachandran restraints generated. 5044 Oldfield, 0 Emsley, 5044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 4268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 623 time to evaluate : 5.039 Fit side-chains REVERT: A 509 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7334 (ttm170) REVERT: A 531 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.6241 (tp30) REVERT: A 549 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7354 (ppt170) REVERT: B 121 ARG cc_start: 0.4335 (OUTLIER) cc_final: 0.4042 (ttp80) REVERT: B 363 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6247 (tp) REVERT: D 531 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6243 (tp30) REVERT: D 549 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7354 (ppt170) REVERT: E 121 ARG cc_start: 0.4334 (OUTLIER) cc_final: 0.4041 (ttp80) REVERT: E 363 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.6249 (tp) REVERT: E 503 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7177 (mt-10) REVERT: a 509 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7363 (ttm170) REVERT: a 531 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.6247 (tp30) REVERT: a 549 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7354 (ppt170) REVERT: b 121 ARG cc_start: 0.4334 (OUTLIER) cc_final: 0.4043 (ttp80) REVERT: b 363 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6252 (tp) REVERT: b 503 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7174 (mt-10) REVERT: d 509 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7364 (ttm170) REVERT: d 531 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.6239 (tp30) REVERT: d 549 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7354 (ppt170) REVERT: e 121 ARG cc_start: 0.4333 (OUTLIER) cc_final: 0.4038 (ttp80) REVERT: e 363 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.6249 (tp) REVERT: e 503 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7175 (mt-10) outliers start: 176 outliers final: 111 residues processed: 742 average time/residue: 3.1169 time to fit residues: 2782.2213 Evaluate side-chains 757 residues out of total 4268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 624 time to evaluate : 5.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 549 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 275 LYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 536 ASP Chi-restraints excluded: chain D residue 549 ARG Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 146 ASP Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 430 SER Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 503 GLU Chi-restraints excluded: chain F residue 30 GLN Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain a residue 26 VAL Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 155 GLU Chi-restraints excluded: chain a residue 238 ILE Chi-restraints excluded: chain a residue 401 SER Chi-restraints excluded: chain a residue 440 ILE Chi-restraints excluded: chain a residue 476 ILE Chi-restraints excluded: chain a residue 509 ARG Chi-restraints excluded: chain a residue 531 GLU Chi-restraints excluded: chain a residue 536 ASP Chi-restraints excluded: chain a residue 549 ARG Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 34 THR Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain b residue 121 ARG Chi-restraints excluded: chain b residue 146 ASP Chi-restraints excluded: chain b residue 172 SER Chi-restraints excluded: chain b residue 275 LYS Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 363 LEU Chi-restraints excluded: chain b residue 365 ASP Chi-restraints excluded: chain b residue 381 THR Chi-restraints excluded: chain b residue 404 LEU Chi-restraints excluded: chain b residue 430 SER Chi-restraints excluded: chain b residue 433 CYS Chi-restraints excluded: chain b residue 455 VAL Chi-restraints excluded: chain b residue 503 GLU Chi-restraints excluded: chain c residue 30 GLN Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain c residue 77 VAL Chi-restraints excluded: chain c residue 134 GLU Chi-restraints excluded: chain c residue 135 VAL Chi-restraints excluded: chain c residue 146 GLU Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 52 ILE Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 238 ILE Chi-restraints excluded: chain d residue 401 SER Chi-restraints excluded: chain d residue 440 ILE Chi-restraints excluded: chain d residue 476 ILE Chi-restraints excluded: chain d residue 509 ARG Chi-restraints excluded: chain d residue 531 GLU Chi-restraints excluded: chain d residue 536 ASP Chi-restraints excluded: chain d residue 549 ARG Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 121 ARG Chi-restraints excluded: chain e residue 146 ASP Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 275 LYS Chi-restraints excluded: chain e residue 349 LEU Chi-restraints excluded: chain e residue 363 LEU Chi-restraints excluded: chain e residue 365 ASP Chi-restraints excluded: chain e residue 381 THR Chi-restraints excluded: chain e residue 404 LEU Chi-restraints excluded: chain e residue 430 SER Chi-restraints excluded: chain e residue 433 CYS Chi-restraints excluded: chain e residue 455 VAL Chi-restraints excluded: chain e residue 503 GLU Chi-restraints excluded: chain f residue 30 GLN Chi-restraints excluded: chain f residue 45 SER Chi-restraints excluded: chain f residue 77 VAL Chi-restraints excluded: chain f residue 134 GLU Chi-restraints excluded: chain f residue 135 VAL Chi-restraints excluded: chain f residue 146 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 252 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 377 optimal weight: 4.9990 chunk 309 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 chunk 454 optimal weight: 10.0000 chunk 491 optimal weight: 4.9990 chunk 405 optimal weight: 5.9990 chunk 451 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 364 optimal weight: 0.0670 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 55 GLN B 145 GLN D 15 ASN D 55 GLN E 145 GLN a 15 ASN a 55 GLN b 145 GLN d 15 ASN d 55 GLN e 145 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.0504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 40612 Z= 0.258 Angle : 0.576 4.978 54892 Z= 0.305 Chirality : 0.043 0.153 6164 Planarity : 0.005 0.052 6992 Dihedral : 8.011 168.851 5681 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.73 % Allowed : 20.69 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.12), residues: 5044 helix: 0.84 (0.11), residues: 2352 sheet: -0.32 (0.21), residues: 544 loop : -0.58 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 344 HIS 0.004 0.001 HIS D 128 PHE 0.013 0.002 PHE D 236 TYR 0.020 0.002 TYR D 459 ARG 0.003 0.001 ARG D 540 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10088 Ramachandran restraints generated. 5044 Oldfield, 0 Emsley, 5044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10088 Ramachandran restraints generated. 5044 Oldfield, 0 Emsley, 5044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 4268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 619 time to evaluate : 5.104 Fit side-chains REVERT: A 509 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7313 (ttm170) REVERT: A 531 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6310 (tp30) REVERT: B 121 ARG cc_start: 0.4364 (OUTLIER) cc_final: 0.4080 (ttp80) REVERT: B 340 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.6731 (mp10) REVERT: B 363 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.6173 (tp) REVERT: D 509 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7305 (ttm170) REVERT: D 531 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6313 (tp30) REVERT: E 121 ARG cc_start: 0.4364 (OUTLIER) cc_final: 0.4082 (ttp80) REVERT: E 340 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.6730 (mp10) REVERT: E 363 LEU cc_start: 0.6621 (OUTLIER) cc_final: 0.6167 (tp) REVERT: a 509 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7367 (ttm170) REVERT: a 531 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.6313 (tp30) REVERT: b 121 ARG cc_start: 0.4361 (OUTLIER) cc_final: 0.4077 (ttp80) REVERT: b 340 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.6732 (mp10) REVERT: b 363 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.6173 (tp) REVERT: c 18 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.7125 (tppt) REVERT: d 509 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7367 (ttm170) REVERT: d 531 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.6307 (tp30) REVERT: e 121 ARG cc_start: 0.4361 (OUTLIER) cc_final: 0.4075 (ttp80) REVERT: e 340 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.6731 (mp10) REVERT: e 363 LEU cc_start: 0.6625 (OUTLIER) cc_final: 0.6173 (tp) outliers start: 156 outliers final: 88 residues processed: 717 average time/residue: 3.1493 time to fit residues: 2711.0263 Evaluate side-chains 714 residues out of total 4268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 605 time to evaluate : 4.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 340 GLN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 509 ARG Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 146 ASP Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 340 GLN Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 430 SER Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 503 GLU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain a residue 26 VAL Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 155 GLU Chi-restraints excluded: chain a residue 238 ILE Chi-restraints excluded: chain a residue 401 SER Chi-restraints excluded: chain a residue 440 ILE Chi-restraints excluded: chain a residue 509 ARG Chi-restraints excluded: chain a residue 531 GLU Chi-restraints excluded: chain b residue 34 THR Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain b residue 121 ARG Chi-restraints excluded: chain b residue 138 ASP Chi-restraints excluded: chain b residue 146 ASP Chi-restraints excluded: chain b residue 172 SER Chi-restraints excluded: chain b residue 340 GLN Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 363 LEU Chi-restraints excluded: chain b residue 365 ASP Chi-restraints excluded: chain b residue 381 THR Chi-restraints excluded: chain b residue 404 LEU Chi-restraints excluded: chain b residue 430 SER Chi-restraints excluded: chain b residue 433 CYS Chi-restraints excluded: chain b residue 455 VAL Chi-restraints excluded: chain b residue 503 GLU Chi-restraints excluded: chain c residue 18 LYS Chi-restraints excluded: chain c residue 77 VAL Chi-restraints excluded: chain c residue 135 VAL Chi-restraints excluded: chain c residue 146 GLU Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 52 ILE Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 238 ILE Chi-restraints excluded: chain d residue 401 SER Chi-restraints excluded: chain d residue 440 ILE Chi-restraints excluded: chain d residue 509 ARG Chi-restraints excluded: chain d residue 531 GLU Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 121 ARG Chi-restraints excluded: chain e residue 138 ASP Chi-restraints excluded: chain e residue 146 ASP Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 340 GLN Chi-restraints excluded: chain e residue 349 LEU Chi-restraints excluded: chain e residue 363 LEU Chi-restraints excluded: chain e residue 365 ASP Chi-restraints excluded: chain e residue 381 THR Chi-restraints excluded: chain e residue 404 LEU Chi-restraints excluded: chain e residue 430 SER Chi-restraints excluded: chain e residue 433 CYS Chi-restraints excluded: chain e residue 455 VAL Chi-restraints excluded: chain e residue 503 GLU Chi-restraints excluded: chain f residue 77 VAL Chi-restraints excluded: chain f residue 134 GLU Chi-restraints excluded: chain f residue 135 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 449 optimal weight: 6.9990 chunk 341 optimal weight: 0.0770 chunk 236 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 217 optimal weight: 7.9990 chunk 305 optimal weight: 6.9990 chunk 456 optimal weight: 7.9990 chunk 483 optimal weight: 4.9990 chunk 238 optimal weight: 8.9990 chunk 432 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 55 GLN B 145 GLN D 15 ASN D 55 GLN E 145 GLN a 15 ASN a 55 GLN b 145 GLN d 15 ASN d 55 GLN e 145 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.0610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 40612 Z= 0.328 Angle : 0.627 5.409 54892 Z= 0.334 Chirality : 0.045 0.157 6164 Planarity : 0.005 0.063 6992 Dihedral : 7.948 168.342 5665 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.59 % Allowed : 20.50 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.12), residues: 5044 helix: 0.65 (0.10), residues: 2356 sheet: -0.34 (0.21), residues: 544 loop : -0.64 (0.14), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP e 344 HIS 0.005 0.001 HIS B 244 PHE 0.017 0.002 PHE a 408 TYR 0.024 0.002 TYR A 459 ARG 0.007 0.001 ARG d 549 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10088 Ramachandran restraints generated. 5044 Oldfield, 0 Emsley, 5044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10088 Ramachandran restraints generated. 5044 Oldfield, 0 Emsley, 5044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 4268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 606 time to evaluate : 4.930 Fit side-chains REVERT: A 509 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7304 (ttm170) REVERT: A 531 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.6037 (tp30) REVERT: A 549 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7366 (ppt170) REVERT: B 121 ARG cc_start: 0.4353 (OUTLIER) cc_final: 0.4055 (ttp80) REVERT: B 340 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.6758 (mp10) REVERT: B 363 LEU cc_start: 0.6676 (OUTLIER) cc_final: 0.6226 (tp) REVERT: D 509 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7132 (ttm170) REVERT: D 531 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6392 (tp30) REVERT: D 549 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7364 (ppt170) REVERT: E 121 ARG cc_start: 0.4352 (OUTLIER) cc_final: 0.4053 (ttp80) REVERT: E 340 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.6774 (mp10) REVERT: E 363 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6224 (tp) REVERT: a 509 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7370 (ttm170) REVERT: a 531 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6042 (tp30) REVERT: a 549 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7366 (ppt170) REVERT: b 121 ARG cc_start: 0.4350 (OUTLIER) cc_final: 0.4053 (ttp80) REVERT: b 340 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.6758 (mp10) REVERT: b 363 LEU cc_start: 0.6676 (OUTLIER) cc_final: 0.6226 (tp) REVERT: c 18 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.6804 (tttt) REVERT: d 509 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7372 (ttm170) REVERT: d 531 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.6387 (tp30) REVERT: d 549 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7366 (ppt170) REVERT: e 121 ARG cc_start: 0.4349 (OUTLIER) cc_final: 0.4049 (ttp80) REVERT: e 340 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.6776 (mp10) REVERT: e 363 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6224 (tp) outliers start: 193 outliers final: 118 residues processed: 734 average time/residue: 3.0872 time to fit residues: 2731.3319 Evaluate side-chains 743 residues out of total 4268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 600 time to evaluate : 4.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 549 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 340 GLN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 451 THR Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain D residue 509 ARG Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 533 ASP Chi-restraints excluded: chain D residue 536 ASP Chi-restraints excluded: chain D residue 549 ARG Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 340 GLN Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 430 SER Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 503 GLU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain a residue 15 ASN Chi-restraints excluded: chain a residue 26 VAL Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 155 GLU Chi-restraints excluded: chain a residue 238 ILE Chi-restraints excluded: chain a residue 401 SER Chi-restraints excluded: chain a residue 440 ILE Chi-restraints excluded: chain a residue 451 THR Chi-restraints excluded: chain a residue 476 ILE Chi-restraints excluded: chain a residue 509 ARG Chi-restraints excluded: chain a residue 531 GLU Chi-restraints excluded: chain a residue 533 ASP Chi-restraints excluded: chain a residue 536 ASP Chi-restraints excluded: chain a residue 549 ARG Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 34 THR Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain b residue 121 ARG Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 172 SER Chi-restraints excluded: chain b residue 180 MET Chi-restraints excluded: chain b residue 340 GLN Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 363 LEU Chi-restraints excluded: chain b residue 365 ASP Chi-restraints excluded: chain b residue 381 THR Chi-restraints excluded: chain b residue 404 LEU Chi-restraints excluded: chain b residue 430 SER Chi-restraints excluded: chain b residue 433 CYS Chi-restraints excluded: chain b residue 455 VAL Chi-restraints excluded: chain b residue 503 GLU Chi-restraints excluded: chain c residue 18 LYS Chi-restraints excluded: chain c residue 77 VAL Chi-restraints excluded: chain c residue 135 VAL Chi-restraints excluded: chain c residue 146 GLU Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 52 ILE Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 238 ILE Chi-restraints excluded: chain d residue 401 SER Chi-restraints excluded: chain d residue 440 ILE Chi-restraints excluded: chain d residue 451 THR Chi-restraints excluded: chain d residue 476 ILE Chi-restraints excluded: chain d residue 509 ARG Chi-restraints excluded: chain d residue 531 GLU Chi-restraints excluded: chain d residue 533 ASP Chi-restraints excluded: chain d residue 536 ASP Chi-restraints excluded: chain d residue 549 ARG Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 121 ARG Chi-restraints excluded: chain e residue 129 THR Chi-restraints excluded: chain e residue 146 ASP Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 180 MET Chi-restraints excluded: chain e residue 340 GLN Chi-restraints excluded: chain e residue 349 LEU Chi-restraints excluded: chain e residue 363 LEU Chi-restraints excluded: chain e residue 365 ASP Chi-restraints excluded: chain e residue 381 THR Chi-restraints excluded: chain e residue 383 MET Chi-restraints excluded: chain e residue 404 LEU Chi-restraints excluded: chain e residue 430 SER Chi-restraints excluded: chain e residue 433 CYS Chi-restraints excluded: chain e residue 455 VAL Chi-restraints excluded: chain e residue 503 GLU Chi-restraints excluded: chain f residue 77 VAL Chi-restraints excluded: chain f residue 134 GLU Chi-restraints excluded: chain f residue 135 VAL Chi-restraints excluded: chain f residue 146 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 402 optimal weight: 6.9990 chunk 274 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 359 optimal weight: 4.9990 chunk 199 optimal weight: 5.9990 chunk 412 optimal weight: 3.9990 chunk 334 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 246 optimal weight: 7.9990 chunk 433 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 55 GLN B 145 GLN D 15 ASN D 55 GLN E 145 GLN a 55 GLN b 145 GLN d 15 ASN d 55 GLN e 145 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 40612 Z= 0.358 Angle : 0.651 6.438 54892 Z= 0.347 Chirality : 0.046 0.156 6164 Planarity : 0.006 0.062 6992 Dihedral : 8.015 168.098 5665 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.80 % Allowed : 20.76 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.12), residues: 5044 helix: 0.52 (0.10), residues: 2356 sheet: -0.35 (0.21), residues: 544 loop : -0.69 (0.14), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP e 344 HIS 0.005 0.001 HIS B 244 PHE 0.017 0.002 PHE d 408 TYR 0.023 0.003 TYR D 459 ARG 0.006 0.001 ARG a 549 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10088 Ramachandran restraints generated. 5044 Oldfield, 0 Emsley, 5044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10088 Ramachandran restraints generated. 5044 Oldfield, 0 Emsley, 5044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 4268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 606 time to evaluate : 5.001 Fit side-chains REVERT: A 509 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7308 (ttm170) REVERT: A 531 GLU cc_start: 0.6339 (OUTLIER) cc_final: 0.6098 (tp30) REVERT: A 549 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7339 (ppt170) REVERT: B 121 ARG cc_start: 0.4350 (OUTLIER) cc_final: 0.4044 (ttp80) REVERT: B 340 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.6758 (mp10) REVERT: B 363 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6220 (tp) REVERT: D 509 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7217 (ttm170) REVERT: D 531 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.6103 (tp30) REVERT: D 549 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7337 (ppt170) REVERT: E 121 ARG cc_start: 0.4339 (OUTLIER) cc_final: 0.4037 (ttp80) REVERT: E 340 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.6772 (mp10) REVERT: E 363 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6218 (tp) REVERT: a 509 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7391 (ttm170) REVERT: a 531 GLU cc_start: 0.6342 (OUTLIER) cc_final: 0.6095 (tp30) REVERT: a 549 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7338 (ppt170) REVERT: b 121 ARG cc_start: 0.4338 (OUTLIER) cc_final: 0.4037 (ttp80) REVERT: b 340 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6757 (mp10) REVERT: b 363 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6220 (tp) REVERT: c 18 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6819 (tttt) REVERT: d 509 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7391 (ttm170) REVERT: d 531 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.6098 (tp30) REVERT: d 549 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7338 (ppt170) REVERT: e 121 ARG cc_start: 0.4348 (OUTLIER) cc_final: 0.4040 (ttp80) REVERT: e 340 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.6774 (mp10) REVERT: e 363 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6219 (tp) outliers start: 202 outliers final: 124 residues processed: 738 average time/residue: 3.1348 time to fit residues: 2780.8720 Evaluate side-chains 751 residues out of total 4268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 602 time to evaluate : 4.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 549 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 340 GLN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 451 THR Chi-restraints excluded: chain D residue 509 ARG Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 533 ASP Chi-restraints excluded: chain D residue 536 ASP Chi-restraints excluded: chain D residue 549 ARG Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 340 GLN Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 430 SER Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 503 GLU Chi-restraints excluded: chain F residue 30 GLN Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain a residue 26 VAL Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 155 GLU Chi-restraints excluded: chain a residue 238 ILE Chi-restraints excluded: chain a residue 401 SER Chi-restraints excluded: chain a residue 440 ILE Chi-restraints excluded: chain a residue 451 THR Chi-restraints excluded: chain a residue 509 ARG Chi-restraints excluded: chain a residue 531 GLU Chi-restraints excluded: chain a residue 533 ASP Chi-restraints excluded: chain a residue 536 ASP Chi-restraints excluded: chain a residue 549 ARG Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 34 THR Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain b residue 121 ARG Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 172 SER Chi-restraints excluded: chain b residue 180 MET Chi-restraints excluded: chain b residue 340 GLN Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 363 LEU Chi-restraints excluded: chain b residue 365 ASP Chi-restraints excluded: chain b residue 381 THR Chi-restraints excluded: chain b residue 404 LEU Chi-restraints excluded: chain b residue 430 SER Chi-restraints excluded: chain b residue 433 CYS Chi-restraints excluded: chain b residue 455 VAL Chi-restraints excluded: chain b residue 503 GLU Chi-restraints excluded: chain c residue 18 LYS Chi-restraints excluded: chain c residue 30 GLN Chi-restraints excluded: chain c residue 77 VAL Chi-restraints excluded: chain c residue 135 VAL Chi-restraints excluded: chain c residue 146 GLU Chi-restraints excluded: chain c residue 151 ILE Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 52 ILE Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 238 ILE Chi-restraints excluded: chain d residue 401 SER Chi-restraints excluded: chain d residue 440 ILE Chi-restraints excluded: chain d residue 451 THR Chi-restraints excluded: chain d residue 509 ARG Chi-restraints excluded: chain d residue 531 GLU Chi-restraints excluded: chain d residue 533 ASP Chi-restraints excluded: chain d residue 536 ASP Chi-restraints excluded: chain d residue 549 ARG Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 121 ARG Chi-restraints excluded: chain e residue 129 THR Chi-restraints excluded: chain e residue 146 ASP Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 180 MET Chi-restraints excluded: chain e residue 340 GLN Chi-restraints excluded: chain e residue 349 LEU Chi-restraints excluded: chain e residue 363 LEU Chi-restraints excluded: chain e residue 365 ASP Chi-restraints excluded: chain e residue 381 THR Chi-restraints excluded: chain e residue 383 MET Chi-restraints excluded: chain e residue 404 LEU Chi-restraints excluded: chain e residue 430 SER Chi-restraints excluded: chain e residue 433 CYS Chi-restraints excluded: chain e residue 455 VAL Chi-restraints excluded: chain e residue 503 GLU Chi-restraints excluded: chain f residue 30 GLN Chi-restraints excluded: chain f residue 77 VAL Chi-restraints excluded: chain f residue 134 GLU Chi-restraints excluded: chain f residue 135 VAL Chi-restraints excluded: chain f residue 146 GLU Chi-restraints excluded: chain f residue 151 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 162 optimal weight: 3.9990 chunk 435 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 283 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 483 optimal weight: 5.9990 chunk 401 optimal weight: 3.9990 chunk 223 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 55 GLN B 145 GLN D 15 ASN D 55 GLN E 145 GLN a 55 GLN b 145 GLN d 15 ASN d 55 GLN e 145 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.0721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 40612 Z= 0.207 Angle : 0.545 6.532 54892 Z= 0.285 Chirality : 0.042 0.150 6164 Planarity : 0.004 0.052 6992 Dihedral : 7.671 167.912 5665 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.50 % Allowed : 21.78 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.12), residues: 5044 helix: 0.92 (0.11), residues: 2352 sheet: -0.30 (0.21), residues: 544 loop : -0.56 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP b 344 HIS 0.005 0.001 HIS a 128 PHE 0.012 0.001 PHE b 96 TYR 0.017 0.002 TYR A 459 ARG 0.002 0.000 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10088 Ramachandran restraints generated. 5044 Oldfield, 0 Emsley, 5044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10088 Ramachandran restraints generated. 5044 Oldfield, 0 Emsley, 5044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 4268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 626 time to evaluate : 5.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7256 (ttm170) REVERT: A 531 GLU cc_start: 0.6202 (OUTLIER) cc_final: 0.5938 (tp30) REVERT: A 549 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7428 (ppt170) REVERT: B 121 ARG cc_start: 0.4344 (OUTLIER) cc_final: 0.4045 (ttp80) REVERT: B 363 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6136 (tp) REVERT: D 509 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7156 (ttm170) REVERT: D 531 GLU cc_start: 0.6197 (OUTLIER) cc_final: 0.5935 (tp30) REVERT: D 549 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7427 (ppt170) REVERT: E 121 ARG cc_start: 0.4332 (OUTLIER) cc_final: 0.4038 (ttp80) REVERT: E 363 LEU cc_start: 0.6611 (OUTLIER) cc_final: 0.6139 (tp) REVERT: a 509 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7365 (ttm170) REVERT: a 531 GLU cc_start: 0.6205 (OUTLIER) cc_final: 0.5941 (tp30) REVERT: a 549 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7429 (ppt170) REVERT: b 121 ARG cc_start: 0.4334 (OUTLIER) cc_final: 0.4038 (ttp80) REVERT: b 363 LEU cc_start: 0.6615 (OUTLIER) cc_final: 0.6143 (tp) REVERT: d 509 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7366 (ttm170) REVERT: d 531 GLU cc_start: 0.6191 (OUTLIER) cc_final: 0.5931 (tp30) REVERT: d 549 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7427 (ppt170) REVERT: e 121 ARG cc_start: 0.4342 (OUTLIER) cc_final: 0.4040 (ttp80) REVERT: e 363 LEU cc_start: 0.6615 (OUTLIER) cc_final: 0.6143 (tp) outliers start: 146 outliers final: 93 residues processed: 719 average time/residue: 3.1636 time to fit residues: 2735.7129 Evaluate side-chains 733 residues out of total 4268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 620 time to evaluate : 5.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 549 ARG Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 509 ARG Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 533 ASP Chi-restraints excluded: chain D residue 549 ARG Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 430 SER Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 503 GLU Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 30 GLN Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain a residue 26 VAL Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 155 GLU Chi-restraints excluded: chain a residue 238 ILE Chi-restraints excluded: chain a residue 440 ILE Chi-restraints excluded: chain a residue 509 ARG Chi-restraints excluded: chain a residue 531 GLU Chi-restraints excluded: chain a residue 533 ASP Chi-restraints excluded: chain a residue 549 ARG Chi-restraints excluded: chain b residue 34 THR Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain b residue 121 ARG Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 172 SER Chi-restraints excluded: chain b residue 180 MET Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 363 LEU Chi-restraints excluded: chain b residue 365 ASP Chi-restraints excluded: chain b residue 381 THR Chi-restraints excluded: chain b residue 430 SER Chi-restraints excluded: chain b residue 433 CYS Chi-restraints excluded: chain b residue 455 VAL Chi-restraints excluded: chain b residue 503 GLU Chi-restraints excluded: chain c residue 18 LYS Chi-restraints excluded: chain c residue 30 GLN Chi-restraints excluded: chain c residue 77 VAL Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 135 VAL Chi-restraints excluded: chain c residue 151 ILE Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 52 ILE Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 238 ILE Chi-restraints excluded: chain d residue 440 ILE Chi-restraints excluded: chain d residue 509 ARG Chi-restraints excluded: chain d residue 531 GLU Chi-restraints excluded: chain d residue 533 ASP Chi-restraints excluded: chain d residue 549 ARG Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 121 ARG Chi-restraints excluded: chain e residue 129 THR Chi-restraints excluded: chain e residue 146 ASP Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 180 MET Chi-restraints excluded: chain e residue 349 LEU Chi-restraints excluded: chain e residue 363 LEU Chi-restraints excluded: chain e residue 365 ASP Chi-restraints excluded: chain e residue 381 THR Chi-restraints excluded: chain e residue 430 SER Chi-restraints excluded: chain e residue 433 CYS Chi-restraints excluded: chain e residue 455 VAL Chi-restraints excluded: chain e residue 503 GLU Chi-restraints excluded: chain f residue 18 LYS Chi-restraints excluded: chain f residue 30 GLN Chi-restraints excluded: chain f residue 77 VAL Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 135 VAL Chi-restraints excluded: chain f residue 151 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 466 optimal weight: 0.0670 chunk 54 optimal weight: 6.9990 chunk 275 optimal weight: 2.9990 chunk 353 optimal weight: 3.9990 chunk 273 optimal weight: 3.9990 chunk 407 optimal weight: 4.9990 chunk 270 optimal weight: 2.9990 chunk 481 optimal weight: 4.9990 chunk 301 optimal weight: 6.9990 chunk 293 optimal weight: 10.0000 chunk 222 optimal weight: 8.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 55 GLN B 145 GLN D 15 ASN D 55 GLN E 145 GLN a 55 GLN b 145 GLN d 15 ASN d 55 GLN e 145 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.0742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 40612 Z= 0.248 Angle : 0.575 6.313 54892 Z= 0.302 Chirality : 0.043 0.152 6164 Planarity : 0.005 0.052 6992 Dihedral : 7.704 167.599 5661 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.29 % Allowed : 22.29 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.12), residues: 5044 helix: 0.86 (0.11), residues: 2352 sheet: -0.33 (0.21), residues: 544 loop : -0.58 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP e 344 HIS 0.005 0.001 HIS d 128 PHE 0.014 0.002 PHE d 408 TYR 0.020 0.002 TYR D 459 ARG 0.004 0.000 ARG D 120 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10088 Ramachandran restraints generated. 5044 Oldfield, 0 Emsley, 5044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10088 Ramachandran restraints generated. 5044 Oldfield, 0 Emsley, 5044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 4268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 634 time to evaluate : 5.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7171 (ttm170) REVERT: A 531 GLU cc_start: 0.6270 (OUTLIER) cc_final: 0.6009 (tp30) REVERT: A 549 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7348 (ppt170) REVERT: B 50 GLU cc_start: 0.4907 (OUTLIER) cc_final: 0.4186 (tt0) REVERT: B 121 ARG cc_start: 0.4348 (OUTLIER) cc_final: 0.4052 (ttp80) REVERT: B 363 LEU cc_start: 0.6638 (OUTLIER) cc_final: 0.6145 (tp) REVERT: D 531 GLU cc_start: 0.6287 (OUTLIER) cc_final: 0.6025 (tp30) REVERT: D 549 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7344 (ppt170) REVERT: E 50 GLU cc_start: 0.4870 (OUTLIER) cc_final: 0.4158 (tt0) REVERT: E 121 ARG cc_start: 0.4333 (OUTLIER) cc_final: 0.4036 (ttp80) REVERT: E 363 LEU cc_start: 0.6646 (OUTLIER) cc_final: 0.6145 (tp) REVERT: F 98 GLU cc_start: 0.5810 (tm-30) cc_final: 0.5560 (tm-30) REVERT: a 509 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7336 (ttm170) REVERT: a 531 GLU cc_start: 0.6273 (OUTLIER) cc_final: 0.6012 (tp30) REVERT: a 549 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7347 (ppt170) REVERT: b 50 GLU cc_start: 0.4909 (OUTLIER) cc_final: 0.4188 (tt0) REVERT: b 121 ARG cc_start: 0.4331 (OUTLIER) cc_final: 0.4036 (ttp80) REVERT: b 363 LEU cc_start: 0.6648 (OUTLIER) cc_final: 0.6146 (tp) REVERT: c 18 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.6790 (tttt) REVERT: d 509 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7337 (ttm170) REVERT: d 531 GLU cc_start: 0.6282 (OUTLIER) cc_final: 0.6025 (tp30) REVERT: d 549 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7346 (ppt170) REVERT: e 50 GLU cc_start: 0.4912 (OUTLIER) cc_final: 0.4192 (tt0) REVERT: e 121 ARG cc_start: 0.4345 (OUTLIER) cc_final: 0.4046 (ttp80) REVERT: e 363 LEU cc_start: 0.6648 (OUTLIER) cc_final: 0.6146 (tp) outliers start: 137 outliers final: 88 residues processed: 723 average time/residue: 3.1935 time to fit residues: 2775.3095 Evaluate side-chains 735 residues out of total 4268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 623 time to evaluate : 5.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 549 ARG Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 509 ARG Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 533 ASP Chi-restraints excluded: chain D residue 549 ARG Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 503 GLU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain a residue 26 VAL Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 155 GLU Chi-restraints excluded: chain a residue 238 ILE Chi-restraints excluded: chain a residue 440 ILE Chi-restraints excluded: chain a residue 509 ARG Chi-restraints excluded: chain a residue 531 GLU Chi-restraints excluded: chain a residue 533 ASP Chi-restraints excluded: chain a residue 549 ARG Chi-restraints excluded: chain b residue 34 THR Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain b residue 121 ARG Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 138 ASP Chi-restraints excluded: chain b residue 172 SER Chi-restraints excluded: chain b residue 180 MET Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 363 LEU Chi-restraints excluded: chain b residue 365 ASP Chi-restraints excluded: chain b residue 381 THR Chi-restraints excluded: chain b residue 404 LEU Chi-restraints excluded: chain b residue 433 CYS Chi-restraints excluded: chain b residue 455 VAL Chi-restraints excluded: chain b residue 503 GLU Chi-restraints excluded: chain c residue 18 LYS Chi-restraints excluded: chain c residue 77 VAL Chi-restraints excluded: chain c residue 134 GLU Chi-restraints excluded: chain c residue 135 VAL Chi-restraints excluded: chain c residue 151 ILE Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 52 ILE Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 238 ILE Chi-restraints excluded: chain d residue 440 ILE Chi-restraints excluded: chain d residue 509 ARG Chi-restraints excluded: chain d residue 531 GLU Chi-restraints excluded: chain d residue 533 ASP Chi-restraints excluded: chain d residue 549 ARG Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 50 GLU Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 121 ARG Chi-restraints excluded: chain e residue 129 THR Chi-restraints excluded: chain e residue 138 ASP Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 180 MET Chi-restraints excluded: chain e residue 349 LEU Chi-restraints excluded: chain e residue 363 LEU Chi-restraints excluded: chain e residue 365 ASP Chi-restraints excluded: chain e residue 381 THR Chi-restraints excluded: chain e residue 404 LEU Chi-restraints excluded: chain e residue 433 CYS Chi-restraints excluded: chain e residue 455 VAL Chi-restraints excluded: chain e residue 503 GLU Chi-restraints excluded: chain f residue 77 VAL Chi-restraints excluded: chain f residue 135 VAL Chi-restraints excluded: chain f residue 151 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 298 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 287 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 306 optimal weight: 9.9990 chunk 328 optimal weight: 5.9990 chunk 238 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 378 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 55 GLN B 145 GLN D 15 ASN D 55 GLN E 145 GLN a 55 GLN b 145 GLN d 15 ASN d 55 GLN e 145 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.0830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 40612 Z= 0.379 Angle : 0.669 7.220 54892 Z= 0.357 Chirality : 0.047 0.166 6164 Planarity : 0.006 0.060 6992 Dihedral : 7.891 167.854 5657 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.71 % Allowed : 21.99 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.12), residues: 5044 helix: 0.53 (0.10), residues: 2356 sheet: -0.37 (0.21), residues: 540 loop : -0.69 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 344 HIS 0.005 0.002 HIS b 244 PHE 0.018 0.002 PHE a 408 TYR 0.025 0.003 TYR A 459 ARG 0.007 0.001 ARG D 549 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10088 Ramachandran restraints generated. 5044 Oldfield, 0 Emsley, 5044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10088 Ramachandran restraints generated. 5044 Oldfield, 0 Emsley, 5044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 4268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 617 time to evaluate : 5.033 Fit side-chains REVERT: A 509 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7247 (ttm170) REVERT: A 531 GLU cc_start: 0.6242 (OUTLIER) cc_final: 0.6028 (tp30) REVERT: A 549 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7358 (ppt170) REVERT: B 50 GLU cc_start: 0.4894 (OUTLIER) cc_final: 0.4165 (tt0) REVERT: B 121 ARG cc_start: 0.4337 (OUTLIER) cc_final: 0.4035 (ttp80) REVERT: B 363 LEU cc_start: 0.6658 (OUTLIER) cc_final: 0.6177 (tp) REVERT: D 509 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7252 (ttm170) REVERT: D 531 GLU cc_start: 0.6249 (OUTLIER) cc_final: 0.6034 (tp30) REVERT: D 549 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7356 (ppt170) REVERT: E 50 GLU cc_start: 0.4890 (OUTLIER) cc_final: 0.4161 (tt0) REVERT: E 121 ARG cc_start: 0.4338 (OUTLIER) cc_final: 0.4041 (ttp80) REVERT: E 363 LEU cc_start: 0.6646 (OUTLIER) cc_final: 0.6155 (tp) REVERT: a 509 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7332 (ttm170) REVERT: a 531 GLU cc_start: 0.6245 (OUTLIER) cc_final: 0.6033 (tp30) REVERT: a 549 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7358 (ppt170) REVERT: b 50 GLU cc_start: 0.4896 (OUTLIER) cc_final: 0.4167 (tt0) REVERT: b 121 ARG cc_start: 0.4334 (OUTLIER) cc_final: 0.4038 (ttp80) REVERT: b 363 LEU cc_start: 0.6648 (OUTLIER) cc_final: 0.6156 (tp) REVERT: d 509 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7333 (ttm170) REVERT: d 531 GLU cc_start: 0.6244 (OUTLIER) cc_final: 0.6024 (tp30) REVERT: d 549 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7358 (ppt170) REVERT: e 50 GLU cc_start: 0.4896 (OUTLIER) cc_final: 0.4178 (tt0) REVERT: e 121 ARG cc_start: 0.4334 (OUTLIER) cc_final: 0.4030 (ttp80) REVERT: e 363 LEU cc_start: 0.6623 (OUTLIER) cc_final: 0.6136 (tp) outliers start: 155 outliers final: 112 residues processed: 715 average time/residue: 3.1592 time to fit residues: 2721.1783 Evaluate side-chains 748 residues out of total 4268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 612 time to evaluate : 5.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASN Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 549 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain D residue 15 ASN Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 509 ARG Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 533 ASP Chi-restraints excluded: chain D residue 549 ARG Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 503 GLU Chi-restraints excluded: chain F residue 30 GLN Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain a residue 26 VAL Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 155 GLU Chi-restraints excluded: chain a residue 238 ILE Chi-restraints excluded: chain a residue 286 GLU Chi-restraints excluded: chain a residue 401 SER Chi-restraints excluded: chain a residue 440 ILE Chi-restraints excluded: chain a residue 476 ILE Chi-restraints excluded: chain a residue 509 ARG Chi-restraints excluded: chain a residue 531 GLU Chi-restraints excluded: chain a residue 533 ASP Chi-restraints excluded: chain a residue 549 ARG Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 34 THR Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain b residue 121 ARG Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 140 THR Chi-restraints excluded: chain b residue 172 SER Chi-restraints excluded: chain b residue 180 MET Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 363 LEU Chi-restraints excluded: chain b residue 365 ASP Chi-restraints excluded: chain b residue 381 THR Chi-restraints excluded: chain b residue 404 LEU Chi-restraints excluded: chain b residue 433 CYS Chi-restraints excluded: chain b residue 455 VAL Chi-restraints excluded: chain b residue 503 GLU Chi-restraints excluded: chain c residue 30 GLN Chi-restraints excluded: chain c residue 77 VAL Chi-restraints excluded: chain c residue 134 GLU Chi-restraints excluded: chain c residue 135 VAL Chi-restraints excluded: chain c residue 151 ILE Chi-restraints excluded: chain d residue 15 ASN Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 52 ILE Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 238 ILE Chi-restraints excluded: chain d residue 286 GLU Chi-restraints excluded: chain d residue 401 SER Chi-restraints excluded: chain d residue 440 ILE Chi-restraints excluded: chain d residue 476 ILE Chi-restraints excluded: chain d residue 509 ARG Chi-restraints excluded: chain d residue 531 GLU Chi-restraints excluded: chain d residue 533 ASP Chi-restraints excluded: chain d residue 549 ARG Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 50 GLU Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 121 ARG Chi-restraints excluded: chain e residue 129 THR Chi-restraints excluded: chain e residue 138 ASP Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 180 MET Chi-restraints excluded: chain e residue 349 LEU Chi-restraints excluded: chain e residue 363 LEU Chi-restraints excluded: chain e residue 365 ASP Chi-restraints excluded: chain e residue 381 THR Chi-restraints excluded: chain e residue 383 MET Chi-restraints excluded: chain e residue 404 LEU Chi-restraints excluded: chain e residue 433 CYS Chi-restraints excluded: chain e residue 455 VAL Chi-restraints excluded: chain e residue 503 GLU Chi-restraints excluded: chain f residue 30 GLN Chi-restraints excluded: chain f residue 77 VAL Chi-restraints excluded: chain f residue 135 VAL Chi-restraints excluded: chain f residue 146 GLU Chi-restraints excluded: chain f residue 151 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 438 optimal weight: 10.0000 chunk 461 optimal weight: 1.9990 chunk 421 optimal weight: 0.9990 chunk 449 optimal weight: 2.9990 chunk 270 optimal weight: 4.9990 chunk 195 optimal weight: 9.9990 chunk 352 optimal weight: 0.9990 chunk 137 optimal weight: 8.9990 chunk 405 optimal weight: 2.9990 chunk 424 optimal weight: 0.7980 chunk 447 optimal weight: 8.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 55 GLN B 145 GLN D 15 ASN D 55 GLN E 145 GLN a 55 GLN b 145 GLN d 15 ASN d 55 GLN e 145 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 40612 Z= 0.187 Angle : 0.552 7.629 54892 Z= 0.287 Chirality : 0.041 0.153 6164 Planarity : 0.004 0.052 6992 Dihedral : 7.612 168.206 5657 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.68 % Allowed : 23.13 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.12), residues: 5044 helix: 0.89 (0.11), residues: 2352 sheet: -0.33 (0.21), residues: 540 loop : -0.59 (0.14), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP b 344 HIS 0.005 0.001 HIS D 128 PHE 0.012 0.001 PHE b 96 TYR 0.017 0.002 TYR F 15 ARG 0.004 0.000 ARG D 120 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10088 Ramachandran restraints generated. 5044 Oldfield, 0 Emsley, 5044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10088 Ramachandran restraints generated. 5044 Oldfield, 0 Emsley, 5044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 4268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 624 time to evaluate : 5.047 Fit side-chains revert: symmetry clash REVERT: A 509 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7167 (ttm170) REVERT: A 531 GLU cc_start: 0.6206 (OUTLIER) cc_final: 0.5932 (tp30) REVERT: A 549 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7454 (ppt170) REVERT: B 1 MET cc_start: 0.1945 (ptt) cc_final: 0.1329 (ptp) REVERT: B 121 ARG cc_start: 0.4340 (OUTLIER) cc_final: 0.4044 (ttp80) REVERT: B 363 LEU cc_start: 0.6578 (OUTLIER) cc_final: 0.6063 (tp) REVERT: D 531 GLU cc_start: 0.6212 (OUTLIER) cc_final: 0.5931 (tp30) REVERT: D 549 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7453 (ppt170) REVERT: E 1 MET cc_start: 0.1947 (ptt) cc_final: 0.1328 (ptp) REVERT: E 121 ARG cc_start: 0.4329 (OUTLIER) cc_final: 0.4036 (ttp80) REVERT: E 363 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.6089 (tp) REVERT: a 509 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7327 (ttm170) REVERT: a 531 GLU cc_start: 0.6210 (OUTLIER) cc_final: 0.5934 (tp30) REVERT: a 549 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7452 (ppt170) REVERT: b 1 MET cc_start: 0.2001 (ptt) cc_final: 0.1364 (ptp) REVERT: b 121 ARG cc_start: 0.4328 (OUTLIER) cc_final: 0.4036 (ttp80) REVERT: b 363 LEU cc_start: 0.6609 (OUTLIER) cc_final: 0.6094 (tp) REVERT: d 509 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7311 (ttm170) REVERT: d 531 GLU cc_start: 0.6205 (OUTLIER) cc_final: 0.5975 (tp30) REVERT: d 549 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7453 (ppt170) REVERT: e 1 MET cc_start: 0.1998 (ptt) cc_final: 0.1363 (ptp) REVERT: e 121 ARG cc_start: 0.4336 (OUTLIER) cc_final: 0.4039 (ttp80) REVERT: e 363 LEU cc_start: 0.6607 (OUTLIER) cc_final: 0.6090 (tp) outliers start: 111 outliers final: 80 residues processed: 697 average time/residue: 3.2548 time to fit residues: 2729.9409 Evaluate side-chains 708 residues out of total 4268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 609 time to evaluate : 4.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 549 ARG Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 509 ARG Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 549 ARG Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 503 GLU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain a residue 26 VAL Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 155 GLU Chi-restraints excluded: chain a residue 238 ILE Chi-restraints excluded: chain a residue 440 ILE Chi-restraints excluded: chain a residue 509 ARG Chi-restraints excluded: chain a residue 531 GLU Chi-restraints excluded: chain a residue 549 ARG Chi-restraints excluded: chain b residue 34 THR Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain b residue 121 ARG Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 138 ASP Chi-restraints excluded: chain b residue 172 SER Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 363 LEU Chi-restraints excluded: chain b residue 365 ASP Chi-restraints excluded: chain b residue 381 THR Chi-restraints excluded: chain b residue 404 LEU Chi-restraints excluded: chain b residue 433 CYS Chi-restraints excluded: chain b residue 455 VAL Chi-restraints excluded: chain b residue 503 GLU Chi-restraints excluded: chain c residue 77 VAL Chi-restraints excluded: chain c residue 135 VAL Chi-restraints excluded: chain c residue 151 ILE Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 52 ILE Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 238 ILE Chi-restraints excluded: chain d residue 440 ILE Chi-restraints excluded: chain d residue 509 ARG Chi-restraints excluded: chain d residue 531 GLU Chi-restraints excluded: chain d residue 533 ASP Chi-restraints excluded: chain d residue 549 ARG Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 121 ARG Chi-restraints excluded: chain e residue 129 THR Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 349 LEU Chi-restraints excluded: chain e residue 363 LEU Chi-restraints excluded: chain e residue 365 ASP Chi-restraints excluded: chain e residue 381 THR Chi-restraints excluded: chain e residue 404 LEU Chi-restraints excluded: chain e residue 433 CYS Chi-restraints excluded: chain e residue 455 VAL Chi-restraints excluded: chain e residue 503 GLU Chi-restraints excluded: chain f residue 77 VAL Chi-restraints excluded: chain f residue 135 VAL Chi-restraints excluded: chain f residue 146 GLU Chi-restraints excluded: chain f residue 151 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 294 optimal weight: 5.9990 chunk 474 optimal weight: 10.0000 chunk 289 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 330 optimal weight: 4.9990 chunk 498 optimal weight: 10.0000 chunk 458 optimal weight: 0.9990 chunk 396 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 306 optimal weight: 10.0000 chunk 243 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 55 GLN B 145 GLN D 15 ASN D 55 GLN E 145 GLN a 55 GLN b 145 GLN d 15 ASN d 55 GLN e 145 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.0806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 40612 Z= 0.211 Angle : 0.556 7.546 54892 Z= 0.290 Chirality : 0.042 0.151 6164 Planarity : 0.004 0.052 6992 Dihedral : 7.543 167.672 5657 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.59 % Allowed : 23.30 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.12), residues: 5044 helix: 1.00 (0.11), residues: 2352 sheet: -0.33 (0.21), residues: 540 loop : -0.55 (0.14), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 344 HIS 0.005 0.001 HIS d 128 PHE 0.012 0.001 PHE A 408 TYR 0.018 0.002 TYR D 459 ARG 0.005 0.000 ARG d 540 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10088 Ramachandran restraints generated. 5044 Oldfield, 0 Emsley, 5044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10088 Ramachandran restraints generated. 5044 Oldfield, 0 Emsley, 5044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 4268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 623 time to evaluate : 5.106 Fit side-chains revert: symmetry clash REVERT: A 509 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7150 (ttm170) REVERT: A 531 GLU cc_start: 0.6250 (OUTLIER) cc_final: 0.6008 (tp30) REVERT: A 549 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7478 (ppt170) REVERT: B 1 MET cc_start: 0.1961 (ptt) cc_final: 0.1336 (ptp) REVERT: B 121 ARG cc_start: 0.4406 (OUTLIER) cc_final: 0.4113 (ttp80) REVERT: B 363 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.6054 (tp) REVERT: D 531 GLU cc_start: 0.6251 (OUTLIER) cc_final: 0.6005 (tp30) REVERT: D 549 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7476 (ppt170) REVERT: E 1 MET cc_start: 0.1961 (ptt) cc_final: 0.1336 (ptp) REVERT: E 121 ARG cc_start: 0.4398 (OUTLIER) cc_final: 0.4102 (ttp80) REVERT: E 363 LEU cc_start: 0.6602 (OUTLIER) cc_final: 0.6080 (tp) REVERT: a 509 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7311 (ttm170) REVERT: a 531 GLU cc_start: 0.6253 (OUTLIER) cc_final: 0.6010 (tp30) REVERT: a 549 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7477 (ppt170) REVERT: b 1 MET cc_start: 0.1953 (ptt) cc_final: 0.1307 (ptp) REVERT: b 121 ARG cc_start: 0.4395 (OUTLIER) cc_final: 0.4103 (ttp80) REVERT: b 363 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.6083 (tp) REVERT: d 509 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7301 (ttm170) REVERT: d 531 GLU cc_start: 0.6247 (OUTLIER) cc_final: 0.6002 (tp30) REVERT: d 549 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7475 (ppt170) REVERT: e 1 MET cc_start: 0.1950 (ptt) cc_final: 0.1305 (ptp) REVERT: e 121 ARG cc_start: 0.4404 (OUTLIER) cc_final: 0.4108 (ttp80) REVERT: e 363 LEU cc_start: 0.6607 (OUTLIER) cc_final: 0.6083 (tp) outliers start: 107 outliers final: 73 residues processed: 689 average time/residue: 3.2966 time to fit residues: 2752.3687 Evaluate side-chains 707 residues out of total 4268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 615 time to evaluate : 4.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 549 ARG Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 509 ARG Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 549 ARG Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 503 GLU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain a residue 26 VAL Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 155 GLU Chi-restraints excluded: chain a residue 238 ILE Chi-restraints excluded: chain a residue 286 GLU Chi-restraints excluded: chain a residue 509 ARG Chi-restraints excluded: chain a residue 531 GLU Chi-restraints excluded: chain a residue 549 ARG Chi-restraints excluded: chain b residue 34 THR Chi-restraints excluded: chain b residue 121 ARG Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 172 SER Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 363 LEU Chi-restraints excluded: chain b residue 365 ASP Chi-restraints excluded: chain b residue 381 THR Chi-restraints excluded: chain b residue 404 LEU Chi-restraints excluded: chain b residue 433 CYS Chi-restraints excluded: chain b residue 455 VAL Chi-restraints excluded: chain b residue 503 GLU Chi-restraints excluded: chain c residue 77 VAL Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 135 VAL Chi-restraints excluded: chain c residue 151 ILE Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 52 ILE Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 238 ILE Chi-restraints excluded: chain d residue 509 ARG Chi-restraints excluded: chain d residue 531 GLU Chi-restraints excluded: chain d residue 549 ARG Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 121 ARG Chi-restraints excluded: chain e residue 129 THR Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 349 LEU Chi-restraints excluded: chain e residue 363 LEU Chi-restraints excluded: chain e residue 365 ASP Chi-restraints excluded: chain e residue 381 THR Chi-restraints excluded: chain e residue 404 LEU Chi-restraints excluded: chain e residue 433 CYS Chi-restraints excluded: chain e residue 455 VAL Chi-restraints excluded: chain e residue 503 GLU Chi-restraints excluded: chain f residue 77 VAL Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 135 VAL Chi-restraints excluded: chain f residue 151 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 315 optimal weight: 9.9990 chunk 422 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 365 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 397 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 407 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 73 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 55 GLN B 145 GLN D 55 GLN E 145 GLN a 55 GLN b 145 GLN d 55 GLN e 145 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.178888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.136227 restraints weight = 112611.700| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.25 r_work: 0.3027 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 40612 Z= 0.326 Angle : 0.635 7.449 54892 Z= 0.336 Chirality : 0.045 0.155 6164 Planarity : 0.005 0.054 6992 Dihedral : 7.735 167.728 5649 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.71 % Allowed : 23.34 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.12), residues: 5044 helix: 0.69 (0.10), residues: 2352 sheet: -0.38 (0.21), residues: 540 loop : -0.65 (0.14), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP E 344 HIS 0.004 0.001 HIS E 555 PHE 0.017 0.002 PHE a 408 TYR 0.024 0.002 TYR A 459 ARG 0.005 0.001 ARG A 549 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 35935.76 seconds wall clock time: 615 minutes 48.22 seconds (36948.22 seconds total)