Starting phenix.real_space_refine on Wed Feb 14 06:08:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oh5_16878/02_2024/8oh5_16878_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oh5_16878/02_2024/8oh5_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_16878/02_2024/8oh5_16878.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oh5_16878/02_2024/8oh5_16878.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oh5_16878/02_2024/8oh5_16878_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oh5_16878/02_2024/8oh5_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-dev-5238/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: 23.07, per 1000 atoms: 0.39 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: 17.38 Conformation dependent library (CDL) restraints added in 7.8 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: 10.97 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: 21.34 Time building geometry restraints manager: 19.30 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.660 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: 0.030 Extract box with map and model: 15.010 Check model and map are aligned: 0.630 Set scattering table: 0.420 Process input model: 136.240 Find NCS groups from input model: 2.920 Set up NCS constraints: 0.420 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:9.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 169.040 ------------------------------------------------------------------------------- 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 : 4.788 Fit side-chains REVERT: A 145 MET cc_start: 0.6654 (tpp) cc_final: 0.6066 (tpp) REVERT: C 502 VAL cc_start: 0.8593 (m) cc_final: 0.8320 (t) REVERT: D 145 MET cc_start: 0.6636 (tpp) cc_final: 0.6357 (mmt) REVERT: F 366 GLU cc_start: 0.7566 (tp30) cc_final: 0.7034 (tp30) REVERT: F 502 VAL cc_start: 0.8587 (m) cc_final: 0.8318 (t) REVERT: G 145 MET cc_start: 0.6626 (tpp) cc_final: 0.6333 (mmt) REVERT: I 502 VAL cc_start: 0.8589 (m) cc_final: 0.8321 (t) REVERT: J 145 MET cc_start: 0.6623 (tpp) cc_final: 0.6329 (mmt) REVERT: L 502 VAL cc_start: 0.8597 (m) cc_final: 0.8328 (t) outliers start: 32 outliers final: 11 residues processed: 638 average time/residue: 1.2762 time to fit residues: 1057.6892 Evaluate side-chains 580 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 569 time to evaluate : 4.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 809 THR Chi-restraints excluded: chain C residue 890 VAL Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain F residue 809 THR Chi-restraints excluded: chain F residue 890 VAL Chi-restraints excluded: chain H residue 183 ASP Chi-restraints excluded: chain I residue 809 THR Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain L residue 809 THR 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: A 42 GLN C 661 GLN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN F 661 GLN ** F 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.0716 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= 0.313 Angle : 0.587 14.116 81180 Z= 0.297 Chirality : 0.046 0.290 9320 Planarity : 0.005 0.054 10340 Dihedral : 8.828 165.580 8708 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.88 % Favored : 95.86 % Rotamer: Outliers : 2.97 % Allowed : 16.37 % Favored : 80.66 % 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: 0.54 (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 L 96 PHE 0.027 0.002 PHE A 76 TYR 0.024 0.001 TYR L 117 ARG 0.005 0.000 ARG I 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 798 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 615 time to evaluate : 4.886 Fit side-chains REVERT: B 227 TYR cc_start: 0.5315 (m-10) cc_final: 0.4982 (m-10) REVERT: C 1 MET cc_start: 0.5448 (ttt) cc_final: 0.5223 (ttt) REVERT: C 19 GLN cc_start: 0.8484 (mt0) cc_final: 0.8276 (mt0) REVERT: C 69 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7271 (mp10) REVERT: C 366 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: C 447 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.7217 (m-30) REVERT: C 502 VAL cc_start: 0.8617 (m) cc_final: 0.8349 (t) REVERT: C 1090 LYS cc_start: 0.8201 (mppt) cc_final: 0.8000 (tppt) REVERT: E 227 TYR cc_start: 0.5318 (m-10) cc_final: 0.4979 (m-10) REVERT: F 19 GLN cc_start: 0.8478 (mt0) cc_final: 0.8272 (mt0) REVERT: F 69 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7229 (mp10) REVERT: F 447 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.7232 (m-30) REVERT: F 502 VAL cc_start: 0.8621 (m) cc_final: 0.8352 (t) REVERT: I 19 GLN cc_start: 0.8481 (mt0) cc_final: 0.8276 (mt0) REVERT: I 69 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7234 (mp10) REVERT: I 366 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: I 447 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7231 (m-30) REVERT: I 502 VAL cc_start: 0.8616 (m) cc_final: 0.8348 (t) REVERT: L 19 GLN cc_start: 0.8479 (mt0) cc_final: 0.8271 (mt0) REVERT: L 69 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7232 (mp10) REVERT: L 308 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8247 (m-30) REVERT: L 364 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7664 (mttt) REVERT: L 366 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: L 447 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7217 (m-30) REVERT: L 502 VAL cc_start: 0.8619 (m) cc_final: 0.8353 (t) outliers start: 183 outliers final: 62 residues processed: 702 average time/residue: 1.2471 time to fit residues: 1145.9489 Evaluate side-chains 638 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 563 time to evaluate : 4.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 831 SER Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 387 SER Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain F residue 676 VAL Chi-restraints excluded: chain F residue 831 SER Chi-restraints excluded: chain F residue 1025 VAL Chi-restraints excluded: chain F residue 1136 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 387 SER Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain H residue 487 LEU Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain I residue 300 MET Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 447 ASP Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 676 VAL Chi-restraints excluded: chain I residue 831 SER Chi-restraints excluded: chain I residue 1025 VAL Chi-restraints excluded: chain I residue 1136 THR Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 127 TYR Chi-restraints excluded: chain K residue 387 SER Chi-restraints excluded: chain K residue 446 ILE Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain L residue 251 LEU Chi-restraints excluded: chain L residue 307 ILE Chi-restraints excluded: chain L residue 308 ASP Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 364 LYS Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain L residue 447 ASP Chi-restraints excluded: chain L residue 516 THR Chi-restraints excluded: chain L residue 676 VAL Chi-restraints excluded: chain L residue 831 SER Chi-restraints excluded: chain L residue 1025 VAL Chi-restraints excluded: chain L residue 1136 THR 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: 7.9990 chunk 574 optimal weight: 6.9990 chunk 469 optimal weight: 4.9990 chunk 190 optimal weight: 20.0000 chunk 691 optimal weight: 0.9990 chunk 746 optimal weight: 7.9990 chunk 615 optimal weight: 8.9990 chunk 685 optimal weight: 6.9990 chunk 235 optimal weight: 8.9990 chunk 554 optimal weight: 0.6980 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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: 0.8132 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 59740 Z= 0.398 Angle : 0.631 10.421 81180 Z= 0.322 Chirality : 0.048 0.299 9320 Planarity : 0.005 0.055 10340 Dihedral : 9.227 164.533 8694 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.16 % Favored : 95.63 % Rotamer: Outliers : 4.90 % Allowed : 16.90 % Favored : 78.20 % 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: -0.28 (0.10), residues: 7600 helix: 0.15 (0.10), residues: 2904 sheet: 0.46 (0.16), residues: 1048 loop : -0.57 (0.10), residues: 3648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP F1122 HIS 0.005 0.001 HIS C 96 PHE 0.029 0.002 PHE J 76 TYR 0.023 0.002 TYR L 117 ARG 0.004 0.001 ARG L 787 *********************** 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 901 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 599 time to evaluate : 4.831 Fit side-chains REVERT: A 145 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6281 (tpp) REVERT: B 207 MET cc_start: 0.4916 (OUTLIER) cc_final: 0.4627 (mtp) REVERT: C 1 MET cc_start: 0.5728 (ttt) cc_final: 0.5494 (ttt) REVERT: C 69 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7254 (mp10) REVERT: C 235 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8795 (mt) REVERT: C 366 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: C 447 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7297 (m-30) REVERT: C 502 VAL cc_start: 0.8770 (m) cc_final: 0.8512 (t) REVERT: C 534 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7194 (tm-30) REVERT: C 685 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.7376 (mmt) REVERT: C 1090 LYS cc_start: 0.8207 (mppt) cc_final: 0.7994 (tppt) REVERT: D 145 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.6263 (tpp) REVERT: E 207 MET cc_start: 0.4934 (OUTLIER) cc_final: 0.4665 (mtp) REVERT: F 69 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7255 (mp10) REVERT: F 235 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8792 (mt) REVERT: F 366 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6962 (mp0) REVERT: F 447 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7299 (m-30) REVERT: F 502 VAL cc_start: 0.8769 (m) cc_final: 0.8512 (t) REVERT: F 685 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.7390 (mmt) REVERT: G 145 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6273 (tpp) REVERT: H 207 MET cc_start: 0.4909 (OUTLIER) cc_final: 0.4606 (mtp) REVERT: I 69 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7256 (mp10) REVERT: I 235 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8792 (mt) REVERT: I 366 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: I 447 ASP cc_start: 0.7588 (OUTLIER) cc_final: 0.7296 (m-30) REVERT: I 502 VAL cc_start: 0.8767 (m) cc_final: 0.8510 (t) REVERT: I 534 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7155 (tm-30) REVERT: I 685 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.7380 (mmt) REVERT: I 1090 LYS cc_start: 0.8201 (mppt) cc_final: 0.7999 (tppt) REVERT: J 145 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6251 (tpp) REVERT: K 207 MET cc_start: 0.4945 (OUTLIER) cc_final: 0.4638 (mtp) REVERT: L 69 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7258 (mp10) REVERT: L 235 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8793 (mt) REVERT: L 366 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: L 447 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.7281 (m-30) REVERT: L 502 VAL cc_start: 0.8769 (m) cc_final: 0.8516 (t) REVERT: L 685 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.7378 (mmt) outliers start: 302 outliers final: 124 residues processed: 796 average time/residue: 1.1980 time to fit residues: 1265.9807 Evaluate side-chains 720 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 568 time to evaluate : 4.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 398 CYS Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 695 CYS Chi-restraints excluded: chain C residue 809 THR Chi-restraints excluded: chain C residue 831 SER Chi-restraints excluded: chain C residue 864 CYS Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 387 SER Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain E residue 528 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 308 ASP Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 398 CYS Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 559 SER Chi-restraints excluded: chain F residue 676 VAL Chi-restraints excluded: chain F residue 685 MET Chi-restraints excluded: chain F residue 695 CYS Chi-restraints excluded: chain F residue 809 THR Chi-restraints excluded: chain F residue 831 SER Chi-restraints excluded: chain F residue 864 CYS Chi-restraints excluded: chain F residue 1025 VAL Chi-restraints excluded: chain F residue 1136 THR Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain H residue 207 MET Chi-restraints excluded: chain H residue 387 SER Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain H residue 452 THR Chi-restraints excluded: chain H residue 487 LEU Chi-restraints excluded: chain H residue 528 THR Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 308 ASP Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain I residue 348 GLU Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 375 VAL Chi-restraints excluded: chain I residue 384 VAL Chi-restraints excluded: chain I residue 398 CYS Chi-restraints excluded: chain I residue 447 ASP Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain I residue 559 SER Chi-restraints excluded: chain I residue 676 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 695 CYS Chi-restraints excluded: chain I residue 809 THR Chi-restraints excluded: chain I residue 831 SER Chi-restraints excluded: chain I residue 864 CYS Chi-restraints excluded: chain I residue 1025 VAL Chi-restraints excluded: chain I residue 1136 THR Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 113 ILE Chi-restraints excluded: chain K residue 127 TYR Chi-restraints excluded: chain K residue 207 MET Chi-restraints excluded: chain K residue 274 GLU Chi-restraints excluded: chain K residue 387 SER Chi-restraints excluded: chain K residue 446 ILE Chi-restraints excluded: chain K residue 452 THR Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain K residue 528 THR Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 251 LEU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 307 ILE Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 348 GLU Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 384 VAL Chi-restraints excluded: chain L residue 398 CYS Chi-restraints excluded: chain L residue 447 ASP Chi-restraints excluded: chain L residue 516 THR Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 559 SER Chi-restraints excluded: chain L residue 676 VAL Chi-restraints excluded: chain L residue 685 MET Chi-restraints excluded: chain L residue 695 CYS Chi-restraints excluded: chain L residue 809 THR Chi-restraints excluded: chain L residue 831 SER Chi-restraints excluded: chain L residue 864 CYS Chi-restraints excluded: chain L residue 1025 VAL Chi-restraints excluded: chain L residue 1136 THR 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: 0.5980 chunk 358 optimal weight: 0.9980 chunk 76 optimal weight: 0.0670 chunk 329 optimal weight: 0.5980 chunk 464 optimal weight: 0.9980 chunk 693 optimal weight: 0.0170 chunk 734 optimal weight: 3.9990 chunk 362 optimal weight: 3.9990 chunk 657 optimal weight: 2.9990 chunk 197 optimal weight: 7.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN B 306 ASN B 382 GLN C 719 ASN D 42 GLN E 306 ASN E 382 GLN F 719 ASN G 42 GLN H 306 ASN H 382 GLN I 719 ASN J 42 GLN K 306 ASN K 382 GLN L 719 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 59740 Z= 0.127 Angle : 0.502 13.429 81180 Z= 0.255 Chirality : 0.042 0.269 9320 Planarity : 0.004 0.048 10340 Dihedral : 8.582 169.531 8694 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.14 % Favored : 96.70 % Rotamer: Outliers : 3.20 % Allowed : 18.82 % Favored : 77.99 % 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: 0.23 (0.10), residues: 7600 helix: 0.72 (0.10), residues: 2840 sheet: 0.54 (0.17), residues: 1008 loop : -0.32 (0.10), residues: 3752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP I1122 HIS 0.001 0.000 HIS C 37 PHE 0.023 0.001 PHE G 76 TYR 0.020 0.001 TYR C 117 ARG 0.002 0.000 ARG L 608 *********************** 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 808 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 611 time to evaluate : 4.823 Fit side-chains REVERT: C 69 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7179 (mp10) REVERT: C 78 THR cc_start: 0.8851 (OUTLIER) cc_final: 0.8579 (m) REVERT: C 366 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: C 502 VAL cc_start: 0.8585 (m) cc_final: 0.8314 (t) REVERT: C 685 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.7396 (mmt) REVERT: D 145 MET cc_start: 0.6664 (OUTLIER) cc_final: 0.6318 (tpp) REVERT: F 69 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7185 (mp10) REVERT: F 78 THR cc_start: 0.8865 (OUTLIER) cc_final: 0.8595 (m) REVERT: F 366 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: F 502 VAL cc_start: 0.8588 (m) cc_final: 0.8317 (t) REVERT: F 685 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.7397 (mmt) REVERT: F 1162 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7684 (mm-30) REVERT: I 69 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7181 (mp10) REVERT: I 78 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8558 (m) REVERT: I 366 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7050 (mp0) REVERT: I 502 VAL cc_start: 0.8584 (m) cc_final: 0.8314 (t) REVERT: I 602 ASN cc_start: 0.7685 (t0) cc_final: 0.7483 (m-40) REVERT: I 685 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.7400 (mmt) REVERT: J 145 MET cc_start: 0.6647 (OUTLIER) cc_final: 0.6304 (tpp) REVERT: L 69 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7185 (mp10) REVERT: L 78 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8559 (m) REVERT: L 366 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: L 502 VAL cc_start: 0.8588 (m) cc_final: 0.8320 (t) REVERT: L 602 ASN cc_start: 0.7687 (t0) cc_final: 0.7487 (m-40) REVERT: L 685 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.7397 (mmt) REVERT: L 1162 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7690 (mm-30) outliers start: 197 outliers final: 69 residues processed: 714 average time/residue: 1.2256 time to fit residues: 1152.8224 Evaluate side-chains 685 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 596 time to evaluate : 4.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 398 CYS Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 695 CYS Chi-restraints excluded: chain C residue 831 SER Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 308 ASP Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 398 CYS Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 681 ILE Chi-restraints excluded: chain F residue 685 MET Chi-restraints excluded: chain F residue 695 CYS Chi-restraints excluded: chain F residue 831 SER Chi-restraints excluded: chain F residue 1025 VAL Chi-restraints excluded: chain F residue 1136 THR Chi-restraints excluded: chain F residue 1162 GLU Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 191 MET Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 487 LEU Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 308 ASP Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 398 CYS Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain I residue 549 THR Chi-restraints excluded: chain I residue 681 ILE Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 695 CYS Chi-restraints excluded: chain I residue 831 SER Chi-restraints excluded: chain I residue 1025 VAL Chi-restraints excluded: chain I residue 1136 THR Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 274 GLU Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 308 ASP Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain L residue 398 CYS Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 549 THR Chi-restraints excluded: chain L residue 681 ILE Chi-restraints excluded: chain L residue 685 MET Chi-restraints excluded: chain L residue 695 CYS Chi-restraints excluded: chain L residue 831 SER Chi-restraints excluded: chain L residue 1025 VAL Chi-restraints excluded: chain L residue 1136 THR Chi-restraints excluded: chain L residue 1162 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 611 optimal weight: 9.9990 chunk 417 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 546 optimal weight: 1.9990 chunk 303 optimal weight: 20.0000 chunk 626 optimal weight: 30.0000 chunk 507 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 375 optimal weight: 1.9990 chunk 659 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 C 719 ASN E 382 GLN F 675 GLN F 719 ASN H 382 GLN I 675 GLN I 719 ASN K 382 GLN ** L 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 675 GLN L 719 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 59740 Z= 0.319 Angle : 0.585 10.661 81180 Z= 0.296 Chirality : 0.046 0.294 9320 Planarity : 0.004 0.052 10340 Dihedral : 8.650 168.250 8692 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.42 % Favored : 95.42 % Rotamer: Outliers : 4.75 % Allowed : 17.70 % Favored : 77.55 % 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: 0.11 (0.10), residues: 7600 helix: 0.62 (0.10), residues: 2868 sheet: 0.59 (0.17), residues: 1000 loop : -0.42 (0.10), residues: 3732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L1122 HIS 0.004 0.001 HIS I 96 PHE 0.029 0.002 PHE A 76 TYR 0.023 0.001 TYR K 47 ARG 0.004 0.000 ARG L 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 874 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 293 poor density : 581 time to evaluate : 4.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7208 (mp10) REVERT: C 235 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8734 (mt) REVERT: C 366 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7014 (mp0) REVERT: C 502 VAL cc_start: 0.8786 (m) cc_final: 0.8528 (t) REVERT: C 534 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7169 (tm-30) REVERT: C 644 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.8032 (ptp) REVERT: C 685 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.7360 (mmt) REVERT: D 145 MET cc_start: 0.6823 (OUTLIER) cc_final: 0.6590 (tpt) REVERT: E 207 MET cc_start: 0.4747 (OUTLIER) cc_final: 0.4070 (mtp) REVERT: F 69 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7213 (mp10) REVERT: F 235 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8735 (mt) REVERT: F 366 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: F 502 VAL cc_start: 0.8786 (m) cc_final: 0.8526 (t) REVERT: F 685 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.7367 (mmt) REVERT: F 1162 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7803 (mm-30) REVERT: H 207 MET cc_start: 0.4737 (OUTLIER) cc_final: 0.4040 (mtp) REVERT: I 69 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7212 (mp10) REVERT: I 235 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8724 (mt) REVERT: I 366 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7047 (mp0) REVERT: I 502 VAL cc_start: 0.8782 (m) cc_final: 0.8525 (t) REVERT: I 534 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7165 (tm-30) REVERT: I 685 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.7364 (mmt) REVERT: J 145 MET cc_start: 0.6809 (OUTLIER) cc_final: 0.6584 (tpt) REVERT: K 207 MET cc_start: 0.4699 (OUTLIER) cc_final: 0.4028 (mtp) REVERT: L 69 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7213 (mp10) REVERT: L 235 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8727 (mt) REVERT: L 366 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: L 502 VAL cc_start: 0.8786 (m) cc_final: 0.8530 (t) REVERT: L 534 GLU cc_start: 0.7335 (mm-30) cc_final: 0.7092 (tm-30) REVERT: L 685 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.7359 (mmt) outliers start: 293 outliers final: 140 residues processed: 784 average time/residue: 1.1904 time to fit residues: 1235.9452 Evaluate side-chains 717 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 554 time to evaluate : 4.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 398 CYS Chi-restraints excluded: chain C residue 495 SER Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 686 ASP Chi-restraints excluded: chain C residue 695 CYS Chi-restraints excluded: chain C residue 809 THR Chi-restraints excluded: chain C residue 831 SER Chi-restraints excluded: chain C residue 875 THR Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 398 CYS Chi-restraints excluded: chain F residue 495 SER Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 559 SER Chi-restraints excluded: chain F residue 681 ILE Chi-restraints excluded: chain F residue 685 MET Chi-restraints excluded: chain F residue 686 ASP Chi-restraints excluded: chain F residue 695 CYS Chi-restraints excluded: chain F residue 762 LEU Chi-restraints excluded: chain F residue 809 THR Chi-restraints excluded: chain F residue 831 SER Chi-restraints excluded: chain F residue 875 THR Chi-restraints excluded: chain F residue 968 VAL Chi-restraints excluded: chain F residue 1025 VAL Chi-restraints excluded: chain F residue 1053 THR Chi-restraints excluded: chain F residue 1136 THR Chi-restraints excluded: chain F residue 1162 GLU Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 207 MET Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 487 LEU Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 375 VAL Chi-restraints excluded: chain I residue 398 CYS Chi-restraints excluded: chain I residue 495 SER Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain I residue 549 THR Chi-restraints excluded: chain I residue 559 SER Chi-restraints excluded: chain I residue 681 ILE Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 686 ASP Chi-restraints excluded: chain I residue 695 CYS Chi-restraints excluded: chain I residue 809 THR Chi-restraints excluded: chain I residue 831 SER Chi-restraints excluded: chain I residue 875 THR Chi-restraints excluded: chain I residue 968 VAL Chi-restraints excluded: chain I residue 1025 VAL Chi-restraints excluded: chain I residue 1053 THR Chi-restraints excluded: chain I residue 1136 THR Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain K residue 48 GLU Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 207 MET Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 251 LEU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 307 ILE Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 398 CYS Chi-restraints excluded: chain L residue 495 SER Chi-restraints excluded: chain L residue 516 THR Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 549 THR Chi-restraints excluded: chain L residue 559 SER Chi-restraints excluded: chain L residue 681 ILE Chi-restraints excluded: chain L residue 685 MET Chi-restraints excluded: chain L residue 686 ASP Chi-restraints excluded: chain L residue 695 CYS Chi-restraints excluded: chain L residue 809 THR Chi-restraints excluded: chain L residue 831 SER Chi-restraints excluded: chain L residue 875 THR Chi-restraints excluded: chain L residue 968 VAL Chi-restraints excluded: chain L residue 1025 VAL Chi-restraints excluded: chain L residue 1053 THR Chi-restraints excluded: chain L residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 247 optimal weight: 7.9990 chunk 661 optimal weight: 9.9990 chunk 145 optimal weight: 0.8980 chunk 431 optimal weight: 8.9990 chunk 181 optimal weight: 1.9990 chunk 735 optimal weight: 4.9990 chunk 610 optimal weight: 7.9990 chunk 340 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 243 optimal weight: 20.0000 chunk 386 optimal weight: 0.6980 overall best weight: 3.3186 ------------------------------------------------------------------------------- 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 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 ASN E 306 ASN E 382 GLN ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 719 ASN ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 306 ASN H 382 GLN ** I 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 719 ASN K 306 ASN K 382 GLN ** L 434 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: 0.8122 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 59740 Z= 0.324 Angle : 0.590 13.228 81180 Z= 0.299 Chirality : 0.046 0.305 9320 Planarity : 0.004 0.052 10340 Dihedral : 8.344 168.439 8692 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.26 % Favored : 95.58 % Rotamer: Outliers : 4.87 % Allowed : 18.06 % Favored : 77.08 % 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: -0.04 (0.10), residues: 7600 helix: 0.52 (0.10), residues: 2892 sheet: 0.45 (0.17), residues: 992 loop : -0.52 (0.10), residues: 3716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP I1122 HIS 0.005 0.001 HIS I 96 PHE 0.029 0.002 PHE A 76 TYR 0.021 0.001 TYR I 117 ARG 0.004 0.000 ARG L 787 *********************** 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 869 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 569 time to evaluate : 4.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.2793 (OUTLIER) cc_final: 0.1273 (mtm) REVERT: C 69 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7220 (mp10) REVERT: C 366 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7052 (mp0) REVERT: C 502 VAL cc_start: 0.8829 (m) cc_final: 0.8586 (t) REVERT: C 644 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.8059 (ptp) REVERT: C 685 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.7398 (mmt) REVERT: F 69 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7224 (mp10) REVERT: F 366 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7048 (mp0) REVERT: F 502 VAL cc_start: 0.8827 (m) cc_final: 0.8586 (t) REVERT: F 534 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7205 (tm-30) REVERT: F 685 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.7406 (mmt) REVERT: I 69 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7220 (mp10) REVERT: I 366 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: I 502 VAL cc_start: 0.8824 (m) cc_final: 0.8583 (t) REVERT: I 644 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.8026 (ptp) REVERT: I 685 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.7389 (mmt) REVERT: L 69 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7220 (mp10) REVERT: L 366 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: L 502 VAL cc_start: 0.8821 (m) cc_final: 0.8579 (t) REVERT: L 534 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7201 (tm-30) REVERT: L 685 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.7354 (mmt) outliers start: 300 outliers final: 171 residues processed: 774 average time/residue: 1.1841 time to fit residues: 1216.7030 Evaluate side-chains 730 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 544 time to evaluate : 4.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 398 CYS Chi-restraints excluded: chain C residue 495 SER Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 686 ASP Chi-restraints excluded: chain C residue 695 CYS Chi-restraints excluded: chain C residue 809 THR Chi-restraints excluded: chain C residue 831 SER Chi-restraints excluded: chain C residue 864 CYS Chi-restraints excluded: chain C residue 875 THR Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain E residue 507 ASP Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 308 ASP Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 398 CYS Chi-restraints excluded: chain F residue 495 SER Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 559 SER Chi-restraints excluded: chain F residue 685 MET Chi-restraints excluded: chain F residue 686 ASP Chi-restraints excluded: chain F residue 695 CYS Chi-restraints excluded: chain F residue 762 LEU Chi-restraints excluded: chain F residue 809 THR Chi-restraints excluded: chain F residue 831 SER Chi-restraints excluded: chain F residue 864 CYS Chi-restraints excluded: chain F residue 875 THR Chi-restraints excluded: chain F residue 968 VAL Chi-restraints excluded: chain F residue 1001 LEU Chi-restraints excluded: chain F residue 1025 VAL Chi-restraints excluded: chain F residue 1053 THR Chi-restraints excluded: chain F residue 1136 THR Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 159 PHE Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 437 THR Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain H residue 487 LEU Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 300 MET Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 308 ASP Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain I residue 348 GLU Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 375 VAL Chi-restraints excluded: chain I residue 398 CYS Chi-restraints excluded: chain I residue 495 SER Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain I residue 549 THR Chi-restraints excluded: chain I residue 559 SER Chi-restraints excluded: chain I residue 644 MET Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 686 ASP Chi-restraints excluded: chain I residue 695 CYS Chi-restraints excluded: chain I residue 762 LEU Chi-restraints excluded: chain I residue 809 THR Chi-restraints excluded: chain I residue 831 SER Chi-restraints excluded: chain I residue 864 CYS Chi-restraints excluded: chain I residue 875 THR Chi-restraints excluded: chain I residue 968 VAL Chi-restraints excluded: chain I residue 1025 VAL Chi-restraints excluded: chain I residue 1053 THR Chi-restraints excluded: chain I residue 1136 THR Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain K residue 48 GLU Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain K residue 113 ILE Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 274 GLU Chi-restraints excluded: chain K residue 437 THR Chi-restraints excluded: chain K residue 446 ILE Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 251 LEU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 307 ILE Chi-restraints excluded: chain L residue 308 ASP Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 348 GLU Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 384 VAL Chi-restraints excluded: chain L residue 398 CYS Chi-restraints excluded: chain L residue 495 SER Chi-restraints excluded: chain L residue 516 THR Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 549 THR Chi-restraints excluded: chain L residue 559 SER Chi-restraints excluded: chain L residue 685 MET Chi-restraints excluded: chain L residue 686 ASP Chi-restraints excluded: chain L residue 695 CYS Chi-restraints excluded: chain L residue 809 THR Chi-restraints excluded: chain L residue 831 SER Chi-restraints excluded: chain L residue 864 CYS Chi-restraints excluded: chain L residue 875 THR Chi-restraints excluded: chain L residue 968 VAL Chi-restraints excluded: chain L residue 1001 LEU Chi-restraints excluded: chain L residue 1025 VAL Chi-restraints excluded: chain L residue 1053 THR Chi-restraints excluded: chain L residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 708 optimal weight: 0.0050 chunk 82 optimal weight: 2.9990 chunk 418 optimal weight: 7.9990 chunk 536 optimal weight: 10.0000 chunk 416 optimal weight: 20.0000 chunk 618 optimal weight: 0.0970 chunk 410 optimal weight: 20.0000 chunk 732 optimal weight: 5.9990 chunk 458 optimal weight: 0.8980 chunk 446 optimal weight: 0.9980 chunk 338 optimal weight: 5.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- 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 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 382 GLN ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 719 ASN ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 59740 Z= 0.149 Angle : 0.520 12.796 81180 Z= 0.264 Chirality : 0.043 0.278 9320 Planarity : 0.004 0.050 10340 Dihedral : 7.965 171.929 8692 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.01 % Favored : 95.83 % Rotamer: Outliers : 3.16 % Allowed : 20.07 % Favored : 76.77 % 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: 0.21 (0.10), residues: 7600 helix: 0.73 (0.10), residues: 2916 sheet: 0.54 (0.17), residues: 1020 loop : -0.38 (0.10), residues: 3664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP L1122 HIS 0.002 0.000 HIS F 96 PHE 0.025 0.001 PHE D 76 TYR 0.022 0.001 TYR H 47 ARG 0.009 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: 195 poor density : 614 time to evaluate : 4.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 TYR cc_start: 0.2438 (p90) cc_final: 0.1648 (m-10) REVERT: C 69 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7225 (mp10) REVERT: C 187 MET cc_start: 0.8069 (mtp) cc_final: 0.7796 (mtm) REVERT: C 366 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7045 (mp0) REVERT: C 401 MET cc_start: 0.8061 (mmm) cc_final: 0.7694 (mtp) REVERT: C 502 VAL cc_start: 0.8737 (m) cc_final: 0.8486 (t) REVERT: C 644 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7979 (ptp) REVERT: C 685 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.7427 (mmt) REVERT: E 62 TYR cc_start: 0.2424 (p90) cc_final: 0.1619 (m-10) REVERT: E 417 MET cc_start: 0.7145 (mmt) cc_final: 0.6927 (mpp) REVERT: F 69 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7187 (mp10) REVERT: F 187 MET cc_start: 0.8070 (mtp) cc_final: 0.7808 (mtm) REVERT: F 366 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: F 401 MET cc_start: 0.8049 (mmm) cc_final: 0.7666 (mtp) REVERT: F 502 VAL cc_start: 0.8745 (m) cc_final: 0.8494 (t) REVERT: F 685 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.7392 (mmt) REVERT: H 48 GLU cc_start: 0.2091 (OUTLIER) cc_final: 0.0845 (pp20) REVERT: H 62 TYR cc_start: 0.2388 (p90) cc_final: 0.1604 (m-10) REVERT: H 417 MET cc_start: 0.7173 (mmt) cc_final: 0.6947 (mpp) REVERT: I 69 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7225 (mp10) REVERT: I 187 MET cc_start: 0.8063 (mtp) cc_final: 0.7790 (mtm) REVERT: I 366 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: I 401 MET cc_start: 0.8045 (mmm) cc_final: 0.7697 (mtm) REVERT: I 502 VAL cc_start: 0.8731 (m) cc_final: 0.8480 (t) REVERT: I 685 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.7404 (mmt) REVERT: K 62 TYR cc_start: 0.2397 (p90) cc_final: 0.1614 (m-10) REVERT: K 417 MET cc_start: 0.7146 (mmt) cc_final: 0.6923 (mpp) REVERT: L 69 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7230 (mp10) REVERT: L 187 MET cc_start: 0.8068 (mtp) cc_final: 0.7805 (mtm) REVERT: L 366 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7088 (mp0) REVERT: L 401 MET cc_start: 0.8066 (mmm) cc_final: 0.7727 (mtm) REVERT: L 502 VAL cc_start: 0.8754 (m) cc_final: 0.8505 (t) REVERT: L 685 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.7391 (mmt) outliers start: 195 outliers final: 118 residues processed: 732 average time/residue: 1.2325 time to fit residues: 1190.5927 Evaluate side-chains 708 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 576 time to evaluate : 4.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 398 CYS Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 686 ASP Chi-restraints excluded: chain C residue 695 CYS Chi-restraints excluded: chain C residue 831 SER Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 308 ASP Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 398 CYS Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 559 SER Chi-restraints excluded: chain F residue 602 ASN Chi-restraints excluded: chain F residue 681 ILE Chi-restraints excluded: chain F residue 685 MET Chi-restraints excluded: chain F residue 686 ASP Chi-restraints excluded: chain F residue 695 CYS Chi-restraints excluded: chain F residue 831 SER Chi-restraints excluded: chain F residue 1025 VAL Chi-restraints excluded: chain F residue 1136 THR Chi-restraints excluded: chain F residue 1149 VAL Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 487 LEU Chi-restraints excluded: chain H residue 507 ASP Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 308 ASP Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain I residue 348 GLU Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 384 VAL Chi-restraints excluded: chain I residue 398 CYS Chi-restraints excluded: chain I residue 420 THR Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain I residue 559 SER Chi-restraints excluded: chain I residue 681 ILE Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 686 ASP Chi-restraints excluded: chain I residue 695 CYS Chi-restraints excluded: chain I residue 831 SER Chi-restraints excluded: chain I residue 1025 VAL Chi-restraints excluded: chain I residue 1136 THR Chi-restraints excluded: chain I residue 1149 VAL Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain K residue 48 GLU Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 274 GLU Chi-restraints excluded: chain K residue 343 LEU Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 307 ILE Chi-restraints excluded: chain L residue 308 ASP Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 348 GLU Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain L residue 398 CYS Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 559 SER Chi-restraints excluded: chain L residue 681 ILE Chi-restraints excluded: chain L residue 685 MET Chi-restraints excluded: chain L residue 686 ASP Chi-restraints excluded: chain L residue 695 CYS Chi-restraints excluded: chain L residue 831 SER Chi-restraints excluded: chain L residue 1025 VAL Chi-restraints excluded: chain L residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 453 optimal weight: 5.9990 chunk 292 optimal weight: 10.0000 chunk 437 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 465 optimal weight: 2.9990 chunk 499 optimal weight: 0.0770 chunk 362 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 chunk 575 optimal weight: 0.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- 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 306 ASN 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** F 719 ASN ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 59740 Z= 0.166 Angle : 0.531 13.059 81180 Z= 0.269 Chirality : 0.043 0.273 9320 Planarity : 0.004 0.051 10340 Dihedral : 7.904 172.898 8692 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.13 % Favored : 95.71 % Rotamer: Outliers : 3.11 % Allowed : 20.38 % 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: 0.28 (0.10), residues: 7600 helix: 0.80 (0.10), residues: 2916 sheet: 0.59 (0.17), residues: 1016 loop : -0.35 (0.10), residues: 3668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F1122 HIS 0.002 0.000 HIS F 149 PHE 0.025 0.001 PHE J 76 TYR 0.019 0.001 TYR E 47 ARG 0.009 0.000 ARG J 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 810 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 618 time to evaluate : 4.929 Fit side-chains REVERT: B 48 GLU cc_start: 0.2283 (OUTLIER) cc_final: 0.0906 (pp20) REVERT: B 62 TYR cc_start: 0.2399 (p90) cc_final: 0.1623 (m-10) REVERT: C 69 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7209 (mp10) REVERT: C 181 ASN cc_start: 0.7729 (OUTLIER) cc_final: 0.7406 (m-40) REVERT: C 187 MET cc_start: 0.8071 (mtp) cc_final: 0.7822 (mtm) REVERT: C 366 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: C 401 MET cc_start: 0.8041 (mmm) cc_final: 0.7647 (mtp) REVERT: C 502 VAL cc_start: 0.8754 (m) cc_final: 0.8499 (t) REVERT: C 644 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7973 (ptp) REVERT: C 685 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.7364 (mmt) REVERT: E 48 GLU cc_start: 0.2149 (OUTLIER) cc_final: 0.0844 (pp20) REVERT: E 62 TYR cc_start: 0.2325 (p90) cc_final: 0.1744 (m-10) REVERT: E 320 MET cc_start: 0.2551 (mmm) cc_final: 0.2197 (tpp) REVERT: F 69 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7202 (mp10) REVERT: F 366 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: F 401 MET cc_start: 0.8046 (mmm) cc_final: 0.7652 (mtp) REVERT: F 502 VAL cc_start: 0.8754 (m) cc_final: 0.8501 (t) REVERT: F 685 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.7368 (mmt) REVERT: G 145 MET cc_start: 0.6020 (tpt) cc_final: 0.5716 (mmt) REVERT: H 48 GLU cc_start: 0.2193 (OUTLIER) cc_final: 0.0893 (pp20) REVERT: H 62 TYR cc_start: 0.2384 (p90) cc_final: 0.1622 (m-10) REVERT: I 69 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7210 (mp10) REVERT: I 187 MET cc_start: 0.8069 (mtp) cc_final: 0.7824 (mtm) REVERT: I 366 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7072 (mp0) REVERT: I 401 MET cc_start: 0.8059 (mmm) cc_final: 0.7662 (mtp) REVERT: I 502 VAL cc_start: 0.8750 (m) cc_final: 0.8496 (t) REVERT: I 685 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.7376 (mmt) REVERT: I 721 ASP cc_start: 0.7881 (m-30) cc_final: 0.7618 (m-30) REVERT: K 48 GLU cc_start: 0.2158 (OUTLIER) cc_final: 0.0855 (pp20) REVERT: K 62 TYR cc_start: 0.2421 (p90) cc_final: 0.1643 (m-10) REVERT: L 69 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7219 (mp10) REVERT: L 366 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: L 401 MET cc_start: 0.8036 (mmm) cc_final: 0.7646 (mtp) REVERT: L 502 VAL cc_start: 0.8756 (m) cc_final: 0.8504 (t) REVERT: L 685 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.7373 (mmt) outliers start: 192 outliers final: 125 residues processed: 732 average time/residue: 1.2362 time to fit residues: 1198.2745 Evaluate side-chains 736 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 593 time to evaluate : 4.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 398 CYS Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 695 CYS Chi-restraints excluded: chain C residue 831 SER Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 308 ASP Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 398 CYS Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 559 SER Chi-restraints excluded: chain F residue 685 MET Chi-restraints excluded: chain F residue 686 ASP Chi-restraints excluded: chain F residue 695 CYS Chi-restraints excluded: chain F residue 831 SER Chi-restraints excluded: chain F residue 1025 VAL Chi-restraints excluded: chain F residue 1053 THR Chi-restraints excluded: chain F residue 1136 THR Chi-restraints excluded: chain F residue 1149 VAL Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 426 MET Chi-restraints excluded: chain H residue 487 LEU Chi-restraints excluded: chain H residue 507 ASP Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain I residue 348 GLU Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 384 VAL Chi-restraints excluded: chain I residue 398 CYS Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain I residue 549 THR Chi-restraints excluded: chain I residue 559 SER Chi-restraints excluded: chain I residue 681 ILE Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 695 CYS Chi-restraints excluded: chain I residue 831 SER Chi-restraints excluded: chain I residue 1025 VAL Chi-restraints excluded: chain I residue 1053 THR Chi-restraints excluded: chain I residue 1136 THR Chi-restraints excluded: chain I residue 1149 VAL Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain K residue 48 GLU Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain K residue 113 ILE Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain K residue 274 GLU Chi-restraints excluded: chain K residue 426 MET Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 251 LEU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 307 ILE Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain L residue 398 CYS Chi-restraints excluded: chain L residue 420 THR Chi-restraints excluded: chain L residue 516 THR Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 549 THR Chi-restraints excluded: chain L residue 559 SER Chi-restraints excluded: chain L residue 685 MET Chi-restraints excluded: chain L residue 686 ASP Chi-restraints excluded: chain L residue 695 CYS Chi-restraints excluded: chain L residue 831 SER Chi-restraints excluded: chain L residue 875 THR Chi-restraints excluded: chain L residue 1025 VAL Chi-restraints excluded: chain L residue 1053 THR Chi-restraints excluded: chain L residue 1136 THR Chi-restraints excluded: chain L residue 1149 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 666 optimal weight: 0.7980 chunk 701 optimal weight: 7.9990 chunk 640 optimal weight: 10.0000 chunk 682 optimal weight: 9.9990 chunk 410 optimal weight: 2.9990 chunk 297 optimal weight: 5.9990 chunk 536 optimal weight: 8.9990 chunk 209 optimal weight: 20.0000 chunk 616 optimal weight: 7.9990 chunk 645 optimal weight: 3.9990 chunk 680 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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 306 ASN 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** F 719 ASN ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 59740 Z= 0.362 Angle : 0.622 11.481 81180 Z= 0.316 Chirality : 0.047 0.297 9320 Planarity : 0.004 0.051 10340 Dihedral : 8.132 169.933 8692 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.74 % Favored : 95.11 % Rotamer: Outliers : 3.99 % Allowed : 19.76 % Favored : 76.25 % 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: 0.04 (0.10), residues: 7600 helix: 0.58 (0.10), residues: 2892 sheet: 0.44 (0.17), residues: 1024 loop : -0.45 (0.10), residues: 3684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C1122 HIS 0.005 0.001 HIS C 149 PHE 0.032 0.002 PHE D 76 TYR 0.021 0.002 TYR F 117 ARG 0.010 0.001 ARG J 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 830 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 584 time to evaluate : 4.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.3007 (OUTLIER) cc_final: 0.1358 (mtm) REVERT: B 48 GLU cc_start: 0.2302 (OUTLIER) cc_final: 0.0874 (pp20) REVERT: B 62 TYR cc_start: 0.2792 (p90) cc_final: 0.1920 (m-10) REVERT: B 417 MET cc_start: 0.7311 (mmt) cc_final: 0.7090 (mpp) REVERT: B 455 MET cc_start: 0.8583 (mtp) cc_final: 0.8314 (mtp) REVERT: C 69 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7272 (mp10) REVERT: C 366 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: C 401 MET cc_start: 0.8082 (mmm) cc_final: 0.7681 (mtp) REVERT: C 502 VAL cc_start: 0.8862 (m) cc_final: 0.8623 (t) REVERT: C 644 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.8057 (ptp) REVERT: C 685 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.7330 (mmt) REVERT: E 48 GLU cc_start: 0.2283 (OUTLIER) cc_final: 0.0858 (pp20) REVERT: E 320 MET cc_start: 0.2472 (mmm) cc_final: 0.2166 (tpp) REVERT: F 69 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7229 (mp10) REVERT: F 366 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: F 401 MET cc_start: 0.8093 (mmm) cc_final: 0.7678 (mtp) REVERT: F 502 VAL cc_start: 0.8862 (m) cc_final: 0.8621 (t) REVERT: F 685 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.7311 (mmt) REVERT: H 44 MET cc_start: 0.5707 (tmt) cc_final: 0.5466 (tmm) REVERT: H 48 GLU cc_start: 0.2326 (OUTLIER) cc_final: 0.0915 (pp20) REVERT: H 455 MET cc_start: 0.8553 (mtp) cc_final: 0.8290 (mtp) REVERT: I 69 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7272 (mp10) REVERT: I 366 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: I 401 MET cc_start: 0.8081 (mmm) cc_final: 0.7675 (mtp) REVERT: I 502 VAL cc_start: 0.8858 (m) cc_final: 0.8618 (t) REVERT: I 685 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.7346 (mmt) REVERT: K 48 GLU cc_start: 0.2299 (OUTLIER) cc_final: 0.0874 (pp20) REVERT: L 69 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7233 (mp10) REVERT: L 366 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: L 401 MET cc_start: 0.8093 (mmm) cc_final: 0.7687 (mtp) REVERT: L 502 VAL cc_start: 0.8858 (m) cc_final: 0.8621 (t) REVERT: L 685 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.7327 (mmt) outliers start: 246 outliers final: 155 residues processed: 758 average time/residue: 1.1889 time to fit residues: 1194.0471 Evaluate side-chains 727 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 554 time to evaluate : 4.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 398 CYS Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 495 SER Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 695 CYS Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 831 SER Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 308 ASP Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 398 CYS Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 495 SER Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 559 SER Chi-restraints excluded: chain F residue 671 CYS Chi-restraints excluded: chain F residue 676 VAL Chi-restraints excluded: chain F residue 685 MET Chi-restraints excluded: chain F residue 686 ASP Chi-restraints excluded: chain F residue 695 CYS Chi-restraints excluded: chain F residue 762 LEU Chi-restraints excluded: chain F residue 831 SER Chi-restraints excluded: chain F residue 875 THR Chi-restraints excluded: chain F residue 968 VAL Chi-restraints excluded: chain F residue 1025 VAL Chi-restraints excluded: chain F residue 1053 THR Chi-restraints excluded: chain F residue 1136 THR Chi-restraints excluded: chain F residue 1149 VAL Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain H residue 487 LEU Chi-restraints excluded: chain H residue 507 ASP Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 308 ASP Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain I residue 348 GLU Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 375 VAL Chi-restraints excluded: chain I residue 384 VAL Chi-restraints excluded: chain I residue 398 CYS Chi-restraints excluded: chain I residue 420 THR Chi-restraints excluded: chain I residue 495 SER Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain I residue 549 THR Chi-restraints excluded: chain I residue 559 SER Chi-restraints excluded: chain I residue 671 CYS Chi-restraints excluded: chain I residue 676 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 695 CYS Chi-restraints excluded: chain I residue 762 LEU Chi-restraints excluded: chain I residue 809 THR Chi-restraints excluded: chain I residue 831 SER Chi-restraints excluded: chain I residue 875 THR Chi-restraints excluded: chain I residue 968 VAL Chi-restraints excluded: chain I residue 1025 VAL Chi-restraints excluded: chain I residue 1053 THR Chi-restraints excluded: chain I residue 1136 THR Chi-restraints excluded: chain I residue 1149 VAL Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain K residue 48 GLU Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain K residue 113 ILE Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain K residue 274 GLU Chi-restraints excluded: chain K residue 446 ILE Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 307 ILE Chi-restraints excluded: chain L residue 308 ASP Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 398 CYS Chi-restraints excluded: chain L residue 420 THR Chi-restraints excluded: chain L residue 495 SER Chi-restraints excluded: chain L residue 516 THR Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 549 THR Chi-restraints excluded: chain L residue 559 SER Chi-restraints excluded: chain L residue 671 CYS Chi-restraints excluded: chain L residue 676 VAL Chi-restraints excluded: chain L residue 685 MET Chi-restraints excluded: chain L residue 686 ASP Chi-restraints excluded: chain L residue 695 CYS Chi-restraints excluded: chain L residue 809 THR Chi-restraints excluded: chain L residue 831 SER Chi-restraints excluded: chain L residue 875 THR Chi-restraints excluded: chain L residue 968 VAL Chi-restraints excluded: chain L residue 1025 VAL Chi-restraints excluded: chain L residue 1053 THR Chi-restraints excluded: chain L residue 1136 THR Chi-restraints excluded: chain L residue 1149 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 448 optimal weight: 1.9990 chunk 721 optimal weight: 0.9990 chunk 440 optimal weight: 2.9990 chunk 342 optimal weight: 0.9990 chunk 501 optimal weight: 0.8980 chunk 757 optimal weight: 0.5980 chunk 696 optimal weight: 8.9990 chunk 602 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 465 optimal weight: 3.9990 chunk 369 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 306 ASN 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 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** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1960 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= 0.161 Angle : 0.538 12.571 81180 Z= 0.273 Chirality : 0.043 0.281 9320 Planarity : 0.004 0.051 10340 Dihedral : 7.923 172.213 8692 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.70 % Favored : 96.14 % Rotamer: Outliers : 2.64 % Allowed : 21.41 % Favored : 75.94 % 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: 0.23 (0.10), residues: 7600 helix: 0.74 (0.10), residues: 2912 sheet: 0.42 (0.17), residues: 1024 loop : -0.31 (0.11), residues: 3664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 165 HIS 0.002 0.000 HIS I 275 PHE 0.026 0.001 PHE J 76 TYR 0.020 0.001 TYR I 117 ARG 0.009 0.000 ARG G 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 750 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 587 time to evaluate : 4.832 Fit side-chains REVERT: B 48 GLU cc_start: 0.2217 (OUTLIER) cc_final: 0.0775 (pp20) REVERT: B 62 TYR cc_start: 0.2712 (p90) cc_final: 0.1849 (m-10) REVERT: C 69 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7209 (mp10) REVERT: C 187 MET cc_start: 0.8051 (mtp) cc_final: 0.7798 (mtm) REVERT: C 366 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7004 (mp0) REVERT: C 401 MET cc_start: 0.8011 (mmm) cc_final: 0.7559 (mtp) REVERT: C 502 VAL cc_start: 0.8755 (m) cc_final: 0.8509 (t) REVERT: C 644 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7976 (ptp) REVERT: C 685 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.7362 (mmt) REVERT: D 145 MET cc_start: 0.6640 (mmp) cc_final: 0.6337 (tpp) REVERT: E 48 GLU cc_start: 0.2125 (OUTLIER) cc_final: 0.0736 (pp20) REVERT: E 62 TYR cc_start: 0.2820 (p90) cc_final: 0.1914 (m-10) REVERT: F 69 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7177 (mp10) REVERT: F 366 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: F 401 MET cc_start: 0.8038 (mmm) cc_final: 0.7577 (mtp) REVERT: F 502 VAL cc_start: 0.8767 (m) cc_final: 0.8521 (t) REVERT: F 685 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.7365 (mmt) REVERT: H 44 MET cc_start: 0.5431 (tmt) cc_final: 0.5205 (tmm) REVERT: H 48 GLU cc_start: 0.2230 (OUTLIER) cc_final: 0.0788 (pp20) REVERT: H 62 TYR cc_start: 0.2788 (p90) cc_final: 0.1904 (m-10) REVERT: I 69 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7216 (mp10) REVERT: I 187 MET cc_start: 0.8045 (mtp) cc_final: 0.7802 (mtm) REVERT: I 366 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: I 401 MET cc_start: 0.8012 (mmm) cc_final: 0.7559 (mtp) REVERT: I 502 VAL cc_start: 0.8749 (m) cc_final: 0.8504 (t) REVERT: I 644 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7958 (ptp) REVERT: I 685 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.7378 (mmt) REVERT: J 145 MET cc_start: 0.6637 (mmp) cc_final: 0.6337 (tpp) REVERT: K 48 GLU cc_start: 0.2152 (OUTLIER) cc_final: 0.0753 (pp20) REVERT: K 62 TYR cc_start: 0.2823 (p90) cc_final: 0.1925 (m-10) REVERT: L 69 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7208 (mp10) REVERT: L 366 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: L 401 MET cc_start: 0.8019 (mmm) cc_final: 0.7653 (mtp) REVERT: L 502 VAL cc_start: 0.8765 (m) cc_final: 0.8522 (t) REVERT: L 685 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.7373 (mmt) outliers start: 163 outliers final: 123 residues processed: 705 average time/residue: 1.2108 time to fit residues: 1132.2482 Evaluate side-chains 703 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 562 time to evaluate : 4.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 398 CYS Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 695 CYS Chi-restraints excluded: chain C residue 831 SER Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 398 CYS Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 559 SER Chi-restraints excluded: chain F residue 671 CYS Chi-restraints excluded: chain F residue 685 MET Chi-restraints excluded: chain F residue 695 CYS Chi-restraints excluded: chain F residue 831 SER Chi-restraints excluded: chain F residue 1025 VAL Chi-restraints excluded: chain F residue 1053 THR Chi-restraints excluded: chain F residue 1136 THR Chi-restraints excluded: chain F residue 1149 VAL Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 426 MET Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain H residue 487 LEU Chi-restraints excluded: chain H residue 507 ASP Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 308 ASP Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain I residue 348 GLU Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 375 VAL Chi-restraints excluded: chain I residue 384 VAL Chi-restraints excluded: chain I residue 398 CYS Chi-restraints excluded: chain I residue 420 THR Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain I residue 549 THR Chi-restraints excluded: chain I residue 559 SER Chi-restraints excluded: chain I residue 644 MET Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 695 CYS Chi-restraints excluded: chain I residue 831 SER Chi-restraints excluded: chain I residue 1025 VAL Chi-restraints excluded: chain I residue 1053 THR Chi-restraints excluded: chain I residue 1136 THR Chi-restraints excluded: chain I residue 1149 VAL Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain K residue 48 GLU Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain K residue 274 GLU Chi-restraints excluded: chain K residue 426 MET Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 308 ASP Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 398 CYS Chi-restraints excluded: chain L residue 420 THR Chi-restraints excluded: chain L residue 516 THR Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 549 THR Chi-restraints excluded: chain L residue 559 SER Chi-restraints excluded: chain L residue 685 MET Chi-restraints excluded: chain L residue 695 CYS Chi-restraints excluded: chain L residue 831 SER Chi-restraints excluded: chain L residue 1025 VAL Chi-restraints excluded: chain L residue 1136 THR Chi-restraints excluded: chain L residue 1149 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 478 optimal weight: 7.9990 chunk 642 optimal weight: 30.0000 chunk 184 optimal weight: 8.9990 chunk 555 optimal weight: 3.9990 chunk 89 optimal weight: 0.0670 chunk 167 optimal weight: 8.9990 chunk 603 optimal weight: 9.9990 chunk 252 optimal weight: 6.9990 chunk 620 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 overall best weight: 3.9924 ------------------------------------------------------------------------------- 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 306 ASN 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 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 ** L 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.182662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.125376 restraints weight = 62895.633| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.44 r_work: 0.3036 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 59740 Z= 0.386 Angle : 0.639 11.862 81180 Z= 0.324 Chirality : 0.048 0.298 9320 Planarity : 0.004 0.051 10340 Dihedral : 8.122 169.466 8692 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.84 % Favored : 95.00 % Rotamer: Outliers : 3.24 % Allowed : 21.03 % Favored : 75.73 % 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: 0.00 (0.10), residues: 7600 helix: 0.56 (0.10), residues: 2888 sheet: 0.36 (0.17), residues: 1024 loop : -0.47 (0.10), residues: 3688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP H 165 HIS 0.005 0.001 HIS F 149 PHE 0.034 0.002 PHE D 76 TYR 0.020 0.002 TYR F 117 ARG 0.010 0.001 ARG G 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18146.48 seconds wall clock time: 316 minutes 33.35 seconds (18993.35 seconds total)