Starting phenix.real_space_refine on Fri Dec 8 17:19:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oh5_16878/12_2023/8oh5_16878_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oh5_16878/12_2023/8oh5_16878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oh5_16878/12_2023/8oh5_16878.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oh5_16878/12_2023/8oh5_16878.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oh5_16878/12_2023/8oh5_16878_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oh5_16878/12_2023/8oh5_16878_neut_updated.pdb" } resolution = 3.0 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= 0.001 sd= 0.054 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: 7 Type Number sf(0) Gaussians Fe 168 7.16 5 Zn 4 6.06 5 P 32 5.49 5 S 616 5.16 5 C 36584 2.51 5 N 9956 2.21 5 O 11264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 183": "OD1" <-> "OD2" Residue "B GLU 184": "OE1" <-> "OE2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "B PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 421": "OD1" <-> "OD2" Residue "B ASP 484": "OD1" <-> "OD2" Residue "C GLU 39": "OE1" <-> "OE2" Residue "C ASP 77": "OD1" <-> "OD2" Residue "C ASP 177": "OD1" <-> "OD2" Residue "C GLU 248": "OE1" <-> "OE2" Residue "C ASP 272": "OD1" <-> "OD2" Residue "C TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 301": "OE1" <-> "OE2" Residue "C GLU 312": "OE1" <-> "OE2" Residue "C GLU 347": "OE1" <-> "OE2" Residue "C GLU 359": "OE1" <-> "OE2" Residue "C GLU 424": "OE1" <-> "OE2" Residue "C PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 535": "OD1" <-> "OD2" Residue "C GLU 607": "OE1" <-> "OE2" Residue "C ASP 624": "OD1" <-> "OD2" Residue "C PHE 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 708": "OD1" <-> "OD2" Residue "C ASP 756": "OD1" <-> "OD2" Residue "C TYR 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 814": "OD1" <-> "OD2" Residue "C GLU 897": "OE1" <-> "OE2" Residue "E ASP 183": "OD1" <-> "OD2" Residue "E GLU 184": "OE1" <-> "OE2" Residue "E ASP 186": "OD1" <-> "OD2" Residue "E PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 421": "OD1" <-> "OD2" Residue "E ASP 484": "OD1" <-> "OD2" Residue "F GLU 39": "OE1" <-> "OE2" Residue "F ASP 77": "OD1" <-> "OD2" Residue "F ASP 177": "OD1" <-> "OD2" Residue "F GLU 248": "OE1" <-> "OE2" Residue "F ASP 272": "OD1" <-> "OD2" Residue "F TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 301": "OE1" <-> "OE2" Residue "F GLU 312": "OE1" <-> "OE2" Residue "F GLU 347": "OE1" <-> "OE2" Residue "F GLU 359": "OE1" <-> "OE2" Residue "F GLU 424": "OE1" <-> "OE2" Residue "F PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 535": "OD1" <-> "OD2" Residue "F GLU 607": "OE1" <-> "OE2" Residue "F ASP 624": "OD1" <-> "OD2" Residue "F PHE 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 708": "OD1" <-> "OD2" Residue "F ASP 756": "OD1" <-> "OD2" Residue "F TYR 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 814": "OD1" <-> "OD2" Residue "F GLU 897": "OE1" <-> "OE2" Residue "H ASP 183": "OD1" <-> "OD2" Residue "H GLU 184": "OE1" <-> "OE2" Residue "H ASP 186": "OD1" <-> "OD2" Residue "H PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 421": "OD1" <-> "OD2" Residue "H ASP 484": "OD1" <-> "OD2" Residue "I GLU 39": "OE1" <-> "OE2" Residue "I ASP 77": "OD1" <-> "OD2" Residue "I ASP 177": "OD1" <-> "OD2" Residue "I GLU 248": "OE1" <-> "OE2" Residue "I ASP 272": "OD1" <-> "OD2" Residue "I TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 301": "OE1" <-> "OE2" Residue "I GLU 312": "OE1" <-> "OE2" Residue "I GLU 347": "OE1" <-> "OE2" Residue "I GLU 359": "OE1" <-> "OE2" Residue "I GLU 424": "OE1" <-> "OE2" Residue "I PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 535": "OD1" <-> "OD2" Residue "I GLU 607": "OE1" <-> "OE2" Residue "I ASP 624": "OD1" <-> "OD2" Residue "I PHE 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 708": "OD1" <-> "OD2" Residue "I ASP 756": "OD1" <-> "OD2" Residue "I TYR 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 814": "OD1" <-> "OD2" Residue "I GLU 897": "OE1" <-> "OE2" Residue "K ASP 183": "OD1" <-> "OD2" Residue "K GLU 184": "OE1" <-> "OE2" Residue "K ASP 186": "OD1" <-> "OD2" Residue "K PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 421": "OD1" <-> "OD2" Residue "K ASP 484": "OD1" <-> "OD2" Residue "L GLU 39": "OE1" <-> "OE2" Residue "L ASP 77": "OD1" <-> "OD2" Residue "L ASP 177": "OD1" <-> "OD2" Residue "L GLU 248": "OE1" <-> "OE2" Residue "L ASP 272": "OD1" <-> "OD2" Residue "L TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 301": "OE1" <-> "OE2" Residue "L GLU 312": "OE1" <-> "OE2" Residue "L GLU 347": "OE1" <-> "OE2" Residue "L GLU 359": "OE1" <-> "OE2" Residue "L GLU 424": "OE1" <-> "OE2" Residue "L PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 535": "OD1" <-> "OD2" Residue "L GLU 607": "OE1" <-> "OE2" Residue "L ASP 624": "OD1" <-> "OD2" Residue "L PHE 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 708": "OD1" <-> "OD2" Residue "L ASP 756": "OD1" <-> "OD2" Residue "L TYR 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 814": "OD1" <-> "OD2" Residue "L GLU 897": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 58624 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1118 Classifications: {'peptide': 150} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 143} Chain: "B" Number of atoms: 4431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4431 Classifications: {'peptide': 584} Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 557} Chain: "C" Number of atoms: 8846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1172, 8846 Classifications: {'peptide': 1172} Link IDs: {'PTRANS': 45, 'TRANS': 1126} Chain: "D" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1118 Classifications: {'peptide': 150} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 143} Chain: "E" Number of atoms: 4431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4431 Classifications: {'peptide': 584} Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 557} Chain: "F" Number of atoms: 8846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1172, 8846 Classifications: {'peptide': 1172} Link IDs: {'PTRANS': 45, 'TRANS': 1126} Chain: "G" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1118 Classifications: {'peptide': 150} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 143} Chain: "H" Number of atoms: 4431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4431 Classifications: {'peptide': 584} Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 557} Chain: "I" Number of atoms: 8846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1172, 8846 Classifications: {'peptide': 1172} Link IDs: {'PTRANS': 45, 'TRANS': 1126} Chain: "J" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1118 Classifications: {'peptide': 150} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 143} Chain: "K" Number of atoms: 4431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4431 Classifications: {'peptide': 584} Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 557} Chain: "L" Number of atoms: 8846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1172, 8846 Classifications: {'peptide': 1172} Link IDs: {'PTRANS': 45, 'TRANS': 1126} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 104 Unusual residues: {' ZN': 1, 'FES': 1, 'FMN': 1, 'NAD': 1, 'SF4': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 153 Unusual residues: {'FAD': 1, 'FES': 1, 'NDP': 1, 'SF4': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 104 Unusual residues: {' ZN': 1, 'FES': 1, 'FMN': 1, 'NAD': 1, 'SF4': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "F" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 153 Unusual residues: {'FAD': 1, 'FES': 1, 'NDP': 1, 'SF4': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 104 Unusual residues: {' ZN': 1, 'FES': 1, 'FMN': 1, 'NAD': 1, 'SF4': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "I" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 153 Unusual residues: {'FAD': 1, 'FES': 1, 'NDP': 1, 'SF4': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "J" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 104 Unusual residues: {' ZN': 1, 'FES': 1, 'FMN': 1, 'NAD': 1, 'SF4': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "L" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 153 Unusual residues: {'FAD': 1, 'FES': 1, 'NDP': 1, 'SF4': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 597 SG CYS A 93 112.975 46.921 31.349 1.00 39.21 S ATOM 628 SG CYS A 98 116.496 46.312 30.951 1.00 41.52 S ATOM 878 SG CYS A 134 111.818 46.355 35.099 1.00 43.97 S ATOM 902 SG CYS A 138 114.558 43.822 35.695 1.00 49.73 S ATOM 4324 SG CYS B 425 129.027 58.984 37.596 1.00 29.89 S ATOM 5065 SG CYS B 518 132.252 59.148 35.692 1.00 48.32 S ATOM 5098 SG CYS B 523 129.209 61.416 34.520 1.00 45.50 S ATOM 1188 SG CYS B 10 113.394 34.912 31.946 1.00 51.88 S ATOM 1443 SG CYS B 45 113.499 35.148 35.804 1.00 56.34 S ATOM 1417 SG CYS B 41 112.581 31.765 36.740 1.00 49.38 S ATOM 1443 SG CYS B 45 113.499 35.148 35.804 1.00 56.34 S ATOM 5272 SG CYS B 546 135.622 58.223 16.210 1.00 60.92 S ATOM 5445 SG CYS B 569 131.913 57.050 19.864 1.00 58.45 S ATOM 5272 SG CYS B 546 135.622 58.223 16.210 1.00 60.92 S ATOM 5423 SG CYS B 566 136.387 61.012 19.428 1.00 55.38 S ATOM 5203 SG CYS B 536 147.334 50.900 18.882 1.00 66.49 S ATOM 5243 SG CYS B 542 141.329 51.748 18.372 1.00 54.81 S ATOM 4464 SG CYS B 442 100.378 63.751 43.714 1.00 0.81 S ATOM 4509 SG CYS B 448 107.050 64.244 44.907 1.00 7.74 S ATOM 4820 SG CYS B 488 102.969 60.224 47.885 1.00 23.54 S ATOM 4483 SG CYS B 445 103.673 67.142 48.022 1.00 0.00 S ATOM 10587 SG CYS C 666 93.918 82.684 42.149 1.00 0.00 S ATOM 10212 SG CYS C 613 97.559 77.844 39.310 1.00 3.97 S ATOM 10251 SG CYS C 619 91.549 76.940 40.162 1.00 0.62 S ATOM 10233 SG CYS C 616 94.935 77.743 45.382 1.00 0.00 S ATOM 9785 SG CYS C 562 99.463 102.842 32.545 1.00 0.00 S ATOM 6698 SG CYS C 155 105.648 104.556 30.498 1.00 1.61 S ATOM 9808 SG CYS C 565 103.697 98.611 31.981 1.00 0.00 S ATOM 6324 SG CYS C 104 104.689 103.234 36.407 1.00 0.00 S ATOM 9875 SG CYS C 573 99.768 87.593 45.476 1.00 0.00 S ATOM 6293 SG CYS C 100 104.864 91.103 43.324 1.00 0.00 S ATOM 9818 SG CYS C 567 99.429 90.656 39.939 1.00 0.00 S ATOM 6671 SG CYS C 151 108.068 109.321 36.497 1.00 0.00 S ATOM 6641 SG CYS C 147 110.853 114.173 39.592 1.00 8.11 S ATOM 6351 SG CYS C 108 108.906 108.581 42.495 1.00 0.00 S ATOM 10540 SG CYS C 659 80.653 80.744 39.257 1.00 0.00 S ATOM 10520 SG CYS C 656 82.601 80.221 33.417 1.00 9.48 S ATOM 10282 SG CYS C 623 83.681 75.365 37.934 1.00 0.00 S ATOM 10559 SG CYS C 662 86.644 81.128 38.398 1.00 0.00 S ATOM 10776 SG CYS C 692 72.292 90.688 43.140 1.00 0.00 S ATOM 11031 SG CYS C 725 73.846 85.406 39.927 1.00 3.86 S ATOM 10798 SG CYS C 695 68.407 86.006 41.235 1.00 13.95 S ATOM 10819 SG CYS C 699 72.962 85.841 46.536 1.00 0.00 S ATOM 5814 SG CYS C 36 96.270 73.957 51.017 1.00 7.15 S ATOM 5903 SG CYS C 47 99.312 75.785 51.943 1.00 0.00 S ATOM 5921 SG CYS C 50 98.109 73.977 57.047 1.00 0.00 S ATOM 6024 SG CYS C 64 95.002 72.438 55.914 1.00 0.00 S ATOM 14992 SG CYS D 93 48.529 214.891 31.372 1.00 39.21 S ATOM 15023 SG CYS D 98 45.008 215.501 30.974 1.00 41.52 S ATOM 15273 SG CYS D 134 49.686 215.456 35.122 1.00 43.97 S ATOM 15297 SG CYS D 138 46.947 217.989 35.719 1.00 49.73 S ATOM 18719 SG CYS E 425 32.476 202.828 37.616 1.00 29.89 S ATOM 19460 SG CYS E 518 29.250 202.666 35.713 1.00 48.32 S ATOM 19493 SG CYS E 523 32.293 200.398 34.540 1.00 45.50 S ATOM 15583 SG CYS E 10 48.112 226.900 31.973 1.00 51.88 S ATOM 15838 SG CYS E 45 48.007 226.663 35.831 1.00 56.34 S ATOM 15812 SG CYS E 41 48.926 230.045 36.768 1.00 49.38 S ATOM 15838 SG CYS E 45 48.007 226.663 35.831 1.00 56.34 S ATOM 19667 SG CYS E 546 25.879 203.597 16.231 1.00 60.92 S ATOM 19840 SG CYS E 569 29.588 204.769 19.885 1.00 58.45 S ATOM 19667 SG CYS E 546 25.879 203.597 16.231 1.00 60.92 S ATOM 19818 SG CYS E 566 25.114 200.808 19.448 1.00 55.38 S ATOM 19598 SG CYS E 536 14.168 210.921 18.907 1.00 66.49 S ATOM 19638 SG CYS E 542 20.173 210.073 18.396 1.00 54.81 S ATOM 18859 SG CYS E 442 61.124 198.055 43.730 1.00 0.81 S ATOM 18904 SG CYS E 448 54.452 197.563 44.924 1.00 7.74 S ATOM 19215 SG CYS E 488 58.534 201.581 47.903 1.00 23.54 S ATOM 18878 SG CYS E 445 57.829 194.663 48.037 1.00 0.00 S ATOM 24982 SG CYS F 666 67.581 179.121 42.158 1.00 0.00 S ATOM 24607 SG CYS F 613 63.941 183.963 39.321 1.00 3.97 S ATOM 24646 SG CYS F 619 69.951 184.866 40.173 1.00 0.62 S ATOM 24628 SG CYS F 616 66.565 184.062 45.393 1.00 0.00 S ATOM 24180 SG CYS F 562 62.032 158.967 32.548 1.00 0.00 S ATOM 21093 SG CYS F 155 55.847 157.255 30.502 1.00 1.61 S ATOM 24203 SG CYS F 565 57.799 163.199 31.986 1.00 0.00 S ATOM 20719 SG CYS F 104 56.806 158.575 36.411 1.00 0.00 S ATOM 24270 SG CYS F 573 61.731 174.212 45.484 1.00 0.00 S ATOM 20688 SG CYS F 100 56.634 170.704 43.332 1.00 0.00 S ATOM 24213 SG CYS F 567 62.069 171.151 39.946 1.00 0.00 S ATOM 21066 SG CYS F 151 53.427 152.489 36.499 1.00 0.00 S ATOM 21036 SG CYS F 147 50.641 147.636 39.593 1.00 8.11 S ATOM 20746 SG CYS F 108 52.589 153.227 42.498 1.00 0.00 S ATOM 24935 SG CYS F 659 80.846 181.060 39.266 1.00 0.00 S ATOM 24915 SG CYS F 656 78.898 181.585 33.426 1.00 9.48 S ATOM 24677 SG CYS F 623 77.819 186.440 37.945 1.00 0.00 S ATOM 24954 SG CYS F 662 74.855 180.677 38.407 1.00 0.00 S ATOM 25171 SG CYS F 692 89.206 171.114 43.145 1.00 0.00 S ATOM 25426 SG CYS F 725 87.653 176.397 39.934 1.00 3.86 S ATOM 25193 SG CYS F 695 93.092 175.796 41.241 1.00 13.95 S ATOM 25214 SG CYS F 699 88.537 175.960 46.542 1.00 0.00 S ATOM 20209 SG CYS F 36 65.231 187.846 51.029 1.00 7.15 S ATOM 20298 SG CYS F 47 62.189 186.018 51.955 1.00 0.00 S ATOM 20316 SG CYS F 50 63.393 187.824 57.060 1.00 0.00 S ATOM 20419 SG CYS F 64 66.500 189.363 55.927 1.00 0.00 S ATOM 29387 SG CYS G 93 112.968 214.887 109.731 1.00 39.21 S ATOM 29418 SG CYS G 98 116.489 215.497 110.129 1.00 41.52 S ATOM 29668 SG CYS G 134 111.811 215.452 105.981 1.00 43.97 S ATOM 29692 SG CYS G 138 114.550 217.985 105.384 1.00 49.73 S ATOM 33114 SG CYS H 425 129.021 202.825 103.486 1.00 29.89 S ATOM 33855 SG CYS H 518 132.246 202.662 105.389 1.00 48.32 S ATOM 33888 SG CYS H 523 129.204 200.394 106.563 1.00 45.50 S ATOM 29978 SG CYS H 10 113.386 226.896 109.131 1.00 51.88 S ATOM 30233 SG CYS H 45 113.490 226.659 105.273 1.00 56.34 S ATOM 30207 SG CYS H 41 112.572 230.042 104.336 1.00 49.38 S ATOM 30233 SG CYS H 45 113.490 226.659 105.273 1.00 56.34 S ATOM 34062 SG CYS H 546 135.619 203.593 124.871 1.00 60.92 S ATOM 34235 SG CYS H 569 131.909 204.764 121.217 1.00 58.45 S ATOM 34062 SG CYS H 546 135.619 203.593 124.871 1.00 60.92 S ATOM 34213 SG CYS H 566 136.384 200.803 121.653 1.00 55.38 S ATOM 33993 SG CYS H 536 147.330 210.917 122.195 1.00 66.49 S ATOM 34033 SG CYS H 542 141.325 210.068 122.706 1.00 54.81 S ATOM 33254 SG CYS H 442 100.372 198.052 97.373 1.00 0.81 S ATOM 33299 SG CYS H 448 107.044 197.560 96.179 1.00 7.74 S ATOM 33610 SG CYS H 488 102.962 201.578 93.201 1.00 23.54 S ATOM 33273 SG CYS H 445 103.667 194.660 93.066 1.00 0.00 S ATOM 39377 SG CYS I 666 93.915 179.119 98.945 1.00 0.00 S ATOM 39002 SG CYS I 613 97.555 183.960 101.782 1.00 3.97 S ATOM 39041 SG CYS I 619 91.545 184.863 100.930 1.00 0.62 S ATOM 39023 SG CYS I 616 94.931 184.059 95.710 1.00 0.00 S ATOM 38575 SG CYS I 562 99.464 158.964 108.554 1.00 0.00 S ATOM 35488 SG CYS I 155 105.649 157.252 110.601 1.00 1.61 S ATOM 38598 SG CYS I 565 103.697 163.196 109.116 1.00 0.00 S ATOM 35114 SG CYS I 104 104.689 158.572 104.691 1.00 0.00 S ATOM 38665 SG CYS I 573 99.765 174.209 95.618 1.00 0.00 S ATOM 35083 SG CYS I 100 104.862 170.701 97.771 1.00 0.00 S ATOM 38608 SG CYS I 567 99.427 171.148 101.156 1.00 0.00 S ATOM 35461 SG CYS I 151 108.069 152.485 104.603 1.00 0.00 S ATOM 35431 SG CYS I 147 110.854 147.633 101.509 1.00 8.11 S ATOM 35141 SG CYS I 108 108.906 153.223 98.604 1.00 0.00 S ATOM 39330 SG CYS I 659 80.650 181.058 101.838 1.00 0.00 S ATOM 39310 SG CYS I 656 82.599 181.583 107.677 1.00 9.48 S ATOM 39072 SG CYS I 623 83.677 186.437 103.159 1.00 0.00 S ATOM 39349 SG CYS I 662 86.641 180.675 102.696 1.00 0.00 S ATOM 39566 SG CYS I 692 72.290 171.111 97.959 1.00 0.00 S ATOM 39821 SG CYS I 725 73.843 176.395 101.170 1.00 3.86 S ATOM 39588 SG CYS I 695 68.404 175.793 99.863 1.00 13.95 S ATOM 39609 SG CYS I 699 72.959 175.957 94.561 1.00 0.00 S ATOM 34604 SG CYS I 36 96.264 187.843 90.074 1.00 7.15 S ATOM 34693 SG CYS I 47 99.307 186.015 89.148 1.00 0.00 S ATOM 34711 SG CYS I 50 98.103 187.822 84.043 1.00 0.00 S ATOM 34814 SG CYS I 64 94.996 189.361 85.176 1.00 0.00 S ATOM 43782 SG CYS J 93 48.531 46.910 109.730 1.00 39.21 S ATOM 43813 SG CYS J 98 45.010 46.300 110.127 1.00 41.52 S ATOM 44063 SG CYS J 134 49.688 46.346 105.980 1.00 43.97 S ATOM 44087 SG CYS J 138 46.949 43.812 105.383 1.00 49.73 S ATOM 47509 SG CYS K 425 32.477 58.972 103.485 1.00 29.89 S ATOM 48250 SG CYS K 518 29.252 59.135 105.389 1.00 48.32 S ATOM 48283 SG CYS K 523 32.295 61.403 106.562 1.00 45.50 S ATOM 44373 SG CYS K 10 48.114 34.901 109.129 1.00 51.88 S ATOM 44628 SG CYS K 45 48.010 35.138 105.271 1.00 56.34 S ATOM 44602 SG CYS K 41 48.928 31.756 104.334 1.00 49.38 S ATOM 44628 SG CYS K 45 48.010 35.138 105.271 1.00 56.34 S ATOM 48457 SG CYS K 546 25.881 58.203 124.870 1.00 60.92 S ATOM 48630 SG CYS K 569 29.590 57.032 121.216 1.00 58.45 S ATOM 48457 SG CYS K 546 25.881 58.203 124.870 1.00 60.92 S ATOM 48608 SG CYS K 566 25.115 60.993 121.653 1.00 55.38 S ATOM 48388 SG CYS K 536 14.170 50.878 122.195 1.00 66.49 S ATOM 48428 SG CYS K 542 20.175 51.727 122.706 1.00 54.81 S ATOM 47649 SG CYS K 442 61.126 63.747 97.371 1.00 0.81 S ATOM 47694 SG CYS K 448 54.454 64.239 96.178 1.00 7.74 S ATOM 48005 SG CYS K 488 58.536 60.220 93.199 1.00 23.54 S ATOM 47668 SG CYS K 445 57.831 67.138 93.064 1.00 0.00 S ATOM 53772 SG CYS L 666 67.582 82.680 98.943 1.00 0.00 S ATOM 53397 SG CYS L 613 63.942 77.839 101.780 1.00 3.97 S ATOM 53436 SG CYS L 619 69.952 76.936 100.928 1.00 0.62 S ATOM 53418 SG CYS L 616 66.566 77.740 95.708 1.00 0.00 S ATOM 52970 SG CYS L 562 62.032 102.834 108.553 1.00 0.00 S ATOM 49883 SG CYS L 155 55.847 104.546 110.600 1.00 1.61 S ATOM 52993 SG CYS L 565 57.799 98.602 109.116 1.00 0.00 S ATOM 49509 SG CYS L 104 56.807 103.226 104.691 1.00 0.00 S ATOM 53060 SG CYS L 573 61.731 87.589 95.617 1.00 0.00 S ATOM 49478 SG CYS L 100 56.635 91.098 97.770 1.00 0.00 S ATOM 53003 SG CYS L 567 62.069 90.651 101.155 1.00 0.00 S ATOM 49856 SG CYS L 151 53.426 109.313 104.603 1.00 0.00 S ATOM 49826 SG CYS L 147 50.641 114.165 101.509 1.00 8.11 S ATOM 49536 SG CYS L 108 52.589 108.575 98.604 1.00 0.00 S ATOM 53725 SG CYS L 659 80.847 80.742 101.836 1.00 0.00 S ATOM 53705 SG CYS L 656 78.899 80.217 107.675 1.00 9.48 S ATOM 53467 SG CYS L 623 77.820 75.362 103.157 1.00 0.00 S ATOM 53744 SG CYS L 662 74.856 81.125 102.694 1.00 0.00 S ATOM 53961 SG CYS L 692 89.207 90.689 97.957 1.00 0.00 S ATOM 54216 SG CYS L 725 87.653 85.405 101.168 1.00 3.86 S ATOM 53983 SG CYS L 695 93.092 86.007 99.860 1.00 13.95 S ATOM 54004 SG CYS L 699 88.538 85.843 94.559 1.00 0.00 S ATOM 48999 SG CYS L 36 65.233 73.956 90.072 1.00 7.15 S ATOM 49088 SG CYS L 47 62.190 75.784 89.146 1.00 0.00 S ATOM 49106 SG CYS L 50 63.394 73.977 84.042 1.00 0.00 S ATOM 49209 SG CYS L 64 66.501 72.439 85.175 1.00 0.00 S Time building chain proxies: 23.51, per 1000 atoms: 0.40 Number of scatterers: 58624 At special positions: 0 Unit cell: (162.35, 262.65, 141.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Fe 168 26.01 S 616 16.00 P 32 15.00 O 11264 8.00 N 9956 7.00 C 36584 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 17.26 Conformation dependent library (CDL) restraints added in 8.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 201 " pdb="FE1 FES A 201 " - pdb=" SG CYS A 98 " pdb="FE2 FES A 201 " - pdb=" SG CYS A 134 " pdb="FE2 FES A 201 " - pdb=" SG CYS A 138 " pdb="FE1 FES A 201 " - pdb=" SG CYS A 93 " pdb=" FES B 602 " pdb="FE2 FES B 602 " - pdb=" SG CYS B 41 " pdb="FE1 FES B 602 " - pdb=" SG CYS B 10 " pdb="FE2 FES B 602 " - pdb=" SG CYS B 45 " pdb=" FES C1209 " pdb="FE2 FES C1209 " - pdb=" SG CYS C 50 " pdb="FE1 FES C1209 " - pdb=" SG CYS C 47 " pdb="FE2 FES C1209 " - pdb=" SG CYS C 64 " pdb="FE1 FES C1209 " - pdb=" SG CYS C 36 " pdb=" FES D 201 " pdb="FE1 FES D 201 " - pdb=" SG CYS D 98 " pdb="FE2 FES D 201 " - pdb=" SG CYS D 134 " pdb="FE2 FES D 201 " - pdb=" SG CYS D 138 " pdb="FE1 FES D 201 " - pdb=" SG CYS D 93 " pdb=" FES E 602 " pdb="FE2 FES E 602 " - pdb=" SG CYS E 41 " pdb="FE1 FES E 602 " - pdb=" SG CYS E 10 " pdb="FE2 FES E 602 " - pdb=" SG CYS E 45 " pdb=" FES F1209 " pdb="FE2 FES F1209 " - pdb=" SG CYS F 50 " pdb="FE1 FES F1209 " - pdb=" SG CYS F 47 " pdb="FE2 FES F1209 " - pdb=" SG CYS F 64 " pdb="FE1 FES F1209 " - pdb=" SG CYS F 36 " pdb=" FES G 201 " pdb="FE1 FES G 201 " - pdb=" SG CYS G 98 " pdb="FE2 FES G 201 " - pdb=" SG CYS G 138 " pdb="FE2 FES G 201 " - pdb=" SG CYS G 134 " pdb="FE1 FES G 201 " - pdb=" SG CYS G 93 " pdb=" FES H 602 " pdb="FE2 FES H 602 " - pdb=" SG CYS H 41 " pdb="FE1 FES H 602 " - pdb=" SG CYS H 10 " pdb="FE2 FES H 602 " - pdb=" SG CYS H 45 " pdb=" FES I1209 " pdb="FE2 FES I1209 " - pdb=" SG CYS I 50 " pdb="FE1 FES I1209 " - pdb=" SG CYS I 47 " pdb="FE2 FES I1209 " - pdb=" SG CYS I 64 " pdb="FE1 FES I1209 " - pdb=" SG CYS I 36 " pdb=" FES J 201 " pdb="FE1 FES J 201 " - pdb=" SG CYS J 98 " pdb="FE2 FES J 201 " - pdb=" SG CYS J 134 " pdb="FE2 FES J 201 " - pdb=" SG CYS J 138 " pdb="FE1 FES J 201 " - pdb=" SG CYS J 93 " pdb=" FES K 602 " pdb="FE2 FES K 602 " - pdb=" SG CYS K 41 " pdb="FE1 FES K 602 " - pdb=" SG CYS K 10 " pdb="FE2 FES K 602 " - pdb=" SG CYS K 45 " pdb=" FES L1209 " pdb="FE2 FES L1209 " - pdb=" SG CYS L 50 " pdb="FE1 FES L1209 " - pdb=" SG CYS L 47 " pdb="FE2 FES L1209 " - pdb=" SG CYS L 64 " pdb="FE1 FES L1209 " - pdb=" SG CYS L 36 " pdb=" SF4 B 604 " pdb="FE3 SF4 B 604 " - pdb=" SG CYS B 569 " pdb="FE4 SF4 B 604 " - pdb=" SG CYS B 566 " pdb="FE4 SF4 B 604 " - pdb=" SG CYS B 546 " pdb=" SF4 B 605 " pdb="FE4 SF4 B 605 " - pdb=" ND1 HIS B 559 " pdb="FE1 SF4 B 605 " - pdb=" SG CYS B 536 " pdb="FE3 SF4 B 605 " - pdb=" SG CYS B 542 " pdb=" SF4 B 607 " pdb="FE4 SF4 B 607 " - pdb=" SG CYS B 445 " pdb="FE1 SF4 B 607 " - pdb=" SG CYS B 442 " pdb="FE2 SF4 B 607 " - pdb=" SG CYS B 448 " pdb="FE3 SF4 B 607 " - pdb=" SG CYS B 488 " pdb=" SF4 C1202 " pdb="FE2 SF4 C1202 " - pdb=" SG CYS C 613 " pdb="FE1 SF4 C1202 " - pdb=" SG CYS C 666 " pdb="FE4 SF4 C1202 " - pdb=" SG CYS C 616 " pdb="FE3 SF4 C1202 " - pdb=" SG CYS C 619 " pdb=" SF4 C1204 " pdb="FE1 SF4 C1204 " - pdb=" SG CYS C 562 " pdb="FE2 SF4 C1204 " - pdb=" SG CYS C 155 " pdb="FE3 SF4 C1204 " - pdb=" SG CYS C 565 " pdb="FE4 SF4 C1204 " - pdb=" SG CYS C 104 " pdb=" SF4 C1205 " pdb="FE4 SF4 C1205 " - pdb=" NE2 HIS C 96 " pdb="FE2 SF4 C1205 " - pdb=" SG CYS C 100 " pdb="FE1 SF4 C1205 " - pdb=" SG CYS C 573 " pdb="FE3 SF4 C1205 " - pdb=" SG CYS C 567 " pdb=" SF4 C1206 " pdb="FE2 SF4 C1206 " - pdb=" SG CYS C 147 " pdb="FE1 SF4 C1206 " - pdb=" SG CYS C 151 " pdb="FE3 SF4 C1206 " - pdb=" SG CYS C 108 " pdb=" SF4 C1207 " pdb="FE1 SF4 C1207 " - pdb=" SG CYS C 659 " pdb="FE2 SF4 C1207 " - pdb=" SG CYS C 656 " pdb="FE3 SF4 C1207 " - pdb=" SG CYS C 623 " pdb="FE4 SF4 C1207 " - pdb=" SG CYS C 662 " pdb=" SF4 C1208 " pdb="FE1 SF4 C1208 " - pdb=" SG CYS C 692 " pdb="FE2 SF4 C1208 " - pdb=" SG CYS C 725 " pdb="FE4 SF4 C1208 " - pdb=" SG CYS C 699 " pdb="FE3 SF4 C1208 " - pdb=" SG CYS C 695 " pdb=" SF4 E 604 " pdb="FE3 SF4 E 604 " - pdb=" SG CYS E 569 " pdb="FE4 SF4 E 604 " - pdb=" SG CYS E 566 " pdb="FE4 SF4 E 604 " - pdb=" SG CYS E 546 " pdb=" SF4 E 605 " pdb="FE4 SF4 E 605 " - pdb=" ND1 HIS E 559 " pdb="FE1 SF4 E 605 " - pdb=" SG CYS E 536 " pdb="FE3 SF4 E 605 " - pdb=" SG CYS E 542 " pdb=" SF4 E 607 " pdb="FE4 SF4 E 607 " - pdb=" SG CYS E 445 " pdb="FE1 SF4 E 607 " - pdb=" SG CYS E 442 " pdb="FE2 SF4 E 607 " - pdb=" SG CYS E 448 " pdb="FE3 SF4 E 607 " - pdb=" SG CYS E 488 " pdb=" SF4 F1202 " pdb="FE2 SF4 F1202 " - pdb=" SG CYS F 613 " pdb="FE1 SF4 F1202 " - pdb=" SG CYS F 666 " pdb="FE4 SF4 F1202 " - pdb=" SG CYS F 616 " pdb="FE3 SF4 F1202 " - pdb=" SG CYS F 619 " pdb=" SF4 F1204 " pdb="FE1 SF4 F1204 " - pdb=" SG CYS F 562 " pdb="FE2 SF4 F1204 " - pdb=" SG CYS F 155 " pdb="FE3 SF4 F1204 " - pdb=" SG CYS F 565 " pdb="FE4 SF4 F1204 " - pdb=" SG CYS F 104 " pdb=" SF4 F1205 " pdb="FE4 SF4 F1205 " - pdb=" NE2 HIS F 96 " pdb="FE2 SF4 F1205 " - pdb=" SG CYS F 100 " pdb="FE1 SF4 F1205 " - pdb=" SG CYS F 573 " pdb="FE3 SF4 F1205 " - pdb=" SG CYS F 567 " pdb=" SF4 F1206 " pdb="FE2 SF4 F1206 " - pdb=" SG CYS F 147 " pdb="FE1 SF4 F1206 " - pdb=" SG CYS F 151 " pdb="FE3 SF4 F1206 " - pdb=" SG CYS F 108 " pdb=" SF4 F1207 " pdb="FE1 SF4 F1207 " - pdb=" SG CYS F 659 " pdb="FE2 SF4 F1207 " - pdb=" SG CYS F 656 " pdb="FE3 SF4 F1207 " - pdb=" SG CYS F 623 " pdb="FE4 SF4 F1207 " - pdb=" SG CYS F 662 " pdb=" SF4 F1208 " pdb="FE1 SF4 F1208 " - pdb=" SG CYS F 692 " pdb="FE2 SF4 F1208 " - pdb=" SG CYS F 725 " pdb="FE4 SF4 F1208 " - pdb=" SG CYS F 699 " pdb="FE3 SF4 F1208 " - pdb=" SG CYS F 695 " pdb=" SF4 H 604 " pdb="FE3 SF4 H 604 " - pdb=" SG CYS H 569 " pdb="FE4 SF4 H 604 " - pdb=" SG CYS H 566 " pdb="FE4 SF4 H 604 " - pdb=" SG CYS H 546 " pdb=" SF4 H 605 " pdb="FE4 SF4 H 605 " - pdb=" ND1 HIS H 559 " pdb="FE1 SF4 H 605 " - pdb=" SG CYS H 536 " pdb="FE3 SF4 H 605 " - pdb=" SG CYS H 542 " pdb=" SF4 H 607 " pdb="FE4 SF4 H 607 " - pdb=" SG CYS H 445 " pdb="FE1 SF4 H 607 " - pdb=" SG CYS H 442 " pdb="FE2 SF4 H 607 " - pdb=" SG CYS H 448 " pdb="FE3 SF4 H 607 " - pdb=" SG CYS H 488 " pdb=" SF4 I1202 " pdb="FE1 SF4 I1202 " - pdb=" SG CYS I 666 " pdb="FE2 SF4 I1202 " - pdb=" SG CYS I 613 " pdb="FE4 SF4 I1202 " - pdb=" SG CYS I 616 " pdb="FE3 SF4 I1202 " - pdb=" SG CYS I 619 " pdb=" SF4 I1204 " pdb="FE1 SF4 I1204 " - pdb=" SG CYS I 562 " pdb="FE2 SF4 I1204 " - pdb=" SG CYS I 155 " pdb="FE3 SF4 I1204 " - pdb=" SG CYS I 565 " pdb="FE4 SF4 I1204 " - pdb=" SG CYS I 104 " pdb=" SF4 I1205 " pdb="FE4 SF4 I1205 " - pdb=" NE2 HIS I 96 " pdb="FE2 SF4 I1205 " - pdb=" SG CYS I 100 " pdb="FE1 SF4 I1205 " - pdb=" SG CYS I 573 " pdb="FE3 SF4 I1205 " - pdb=" SG CYS I 567 " pdb=" SF4 I1206 " pdb="FE2 SF4 I1206 " - pdb=" SG CYS I 147 " pdb="FE1 SF4 I1206 " - pdb=" SG CYS I 151 " pdb="FE3 SF4 I1206 " - pdb=" SG CYS I 108 " pdb=" SF4 I1207 " pdb="FE1 SF4 I1207 " - pdb=" SG CYS I 659 " pdb="FE2 SF4 I1207 " - pdb=" SG CYS I 656 " pdb="FE3 SF4 I1207 " - pdb=" SG CYS I 623 " pdb="FE4 SF4 I1207 " - pdb=" SG CYS I 662 " pdb=" SF4 I1208 " pdb="FE1 SF4 I1208 " - pdb=" SG CYS I 692 " pdb="FE2 SF4 I1208 " - pdb=" SG CYS I 725 " pdb="FE4 SF4 I1208 " - pdb=" SG CYS I 699 " pdb="FE3 SF4 I1208 " - pdb=" SG CYS I 695 " pdb=" SF4 K 604 " pdb="FE3 SF4 K 604 " - pdb=" SG CYS K 569 " pdb="FE4 SF4 K 604 " - pdb=" SG CYS K 566 " pdb="FE4 SF4 K 604 " - pdb=" SG CYS K 546 " pdb=" SF4 K 605 " pdb="FE4 SF4 K 605 " - pdb=" ND1 HIS K 559 " pdb="FE1 SF4 K 605 " - pdb=" SG CYS K 536 " pdb="FE3 SF4 K 605 " - pdb=" SG CYS K 542 " pdb=" SF4 K 607 " pdb="FE4 SF4 K 607 " - pdb=" SG CYS K 445 " pdb="FE1 SF4 K 607 " - pdb=" SG CYS K 442 " pdb="FE2 SF4 K 607 " - pdb=" SG CYS K 448 " pdb="FE3 SF4 K 607 " - pdb=" SG CYS K 488 " pdb=" SF4 L1202 " pdb="FE2 SF4 L1202 " - pdb=" SG CYS L 613 " pdb="FE1 SF4 L1202 " - pdb=" SG CYS L 666 " pdb="FE4 SF4 L1202 " - pdb=" SG CYS L 616 " pdb="FE3 SF4 L1202 " - pdb=" SG CYS L 619 " pdb=" SF4 L1204 " pdb="FE1 SF4 L1204 " - pdb=" SG CYS L 562 " pdb="FE2 SF4 L1204 " - pdb=" SG CYS L 155 " pdb="FE3 SF4 L1204 " - pdb=" SG CYS L 565 " pdb="FE4 SF4 L1204 " - pdb=" SG CYS L 104 " pdb=" SF4 L1205 " pdb="FE4 SF4 L1205 " - pdb=" NE2 HIS L 96 " pdb="FE2 SF4 L1205 " - pdb=" SG CYS L 100 " pdb="FE1 SF4 L1205 " - pdb=" SG CYS L 573 " pdb="FE3 SF4 L1205 " - pdb=" SG CYS L 567 " pdb=" SF4 L1206 " pdb="FE2 SF4 L1206 " - pdb=" SG CYS L 147 " pdb="FE1 SF4 L1206 " - pdb=" SG CYS L 151 " pdb="FE3 SF4 L1206 " - pdb=" SG CYS L 108 " pdb=" SF4 L1207 " pdb="FE1 SF4 L1207 " - pdb=" SG CYS L 659 " pdb="FE2 SF4 L1207 " - pdb=" SG CYS L 656 " pdb="FE3 SF4 L1207 " - pdb=" SG CYS L 623 " pdb="FE4 SF4 L1207 " - pdb=" SG CYS L 662 " pdb=" SF4 L1208 " pdb="FE1 SF4 L1208 " - pdb=" SG CYS L 692 " pdb="FE2 SF4 L1208 " - pdb=" SG CYS L 725 " pdb="FE4 SF4 L1208 " - pdb=" SG CYS L 699 " pdb="FE3 SF4 L1208 " - pdb=" SG CYS L 695 " Number of angles added : 440 Zn2+ tetrahedral coordination pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS B 512 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 425 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 518 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 523 " pdb=" ZN E 601 " pdb="ZN ZN E 601 " - pdb=" NE2 HIS E 512 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 425 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 518 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 523 " pdb=" ZN H 601 " pdb="ZN ZN H 601 " - pdb=" NE2 HIS H 512 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 425 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 518 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 523 " pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 512 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 425 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 518 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 523 " Number of angles added : 12 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13824 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 343 helices and 64 sheets defined 36.2% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.15 Creating SS restraints... Processing helix chain 'A' and resid 20 through 29 Proline residue: A 25 - end of helix Processing helix chain 'A' and resid 37 through 48 Processing helix chain 'A' and resid 53 through 60 Processing helix chain 'A' and resid 67 through 75 Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 103 through 114 Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 156 through 166 Processing helix chain 'B' and resid 9 through 12 No H-bonds generated for 'chain 'B' and resid 9 through 12' Processing helix chain 'B' and resid 17 through 30 Processing helix chain 'B' and resid 67 through 76 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 118 through 124 Processing helix chain 'B' and resid 128 through 136 Processing helix chain 'B' and resid 139 through 149 Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 191 through 198 Processing helix chain 'B' and resid 200 through 214 Processing helix chain 'B' and resid 228 through 243 Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 276 through 281 Processing helix chain 'B' and resid 300 through 302 No H-bonds generated for 'chain 'B' and resid 300 through 302' Processing helix chain 'B' and resid 310 through 322 Proline residue: B 317 - end of helix removed outlier: 3.799A pdb=" N ASN B 322 " --> pdb=" O TRP B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 327 No H-bonds generated for 'chain 'B' and resid 324 through 327' Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 385 through 387 No H-bonds generated for 'chain 'B' and resid 385 through 387' Processing helix chain 'B' and resid 402 through 407 Processing helix chain 'B' and resid 426 through 438 Processing helix chain 'B' and resid 446 through 462 removed outlier: 4.534A pdb=" N THR B 452 " --> pdb=" O CYS B 448 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LYS B 453 " --> pdb=" O ARG B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 485 removed outlier: 3.556A pdb=" N SER B 481 " --> pdb=" O GLU B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 492 No H-bonds generated for 'chain 'B' and resid 489 through 492' Processing helix chain 'B' and resid 496 through 501 Processing helix chain 'B' and resid 506 through 513 removed outlier: 3.601A pdb=" N GLU B 510 " --> pdb=" O ARG B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 544 No H-bonds generated for 'chain 'B' and resid 541 through 544' Processing helix chain 'C' and resid 21 through 27 Processing helix chain 'C' and resid 79 through 95 removed outlier: 4.019A pdb=" N ASP C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 114 through 122 Processing helix chain 'C' and resid 126 through 135 removed outlier: 3.660A pdb=" N ASP C 135 " --> pdb=" O LYS C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 146 Processing helix chain 'C' and resid 150 through 153 No H-bonds generated for 'chain 'C' and resid 150 through 153' Processing helix chain 'C' and resid 156 through 159 Processing helix chain 'C' and resid 166 through 178 Processing helix chain 'C' and resid 202 through 212 Processing helix chain 'C' and resid 229 through 233 removed outlier: 3.942A pdb=" N TYR C 233 " --> pdb=" O MET C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 255 removed outlier: 3.835A pdb=" N MET C 255 " --> pdb=" O LEU C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 277 Processing helix chain 'C' and resid 306 through 314 Processing helix chain 'C' and resid 332 through 343 Processing helix chain 'C' and resid 364 through 373 Processing helix chain 'C' and resid 470 through 474 removed outlier: 4.120A pdb=" N THR C 474 " --> pdb=" O ASP C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 498 removed outlier: 3.515A pdb=" N ASN C 498 " --> pdb=" O ASP C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 520 No H-bonds generated for 'chain 'C' and resid 518 through 520' Processing helix chain 'C' and resid 536 through 539 No H-bonds generated for 'chain 'C' and resid 536 through 539' Processing helix chain 'C' and resid 552 through 561 removed outlier: 4.216A pdb=" N ARG C 561 " --> pdb=" O ARG C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 581 Processing helix chain 'C' and resid 610 through 612 No H-bonds generated for 'chain 'C' and resid 610 through 612' Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 638 through 640 No H-bonds generated for 'chain 'C' and resid 638 through 640' Processing helix chain 'C' and resid 646 through 648 No H-bonds generated for 'chain 'C' and resid 646 through 648' Processing helix chain 'C' and resid 651 through 653 No H-bonds generated for 'chain 'C' and resid 651 through 653' Processing helix chain 'C' and resid 661 through 665 Processing helix chain 'C' and resid 726 through 729 No H-bonds generated for 'chain 'C' and resid 726 through 729' Processing helix chain 'C' and resid 733 through 736 Processing helix chain 'C' and resid 757 through 775 Processing helix chain 'C' and resid 790 through 802 Processing helix chain 'C' and resid 819 through 823 Processing helix chain 'C' and resid 832 through 834 No H-bonds generated for 'chain 'C' and resid 832 through 834' Processing helix chain 'C' and resid 847 through 850 No H-bonds generated for 'chain 'C' and resid 847 through 850' Processing helix chain 'C' and resid 852 through 861 Processing helix chain 'C' and resid 875 through 887 Processing helix chain 'C' and resid 892 through 898 Processing helix chain 'C' and resid 902 through 909 Processing helix chain 'C' and resid 916 through 927 Processing helix chain 'C' and resid 942 through 955 Processing helix chain 'C' and resid 974 through 979 Processing helix chain 'C' and resid 986 through 994 Processing helix chain 'C' and resid 1008 through 1010 No H-bonds generated for 'chain 'C' and resid 1008 through 1010' Processing helix chain 'C' and resid 1012 through 1020 removed outlier: 3.960A pdb=" N LYS C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1036 No H-bonds generated for 'chain 'C' and resid 1033 through 1036' Processing helix chain 'C' and resid 1047 through 1049 No H-bonds generated for 'chain 'C' and resid 1047 through 1049' Processing helix chain 'C' and resid 1076 through 1087 Processing helix chain 'C' and resid 1094 through 1104 Processing helix chain 'C' and resid 1160 through 1169 Processing helix chain 'D' and resid 20 through 29 Proline residue: D 25 - end of helix Processing helix chain 'D' and resid 37 through 48 Processing helix chain 'D' and resid 53 through 60 Processing helix chain 'D' and resid 67 through 75 Processing helix chain 'D' and resid 96 through 100 Processing helix chain 'D' and resid 103 through 114 Processing helix chain 'D' and resid 138 through 140 No H-bonds generated for 'chain 'D' and resid 138 through 140' Processing helix chain 'D' and resid 156 through 166 Processing helix chain 'E' and resid 9 through 12 No H-bonds generated for 'chain 'E' and resid 9 through 12' Processing helix chain 'E' and resid 17 through 30 Processing helix chain 'E' and resid 67 through 76 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'E' and resid 128 through 136 Processing helix chain 'E' and resid 139 through 149 Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 165 through 170 Processing helix chain 'E' and resid 191 through 198 Processing helix chain 'E' and resid 200 through 214 Processing helix chain 'E' and resid 228 through 243 Processing helix chain 'E' and resid 251 through 253 No H-bonds generated for 'chain 'E' and resid 251 through 253' Processing helix chain 'E' and resid 276 through 281 Processing helix chain 'E' and resid 300 through 302 No H-bonds generated for 'chain 'E' and resid 300 through 302' Processing helix chain 'E' and resid 310 through 322 Proline residue: E 317 - end of helix removed outlier: 3.799A pdb=" N ASN E 322 " --> pdb=" O TRP E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 327 No H-bonds generated for 'chain 'E' and resid 324 through 327' Processing helix chain 'E' and resid 361 through 365 Processing helix chain 'E' and resid 373 through 375 No H-bonds generated for 'chain 'E' and resid 373 through 375' Processing helix chain 'E' and resid 385 through 387 No H-bonds generated for 'chain 'E' and resid 385 through 387' Processing helix chain 'E' and resid 402 through 407 Processing helix chain 'E' and resid 426 through 438 Processing helix chain 'E' and resid 446 through 462 removed outlier: 4.534A pdb=" N THR E 452 " --> pdb=" O CYS E 448 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LYS E 453 " --> pdb=" O ARG E 449 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 485 removed outlier: 3.556A pdb=" N SER E 481 " --> pdb=" O GLU E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 492 No H-bonds generated for 'chain 'E' and resid 489 through 492' Processing helix chain 'E' and resid 496 through 501 Processing helix chain 'E' and resid 506 through 513 removed outlier: 3.600A pdb=" N GLU E 510 " --> pdb=" O ARG E 506 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 544 No H-bonds generated for 'chain 'E' and resid 541 through 544' Processing helix chain 'F' and resid 21 through 27 Processing helix chain 'F' and resid 79 through 95 removed outlier: 4.020A pdb=" N ASP F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 107 Processing helix chain 'F' and resid 114 through 122 Processing helix chain 'F' and resid 126 through 135 removed outlier: 3.660A pdb=" N ASP F 135 " --> pdb=" O LYS F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 146 Processing helix chain 'F' and resid 150 through 153 No H-bonds generated for 'chain 'F' and resid 150 through 153' Processing helix chain 'F' and resid 156 through 159 Processing helix chain 'F' and resid 166 through 178 Processing helix chain 'F' and resid 202 through 212 Processing helix chain 'F' and resid 229 through 233 removed outlier: 3.942A pdb=" N TYR F 233 " --> pdb=" O MET F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 255 removed outlier: 3.835A pdb=" N MET F 255 " --> pdb=" O LEU F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 277 Processing helix chain 'F' and resid 306 through 314 Processing helix chain 'F' and resid 332 through 343 Processing helix chain 'F' and resid 364 through 373 Processing helix chain 'F' and resid 470 through 474 removed outlier: 4.120A pdb=" N THR F 474 " --> pdb=" O ASP F 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 498 removed outlier: 3.514A pdb=" N ASN F 498 " --> pdb=" O ASP F 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 520 No H-bonds generated for 'chain 'F' and resid 518 through 520' Processing helix chain 'F' and resid 536 through 539 No H-bonds generated for 'chain 'F' and resid 536 through 539' Processing helix chain 'F' and resid 552 through 561 removed outlier: 4.215A pdb=" N ARG F 561 " --> pdb=" O ARG F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 575 through 581 Processing helix chain 'F' and resid 610 through 612 No H-bonds generated for 'chain 'F' and resid 610 through 612' Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 638 through 640 No H-bonds generated for 'chain 'F' and resid 638 through 640' Processing helix chain 'F' and resid 646 through 648 No H-bonds generated for 'chain 'F' and resid 646 through 648' Processing helix chain 'F' and resid 651 through 653 No H-bonds generated for 'chain 'F' and resid 651 through 653' Processing helix chain 'F' and resid 661 through 665 Processing helix chain 'F' and resid 726 through 729 No H-bonds generated for 'chain 'F' and resid 726 through 729' Processing helix chain 'F' and resid 733 through 736 Processing helix chain 'F' and resid 757 through 775 Processing helix chain 'F' and resid 790 through 802 Processing helix chain 'F' and resid 819 through 823 Processing helix chain 'F' and resid 832 through 834 No H-bonds generated for 'chain 'F' and resid 832 through 834' Processing helix chain 'F' and resid 847 through 850 No H-bonds generated for 'chain 'F' and resid 847 through 850' Processing helix chain 'F' and resid 852 through 861 Processing helix chain 'F' and resid 875 through 887 Processing helix chain 'F' and resid 892 through 898 Processing helix chain 'F' and resid 902 through 909 Processing helix chain 'F' and resid 916 through 927 Processing helix chain 'F' and resid 942 through 955 Processing helix chain 'F' and resid 974 through 979 Processing helix chain 'F' and resid 986 through 994 Processing helix chain 'F' and resid 1008 through 1010 No H-bonds generated for 'chain 'F' and resid 1008 through 1010' Processing helix chain 'F' and resid 1012 through 1020 removed outlier: 3.960A pdb=" N LYS F1020 " --> pdb=" O ALA F1016 " (cutoff:3.500A) Processing helix chain 'F' and resid 1033 through 1036 No H-bonds generated for 'chain 'F' and resid 1033 through 1036' Processing helix chain 'F' and resid 1047 through 1049 No H-bonds generated for 'chain 'F' and resid 1047 through 1049' Processing helix chain 'F' and resid 1076 through 1087 Processing helix chain 'F' and resid 1094 through 1104 Processing helix chain 'F' and resid 1160 through 1169 Processing helix chain 'G' and resid 20 through 29 Proline residue: G 25 - end of helix Processing helix chain 'G' and resid 37 through 48 Processing helix chain 'G' and resid 53 through 60 Processing helix chain 'G' and resid 67 through 75 Processing helix chain 'G' and resid 96 through 100 Processing helix chain 'G' and resid 103 through 114 Processing helix chain 'G' and resid 138 through 140 No H-bonds generated for 'chain 'G' and resid 138 through 140' Processing helix chain 'G' and resid 156 through 166 Processing helix chain 'H' and resid 9 through 12 No H-bonds generated for 'chain 'H' and resid 9 through 12' Processing helix chain 'H' and resid 17 through 30 Processing helix chain 'H' and resid 67 through 76 Processing helix chain 'H' and resid 118 through 124 Processing helix chain 'H' and resid 128 through 136 Processing helix chain 'H' and resid 139 through 149 Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 165 through 170 Processing helix chain 'H' and resid 191 through 198 Processing helix chain 'H' and resid 200 through 214 Processing helix chain 'H' and resid 228 through 243 Processing helix chain 'H' and resid 251 through 253 No H-bonds generated for 'chain 'H' and resid 251 through 253' Processing helix chain 'H' and resid 276 through 281 Processing helix chain 'H' and resid 300 through 302 No H-bonds generated for 'chain 'H' and resid 300 through 302' Processing helix chain 'H' and resid 310 through 322 Proline residue: H 317 - end of helix removed outlier: 3.799A pdb=" N ASN H 322 " --> pdb=" O TRP H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 327 No H-bonds generated for 'chain 'H' and resid 324 through 327' Processing helix chain 'H' and resid 361 through 365 Processing helix chain 'H' and resid 373 through 375 No H-bonds generated for 'chain 'H' and resid 373 through 375' Processing helix chain 'H' and resid 385 through 387 No H-bonds generated for 'chain 'H' and resid 385 through 387' Processing helix chain 'H' and resid 402 through 407 Processing helix chain 'H' and resid 426 through 438 Processing helix chain 'H' and resid 446 through 462 removed outlier: 4.534A pdb=" N THR H 452 " --> pdb=" O CYS H 448 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LYS H 453 " --> pdb=" O ARG H 449 " (cutoff:3.500A) Processing helix chain 'H' and resid 471 through 485 removed outlier: 3.556A pdb=" N SER H 481 " --> pdb=" O GLU H 477 " (cutoff:3.500A) Processing helix chain 'H' and resid 489 through 492 No H-bonds generated for 'chain 'H' and resid 489 through 492' Processing helix chain 'H' and resid 496 through 501 Processing helix chain 'H' and resid 506 through 513 removed outlier: 3.600A pdb=" N GLU H 510 " --> pdb=" O ARG H 506 " (cutoff:3.500A) Processing helix chain 'H' and resid 541 through 544 No H-bonds generated for 'chain 'H' and resid 541 through 544' Processing helix chain 'I' and resid 21 through 27 Processing helix chain 'I' and resid 79 through 95 removed outlier: 4.020A pdb=" N ASP I 95 " --> pdb=" O LEU I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 107 Processing helix chain 'I' and resid 114 through 122 Processing helix chain 'I' and resid 126 through 135 removed outlier: 3.661A pdb=" N ASP I 135 " --> pdb=" O LYS I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 146 Processing helix chain 'I' and resid 150 through 153 No H-bonds generated for 'chain 'I' and resid 150 through 153' Processing helix chain 'I' and resid 156 through 159 Processing helix chain 'I' and resid 166 through 178 Processing helix chain 'I' and resid 202 through 212 Processing helix chain 'I' and resid 229 through 233 removed outlier: 3.942A pdb=" N TYR I 233 " --> pdb=" O MET I 230 " (cutoff:3.500A) Processing helix chain 'I' and resid 242 through 255 removed outlier: 3.835A pdb=" N MET I 255 " --> pdb=" O LEU I 251 " (cutoff:3.500A) Processing helix chain 'I' and resid 271 through 277 Processing helix chain 'I' and resid 306 through 314 Processing helix chain 'I' and resid 332 through 343 Processing helix chain 'I' and resid 364 through 373 Processing helix chain 'I' and resid 470 through 474 removed outlier: 4.120A pdb=" N THR I 474 " --> pdb=" O ASP I 471 " (cutoff:3.500A) Processing helix chain 'I' and resid 479 through 498 removed outlier: 3.514A pdb=" N ASN I 498 " --> pdb=" O ASP I 494 " (cutoff:3.500A) Processing helix chain 'I' and resid 518 through 520 No H-bonds generated for 'chain 'I' and resid 518 through 520' Processing helix chain 'I' and resid 536 through 539 No H-bonds generated for 'chain 'I' and resid 536 through 539' Processing helix chain 'I' and resid 552 through 561 removed outlier: 4.216A pdb=" N ARG I 561 " --> pdb=" O ARG I 557 " (cutoff:3.500A) Processing helix chain 'I' and resid 575 through 581 Processing helix chain 'I' and resid 610 through 612 No H-bonds generated for 'chain 'I' and resid 610 through 612' Processing helix chain 'I' and resid 618 through 625 Processing helix chain 'I' and resid 638 through 640 No H-bonds generated for 'chain 'I' and resid 638 through 640' Processing helix chain 'I' and resid 646 through 648 No H-bonds generated for 'chain 'I' and resid 646 through 648' Processing helix chain 'I' and resid 651 through 653 No H-bonds generated for 'chain 'I' and resid 651 through 653' Processing helix chain 'I' and resid 661 through 665 Processing helix chain 'I' and resid 726 through 729 No H-bonds generated for 'chain 'I' and resid 726 through 729' Processing helix chain 'I' and resid 733 through 736 Processing helix chain 'I' and resid 757 through 775 Processing helix chain 'I' and resid 790 through 802 Processing helix chain 'I' and resid 819 through 823 Processing helix chain 'I' and resid 832 through 834 No H-bonds generated for 'chain 'I' and resid 832 through 834' Processing helix chain 'I' and resid 847 through 850 No H-bonds generated for 'chain 'I' and resid 847 through 850' Processing helix chain 'I' and resid 852 through 861 Processing helix chain 'I' and resid 875 through 887 Processing helix chain 'I' and resid 892 through 898 Processing helix chain 'I' and resid 902 through 909 Processing helix chain 'I' and resid 916 through 927 Processing helix chain 'I' and resid 942 through 955 Processing helix chain 'I' and resid 974 through 979 Processing helix chain 'I' and resid 986 through 994 Processing helix chain 'I' and resid 1008 through 1010 No H-bonds generated for 'chain 'I' and resid 1008 through 1010' Processing helix chain 'I' and resid 1012 through 1020 removed outlier: 3.960A pdb=" N LYS I1020 " --> pdb=" O ALA I1016 " (cutoff:3.500A) Processing helix chain 'I' and resid 1033 through 1036 No H-bonds generated for 'chain 'I' and resid 1033 through 1036' Processing helix chain 'I' and resid 1047 through 1049 No H-bonds generated for 'chain 'I' and resid 1047 through 1049' Processing helix chain 'I' and resid 1076 through 1087 Processing helix chain 'I' and resid 1094 through 1104 Processing helix chain 'I' and resid 1160 through 1169 Processing helix chain 'J' and resid 20 through 29 Proline residue: J 25 - end of helix Processing helix chain 'J' and resid 37 through 48 Processing helix chain 'J' and resid 53 through 60 Processing helix chain 'J' and resid 67 through 75 Processing helix chain 'J' and resid 96 through 100 Processing helix chain 'J' and resid 103 through 114 Processing helix chain 'J' and resid 138 through 140 No H-bonds generated for 'chain 'J' and resid 138 through 140' Processing helix chain 'J' and resid 156 through 166 Processing helix chain 'K' and resid 9 through 12 No H-bonds generated for 'chain 'K' and resid 9 through 12' Processing helix chain 'K' and resid 17 through 30 Processing helix chain 'K' and resid 67 through 76 Processing helix chain 'K' and resid 98 through 100 No H-bonds generated for 'chain 'K' and resid 98 through 100' Processing helix chain 'K' and resid 118 through 124 Processing helix chain 'K' and resid 128 through 136 Processing helix chain 'K' and resid 139 through 149 Processing helix chain 'K' and resid 161 through 163 No H-bonds generated for 'chain 'K' and resid 161 through 163' Processing helix chain 'K' and resid 165 through 170 Processing helix chain 'K' and resid 191 through 198 Processing helix chain 'K' and resid 200 through 214 Processing helix chain 'K' and resid 228 through 243 Processing helix chain 'K' and resid 251 through 253 No H-bonds generated for 'chain 'K' and resid 251 through 253' Processing helix chain 'K' and resid 276 through 281 Processing helix chain 'K' and resid 300 through 302 No H-bonds generated for 'chain 'K' and resid 300 through 302' Processing helix chain 'K' and resid 310 through 322 Proline residue: K 317 - end of helix removed outlier: 3.799A pdb=" N ASN K 322 " --> pdb=" O TRP K 318 " (cutoff:3.500A) Processing helix chain 'K' and resid 324 through 327 No H-bonds generated for 'chain 'K' and resid 324 through 327' Processing helix chain 'K' and resid 361 through 365 Processing helix chain 'K' and resid 373 through 375 No H-bonds generated for 'chain 'K' and resid 373 through 375' Processing helix chain 'K' and resid 385 through 387 No H-bonds generated for 'chain 'K' and resid 385 through 387' Processing helix chain 'K' and resid 402 through 407 Processing helix chain 'K' and resid 426 through 438 Processing helix chain 'K' and resid 446 through 462 removed outlier: 4.534A pdb=" N THR K 452 " --> pdb=" O CYS K 448 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LYS K 453 " --> pdb=" O ARG K 449 " (cutoff:3.500A) Processing helix chain 'K' and resid 471 through 485 removed outlier: 3.556A pdb=" N SER K 481 " --> pdb=" O GLU K 477 " (cutoff:3.500A) Processing helix chain 'K' and resid 489 through 492 No H-bonds generated for 'chain 'K' and resid 489 through 492' Processing helix chain 'K' and resid 496 through 501 Processing helix chain 'K' and resid 506 through 513 removed outlier: 3.601A pdb=" N GLU K 510 " --> pdb=" O ARG K 506 " (cutoff:3.500A) Processing helix chain 'K' and resid 541 through 544 No H-bonds generated for 'chain 'K' and resid 541 through 544' Processing helix chain 'L' and resid 21 through 27 Processing helix chain 'L' and resid 79 through 95 removed outlier: 4.020A pdb=" N ASP L 95 " --> pdb=" O LEU L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 107 Processing helix chain 'L' and resid 114 through 122 Processing helix chain 'L' and resid 126 through 135 removed outlier: 3.660A pdb=" N ASP L 135 " --> pdb=" O LYS L 131 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 146 Processing helix chain 'L' and resid 150 through 153 No H-bonds generated for 'chain 'L' and resid 150 through 153' Processing helix chain 'L' and resid 156 through 159 Processing helix chain 'L' and resid 166 through 178 Processing helix chain 'L' and resid 202 through 212 Processing helix chain 'L' and resid 229 through 233 removed outlier: 3.942A pdb=" N TYR L 233 " --> pdb=" O MET L 230 " (cutoff:3.500A) Processing helix chain 'L' and resid 242 through 255 removed outlier: 3.835A pdb=" N MET L 255 " --> pdb=" O LEU L 251 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 277 Processing helix chain 'L' and resid 306 through 314 Processing helix chain 'L' and resid 332 through 343 Processing helix chain 'L' and resid 364 through 373 Processing helix chain 'L' and resid 470 through 474 removed outlier: 4.120A pdb=" N THR L 474 " --> pdb=" O ASP L 471 " (cutoff:3.500A) Processing helix chain 'L' and resid 479 through 498 removed outlier: 3.514A pdb=" N ASN L 498 " --> pdb=" O ASP L 494 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 520 No H-bonds generated for 'chain 'L' and resid 518 through 520' Processing helix chain 'L' and resid 536 through 539 No H-bonds generated for 'chain 'L' and resid 536 through 539' Processing helix chain 'L' and resid 552 through 561 removed outlier: 4.216A pdb=" N ARG L 561 " --> pdb=" O ARG L 557 " (cutoff:3.500A) Processing helix chain 'L' and resid 575 through 581 Processing helix chain 'L' and resid 610 through 612 No H-bonds generated for 'chain 'L' and resid 610 through 612' Processing helix chain 'L' and resid 618 through 625 Processing helix chain 'L' and resid 638 through 640 No H-bonds generated for 'chain 'L' and resid 638 through 640' Processing helix chain 'L' and resid 646 through 648 No H-bonds generated for 'chain 'L' and resid 646 through 648' Processing helix chain 'L' and resid 651 through 653 No H-bonds generated for 'chain 'L' and resid 651 through 653' Processing helix chain 'L' and resid 661 through 665 Processing helix chain 'L' and resid 726 through 729 No H-bonds generated for 'chain 'L' and resid 726 through 729' Processing helix chain 'L' and resid 733 through 736 Processing helix chain 'L' and resid 757 through 775 Processing helix chain 'L' and resid 790 through 802 Processing helix chain 'L' and resid 819 through 823 Processing helix chain 'L' and resid 832 through 834 No H-bonds generated for 'chain 'L' and resid 832 through 834' Processing helix chain 'L' and resid 847 through 850 No H-bonds generated for 'chain 'L' and resid 847 through 850' Processing helix chain 'L' and resid 852 through 861 Processing helix chain 'L' and resid 875 through 887 Processing helix chain 'L' and resid 892 through 898 Processing helix chain 'L' and resid 902 through 909 Processing helix chain 'L' and resid 916 through 927 Processing helix chain 'L' and resid 942 through 955 Processing helix chain 'L' and resid 974 through 979 Processing helix chain 'L' and resid 986 through 994 Processing helix chain 'L' and resid 1008 through 1010 No H-bonds generated for 'chain 'L' and resid 1008 through 1010' Processing helix chain 'L' and resid 1012 through 1020 removed outlier: 3.960A pdb=" N LYS L1020 " --> pdb=" O ALA L1016 " (cutoff:3.500A) Processing helix chain 'L' and resid 1033 through 1036 No H-bonds generated for 'chain 'L' and resid 1033 through 1036' Processing helix chain 'L' and resid 1047 through 1049 No H-bonds generated for 'chain 'L' and resid 1047 through 1049' Processing helix chain 'L' and resid 1076 through 1087 Processing helix chain 'L' and resid 1094 through 1104 Processing helix chain 'L' and resid 1160 through 1169 Processing sheet with id= A, first strand: chain 'A' and resid 127 through 132 removed outlier: 7.102A pdb=" N TYR A 88 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N GLU A 130 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE A 90 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL A 132 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLN A 92 " --> pdb=" O VAL A 132 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 35 through 38 removed outlier: 3.954A pdb=" N LYS B 2 " --> pdb=" O PHE B 54 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 305 through 309 removed outlier: 6.482A pdb=" N TYR B 177 " --> pdb=" O ASN B 306 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ASN B 308 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL B 179 " --> pdb=" O ASN B 308 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLU B 218 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N CYS B 180 " --> pdb=" O GLU B 218 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N HIS B 220 " --> pdb=" O CYS B 180 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ALA B 182 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N TYR B 222 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASP B 259 " --> pdb=" O GLY B 219 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ILE B 221 " --> pdb=" O ASP B 259 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LYS B 261 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N CYS B 223 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LYS B 263 " --> pdb=" O CYS B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 351 through 355 Processing sheet with id= E, first strand: chain 'B' and resid 528 through 531 Processing sheet with id= F, first strand: chain 'C' and resid 5 through 8 Processing sheet with id= G, first strand: chain 'C' and resid 466 through 468 removed outlier: 6.394A pdb=" N VAL C 281 " --> pdb=" O PHE C 467 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LYS C 217 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL C 197 " --> pdb=" O LYS C 217 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL C 219 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLU C 258 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 303 through 305 removed outlier: 6.468A pdb=" N ILE C 428 " --> pdb=" O LEU C 304 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU C 348 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL C 327 " --> pdb=" O GLU C 348 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR C 350 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LYS C 376 " --> pdb=" O ILE C 351 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 420 through 424 removed outlier: 5.354A pdb=" N GLU C 399 " --> pdb=" O PRO C 383 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 606 through 608 Processing sheet with id= K, first strand: chain 'C' and resid 632 through 635 Processing sheet with id= L, first strand: chain 'C' and resid 686 through 691 Processing sheet with id= M, first strand: chain 'C' and resid 745 through 748 Processing sheet with id= N, first strand: chain 'C' and resid 807 through 809 removed outlier: 4.610A pdb=" N ILE C 807 " --> pdb=" O ILE C 780 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA C1000 " --> pdb=" O GLY C 781 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N VAL C 783 " --> pdb=" O ALA C1000 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL C1002 " --> pdb=" O VAL C 783 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE C1023 " --> pdb=" O LEU C1001 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL C1003 " --> pdb=" O PHE C1023 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL C1025 " --> pdb=" O VAL C1003 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N MET C1040 " --> pdb=" O VAL C1026 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASP C1028 " --> pdb=" O MET C1040 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL C1042 " --> pdb=" O ASP C1028 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 865 through 867 removed outlier: 6.222A pdb=" N VAL C 841 " --> pdb=" O VAL C 866 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLY C 964 " --> pdb=" O ILE C 933 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ILE C 935 " --> pdb=" O GLY C 964 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE C 966 " --> pdb=" O ILE C 935 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 1052 through 1055 Processing sheet with id= Q, first strand: chain 'D' and resid 127 through 132 removed outlier: 7.102A pdb=" N TYR D 88 " --> pdb=" O THR D 128 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N GLU D 130 " --> pdb=" O TYR D 88 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE D 90 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL D 132 " --> pdb=" O ILE D 90 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLN D 92 " --> pdb=" O VAL D 132 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 35 through 38 removed outlier: 3.955A pdb=" N LYS E 2 " --> pdb=" O PHE E 54 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 305 through 309 removed outlier: 6.482A pdb=" N TYR E 177 " --> pdb=" O ASN E 306 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ASN E 308 " --> pdb=" O TYR E 177 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL E 179 " --> pdb=" O ASN E 308 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLU E 218 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N CYS E 180 " --> pdb=" O GLU E 218 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N HIS E 220 " --> pdb=" O CYS E 180 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ALA E 182 " --> pdb=" O HIS E 220 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N TYR E 222 " --> pdb=" O ALA E 182 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASP E 259 " --> pdb=" O GLY E 219 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ILE E 221 " --> pdb=" O ASP E 259 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LYS E 261 " --> pdb=" O ILE E 221 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N CYS E 223 " --> pdb=" O LYS E 261 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LYS E 263 " --> pdb=" O CYS E 223 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'E' and resid 351 through 355 Processing sheet with id= U, first strand: chain 'E' and resid 528 through 531 Processing sheet with id= V, first strand: chain 'F' and resid 5 through 8 Processing sheet with id= W, first strand: chain 'F' and resid 466 through 468 removed outlier: 6.394A pdb=" N VAL F 281 " --> pdb=" O PHE F 467 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LYS F 217 " --> pdb=" O VAL F 195 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL F 197 " --> pdb=" O LYS F 217 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL F 219 " --> pdb=" O VAL F 197 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLU F 258 " --> pdb=" O ILE F 220 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 303 through 305 removed outlier: 6.468A pdb=" N ILE F 428 " --> pdb=" O LEU F 304 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU F 348 " --> pdb=" O VAL F 325 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL F 327 " --> pdb=" O GLU F 348 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR F 350 " --> pdb=" O VAL F 327 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LYS F 376 " --> pdb=" O ILE F 351 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 420 through 424 removed outlier: 5.354A pdb=" N GLU F 399 " --> pdb=" O PRO F 383 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 606 through 608 Processing sheet with id= AA, first strand: chain 'F' and resid 632 through 635 Processing sheet with id= AB, first strand: chain 'F' and resid 686 through 691 Processing sheet with id= AC, first strand: chain 'F' and resid 745 through 748 Processing sheet with id= AD, first strand: chain 'F' and resid 807 through 809 removed outlier: 4.610A pdb=" N ILE F 807 " --> pdb=" O ILE F 780 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA F1000 " --> pdb=" O GLY F 781 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N VAL F 783 " --> pdb=" O ALA F1000 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL F1002 " --> pdb=" O VAL F 783 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE F1023 " --> pdb=" O LEU F1001 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL F1003 " --> pdb=" O PHE F1023 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL F1025 " --> pdb=" O VAL F1003 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N MET F1040 " --> pdb=" O VAL F1026 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ASP F1028 " --> pdb=" O MET F1040 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL F1042 " --> pdb=" O ASP F1028 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 865 through 867 removed outlier: 6.222A pdb=" N VAL F 841 " --> pdb=" O VAL F 866 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLY F 964 " --> pdb=" O ILE F 933 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ILE F 935 " --> pdb=" O GLY F 964 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE F 966 " --> pdb=" O ILE F 935 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 1052 through 1055 Processing sheet with id= AG, first strand: chain 'G' and resid 127 through 132 removed outlier: 7.102A pdb=" N TYR G 88 " --> pdb=" O THR G 128 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N GLU G 130 " --> pdb=" O TYR G 88 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE G 90 " --> pdb=" O GLU G 130 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL G 132 " --> pdb=" O ILE G 90 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLN G 92 " --> pdb=" O VAL G 132 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'H' and resid 35 through 38 removed outlier: 3.954A pdb=" N LYS H 2 " --> pdb=" O PHE H 54 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'H' and resid 305 through 309 removed outlier: 6.482A pdb=" N TYR H 177 " --> pdb=" O ASN H 306 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ASN H 308 " --> pdb=" O TYR H 177 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL H 179 " --> pdb=" O ASN H 308 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLU H 218 " --> pdb=" O VAL H 178 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N CYS H 180 " --> pdb=" O GLU H 218 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N HIS H 220 " --> pdb=" O CYS H 180 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ALA H 182 " --> pdb=" O HIS H 220 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N TYR H 222 " --> pdb=" O ALA H 182 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASP H 259 " --> pdb=" O GLY H 219 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ILE H 221 " --> pdb=" O ASP H 259 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LYS H 261 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N CYS H 223 " --> pdb=" O LYS H 261 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LYS H 263 " --> pdb=" O CYS H 223 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'H' and resid 351 through 355 Processing sheet with id= AK, first strand: chain 'H' and resid 528 through 531 Processing sheet with id= AL, first strand: chain 'I' and resid 5 through 8 Processing sheet with id= AM, first strand: chain 'I' and resid 466 through 468 removed outlier: 6.394A pdb=" N VAL I 281 " --> pdb=" O PHE I 467 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LYS I 217 " --> pdb=" O VAL I 195 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL I 197 " --> pdb=" O LYS I 217 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL I 219 " --> pdb=" O VAL I 197 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLU I 258 " --> pdb=" O ILE I 220 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'I' and resid 303 through 305 removed outlier: 6.468A pdb=" N ILE I 428 " --> pdb=" O LEU I 304 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU I 348 " --> pdb=" O VAL I 325 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL I 327 " --> pdb=" O GLU I 348 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR I 350 " --> pdb=" O VAL I 327 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LYS I 376 " --> pdb=" O ILE I 351 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'I' and resid 420 through 424 removed outlier: 5.354A pdb=" N GLU I 399 " --> pdb=" O PRO I 383 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'I' and resid 606 through 608 Processing sheet with id= AQ, first strand: chain 'I' and resid 632 through 635 Processing sheet with id= AR, first strand: chain 'I' and resid 686 through 691 Processing sheet with id= AS, first strand: chain 'I' and resid 745 through 748 Processing sheet with id= AT, first strand: chain 'I' and resid 807 through 809 removed outlier: 4.610A pdb=" N ILE I 807 " --> pdb=" O ILE I 780 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA I1000 " --> pdb=" O GLY I 781 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N VAL I 783 " --> pdb=" O ALA I1000 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL I1002 " --> pdb=" O VAL I 783 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE I1023 " --> pdb=" O LEU I1001 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL I1003 " --> pdb=" O PHE I1023 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL I1025 " --> pdb=" O VAL I1003 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N MET I1040 " --> pdb=" O VAL I1026 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ASP I1028 " --> pdb=" O MET I1040 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL I1042 " --> pdb=" O ASP I1028 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'I' and resid 865 through 867 removed outlier: 6.222A pdb=" N VAL I 841 " --> pdb=" O VAL I 866 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY I 964 " --> pdb=" O ILE I 933 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ILE I 935 " --> pdb=" O GLY I 964 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE I 966 " --> pdb=" O ILE I 935 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'I' and resid 1052 through 1055 Processing sheet with id= AW, first strand: chain 'J' and resid 127 through 132 removed outlier: 7.102A pdb=" N TYR J 88 " --> pdb=" O THR J 128 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N GLU J 130 " --> pdb=" O TYR J 88 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE J 90 " --> pdb=" O GLU J 130 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL J 132 " --> pdb=" O ILE J 90 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLN J 92 " --> pdb=" O VAL J 132 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'K' and resid 35 through 38 removed outlier: 3.955A pdb=" N LYS K 2 " --> pdb=" O PHE K 54 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'K' and resid 305 through 309 removed outlier: 6.482A pdb=" N TYR K 177 " --> pdb=" O ASN K 306 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ASN K 308 " --> pdb=" O TYR K 177 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL K 179 " --> pdb=" O ASN K 308 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLU K 218 " --> pdb=" O VAL K 178 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N CYS K 180 " --> pdb=" O GLU K 218 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N HIS K 220 " --> pdb=" O CYS K 180 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ALA K 182 " --> pdb=" O HIS K 220 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N TYR K 222 " --> pdb=" O ALA K 182 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASP K 259 " --> pdb=" O GLY K 219 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ILE K 221 " --> pdb=" O ASP K 259 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LYS K 261 " --> pdb=" O ILE K 221 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N CYS K 223 " --> pdb=" O LYS K 261 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LYS K 263 " --> pdb=" O CYS K 223 " (cutoff:3.500A) No H-bonds generated for sheet with id= AY Processing sheet with id= AZ, first strand: chain 'K' and resid 351 through 355 Processing sheet with id= BA, first strand: chain 'K' and resid 528 through 531 Processing sheet with id= BB, first strand: chain 'L' and resid 5 through 8 Processing sheet with id= BC, first strand: chain 'L' and resid 466 through 468 removed outlier: 6.394A pdb=" N VAL L 281 " --> pdb=" O PHE L 467 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LYS L 217 " --> pdb=" O VAL L 195 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL L 197 " --> pdb=" O LYS L 217 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL L 219 " --> pdb=" O VAL L 197 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLU L 258 " --> pdb=" O ILE L 220 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'L' and resid 303 through 305 removed outlier: 6.468A pdb=" N ILE L 428 " --> pdb=" O LEU L 304 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU L 348 " --> pdb=" O VAL L 325 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL L 327 " --> pdb=" O GLU L 348 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR L 350 " --> pdb=" O VAL L 327 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LYS L 376 " --> pdb=" O ILE L 351 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'L' and resid 420 through 424 removed outlier: 5.354A pdb=" N GLU L 399 " --> pdb=" O PRO L 383 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'L' and resid 606 through 608 Processing sheet with id= BG, first strand: chain 'L' and resid 632 through 635 Processing sheet with id= BH, first strand: chain 'L' and resid 686 through 691 Processing sheet with id= BI, first strand: chain 'L' and resid 745 through 748 Processing sheet with id= BJ, first strand: chain 'L' and resid 807 through 809 removed outlier: 4.609A pdb=" N ILE L 807 " --> pdb=" O ILE L 780 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA L1000 " --> pdb=" O GLY L 781 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL L 783 " --> pdb=" O ALA L1000 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL L1002 " --> pdb=" O VAL L 783 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE L1023 " --> pdb=" O LEU L1001 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL L1003 " --> pdb=" O PHE L1023 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL L1025 " --> pdb=" O VAL L1003 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N MET L1040 " --> pdb=" O VAL L1026 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ASP L1028 " --> pdb=" O MET L1040 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL L1042 " --> pdb=" O ASP L1028 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'L' and resid 865 through 867 removed outlier: 6.222A pdb=" N VAL L 841 " --> pdb=" O VAL L 866 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY L 964 " --> pdb=" O ILE L 933 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ILE L 935 " --> pdb=" O GLY L 964 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE L 966 " --> pdb=" O ILE L 935 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'L' and resid 1052 through 1055 1740 hydrogen bonds defined for protein. 4992 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: 22.62 Time building geometry restraints manager: 18.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.41: 23219 1.41 - 1.63: 35393 1.63 - 1.85: 648 1.85 - 2.07: 0 2.07 - 2.28: 480 Bond restraints: 59740 Sorted by residual: bond pdb=" C3N NAD B 606 " pdb=" C4N NAD B 606 " ideal model delta sigma weight residual 1.390 1.506 -0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" C3N NAD K 606 " pdb=" C4N NAD K 606 " ideal model delta sigma weight residual 1.390 1.506 -0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" C3N NAD H 606 " pdb=" C4N NAD H 606 " ideal model delta sigma weight residual 1.390 1.506 -0.116 2.00e-02 2.50e+03 3.35e+01 bond pdb=" C3N NAD E 606 " pdb=" C4N NAD E 606 " ideal model delta sigma weight residual 1.390 1.506 -0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" O2B NDP L1203 " pdb=" P2B NDP L1203 " ideal model delta sigma weight residual 1.833 1.631 0.202 3.80e-02 6.93e+02 2.81e+01 ... (remaining 59735 not shown) Histogram of bond angle deviations from ideal: 73.42 - 86.57: 456 86.57 - 99.72: 40 99.72 - 112.87: 33542 112.87 - 126.02: 46492 126.02 - 139.18: 650 Bond angle restraints: 81180 Sorted by residual: angle pdb=" C5B NDP I1203 " pdb=" O5B NDP I1203 " pdb=" PA NDP I1203 " ideal model delta sigma weight residual 103.84 122.80 -18.96 1.91e+00 2.73e-01 9.81e+01 angle pdb=" C5B NDP C1203 " pdb=" O5B NDP C1203 " pdb=" PA NDP C1203 " ideal model delta sigma weight residual 103.84 122.80 -18.96 1.91e+00 2.73e-01 9.81e+01 angle pdb=" C5B NDP F1203 " pdb=" O5B NDP F1203 " pdb=" PA NDP F1203 " ideal model delta sigma weight residual 103.84 122.80 -18.96 1.91e+00 2.73e-01 9.81e+01 angle pdb=" C5B NDP L1203 " pdb=" O5B NDP L1203 " pdb=" PA NDP L1203 " ideal model delta sigma weight residual 103.84 122.77 -18.93 1.91e+00 2.73e-01 9.77e+01 angle pdb=" PA NDP L1203 " pdb=" O3 NDP L1203 " pdb=" PN NDP L1203 " ideal model delta sigma weight residual 107.74 125.45 -17.71 1.95e+00 2.62e-01 8.21e+01 ... (remaining 81175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.68: 34933 33.68 - 67.35: 1091 67.35 - 101.03: 100 101.03 - 134.70: 4 134.70 - 168.38: 4 Dihedral angle restraints: 36132 sinusoidal: 14448 harmonic: 21684 Sorted by residual: dihedral pdb=" C10 FMN K 603 " pdb=" C1' FMN K 603 " pdb=" N10 FMN K 603 " pdb=" C2' FMN K 603 " ideal model delta sinusoidal sigma weight residual -102.41 65.97 -168.38 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C10 FMN B 603 " pdb=" C1' FMN B 603 " pdb=" N10 FMN B 603 " pdb=" C2' FMN B 603 " ideal model delta sinusoidal sigma weight residual -102.41 65.93 -168.34 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C10 FMN E 603 " pdb=" C1' FMN E 603 " pdb=" N10 FMN E 603 " pdb=" C2' FMN E 603 " ideal model delta sinusoidal sigma weight residual -102.41 65.92 -168.33 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 36129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 8447 0.084 - 0.169: 837 0.169 - 0.253: 20 0.253 - 0.338: 12 0.338 - 0.422: 4 Chirality restraints: 9320 Sorted by residual: chirality pdb=" C2D NDP L1203 " pdb=" C1D NDP L1203 " pdb=" C3D NDP L1203 " pdb=" O2D NDP L1203 " both_signs ideal model delta sigma weight residual False -2.71 -2.28 -0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" C2D NDP F1203 " pdb=" C1D NDP F1203 " pdb=" C3D NDP F1203 " pdb=" O2D NDP F1203 " both_signs ideal model delta sigma weight residual False -2.71 -2.28 -0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" C2D NDP C1203 " pdb=" C1D NDP C1203 " pdb=" C3D NDP C1203 " pdb=" O2D NDP C1203 " both_signs ideal model delta sigma weight residual False -2.71 -2.29 -0.42 2.00e-01 2.50e+01 4.43e+00 ... (remaining 9317 not shown) Planarity restraints: 10340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP F1203 " 0.329 2.00e-02 2.50e+03 2.42e-01 7.31e+02 pdb=" C3N NDP F1203 " 0.204 2.00e-02 2.50e+03 pdb=" C4N NDP F1203 " -0.004 2.00e-02 2.50e+03 pdb=" C7N NDP F1203 " -0.234 2.00e-02 2.50e+03 pdb=" N1N NDP F1203 " -0.296 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP L1203 " -0.329 2.00e-02 2.50e+03 2.42e-01 7.31e+02 pdb=" C3N NDP L1203 " -0.204 2.00e-02 2.50e+03 pdb=" C4N NDP L1203 " 0.004 2.00e-02 2.50e+03 pdb=" C7N NDP L1203 " 0.233 2.00e-02 2.50e+03 pdb=" N1N NDP L1203 " 0.296 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP C1203 " -0.329 2.00e-02 2.50e+03 2.42e-01 7.30e+02 pdb=" C3N NDP C1203 " -0.204 2.00e-02 2.50e+03 pdb=" C4N NDP C1203 " 0.004 2.00e-02 2.50e+03 pdb=" C7N NDP C1203 " 0.233 2.00e-02 2.50e+03 pdb=" N1N NDP C1203 " 0.296 2.00e-02 2.50e+03 ... (remaining 10337 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 3581 2.73 - 3.27: 55837 3.27 - 3.82: 94803 3.82 - 4.36: 119432 4.36 - 4.90: 203271 Nonbonded interactions: 476924 Sorted by model distance: nonbonded pdb=" O TRP E 318 " pdb=" OH TYR E 327 " model vdw 2.190 2.440 nonbonded pdb=" O TRP B 318 " pdb=" OH TYR B 327 " model vdw 2.191 2.440 nonbonded pdb=" O TRP K 318 " pdb=" OH TYR K 327 " model vdw 2.191 2.440 nonbonded pdb=" O TRP H 318 " pdb=" OH TYR H 327 " model vdw 2.191 2.440 nonbonded pdb=" ND2 ASN F 332 " pdb=" O7N NDP F1203 " model vdw 2.224 2.520 ... (remaining 476919 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 15.270 Check model and map are aligned: 0.670 Set scattering table: 0.410 Process input model: 136.910 Find NCS groups from input model: 2.960 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 169.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 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 : 0.007 0.202 59740 Z= 0.439 Angle : 0.899 18.963 81180 Z= 0.453 Chirality : 0.050 0.422 9320 Planarity : 0.010 0.340 10340 Dihedral : 16.084 168.379 22308 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.37 % Favored : 95.32 % Rotamer: Outliers : 0.52 % Allowed : 15.20 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -0.48 (0.09), residues: 7600 helix: -0.22 (0.09), residues: 2876 sheet: 0.50 (0.17), residues: 1020 loop : -0.51 (0.10), residues: 3704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP L1122 HIS 0.004 0.001 HIS F 96 PHE 0.031 0.002 PHE G 76 TYR 0.026 0.002 TYR F 117 ARG 0.007 0.001 ARG L 427 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 624 time to evaluate : 5.046 Fit side-chains outliers start: 32 outliers final: 11 residues processed: 638 average time/residue: 1.2810 time to fit residues: 1064.3286 Evaluate side-chains 580 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 569 time to evaluate : 4.933 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 0.4965 time to fit residues: 10.3039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 641 optimal weight: 30.0000 chunk 576 optimal weight: 4.9990 chunk 319 optimal weight: 2.9990 chunk 196 optimal weight: 0.4980 chunk 388 optimal weight: 9.9990 chunk 307 optimal weight: 3.9990 chunk 595 optimal weight: 30.0000 chunk 230 optimal weight: 7.9990 chunk 362 optimal weight: 9.9990 chunk 443 optimal weight: 5.9990 chunk 690 optimal weight: 2.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 661 GLN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 661 GLN ** F 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 661 GLN ** I 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 661 GLN ** L 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.0698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 59740 Z= 0.312 Angle : 0.589 15.051 81180 Z= 0.298 Chirality : 0.046 0.288 9320 Planarity : 0.005 0.053 10340 Dihedral : 8.788 165.940 8692 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.80 % Favored : 95.93 % Rotamer: Outliers : 3.20 % Allowed : 16.04 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.10), residues: 7600 helix: 0.15 (0.10), residues: 2888 sheet: 0.53 (0.17), residues: 972 loop : -0.43 (0.10), residues: 3740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C1122 HIS 0.004 0.001 HIS C 96 PHE 0.027 0.002 PHE A 76 TYR 0.024 0.001 TYR L 117 ARG 0.005 0.000 ARG F 787 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 605 time to evaluate : 5.177 Fit side-chains outliers start: 197 outliers final: 70 residues processed: 700 average time/residue: 1.2801 time to fit residues: 1171.8837 Evaluate side-chains 631 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 561 time to evaluate : 5.023 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 47 residues processed: 23 average time/residue: 0.5347 time to fit residues: 28.2805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 383 optimal weight: 9.9990 chunk 214 optimal weight: 1.9990 chunk 574 optimal weight: 9.9990 chunk 469 optimal weight: 1.9990 chunk 190 optimal weight: 20.0000 chunk 691 optimal weight: 0.8980 chunk 746 optimal weight: 7.9990 chunk 615 optimal weight: 1.9990 chunk 685 optimal weight: 6.9990 chunk 235 optimal weight: 0.9990 chunk 554 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN B 382 GLN C 19 GLN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN E 382 GLN F 19 GLN H 382 GLN ** I 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 382 GLN L 19 GLN ** L 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 59740 Z= 0.170 Angle : 0.509 10.194 81180 Z= 0.260 Chirality : 0.043 0.275 9320 Planarity : 0.004 0.050 10340 Dihedral : 8.622 168.321 8692 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.43 % Favored : 96.36 % Rotamer: Outliers : 2.79 % Allowed : 18.01 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: 0.16 (0.10), residues: 7600 helix: 0.55 (0.10), residues: 2872 sheet: 0.60 (0.17), residues: 980 loop : -0.28 (0.10), residues: 3748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP F1122 HIS 0.002 0.000 HIS C 96 PHE 0.025 0.001 PHE G 76 TYR 0.028 0.001 TYR H 47 ARG 0.002 0.000 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 619 time to evaluate : 5.167 Fit side-chains outliers start: 172 outliers final: 87 residues processed: 735 average time/residue: 1.2300 time to fit residues: 1196.3863 Evaluate side-chains 653 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 566 time to evaluate : 4.918 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 83 residues processed: 4 average time/residue: 0.4100 time to fit residues: 9.9430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 683 optimal weight: 20.0000 chunk 519 optimal weight: 2.9990 chunk 358 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 329 optimal weight: 2.9990 chunk 464 optimal weight: 6.9990 chunk 693 optimal weight: 0.0770 chunk 734 optimal weight: 20.0000 chunk 362 optimal weight: 9.9990 chunk 657 optimal weight: 1.9990 chunk 197 optimal weight: 20.0000 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 382 GLN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 680 GLN E 382 GLN ** F 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 680 GLN H 382 GLN ** I 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 680 GLN K 382 GLN ** L 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 680 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 59740 Z= 0.256 Angle : 0.551 15.472 81180 Z= 0.279 Chirality : 0.044 0.279 9320 Planarity : 0.004 0.048 10340 Dihedral : 8.640 168.086 8692 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.25 % Favored : 95.59 % Rotamer: Outliers : 4.23 % Allowed : 17.75 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: 0.16 (0.10), residues: 7600 helix: 0.63 (0.10), residues: 2880 sheet: 0.63 (0.17), residues: 1008 loop : -0.37 (0.10), residues: 3712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP L1122 HIS 0.003 0.001 HIS C 96 PHE 0.027 0.001 PHE J 76 TYR 0.019 0.001 TYR F 117 ARG 0.003 0.000 ARG L 787 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 584 time to evaluate : 5.052 Fit side-chains outliers start: 261 outliers final: 118 residues processed: 760 average time/residue: 1.1877 time to fit residues: 1207.9173 Evaluate side-chains 686 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 568 time to evaluate : 4.965 Switching outliers to nearest non-outliers outliers start: 118 outliers final: 94 residues processed: 24 average time/residue: 0.4714 time to fit residues: 27.4812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 611 optimal weight: 6.9990 chunk 417 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 546 optimal weight: 9.9990 chunk 303 optimal weight: 7.9990 chunk 626 optimal weight: 30.0000 chunk 507 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 375 optimal weight: 3.9990 chunk 659 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 ASN B 382 GLN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 ASN E 306 ASN E 382 GLN ** F 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 719 ASN H 306 ASN H 382 GLN ** I 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 719 ASN K 306 ASN K 382 GLN ** L 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 719 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 59740 Z= 0.488 Angle : 0.690 12.641 81180 Z= 0.349 Chirality : 0.051 0.305 9320 Planarity : 0.005 0.063 10340 Dihedral : 9.177 164.007 8692 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.95 % Favored : 94.89 % Rotamer: Outliers : 5.60 % Allowed : 16.97 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.30 (0.10), residues: 7600 helix: 0.24 (0.10), residues: 2876 sheet: 0.42 (0.16), residues: 1076 loop : -0.66 (0.10), residues: 3648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP L1122 HIS 0.005 0.001 HIS C 149 PHE 0.032 0.002 PHE G 76 TYR 0.026 0.002 TYR K 47 ARG 0.005 0.001 ARG F 787 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 345 poor density : 583 time to evaluate : 5.054 Fit side-chains revert: symmetry clash outliers start: 345 outliers final: 156 residues processed: 822 average time/residue: 1.1534 time to fit residues: 1278.9337 Evaluate side-chains 705 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 549 time to evaluate : 5.036 Switching outliers to nearest non-outliers outliers start: 156 outliers final: 147 residues processed: 9 average time/residue: 0.4387 time to fit residues: 14.4267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 247 optimal weight: 10.0000 chunk 661 optimal weight: 10.0000 chunk 145 optimal weight: 0.9990 chunk 431 optimal weight: 0.2980 chunk 181 optimal weight: 4.9990 chunk 735 optimal weight: 4.9990 chunk 610 optimal weight: 0.5980 chunk 340 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 chunk 243 optimal weight: 20.0000 chunk 386 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 382 GLN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 ASN E 382 GLN ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 382 GLN ** I 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 719 ASN K 382 GLN ** L 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 719 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 59740 Z= 0.139 Angle : 0.519 12.778 81180 Z= 0.264 Chirality : 0.042 0.279 9320 Planarity : 0.004 0.049 10340 Dihedral : 8.578 169.687 8692 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.49 % Favored : 96.36 % Rotamer: Outliers : 4.43 % Allowed : 18.25 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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 (0.10), residues: 7600 helix: 0.70 (0.10), residues: 2860 sheet: 0.52 (0.17), residues: 992 loop : -0.38 (0.10), residues: 3748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP I1122 HIS 0.002 0.000 HIS C 96 PHE 0.024 0.001 PHE D 76 TYR 0.021 0.001 TYR F 117 ARG 0.002 0.000 ARG K 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 599 time to evaluate : 5.101 Fit side-chains revert: symmetry clash outliers start: 273 outliers final: 162 residues processed: 791 average time/residue: 1.1983 time to fit residues: 1267.7780 Evaluate side-chains 725 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 563 time to evaluate : 4.982 Switching outliers to nearest non-outliers outliers start: 162 outliers final: 146 residues processed: 20 average time/residue: 0.5583 time to fit residues: 25.7550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 708 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 418 optimal weight: 6.9990 chunk 536 optimal weight: 9.9990 chunk 416 optimal weight: 20.0000 chunk 618 optimal weight: 2.9990 chunk 410 optimal weight: 20.0000 chunk 732 optimal weight: 5.9990 chunk 458 optimal weight: 0.8980 chunk 446 optimal weight: 8.9990 chunk 338 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 GLN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 ASN ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 382 GLN ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 382 GLN ** I 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 719 ASN ** K 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 382 GLN ** L 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 719 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 59740 Z= 0.283 Angle : 0.578 13.359 81180 Z= 0.292 Chirality : 0.045 0.300 9320 Planarity : 0.004 0.049 10340 Dihedral : 8.659 169.750 8692 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.57 % Favored : 95.28 % Rotamer: Outliers : 3.73 % Allowed : 19.52 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.08 (0.10), residues: 7600 helix: 0.61 (0.10), residues: 2892 sheet: 0.53 (0.17), residues: 1020 loop : -0.45 (0.10), residues: 3688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F1122 HIS 0.003 0.001 HIS C 149 PHE 0.030 0.002 PHE G 76 TYR 0.020 0.001 TYR C 117 ARG 0.003 0.000 ARG D 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 579 time to evaluate : 5.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 230 outliers final: 166 residues processed: 756 average time/residue: 1.2108 time to fit residues: 1224.1211 Evaluate side-chains 715 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 549 time to evaluate : 5.001 Switching outliers to nearest non-outliers outliers start: 166 outliers final: 157 residues processed: 9 average time/residue: 0.6344 time to fit residues: 16.1037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 453 optimal weight: 4.9990 chunk 292 optimal weight: 9.9990 chunk 437 optimal weight: 0.9990 chunk 220 optimal weight: 20.0000 chunk 143 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 465 optimal weight: 0.9980 chunk 499 optimal weight: 6.9990 chunk 362 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 575 optimal weight: 0.4980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 GLN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 ASN ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 382 GLN ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 382 GLN ** I 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 719 ASN ** K 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 382 GLN ** L 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 719 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 59740 Z= 0.242 Angle : 0.557 11.382 81180 Z= 0.283 Chirality : 0.045 0.296 9320 Planarity : 0.004 0.049 10340 Dihedral : 8.605 170.724 8692 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.01 % Favored : 95.83 % Rotamer: Outliers : 3.76 % Allowed : 19.73 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: 0.17 (0.10), residues: 7600 helix: 0.72 (0.10), residues: 2856 sheet: 0.49 (0.17), residues: 1024 loop : -0.40 (0.10), residues: 3720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C1122 HIS 0.003 0.001 HIS C 96 PHE 0.029 0.001 PHE G 76 TYR 0.025 0.001 TYR E 47 ARG 0.005 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 585 time to evaluate : 5.459 Fit side-chains outliers start: 232 outliers final: 167 residues processed: 764 average time/residue: 1.2240 time to fit residues: 1253.6920 Evaluate side-chains 730 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 563 time to evaluate : 5.019 Switching outliers to nearest non-outliers outliers start: 167 outliers final: 162 residues processed: 7 average time/residue: 0.7555 time to fit residues: 14.9130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 666 optimal weight: 0.2980 chunk 701 optimal weight: 0.1980 chunk 640 optimal weight: 7.9990 chunk 682 optimal weight: 10.0000 chunk 410 optimal weight: 20.0000 chunk 297 optimal weight: 5.9990 chunk 536 optimal weight: 7.9990 chunk 209 optimal weight: 10.0000 chunk 616 optimal weight: 0.0270 chunk 645 optimal weight: 5.9990 chunk 680 optimal weight: 4.9990 overall best weight: 2.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 GLN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 ASN ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 382 GLN ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 382 GLN ** I 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 719 ASN ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 382 GLN ** L 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 719 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 59740 Z= 0.247 Angle : 0.570 12.589 81180 Z= 0.289 Chirality : 0.045 0.289 9320 Planarity : 0.004 0.049 10340 Dihedral : 8.607 171.106 8692 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.47 % Favored : 95.37 % Rotamer: Outliers : 3.34 % Allowed : 20.39 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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 (0.10), residues: 7600 helix: 0.66 (0.10), residues: 2876 sheet: 0.47 (0.17), residues: 1024 loop : -0.42 (0.10), residues: 3700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP K 165 HIS 0.003 0.001 HIS C 96 PHE 0.029 0.001 PHE G 76 TYR 0.023 0.001 TYR E 47 ARG 0.007 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 579 time to evaluate : 5.476 Fit side-chains outliers start: 206 outliers final: 176 residues processed: 755 average time/residue: 1.2133 time to fit residues: 1231.0946 Evaluate side-chains 741 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 565 time to evaluate : 5.064 Switching outliers to nearest non-outliers outliers start: 176 outliers final: 165 residues processed: 13 average time/residue: 0.7456 time to fit residues: 21.8468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 448 optimal weight: 2.9990 chunk 721 optimal weight: 3.9990 chunk 440 optimal weight: 6.9990 chunk 342 optimal weight: 2.9990 chunk 501 optimal weight: 1.9990 chunk 757 optimal weight: 3.9990 chunk 696 optimal weight: 8.9990 chunk 602 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 465 optimal weight: 3.9990 chunk 369 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 GLN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 ASN ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 382 GLN ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 382 GLN ** I 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 719 ASN ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 382 GLN ** L 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 719 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 59740 Z= 0.318 Angle : 0.611 12.491 81180 Z= 0.309 Chirality : 0.046 0.297 9320 Planarity : 0.004 0.049 10340 Dihedral : 8.543 169.953 8692 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.38 % Favored : 95.46 % Rotamer: Outliers : 3.50 % Allowed : 20.34 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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 (0.10), residues: 7600 helix: 0.60 (0.10), residues: 2852 sheet: 0.38 (0.17), residues: 1024 loop : -0.48 (0.10), residues: 3724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP K 165 HIS 0.003 0.001 HIS C 96 PHE 0.032 0.002 PHE G 76 TYR 0.023 0.002 TYR H 62 ARG 0.007 0.000 ARG D 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 561 time to evaluate : 5.026 Fit side-chains outliers start: 216 outliers final: 170 residues processed: 746 average time/residue: 1.2186 time to fit residues: 1224.1916 Evaluate side-chains 713 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 543 time to evaluate : 5.036 Switching outliers to nearest non-outliers outliers start: 170 outliers final: 163 residues processed: 7 average time/residue: 0.7238 time to fit residues: 15.0112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 478 optimal weight: 0.9980 chunk 642 optimal weight: 0.0020 chunk 184 optimal weight: 8.9990 chunk 555 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 167 optimal weight: 0.4980 chunk 603 optimal weight: 20.0000 chunk 252 optimal weight: 5.9990 chunk 620 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 GLN ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 382 GLN H 77 HIS ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 382 GLN ** I 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 382 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.186742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.143570 restraints weight = 62630.322| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.05 r_work: 0.3133 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 59740 Z= 0.145 Angle : 0.530 11.480 81180 Z= 0.269 Chirality : 0.043 0.274 9320 Planarity : 0.004 0.049 10340 Dihedral : 8.060 173.532 8692 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.97 % Favored : 95.87 % Rotamer: Outliers : 3.11 % Allowed : 20.83 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: 0.27 (0.10), residues: 7600 helix: 0.80 (0.10), residues: 2880 sheet: 0.43 (0.17), residues: 1024 loop : -0.30 (0.11), residues: 3696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 165 HIS 0.001 0.000 HIS C 96 PHE 0.025 0.001 PHE G 76 TYR 0.030 0.001 TYR K 47 ARG 0.009 0.000 ARG J 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18220.31 seconds wall clock time: 317 minutes 39.15 seconds (19059.15 seconds total)