Starting phenix.real_space_refine on Wed Feb 14 04:43:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oh9_16879/02_2024/8oh9_16879_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oh9_16879/02_2024/8oh9_16879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oh9_16879/02_2024/8oh9_16879.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oh9_16879/02_2024/8oh9_16879.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oh9_16879/02_2024/8oh9_16879_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oh9_16879/02_2024/8oh9_16879_updated.pdb" } resolution = 3.2 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= 0.007 sd= 0.164 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 8 5.49 5 S 616 5.16 5 C 36348 2.51 5 N 9884 2.21 5 O 11104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 52": "OD1" <-> "OD2" Residue "B TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B GLU 184": "OE1" <-> "OE2" Residue "B ASP 192": "OD1" <-> "OD2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B GLU 476": "OE1" <-> "OE2" Residue "B GLU 477": "OE1" <-> "OE2" Residue "B TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C ASP 77": "OD1" <-> "OD2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C ASP 246": "OD1" <-> "OD2" Residue "C GLU 248": "OE1" <-> "OE2" Residue "C GLU 385": "OE1" <-> "OE2" Residue "C GLU 553": "OE1" <-> "OE2" Residue "C ASP 589": "OD1" <-> "OD2" Residue "C ASP 720": "OD1" <-> "OD2" Residue "C ASP 814": "OD1" <-> "OD2" Residue "C GLU 904": "OE1" <-> "OE2" Residue "C GLU 917": "OE1" <-> "OE2" Residue "C GLU 943": "OE1" <-> "OE2" Residue "C ASP 1007": "OD1" <-> "OD2" Residue "C GLU 1082": "OE1" <-> "OE2" Residue "D PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 61": "OD1" <-> "OD2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 52": "OD1" <-> "OD2" Residue "E PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 68": "OD1" <-> "OD2" Residue "E GLU 184": "OE1" <-> "OE2" Residue "E ASP 192": "OD1" <-> "OD2" Residue "E GLU 469": "OE1" <-> "OE2" Residue "E GLU 477": "OE1" <-> "OE2" Residue "F GLU 27": "OE1" <-> "OE2" Residue "F ASP 77": "OD1" <-> "OD2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "F ASP 177": "OD1" <-> "OD2" Residue "F GLU 248": "OE1" <-> "OE2" Residue "F GLU 385": "OE1" <-> "OE2" Residue "F TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 534": "OE1" <-> "OE2" Residue "F GLU 607": "OE1" <-> "OE2" Residue "F ASP 720": "OD1" <-> "OD2" Residue "F ASP 814": "OD1" <-> "OD2" Residue "F GLU 904": "OE1" <-> "OE2" Residue "F GLU 1082": "OE1" <-> "OE2" Residue "G TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 26": "OE1" <-> "OE2" Residue "H ASP 52": "OD1" <-> "OD2" Residue "H ASP 68": "OD1" <-> "OD2" Residue "H ASP 192": "OD1" <-> "OD2" Residue "H GLU 476": "OE1" <-> "OE2" Residue "H GLU 477": "OE1" <-> "OE2" Residue "I GLU 27": "OE1" <-> "OE2" Residue "I ASP 77": "OD1" <-> "OD2" Residue "I GLU 158": "OE1" <-> "OE2" Residue "I ASP 177": "OD1" <-> "OD2" Residue "I GLU 248": "OE1" <-> "OE2" Residue "I GLU 385": "OE1" <-> "OE2" Residue "I GLU 593": "OE1" <-> "OE2" Residue "I ASP 720": "OD1" <-> "OD2" Residue "I ASP 814": "OD1" <-> "OD2" Residue "I GLU 904": "OE1" <-> "OE2" Residue "I GLU 1082": "OE1" <-> "OE2" Residue "J PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 68": "OD1" <-> "OD2" Residue "K TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 174": "OE1" <-> "OE2" Residue "K ASP 192": "OD1" <-> "OD2" Residue "K GLU 469": "OE1" <-> "OE2" Residue "K GLU 473": "OE1" <-> "OE2" Residue "L ASP 77": "OD1" <-> "OD2" Residue "L GLU 158": "OE1" <-> "OE2" Residue "L ASP 177": "OD1" <-> "OD2" Residue "L ASP 246": "OD1" <-> "OD2" Residue "L GLU 248": "OE1" <-> "OE2" Residue "L GLU 359": "OE1" <-> "OE2" Residue "L GLU 385": "OE1" <-> "OE2" Residue "L GLU 607": "OE1" <-> "OE2" Residue "L PHE 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 720": "OD1" <-> "OD2" Residue "L ASP 814": "OD1" <-> "OD2" Residue "L GLU 904": "OE1" <-> "OE2" Residue "L GLU 917": "OE1" <-> "OE2" Residue "L ASP 1007": "OD1" <-> "OD2" Residue "L GLU 1082": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 58132 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' ZN': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 105 Unusual residues: {'FAD': 1, 'FES': 1, 'SF4': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' ZN': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 105 Unusual residues: {'FAD': 1, 'FES': 1, 'SF4': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' ZN': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "I" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 105 Unusual residues: {'FAD': 1, 'FES': 1, 'SF4': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' ZN': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "L" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 105 Unusual residues: {'FAD': 1, 'FES': 1, 'SF4': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 597 SG CYS A 93 111.789 114.784 214.772 1.00 72.82 S ATOM 628 SG CYS A 98 110.841 117.499 213.568 1.00 73.25 S ATOM 878 SG CYS A 134 107.869 113.936 215.231 1.00 77.06 S ATOM 902 SG CYS A 138 106.990 116.456 217.829 1.00 81.43 S ATOM 5065 SG CYS B 518 107.136 133.386 202.515 1.00 70.25 S ATOM 5098 SG CYS B 523 108.399 130.059 200.580 1.00 70.44 S ATOM 1188 SG CYS B 10 109.100 112.996 225.546 1.00 82.70 S ATOM 1443 SG CYS B 45 108.584 115.019 227.831 1.00 82.73 S ATOM 1417 SG CYS B 41 105.962 114.005 229.495 1.00 82.31 S ATOM 4464 SG CYS B 442 99.090 101.984 198.697 1.00 27.12 S ATOM 4509 SG CYS B 448 97.988 108.338 197.617 1.00 19.68 S ATOM 4820 SG CYS B 488 94.445 104.636 201.524 1.00 35.28 S ATOM 4483 SG CYS B 445 94.534 105.196 194.867 1.00 17.72 S ATOM 5423 SG CYS B 566 121.943 137.403 198.187 1.00 97.71 S ATOM 5272 SG CYS B 546 128.493 137.181 199.582 1.00 88.62 S ATOM 5445 SG CYS B 569 125.027 133.550 203.078 1.00 91.19 S ATOM 5463 SG CYS B 572 126.290 138.849 202.968 1.00100.97 S ATOM 5487 SG CYS B 576 123.366 145.299 209.556 1.00 98.18 S ATOM 5203 SG CYS B 536 124.536 150.017 205.905 1.00105.44 S ATOM 5243 SG CYS B 542 126.596 143.438 206.429 1.00 95.35 S ATOM 5222 SG CYS B 539 129.887 147.579 208.544 1.00 94.18 S ATOM 10212 SG CYS C 613 103.127 98.693 184.222 1.00 15.49 S ATOM 10233 SG CYS C 616 97.172 96.092 184.217 1.00 13.44 S ATOM 10251 SG CYS C 619 102.426 92.661 184.990 1.00 22.67 S ATOM 10587 SG CYS C 666 100.316 95.124 179.269 1.00 9.55 S ATOM 9785 SG CYS C 562 109.985 100.690 159.084 1.00 11.14 S ATOM 6698 SG CYS C 155 112.052 106.696 157.397 1.00 13.91 S ATOM 9808 SG CYS C 565 110.553 104.774 163.346 1.00 9.12 S ATOM 6324 SG CYS C 104 106.051 105.877 158.616 1.00 8.95 S ATOM 6293 SG CYS C 100 99.219 105.980 170.873 1.00 13.21 S ATOM 9818 SG CYS C 567 102.531 100.472 171.153 1.00 9.67 S ATOM 9875 SG CYS C 573 96.874 101.147 174.266 1.00 13.85 S ATOM 6671 SG CYS C 151 105.847 109.104 152.675 1.00 10.06 S ATOM 6641 SG CYS C 147 103.176 112.132 147.730 1.00 8.02 S ATOM 6351 SG CYS C 108 100.179 110.092 153.160 1.00 21.36 S ATOM 10282 SG CYS C 623 104.640 85.000 186.617 1.00 15.86 S ATOM 10540 SG CYS C 659 103.167 81.942 181.313 1.00 14.46 S ATOM 10520 SG CYS C 656 109.141 83.928 181.900 1.00 17.85 S ATOM 10559 SG CYS C 662 104.105 87.948 180.922 1.00 24.42 S ATOM 10776 SG CYS C 692 99.354 73.120 171.408 1.00 19.02 S ATOM 11031 SG CYS C 725 102.639 74.839 176.446 1.00 19.02 S ATOM 10798 SG CYS C 695 101.602 69.583 175.764 1.00 23.25 S ATOM 10819 SG CYS C 699 95.984 73.999 176.216 1.00 36.46 S ATOM 5814 SG CYS C 36 91.527 97.377 188.207 1.00 10.11 S ATOM 5903 SG CYS C 47 90.656 100.261 186.393 1.00 10.46 S ATOM 5921 SG CYS C 50 85.659 99.198 187.927 1.00 36.46 S ATOM 6024 SG CYS C 64 86.643 96.016 189.776 1.00 10.37 S ATOM 14992 SG CYS D 93 111.634 48.671 46.950 1.00 69.76 S ATOM 15023 SG CYS D 98 110.796 45.965 48.050 1.00 73.68 S ATOM 15273 SG CYS D 134 107.780 49.621 46.383 1.00 76.10 S ATOM 15297 SG CYS D 138 106.934 46.995 43.773 1.00 83.62 S ATOM 19460 SG CYS E 518 107.099 30.060 59.088 1.00 70.64 S ATOM 19493 SG CYS E 523 108.394 33.409 61.024 1.00 69.65 S ATOM 15583 SG CYS E 10 109.005 50.378 36.186 1.00 82.32 S ATOM 15838 SG CYS E 45 108.778 48.455 34.534 1.00 84.56 S ATOM 15812 SG CYS E 41 106.011 49.588 32.077 1.00 81.64 S ATOM 18859 SG CYS E 442 99.068 61.454 62.881 1.00 27.03 S ATOM 18904 SG CYS E 448 98.004 55.036 63.962 1.00 21.47 S ATOM 19215 SG CYS E 488 94.434 58.857 60.105 1.00 33.21 S ATOM 18878 SG CYS E 445 94.526 58.258 66.718 1.00 18.92 S ATOM 19840 SG CYS E 569 124.995 29.889 58.553 1.00 90.62 S ATOM 19858 SG CYS E 572 126.202 24.565 58.637 1.00 96.49 S ATOM 19818 SG CYS E 566 121.807 26.148 63.447 1.00 96.83 S ATOM 19667 SG CYS E 546 128.411 26.308 61.992 1.00 88.98 S ATOM 19882 SG CYS E 576 123.371 18.062 51.957 1.00 98.06 S ATOM 19598 SG CYS E 536 124.595 13.332 55.792 1.00106.25 S ATOM 19638 SG CYS E 542 126.588 19.994 55.230 1.00 95.57 S ATOM 19617 SG CYS E 539 129.836 15.836 53.050 1.00 95.34 S ATOM 24607 SG CYS F 613 103.122 64.765 77.375 1.00 14.97 S ATOM 24628 SG CYS F 616 97.159 67.359 77.383 1.00 9.52 S ATOM 24646 SG CYS F 619 102.422 70.801 76.607 1.00 15.23 S ATOM 24982 SG CYS F 666 100.315 68.336 82.320 1.00 10.01 S ATOM 21093 SG CYS F 155 112.050 56.771 104.180 1.00 15.15 S ATOM 24180 SG CYS F 562 109.976 62.779 102.518 1.00 11.85 S ATOM 20719 SG CYS F 104 106.030 57.589 102.987 1.00 10.96 S ATOM 24203 SG CYS F 565 110.562 58.706 98.265 1.00 7.51 S ATOM 20688 SG CYS F 100 99.214 57.476 90.714 1.00 15.01 S ATOM 24213 SG CYS F 567 102.528 62.988 90.447 1.00 14.51 S ATOM 24270 SG CYS F 573 96.873 62.309 87.324 1.00 16.87 S ATOM 21066 SG CYS F 151 105.850 54.357 108.925 1.00 8.15 S ATOM 21036 SG CYS F 147 103.171 51.324 113.868 1.00 8.19 S ATOM 20746 SG CYS F 108 100.172 53.400 108.427 1.00 15.57 S ATOM 24915 SG CYS F 656 109.143 79.570 79.693 1.00 18.37 S ATOM 24935 SG CYS F 659 103.163 81.537 80.276 1.00 14.90 S ATOM 24954 SG CYS F 662 104.104 75.522 80.675 1.00 26.04 S ATOM 24677 SG CYS F 623 104.630 78.487 74.989 1.00 16.78 S ATOM 25171 SG CYS F 692 99.331 90.301 90.229 1.00 18.84 S ATOM 25426 SG CYS F 725 102.631 88.641 85.159 1.00 19.19 S ATOM 25193 SG CYS F 695 100.771 94.033 86.029 1.00 18.38 S ATOM 25214 SG CYS F 699 95.825 89.379 85.277 1.00 36.46 S ATOM 20316 SG CYS F 50 85.671 64.094 73.307 1.00 9.07 S ATOM 20419 SG CYS F 64 86.626 67.511 71.937 1.00 8.62 S ATOM 20209 SG CYS F 36 91.588 66.092 73.377 1.00 8.26 S ATOM 20298 SG CYS F 47 90.553 63.189 75.136 1.00 14.28 S ATOM 29387 SG CYS G 93 32.259 48.668 214.650 1.00 70.31 S ATOM 29418 SG CYS G 98 33.067 45.928 213.571 1.00 74.31 S ATOM 29668 SG CYS G 134 36.107 49.634 215.231 1.00 75.03 S ATOM 29692 SG CYS G 138 36.959 46.998 217.821 1.00 84.56 S ATOM 33855 SG CYS H 518 36.756 30.033 202.522 1.00 69.06 S ATOM 33888 SG CYS H 523 35.498 33.391 200.580 1.00 68.45 S ATOM 29978 SG CYS H 10 34.901 50.376 225.396 1.00 81.96 S ATOM 30233 SG CYS H 45 34.572 47.295 227.195 1.00 82.72 S ATOM 30207 SG CYS H 41 37.888 49.582 229.524 1.00 81.71 S ATOM 33254 SG CYS H 442 44.810 61.461 198.728 1.00 26.58 S ATOM 33299 SG CYS H 448 45.906 55.028 197.682 1.00 19.85 S ATOM 33610 SG CYS H 488 49.446 58.858 201.492 1.00 33.74 S ATOM 33273 SG CYS H 445 49.360 58.271 194.878 1.00 17.96 S ATOM 34213 SG CYS H 566 22.149 26.148 198.136 1.00 98.72 S ATOM 34062 SG CYS H 546 15.568 26.452 199.714 1.00 89.34 S ATOM 34235 SG CYS H 569 18.915 29.873 203.089 1.00 90.20 S ATOM 34253 SG CYS H 572 17.822 24.493 202.968 1.00 98.57 S ATOM 34277 SG CYS H 576 20.624 18.175 209.628 1.00 98.68 S ATOM 34033 SG CYS H 542 17.294 20.228 206.555 1.00 95.78 S ATOM 34012 SG CYS H 539 13.966 15.866 208.570 1.00 94.02 S ATOM 39002 SG CYS I 613 40.756 64.782 184.224 1.00 14.46 S ATOM 39023 SG CYS I 616 46.734 67.390 184.213 1.00 12.75 S ATOM 39041 SG CYS I 619 41.457 70.805 184.999 1.00 22.38 S ATOM 39377 SG CYS I 666 43.566 68.351 179.276 1.00 10.01 S ATOM 35488 SG CYS I 155 31.827 56.768 157.412 1.00 14.44 S ATOM 38575 SG CYS I 562 33.894 62.774 159.080 1.00 11.88 S ATOM 35114 SG CYS I 104 37.832 57.594 158.625 1.00 16.67 S ATOM 38598 SG CYS I 565 33.318 58.708 163.353 1.00 14.50 S ATOM 35083 SG CYS I 100 44.668 57.486 170.883 1.00 17.29 S ATOM 38608 SG CYS I 567 41.345 63.000 171.154 1.00 14.89 S ATOM 38665 SG CYS I 573 47.004 62.318 174.273 1.00 14.73 S ATOM 35461 SG CYS I 151 38.028 54.360 152.677 1.00 10.78 S ATOM 35431 SG CYS I 147 40.707 51.329 147.733 1.00 9.21 S ATOM 35141 SG CYS I 108 43.707 53.405 153.174 1.00 15.05 S ATOM 39310 SG CYS I 656 34.736 79.571 181.902 1.00 17.89 S ATOM 39330 SG CYS I 659 40.717 81.545 181.322 1.00 14.35 S ATOM 39349 SG CYS I 662 39.776 75.531 180.925 1.00 25.94 S ATOM 39072 SG CYS I 623 39.247 78.492 186.610 1.00 14.94 S ATOM 39566 SG CYS I 692 44.531 90.350 171.408 1.00 19.50 S ATOM 39821 SG CYS I 725 41.246 88.632 176.451 1.00 18.50 S ATOM 39588 SG CYS I 695 42.279 93.889 175.766 1.00 23.72 S ATOM 39609 SG CYS I 699 47.896 89.469 176.217 1.00 36.46 S ATOM 34711 SG CYS I 50 58.209 64.106 188.292 1.00 10.08 S ATOM 34814 SG CYS I 64 57.253 67.515 189.663 1.00 8.70 S ATOM 34604 SG CYS I 36 52.281 66.102 188.220 1.00 9.89 S ATOM 34693 SG CYS I 47 53.311 63.211 186.452 1.00 14.01 S ATOM 43782 SG CYS J 93 32.104 114.858 47.011 1.00 71.19 S ATOM 43813 SG CYS J 98 31.346 118.010 47.214 1.00 75.06 S ATOM 44063 SG CYS J 134 35.979 113.809 46.206 1.00 70.88 S ATOM 44087 SG CYS J 138 36.876 116.345 43.663 1.00 83.78 S ATOM 48250 SG CYS K 518 36.736 133.433 59.070 1.00 70.88 S ATOM 48283 SG CYS K 523 35.481 130.030 61.023 1.00 69.49 S ATOM 44373 SG CYS K 10 34.747 113.093 36.116 1.00 81.19 S ATOM 44628 SG CYS K 45 35.053 115.007 34.520 1.00 82.29 S ATOM 44602 SG CYS K 41 37.839 113.919 32.048 1.00 82.80 S ATOM 47649 SG CYS K 442 44.815 102.006 62.879 1.00 27.36 S ATOM 47694 SG CYS K 448 45.870 108.444 63.928 1.00 20.88 S ATOM 48005 SG CYS K 488 49.430 104.612 60.096 1.00 33.95 S ATOM 47668 SG CYS K 445 49.350 105.181 66.719 1.00 18.89 S ATOM 48608 SG CYS K 566 22.063 137.328 63.436 1.00 99.56 S ATOM 48457 SG CYS K 546 15.458 137.174 61.975 1.00 89.82 S ATOM 48630 SG CYS K 569 18.876 133.586 58.544 1.00 91.68 S ATOM 48648 SG CYS K 572 17.660 138.905 58.629 1.00 97.39 S ATOM 48672 SG CYS K 576 20.514 145.376 52.046 1.00 97.53 S ATOM 48388 SG CYS K 536 19.298 150.124 55.808 1.00103.83 S ATOM 48428 SG CYS K 542 17.277 143.518 55.192 1.00 95.03 S ATOM 48407 SG CYS K 539 14.012 147.659 53.059 1.00 93.58 S ATOM 53397 SG CYS L 613 40.750 98.680 77.367 1.00 14.86 S ATOM 53418 SG CYS L 616 46.724 96.067 77.380 1.00 10.08 S ATOM 53436 SG CYS L 619 41.450 92.659 76.591 1.00 15.05 S ATOM 53772 SG CYS L 666 43.561 95.120 82.322 1.00 10.51 S ATOM 52970 SG CYS L 562 33.893 100.684 102.515 1.00 11.27 S ATOM 49883 SG CYS L 155 31.823 106.693 104.186 1.00 14.42 S ATOM 52993 SG CYS L 565 33.327 104.772 98.245 1.00 9.44 S ATOM 49509 SG CYS L 104 37.827 105.871 102.973 1.00 13.05 S ATOM 49478 SG CYS L 100 44.666 105.970 90.720 1.00 11.76 S ATOM 53003 SG CYS L 567 41.339 100.462 90.443 1.00 13.31 S ATOM 53060 SG CYS L 573 46.993 101.140 87.328 1.00 14.34 S ATOM 49856 SG CYS L 151 38.026 109.100 108.916 1.00 10.21 S ATOM 49826 SG CYS L 147 40.702 112.129 113.862 1.00 8.32 S ATOM 49536 SG CYS L 108 43.696 110.091 108.432 1.00 16.03 S ATOM 53725 SG CYS L 659 40.709 81.915 80.274 1.00 13.37 S ATOM 53705 SG CYS L 656 34.722 83.930 79.685 1.00 18.89 S ATOM 53467 SG CYS L 623 39.239 84.990 74.988 1.00 17.19 S ATOM 53744 SG CYS L 662 39.772 87.935 80.675 1.00 17.04 S ATOM 53961 SG CYS L 692 44.524 73.114 90.189 1.00 18.77 S ATOM 54216 SG CYS L 725 41.238 74.832 85.154 1.00 19.01 S ATOM 53983 SG CYS L 695 42.276 69.573 85.833 1.00 23.47 S ATOM 54004 SG CYS L 699 47.893 73.986 85.374 1.00 36.46 S ATOM 48999 SG CYS L 36 52.341 97.355 73.382 1.00 8.55 S ATOM 49088 SG CYS L 47 53.191 100.197 75.211 1.00 14.42 S ATOM 49106 SG CYS L 50 58.248 99.197 73.626 1.00 9.42 S ATOM 49209 SG CYS L 64 57.233 96.016 71.820 1.00 8.54 S Time building chain proxies: 25.60, per 1000 atoms: 0.44 Number of scatterers: 58132 At special positions: 0 Unit cell: (144.97, 164.59, 262.69, 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 8 15.00 O 11104 8.00 N 9884 7.00 C 36348 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.75 Conformation dependent library (CDL) restraints added in 8.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 201 " pdb="FE1 FES A 201 " - pdb=" SG CYS A 93 " pdb="FE2 FES A 201 " - pdb=" SG CYS A 138 " pdb="FE1 FES A 201 " - pdb=" SG CYS A 98 " pdb="FE2 FES A 201 " - pdb=" SG CYS A 134 " pdb=" FES B 602 " pdb="FE1 FES B 602 " - pdb=" SG CYS B 45 " pdb="FE2 FES B 602 " - pdb=" SG CYS B 41 " pdb="FE1 FES B 602 " - pdb=" SG CYS B 10 " pdb=" FES C1208 " pdb="FE2 FES C1208 " - pdb=" SG CYS C 50 " pdb="FE1 FES C1208 " - pdb=" SG CYS C 47 " pdb="FE2 FES C1208 " - pdb=" SG CYS C 64 " pdb="FE1 FES C1208 " - pdb=" SG CYS C 36 " pdb=" FES D 201 " pdb="FE1 FES D 201 " - pdb=" SG CYS D 93 " pdb="FE2 FES D 201 " - pdb=" SG CYS D 138 " pdb="FE1 FES D 201 " - pdb=" SG CYS D 98 " pdb="FE2 FES D 201 " - pdb=" SG CYS D 134 " pdb=" FES E 602 " pdb="FE1 FES E 602 " - pdb=" SG CYS E 45 " pdb="FE2 FES E 602 " - pdb=" SG CYS E 41 " pdb="FE1 FES E 602 " - pdb=" SG CYS E 10 " pdb=" FES F1208 " pdb="FE1 FES F1208 " - pdb=" SG CYS F 50 " pdb="FE2 FES F1208 " - pdb=" SG CYS F 47 " pdb="FE2 FES F1208 " - pdb=" SG CYS F 36 " pdb="FE1 FES F1208 " - pdb=" SG CYS F 64 " pdb=" FES G 201 " pdb="FE1 FES G 201 " - pdb=" SG CYS G 93 " pdb="FE2 FES G 201 " - pdb=" SG CYS G 138 " pdb="FE1 FES G 201 " - pdb=" SG CYS G 98 " pdb="FE2 FES G 201 " - pdb=" SG CYS G 134 " pdb=" FES H 602 " pdb="FE1 FES H 602 " - pdb=" SG CYS H 45 " pdb="FE2 FES H 602 " - pdb=" SG CYS H 41 " pdb="FE1 FES H 602 " - pdb=" SG CYS H 10 " pdb=" FES I1208 " pdb="FE2 FES I1208 " - pdb=" SG CYS I 47 " pdb="FE1 FES I1208 " - pdb=" SG CYS I 50 " pdb="FE2 FES I1208 " - pdb=" SG CYS I 36 " pdb="FE1 FES I1208 " - pdb=" SG CYS I 64 " pdb=" FES J 201 " pdb="FE1 FES J 201 " - pdb=" SG CYS J 93 " pdb="FE2 FES J 201 " - pdb=" SG CYS J 138 " pdb="FE2 FES J 201 " - pdb=" SG CYS J 134 " pdb="FE1 FES J 201 " - pdb=" SG CYS J 98 " pdb=" FES K 602 " pdb="FE1 FES K 602 " - pdb=" SG CYS K 45 " pdb="FE2 FES K 602 " - pdb=" SG CYS K 41 " pdb="FE1 FES K 602 " - pdb=" SG CYS K 10 " pdb=" FES L1208 " pdb="FE2 FES L1208 " - pdb=" SG CYS L 50 " pdb="FE1 FES L1208 " - pdb=" SG CYS L 47 " pdb="FE2 FES L1208 " - pdb=" SG CYS L 64 " pdb="FE1 FES L1208 " - pdb=" SG CYS L 36 " pdb=" SF4 B 603 " pdb="FE1 SF4 B 603 " - pdb=" SG CYS B 442 " pdb="FE4 SF4 B 603 " - pdb=" SG CYS B 445 " pdb="FE3 SF4 B 603 " - pdb=" SG CYS B 488 " pdb="FE2 SF4 B 603 " - pdb=" SG CYS B 448 " pdb=" SF4 B 604 " pdb="FE4 SF4 B 604 " - pdb=" SG CYS B 572 " pdb="FE1 SF4 B 604 " - pdb=" SG CYS B 566 " pdb="FE2 SF4 B 604 " - pdb=" SG CYS B 546 " pdb="FE3 SF4 B 604 " - pdb=" SG CYS B 569 " pdb=" SF4 B 605 " pdb="FE3 SF4 B 605 " - pdb=" SG CYS B 542 " pdb="FE4 SF4 B 605 " - pdb=" SG CYS B 539 " pdb="FE2 SF4 B 605 " - pdb=" SG CYS B 536 " pdb="FE1 SF4 B 605 " - pdb=" SG CYS B 576 " pdb=" SF4 C1202 " pdb="FE2 SF4 C1202 " - pdb=" SG CYS C 616 " pdb="FE4 SF4 C1202 " - pdb=" SG CYS C 666 " pdb="FE1 SF4 C1202 " - pdb=" SG CYS C 613 " pdb="FE3 SF4 C1202 " - pdb=" SG CYS C 619 " pdb=" SF4 C1203 " pdb="FE2 SF4 C1203 " - pdb=" SG CYS C 155 " pdb="FE3 SF4 C1203 " - pdb=" SG CYS C 565 " pdb="FE1 SF4 C1203 " - pdb=" SG CYS C 562 " pdb="FE4 SF4 C1203 " - pdb=" SG CYS C 104 " pdb=" SF4 C1204 " pdb="FE2 SF4 C1204 " - pdb=" NE2 HIS C 96 " pdb="FE1 SF4 C1204 " - pdb=" SG CYS C 100 " pdb="FE4 SF4 C1204 " - pdb=" SG CYS C 573 " pdb="FE3 SF4 C1204 " - pdb=" SG CYS C 567 " pdb=" SF4 C1205 " pdb="FE1 SF4 C1205 " - pdb=" SG CYS C 151 " pdb="FE3 SF4 C1205 " - pdb=" SG CYS C 108 " pdb="FE2 SF4 C1205 " - pdb=" SG CYS C 147 " pdb=" SF4 C1206 " pdb="FE3 SF4 C1206 " - pdb=" SG CYS C 656 " pdb="FE2 SF4 C1206 " - pdb=" SG CYS C 659 " pdb="FE1 SF4 C1206 " - pdb=" SG CYS C 623 " pdb="FE4 SF4 C1206 " - pdb=" SG CYS C 662 " pdb=" SF4 C1207 " pdb="FE2 SF4 C1207 " - pdb=" SG CYS C 725 " pdb="FE1 SF4 C1207 " - pdb=" SG CYS C 692 " pdb="FE4 SF4 C1207 " - pdb=" SG CYS C 699 " pdb="FE3 SF4 C1207 " - pdb=" SG CYS C 695 " pdb=" SF4 E 603 " pdb="FE1 SF4 E 603 " - pdb=" SG CYS E 442 " pdb="FE4 SF4 E 603 " - pdb=" SG CYS E 445 " pdb="FE3 SF4 E 603 " - pdb=" SG CYS E 488 " pdb="FE2 SF4 E 603 " - pdb=" SG CYS E 448 " pdb=" SF4 E 604 " pdb="FE2 SF4 E 604 " - pdb=" SG CYS E 572 " pdb="FE4 SF4 E 604 " - pdb=" SG CYS E 546 " pdb="FE3 SF4 E 604 " - pdb=" SG CYS E 566 " pdb="FE1 SF4 E 604 " - pdb=" SG CYS E 569 " pdb=" SF4 E 605 " pdb="FE3 SF4 E 605 " - pdb=" SG CYS E 542 " pdb="FE4 SF4 E 605 " - pdb=" SG CYS E 539 " pdb="FE2 SF4 E 605 " - pdb=" SG CYS E 536 " pdb="FE1 SF4 E 605 " - pdb=" SG CYS E 576 " pdb=" SF4 F1202 " pdb="FE4 SF4 F1202 " - pdb=" SG CYS F 666 " pdb="FE1 SF4 F1202 " - pdb=" SG CYS F 613 " pdb="FE2 SF4 F1202 " - pdb=" SG CYS F 616 " pdb="FE3 SF4 F1202 " - pdb=" SG CYS F 619 " pdb=" SF4 F1203 " pdb="FE1 SF4 F1203 " - pdb=" SG CYS F 155 " pdb="FE4 SF4 F1203 " - pdb=" SG CYS F 565 " pdb="FE2 SF4 F1203 " - pdb=" SG CYS F 562 " pdb="FE3 SF4 F1203 " - pdb=" SG CYS F 104 " pdb=" SF4 F1204 " pdb="FE2 SF4 F1204 " - pdb=" NE2 HIS F 96 " pdb="FE1 SF4 F1204 " - pdb=" SG CYS F 100 " pdb="FE4 SF4 F1204 " - pdb=" SG CYS F 573 " pdb="FE3 SF4 F1204 " - pdb=" SG CYS F 567 " pdb=" SF4 F1205 " pdb="FE1 SF4 F1205 " - pdb=" SG CYS F 151 " pdb="FE3 SF4 F1205 " - pdb=" SG CYS F 108 " pdb="FE2 SF4 F1205 " - pdb=" SG CYS F 147 " pdb=" SF4 F1206 " pdb="FE1 SF4 F1206 " - pdb=" SG CYS F 656 " pdb="FE2 SF4 F1206 " - pdb=" SG CYS F 659 " pdb="FE4 SF4 F1206 " - pdb=" SG CYS F 623 " pdb="FE3 SF4 F1206 " - pdb=" SG CYS F 662 " pdb=" SF4 F1207 " pdb="FE3 SF4 F1207 " - pdb=" SG CYS F 695 " pdb="FE1 SF4 F1207 " - pdb=" SG CYS F 692 " pdb="FE2 SF4 F1207 " - pdb=" SG CYS F 725 " pdb="FE4 SF4 F1207 " - pdb=" SG CYS F 699 " pdb=" SF4 H 603 " pdb="FE1 SF4 H 603 " - pdb=" SG CYS H 442 " pdb="FE4 SF4 H 603 " - pdb=" SG CYS H 445 " pdb="FE3 SF4 H 603 " - pdb=" SG CYS H 488 " pdb="FE2 SF4 H 603 " - pdb=" SG CYS H 448 " pdb=" SF4 H 604 " pdb="FE2 SF4 H 604 " - pdb=" SG CYS H 546 " pdb="FE4 SF4 H 604 " - pdb=" SG CYS H 572 " pdb="FE1 SF4 H 604 " - pdb=" SG CYS H 566 " pdb="FE3 SF4 H 604 " - pdb=" SG CYS H 569 " pdb=" SF4 H 605 " pdb="FE3 SF4 H 605 " - pdb=" SG CYS H 542 " pdb="FE4 SF4 H 605 " - pdb=" SG CYS H 539 " pdb="FE1 SF4 H 605 " - pdb=" SG CYS H 576 " pdb=" SF4 I1202 " pdb="FE1 SF4 I1202 " - pdb=" SG CYS I 613 " pdb="FE4 SF4 I1202 " - pdb=" SG CYS I 666 " pdb="FE3 SF4 I1202 " - pdb=" SG CYS I 619 " pdb="FE2 SF4 I1202 " - pdb=" SG CYS I 616 " pdb=" SF4 I1203 " pdb="FE1 SF4 I1203 " - pdb=" SG CYS I 155 " pdb="FE4 SF4 I1203 " - pdb=" SG CYS I 565 " pdb="FE2 SF4 I1203 " - pdb=" SG CYS I 562 " pdb="FE3 SF4 I1203 " - pdb=" SG CYS I 104 " pdb=" SF4 I1204 " pdb="FE2 SF4 I1204 " - pdb=" NE2 HIS I 96 " pdb="FE1 SF4 I1204 " - pdb=" SG CYS I 100 " pdb="FE4 SF4 I1204 " - pdb=" SG CYS I 573 " pdb="FE3 SF4 I1204 " - pdb=" SG CYS I 567 " pdb=" SF4 I1205 " pdb="FE1 SF4 I1205 " - pdb=" SG CYS I 151 " pdb="FE3 SF4 I1205 " - pdb=" SG CYS I 108 " pdb="FE2 SF4 I1205 " - pdb=" SG CYS I 147 " pdb=" SF4 I1206 " pdb="FE1 SF4 I1206 " - pdb=" SG CYS I 656 " pdb="FE4 SF4 I1206 " - pdb=" SG CYS I 623 " pdb="FE2 SF4 I1206 " - pdb=" SG CYS I 659 " pdb="FE3 SF4 I1206 " - pdb=" SG CYS I 662 " pdb=" SF4 I1207 " pdb="FE2 SF4 I1207 " - pdb=" SG CYS I 725 " pdb="FE1 SF4 I1207 " - pdb=" SG CYS I 692 " pdb="FE4 SF4 I1207 " - pdb=" SG CYS I 699 " pdb="FE3 SF4 I1207 " - pdb=" SG CYS I 695 " pdb=" SF4 K 603 " pdb="FE1 SF4 K 603 " - pdb=" SG CYS K 442 " pdb="FE4 SF4 K 603 " - pdb=" SG CYS K 445 " pdb="FE3 SF4 K 603 " - pdb=" SG CYS K 488 " pdb="FE2 SF4 K 603 " - pdb=" SG CYS K 448 " pdb=" SF4 K 604 " pdb="FE4 SF4 K 604 " - pdb=" SG CYS K 572 " pdb="FE2 SF4 K 604 " - pdb=" SG CYS K 546 " pdb="FE1 SF4 K 604 " - pdb=" SG CYS K 566 " pdb="FE3 SF4 K 604 " - pdb=" SG CYS K 569 " pdb=" SF4 K 605 " pdb="FE3 SF4 K 605 " - pdb=" SG CYS K 542 " pdb="FE4 SF4 K 605 " - pdb=" SG CYS K 539 " pdb="FE2 SF4 K 605 " - pdb=" SG CYS K 536 " pdb="FE1 SF4 K 605 " - pdb=" SG CYS K 576 " pdb=" SF4 L1202 " pdb="FE1 SF4 L1202 " - pdb=" SG CYS L 613 " pdb="FE4 SF4 L1202 " - pdb=" SG CYS L 666 " pdb="FE3 SF4 L1202 " - pdb=" SG CYS L 619 " pdb="FE2 SF4 L1202 " - pdb=" SG CYS L 616 " pdb=" SF4 L1203 " pdb="FE2 SF4 L1203 " - pdb=" SG CYS L 155 " pdb="FE3 SF4 L1203 " - pdb=" SG CYS L 565 " pdb="FE1 SF4 L1203 " - pdb=" SG CYS L 562 " pdb="FE4 SF4 L1203 " - pdb=" SG CYS L 104 " pdb=" SF4 L1204 " pdb="FE2 SF4 L1204 " - pdb=" NE2 HIS L 96 " pdb="FE1 SF4 L1204 " - pdb=" SG CYS L 100 " pdb="FE4 SF4 L1204 " - pdb=" SG CYS L 573 " pdb="FE3 SF4 L1204 " - pdb=" SG CYS L 567 " pdb=" SF4 L1205 " pdb="FE1 SF4 L1205 " - pdb=" SG CYS L 151 " pdb="FE3 SF4 L1205 " - pdb=" SG CYS L 108 " pdb="FE2 SF4 L1205 " - pdb=" SG CYS L 147 " pdb=" SF4 L1206 " pdb="FE2 SF4 L1206 " - pdb=" SG CYS L 656 " pdb="FE3 SF4 L1206 " - pdb=" SG CYS L 623 " pdb="FE1 SF4 L1206 " - pdb=" SG CYS L 659 " pdb="FE4 SF4 L1206 " - pdb=" SG CYS L 662 " pdb=" SF4 L1207 " pdb="FE2 SF4 L1207 " - pdb=" SG CYS L 725 " pdb="FE1 SF4 L1207 " - pdb=" SG CYS L 692 " pdb="FE4 SF4 L1207 " - pdb=" SG CYS L 699 " pdb="FE3 SF4 L1207 " - pdb=" SG CYS L 695 " Number of angles added : 484 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 523 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 518 " pdb=" ZN E 601 " pdb="ZN ZN E 601 " - pdb=" NE2 HIS E 512 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 523 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 518 " pdb=" ZN H 601 " pdb="ZN ZN H 601 " - pdb=" NE2 HIS H 512 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 523 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 518 " pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 512 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 523 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 518 " 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: 339 helices and 64 sheets defined 37.5% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.78 Creating SS restraints... Processing helix chain 'A' and resid 20 through 30 Proline residue: A 25 - end of helix Processing helix chain 'A' and resid 37 through 48 Processing helix chain 'A' and resid 53 through 63 Processing helix chain 'A' and resid 68 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 11 through 14 No H-bonds generated for 'chain 'B' and resid 11 through 14' Processing helix chain 'B' and resid 16 through 30 Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 67 through 76 Processing helix chain 'B' and resid 97 through 100 No H-bonds generated for 'chain 'B' and resid 97 through 100' Processing helix chain 'B' and resid 118 through 123 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 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 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 274 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 Processing helix chain 'B' and resid 324 through 328 Processing helix chain 'B' and resid 361 through 366 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 439 Processing helix chain 'B' and resid 446 through 463 removed outlier: 3.742A pdb=" N THR B 452 " --> pdb=" O CYS B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 485 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 494 through 513 Proline residue: B 497 - end of helix removed outlier: 4.072A pdb=" N THR B 500 " --> pdb=" O PRO B 497 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TYR B 504 " --> pdb=" O THR B 501 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ARG B 506 " --> pdb=" O ARG B 503 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ASP B 507 " --> pdb=" O TYR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 526 No H-bonds generated for 'chain 'B' and resid 524 through 526' Processing helix chain 'B' and resid 541 through 544 No H-bonds generated for 'chain 'B' and resid 541 through 544' Processing helix chain 'B' and resid 571 through 574 No H-bonds generated for 'chain 'B' and resid 571 through 574' Processing helix chain 'C' and resid 21 through 27 Processing helix chain 'C' and resid 79 through 94 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: 3.804A 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 156 through 159 Processing helix chain 'C' and resid 166 through 179 Processing helix chain 'C' and resid 202 through 214 removed outlier: 4.003A pdb=" N ASP C 214 " --> pdb=" O PHE C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 233 removed outlier: 4.130A pdb=" N TYR C 233 " --> pdb=" O MET C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 255 removed outlier: 3.731A 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 357 through 359 No H-bonds generated for 'chain 'C' and resid 357 through 359' Processing helix chain 'C' and resid 364 through 373 Processing helix chain 'C' and resid 470 through 474 removed outlier: 4.026A pdb=" N THR C 474 " --> pdb=" O ASP C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 498 removed outlier: 3.598A pdb=" N ASN C 498 " --> pdb=" O ASP C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 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: 4.267A pdb=" N ARG C 561 " --> pdb=" O ARG C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 582 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 661 through 665 Processing helix chain 'C' and resid 726 through 730 Processing helix chain 'C' and resid 732 through 736 removed outlier: 3.620A pdb=" N ASN C 736 " --> pdb=" O GLY C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 775 Processing helix chain 'C' and resid 790 through 802 Processing helix chain 'C' and resid 820 through 823 No H-bonds generated for 'chain 'C' and resid 820 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 888 Processing helix chain 'C' and resid 892 through 898 Processing helix chain 'C' and resid 902 through 908 Processing helix chain 'C' and resid 916 through 927 Processing helix chain 'C' and resid 942 through 954 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: 3.827A 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 1076 through 1087 Processing helix chain 'C' and resid 1094 through 1104 Processing helix chain 'C' and resid 1160 through 1171 removed outlier: 3.771A pdb=" N VAL C1166 " --> pdb=" O GLU C1162 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN C1170 " --> pdb=" O VAL C1166 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER C1171 " --> pdb=" O ASN C1167 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 30 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 11 through 14 No H-bonds generated for 'chain 'E' and resid 11 through 14' Processing helix chain 'E' and resid 16 through 30 removed outlier: 5.319A pdb=" N ASP E 21 " --> pdb=" O LYS E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 76 Processing helix chain 'E' and resid 118 through 123 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 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 270 through 272 No H-bonds generated for 'chain 'E' and resid 270 through 272' Processing helix chain 'E' and resid 274 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 Processing helix chain 'E' and resid 324 through 329 Processing helix chain 'E' and resid 361 through 366 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 439 Processing helix chain 'E' and resid 446 through 463 removed outlier: 4.068A pdb=" N THR E 452 " --> pdb=" O CYS E 448 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS E 453 " --> pdb=" O ARG E 449 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 485 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 494 through 513 Proline residue: E 497 - end of helix removed outlier: 3.812A pdb=" N THR E 500 " --> pdb=" O PRO E 497 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR E 501 " --> pdb=" O VAL E 498 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR E 504 " --> pdb=" O THR E 501 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ARG E 506 " --> pdb=" O ARG E 503 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASP E 507 " --> pdb=" O TYR E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 526 No H-bonds generated for 'chain 'E' and resid 524 through 526' Processing helix chain 'E' and resid 541 through 544 No H-bonds generated for 'chain 'E' and resid 541 through 544' Processing helix chain 'E' and resid 571 through 574 No H-bonds generated for 'chain 'E' and resid 571 through 574' Processing helix chain 'F' and resid 21 through 27 Processing helix chain 'F' and resid 79 through 94 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: 3.825A 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 156 through 159 Processing helix chain 'F' and resid 166 through 179 Processing helix chain 'F' and resid 202 through 214 removed outlier: 4.009A pdb=" N ASP F 214 " --> pdb=" O PHE F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 233 removed outlier: 4.069A pdb=" N TYR F 233 " --> pdb=" O MET F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 255 removed outlier: 3.687A 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 357 through 359 No H-bonds generated for 'chain 'F' and resid 357 through 359' Processing helix chain 'F' and resid 364 through 373 Processing helix chain 'F' and resid 470 through 474 removed outlier: 4.048A pdb=" N THR F 474 " --> pdb=" O ASP F 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 498 removed outlier: 3.589A pdb=" N ASN F 498 " --> pdb=" O ASP F 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 517 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: 4.251A pdb=" N ARG F 561 " --> pdb=" O ARG F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 582 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 661 through 665 Processing helix chain 'F' and resid 726 through 730 Processing helix chain 'F' and resid 732 through 736 removed outlier: 3.617A pdb=" N ASN F 736 " --> pdb=" O GLY F 733 " (cutoff:3.500A) Processing helix chain 'F' and resid 757 through 775 Processing helix chain 'F' and resid 790 through 802 Processing helix chain 'F' and resid 820 through 823 No H-bonds generated for 'chain 'F' and resid 820 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 888 Processing helix chain 'F' and resid 892 through 898 Processing helix chain 'F' and resid 902 through 908 Processing helix chain 'F' and resid 916 through 927 Processing helix chain 'F' and resid 942 through 954 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: 3.795A 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 1076 through 1087 Processing helix chain 'F' and resid 1094 through 1104 Processing helix chain 'F' and resid 1160 through 1171 removed outlier: 3.800A pdb=" N GLN F1170 " --> pdb=" O VAL F1166 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER F1171 " --> pdb=" O ASN F1167 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 30 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 11 through 14 No H-bonds generated for 'chain 'H' and resid 11 through 14' Processing helix chain 'H' and resid 16 through 30 removed outlier: 5.285A pdb=" N ASP H 21 " --> pdb=" O LYS H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 76 Processing helix chain 'H' and resid 99 through 101 No H-bonds generated for 'chain 'H' and resid 99 through 101' Processing helix chain 'H' and resid 118 through 123 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 170 Processing helix chain 'H' and resid 191 through 196 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 270 through 272 No H-bonds generated for 'chain 'H' and resid 270 through 272' Processing helix chain 'H' and resid 274 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 Processing helix chain 'H' and resid 324 through 329 Processing helix chain 'H' and resid 361 through 366 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 393 through 395 No H-bonds generated for 'chain 'H' and resid 393 through 395' Processing helix chain 'H' and resid 402 through 407 Processing helix chain 'H' and resid 426 through 439 Processing helix chain 'H' and resid 446 through 463 removed outlier: 4.053A pdb=" N THR H 452 " --> pdb=" O CYS H 448 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS H 453 " --> pdb=" O ARG H 449 " (cutoff:3.500A) Processing helix chain 'H' and resid 471 through 485 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 494 through 513 Proline residue: H 497 - end of helix removed outlier: 3.789A pdb=" N THR H 500 " --> pdb=" O PRO H 497 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR H 501 " --> pdb=" O VAL H 498 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TYR H 504 " --> pdb=" O THR H 501 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ARG H 506 " --> pdb=" O ARG H 503 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASP H 507 " --> pdb=" O TYR H 504 " (cutoff:3.500A) Processing helix chain 'H' and resid 524 through 526 No H-bonds generated for 'chain 'H' and resid 524 through 526' Processing helix chain 'H' and resid 541 through 544 No H-bonds generated for 'chain 'H' and resid 541 through 544' Processing helix chain 'H' and resid 571 through 574 No H-bonds generated for 'chain 'H' and resid 571 through 574' Processing helix chain 'I' and resid 21 through 27 Processing helix chain 'I' and resid 79 through 94 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: 3.825A 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 156 through 159 Processing helix chain 'I' and resid 166 through 179 Processing helix chain 'I' and resid 202 through 214 removed outlier: 4.006A pdb=" N ASP I 214 " --> pdb=" O PHE I 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 229 through 233 removed outlier: 4.092A pdb=" N TYR I 233 " --> pdb=" O MET I 230 " (cutoff:3.500A) Processing helix chain 'I' and resid 242 through 255 removed outlier: 3.701A 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 357 through 359 No H-bonds generated for 'chain 'I' and resid 357 through 359' Processing helix chain 'I' and resid 364 through 373 Processing helix chain 'I' and resid 470 through 474 removed outlier: 4.019A pdb=" N THR I 474 " --> pdb=" O ASP I 471 " (cutoff:3.500A) Processing helix chain 'I' and resid 479 through 498 removed outlier: 3.592A pdb=" N ASN I 498 " --> pdb=" O ASP I 494 " (cutoff:3.500A) Processing helix chain 'I' and resid 517 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: 4.234A pdb=" N ARG I 561 " --> pdb=" O ARG I 557 " (cutoff:3.500A) Processing helix chain 'I' and resid 574 through 582 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 661 through 665 Processing helix chain 'I' and resid 726 through 730 Processing helix chain 'I' and resid 732 through 736 removed outlier: 3.618A pdb=" N ASN I 736 " --> pdb=" O GLY I 733 " (cutoff:3.500A) Processing helix chain 'I' and resid 757 through 775 Processing helix chain 'I' and resid 790 through 802 Processing helix chain 'I' and resid 820 through 823 No H-bonds generated for 'chain 'I' and resid 820 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 888 Processing helix chain 'I' and resid 892 through 898 Processing helix chain 'I' and resid 902 through 908 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 1012 through 1020 removed outlier: 3.807A 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 1076 through 1087 Processing helix chain 'I' and resid 1094 through 1104 Processing helix chain 'I' and resid 1160 through 1171 removed outlier: 3.771A pdb=" N GLN I1170 " --> pdb=" O VAL I1166 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER I1171 " --> pdb=" O ASN I1167 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 30 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 11 through 14 No H-bonds generated for 'chain 'K' and resid 11 through 14' Processing helix chain 'K' and resid 16 through 30 Processing helix chain 'K' and resid 67 through 76 Processing helix chain 'K' and resid 97 through 100 No H-bonds generated for 'chain 'K' and resid 97 through 100' Processing helix chain 'K' and resid 118 through 123 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 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 270 through 272 No H-bonds generated for 'chain 'K' and resid 270 through 272' Processing helix chain 'K' and resid 274 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 Processing helix chain 'K' and resid 324 through 329 Processing helix chain 'K' and resid 361 through 366 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 439 Processing helix chain 'K' and resid 446 through 463 removed outlier: 3.738A pdb=" N THR K 452 " --> pdb=" O CYS K 448 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS K 453 " --> pdb=" O ARG K 449 " (cutoff:3.500A) Processing helix chain 'K' and resid 471 through 485 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 494 through 513 Proline residue: K 497 - end of helix removed outlier: 3.787A pdb=" N THR K 500 " --> pdb=" O PRO K 497 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR K 501 " --> pdb=" O VAL K 498 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TYR K 504 " --> pdb=" O THR K 501 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ARG K 506 " --> pdb=" O ARG K 503 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ASP K 507 " --> pdb=" O TYR K 504 " (cutoff:3.500A) Processing helix chain 'K' and resid 524 through 526 No H-bonds generated for 'chain 'K' and resid 524 through 526' Processing helix chain 'K' and resid 541 through 544 No H-bonds generated for 'chain 'K' and resid 541 through 544' Processing helix chain 'K' and resid 571 through 574 No H-bonds generated for 'chain 'K' and resid 571 through 574' Processing helix chain 'L' and resid 21 through 27 Processing helix chain 'L' and resid 79 through 94 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: 3.809A 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 156 through 159 Processing helix chain 'L' and resid 166 through 179 Processing helix chain 'L' and resid 202 through 214 removed outlier: 4.004A pdb=" N ASP L 214 " --> pdb=" O PHE L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 229 through 233 removed outlier: 4.072A pdb=" N TYR L 233 " --> pdb=" O MET L 230 " (cutoff:3.500A) Processing helix chain 'L' and resid 242 through 255 removed outlier: 3.760A 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 357 through 359 No H-bonds generated for 'chain 'L' and resid 357 through 359' Processing helix chain 'L' and resid 364 through 373 Processing helix chain 'L' and resid 470 through 474 removed outlier: 4.054A pdb=" N THR L 474 " --> pdb=" O ASP L 471 " (cutoff:3.500A) Processing helix chain 'L' and resid 479 through 498 removed outlier: 3.599A pdb=" N ASN L 498 " --> pdb=" O ASP L 494 " (cutoff:3.500A) Processing helix chain 'L' and resid 517 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: 4.250A pdb=" N ARG L 561 " --> pdb=" O ARG L 557 " (cutoff:3.500A) Processing helix chain 'L' and resid 574 through 582 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 646 through 648 No H-bonds generated for 'chain 'L' and resid 646 through 648' Processing helix chain 'L' and resid 661 through 665 Processing helix chain 'L' and resid 726 through 730 Processing helix chain 'L' and resid 732 through 736 removed outlier: 3.618A pdb=" N ASN L 736 " --> pdb=" O GLY L 733 " (cutoff:3.500A) Processing helix chain 'L' and resid 757 through 775 Processing helix chain 'L' and resid 790 through 802 Processing helix chain 'L' and resid 820 through 823 No H-bonds generated for 'chain 'L' and resid 820 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 888 Processing helix chain 'L' and resid 892 through 898 Processing helix chain 'L' and resid 902 through 908 Processing helix chain 'L' and resid 916 through 927 Processing helix chain 'L' and resid 942 through 954 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: 3.795A 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 1076 through 1087 Processing helix chain 'L' and resid 1094 through 1104 Processing helix chain 'L' and resid 1160 through 1171 removed outlier: 3.789A pdb=" N GLN L1170 " --> pdb=" O VAL L1166 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER L1171 " --> pdb=" O ASN L1167 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 127 through 132 removed outlier: 6.944A pdb=" N TYR A 88 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLU A 130 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE A 90 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL A 132 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLN A 92 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL A 143 " --> pdb=" O CYS A 93 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 35 through 38 removed outlier: 3.951A 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: 6.709A pdb=" N TYR B 177 " --> pdb=" O ASN B 306 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ASN B 308 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL B 179 " --> pdb=" O ASN B 308 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLU B 218 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N CYS B 180 " --> pdb=" O GLU B 218 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N HIS B 220 " --> pdb=" O CYS B 180 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP B 259 " --> pdb=" O GLY B 219 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ILE B 221 " --> pdb=" O ASP B 259 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LYS B 261 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N CYS B 223 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 5.861A 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 356 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: 6.450A pdb=" N VAL C 281 " --> pdb=" O PHE C 467 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LYS C 217 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N VAL C 197 " --> pdb=" O LYS C 217 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL C 219 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 6.667A 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: 6.503A pdb=" N ILE C 428 " --> pdb=" O LEU C 304 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLU C 348 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N VAL C 327 " --> pdb=" O GLU C 348 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N THR C 350 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LYS C 376 " --> pdb=" O ILE C 351 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 606 through 608 Processing sheet with id= J, first strand: chain 'C' and resid 632 through 635 Processing sheet with id= K, first strand: chain 'C' and resid 686 through 691 Processing sheet with id= L, first strand: chain 'C' and resid 745 through 748 Processing sheet with id= M, first strand: chain 'C' and resid 807 through 809 removed outlier: 4.483A pdb=" N ILE C 807 " --> pdb=" O ILE C 780 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA C1000 " --> pdb=" O GLY C 781 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL C 783 " --> pdb=" O ALA C1000 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N VAL C1002 " --> pdb=" O VAL C 783 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE C1023 " --> pdb=" O LEU C1001 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL C1003 " --> pdb=" O PHE C1023 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL C1025 " --> pdb=" O VAL C1003 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N MET C1040 " --> pdb=" O VAL C1026 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ASP C1028 " --> pdb=" O MET C1040 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL C1042 " --> pdb=" O ASP C1028 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 865 through 867 removed outlier: 6.286A pdb=" N VAL C 841 " --> pdb=" O VAL C 866 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLY C 964 " --> pdb=" O ILE C 933 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ILE C 935 " --> pdb=" O GLY C 964 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE C 966 " --> pdb=" O ILE C 935 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 1052 through 1055 Processing sheet with id= P, first strand: chain 'C' and resid 381 through 387 removed outlier: 3.569A pdb=" N ALA C 382 " --> pdb=" O GLU C 399 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LYS C 397 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N VAL C 386 " --> pdb=" O ALA C 395 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ALA C 395 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLU C 419 " --> pdb=" O ILE C 400 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ARG C 402 " --> pdb=" O THR C 417 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N THR C 417 " --> pdb=" O ARG C 402 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.857A pdb=" N TYR D 88 " --> pdb=" O THR D 128 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N GLU D 130 " --> pdb=" O TYR D 88 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE D 90 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL D 132 " --> pdb=" O ILE D 90 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN D 92 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N VAL D 143 " --> pdb=" O CYS D 93 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 35 through 39 removed outlier: 4.180A pdb=" N LYS E 2 " --> pdb=" O PHE E 54 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE E 50 " --> pdb=" O GLY E 6 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 305 through 309 removed outlier: 6.784A pdb=" N TYR E 177 " --> pdb=" O ASN E 306 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N ASN E 308 " --> pdb=" O TYR E 177 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL E 179 " --> pdb=" O ASN E 308 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLU E 218 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N CYS E 180 " --> pdb=" O GLU E 218 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N HIS E 220 " --> pdb=" O CYS E 180 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASP E 259 " --> pdb=" O GLY E 219 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ILE E 221 " --> pdb=" O ASP E 259 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS E 261 " --> pdb=" O ILE E 221 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N CYS E 223 " --> pdb=" O LYS E 261 " (cutoff:3.500A) removed outlier: 5.862A 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 356 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: 6.430A pdb=" N VAL F 281 " --> pdb=" O PHE F 467 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LYS F 217 " --> pdb=" O VAL F 195 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL F 197 " --> pdb=" O LYS F 217 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL F 219 " --> pdb=" O VAL F 197 " (cutoff:3.500A) removed outlier: 6.685A 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: 6.508A pdb=" N ILE F 428 " --> pdb=" O LEU F 304 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU F 348 " --> pdb=" O VAL F 325 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N VAL F 327 " --> pdb=" O GLU F 348 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N THR F 350 " --> pdb=" O VAL F 327 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LYS F 376 " --> pdb=" O ILE F 351 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 606 through 608 Processing sheet with id= Z, first strand: chain 'F' and resid 632 through 635 Processing sheet with id= AA, first strand: chain 'F' and resid 686 through 691 Processing sheet with id= AB, first strand: chain 'F' and resid 745 through 748 Processing sheet with id= AC, first strand: chain 'F' and resid 807 through 809 removed outlier: 4.479A pdb=" N ILE F 807 " --> pdb=" O ILE F 780 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA F1000 " --> pdb=" O GLY F 781 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N VAL F 783 " --> pdb=" O ALA F1000 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL F1002 " --> pdb=" O VAL F 783 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE F1023 " --> pdb=" O LEU F1001 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL F1003 " --> pdb=" O PHE F1023 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL F1025 " --> pdb=" O VAL F1003 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N MET F1040 " --> pdb=" O VAL F1026 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ASP F1028 " --> pdb=" O MET F1040 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N VAL F1042 " --> pdb=" O ASP F1028 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 865 through 867 removed outlier: 6.286A pdb=" N VAL F 841 " --> pdb=" O VAL F 866 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY F 964 " --> pdb=" O ILE F 933 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ILE F 935 " --> pdb=" O GLY F 964 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE F 966 " --> pdb=" O ILE F 935 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 1052 through 1055 Processing sheet with id= AF, first strand: chain 'F' and resid 381 through 387 removed outlier: 3.510A pdb=" N ALA F 382 " --> pdb=" O GLU F 399 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LYS F 397 " --> pdb=" O VAL F 384 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N VAL F 386 " --> pdb=" O ALA F 395 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ALA F 395 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU F 419 " --> pdb=" O ILE F 400 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ARG F 402 " --> pdb=" O THR F 417 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR F 417 " --> pdb=" O ARG F 402 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 127 through 132 removed outlier: 6.837A pdb=" N TYR G 88 " --> pdb=" O THR G 128 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N GLU G 130 " --> pdb=" O TYR G 88 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE G 90 " --> pdb=" O GLU G 130 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL G 132 " --> pdb=" O ILE G 90 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLN G 92 " --> pdb=" O VAL G 132 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N VAL G 143 " --> pdb=" O CYS G 93 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'H' and resid 35 through 38 removed outlier: 4.091A pdb=" N LYS H 2 " --> pdb=" O PHE H 54 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE H 50 " --> pdb=" O GLY H 6 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'H' and resid 304 through 309 removed outlier: 6.860A pdb=" N GLU H 218 " --> pdb=" O VAL H 178 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N CYS H 180 " --> pdb=" O GLU H 218 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N HIS H 220 " --> pdb=" O CYS H 180 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASP H 259 " --> pdb=" O GLY H 219 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ILE H 221 " --> pdb=" O ASP H 259 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LYS H 261 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N CYS H 223 " --> pdb=" O LYS H 261 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LYS H 263 " --> pdb=" O CYS H 223 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 351 through 356 removed outlier: 3.676A pdb=" N ALA H 380 " --> pdb=" O MET H 420 " (cutoff:3.500A) 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: 6.463A pdb=" N VAL I 281 " --> pdb=" O PHE I 467 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LYS I 217 " --> pdb=" O VAL I 195 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N VAL I 197 " --> pdb=" O LYS I 217 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL I 219 " --> pdb=" O VAL I 197 " (cutoff:3.500A) removed outlier: 6.676A 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: 6.501A pdb=" N ILE I 428 " --> pdb=" O LEU I 304 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLU I 348 " --> pdb=" O VAL I 325 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL I 327 " --> pdb=" O GLU I 348 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR I 350 " --> pdb=" O VAL I 327 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LYS I 376 " --> pdb=" O ILE I 351 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'I' and resid 606 through 608 Processing sheet with id= AP, first strand: chain 'I' and resid 632 through 635 Processing sheet with id= AQ, first strand: chain 'I' and resid 686 through 691 Processing sheet with id= AR, first strand: chain 'I' and resid 745 through 748 Processing sheet with id= AS, first strand: chain 'I' and resid 807 through 809 removed outlier: 4.470A pdb=" N ILE I 807 " --> pdb=" O ILE I 780 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA I1000 " --> pdb=" O GLY I 781 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL I 783 " --> pdb=" O ALA I1000 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL I1002 " --> pdb=" O VAL I 783 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE I1023 " --> pdb=" O LEU I1001 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N VAL I1003 " --> pdb=" O PHE I1023 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL I1025 " --> pdb=" O VAL I1003 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N MET I1040 " --> pdb=" O VAL I1026 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ASP I1028 " --> pdb=" O MET I1040 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N VAL I1042 " --> pdb=" O ASP I1028 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'I' and resid 865 through 867 removed outlier: 6.286A pdb=" N VAL I 841 " --> pdb=" O VAL I 866 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY I 964 " --> pdb=" O ILE I 933 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ILE I 935 " --> pdb=" O GLY I 964 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE I 966 " --> pdb=" O ILE I 935 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'I' and resid 1052 through 1055 Processing sheet with id= AV, first strand: chain 'I' and resid 381 through 387 removed outlier: 3.506A pdb=" N ALA I 382 " --> pdb=" O GLU I 399 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LYS I 397 " --> pdb=" O VAL I 384 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N VAL I 386 " --> pdb=" O ALA I 395 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ALA I 395 " --> pdb=" O VAL I 386 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLU I 419 " --> pdb=" O ILE I 400 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ARG I 402 " --> pdb=" O THR I 417 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N THR I 417 " --> pdb=" O ARG I 402 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'J' and resid 127 through 132 removed outlier: 6.892A pdb=" N TYR J 88 " --> pdb=" O THR J 128 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N GLU J 130 " --> pdb=" O TYR J 88 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE J 90 " --> pdb=" O GLU J 130 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL J 132 " --> pdb=" O ILE J 90 " (cutoff:3.500A) removed outlier: 6.385A 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 39 removed outlier: 4.008A pdb=" N LYS K 2 " --> pdb=" O PHE K 54 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE K 50 " --> pdb=" O GLY K 6 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'K' and resid 305 through 308 removed outlier: 6.745A pdb=" N TYR K 177 " --> pdb=" O ASN K 306 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ASN K 308 " --> pdb=" O TYR K 177 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL K 179 " --> pdb=" O ASN K 308 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLU K 218 " --> pdb=" O VAL K 178 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N CYS K 180 " --> pdb=" O GLU K 218 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N HIS K 220 " --> pdb=" O CYS K 180 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASP K 259 " --> pdb=" O GLY K 219 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ILE K 221 " --> pdb=" O ASP K 259 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LYS K 261 " --> pdb=" O ILE K 221 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N CYS K 223 " --> pdb=" O LYS K 261 " (cutoff:3.500A) removed outlier: 5.851A 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 356 removed outlier: 3.623A pdb=" N ALA K 380 " --> pdb=" O MET K 420 " (cutoff:3.500A) 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 4 through 8 removed outlier: 4.125A pdb=" N ILE L 4 " --> pdb=" O VAL L 15 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'L' and resid 466 through 468 removed outlier: 6.431A pdb=" N VAL L 281 " --> pdb=" O PHE L 467 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LYS L 217 " --> pdb=" O VAL L 195 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL L 197 " --> pdb=" O LYS L 217 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL L 219 " --> pdb=" O VAL L 197 " (cutoff:3.500A) removed outlier: 6.669A 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: 6.505A pdb=" N ILE L 428 " --> pdb=" O LEU L 304 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU L 348 " --> pdb=" O VAL L 325 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL L 327 " --> pdb=" O GLU L 348 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N THR L 350 " --> pdb=" O VAL L 327 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LYS L 376 " --> pdb=" O ILE L 351 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'L' and resid 606 through 608 Processing sheet with id= BF, first strand: chain 'L' and resid 632 through 635 Processing sheet with id= BG, first strand: chain 'L' and resid 686 through 691 Processing sheet with id= BH, first strand: chain 'L' and resid 745 through 748 Processing sheet with id= BI, first strand: chain 'L' and resid 807 through 809 removed outlier: 4.491A pdb=" N ILE L 807 " --> pdb=" O ILE L 780 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA L1000 " --> pdb=" O GLY L 781 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL L 783 " --> pdb=" O ALA L1000 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL L1002 " --> pdb=" O VAL L 783 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE L1023 " --> pdb=" O LEU L1001 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N VAL L1003 " --> pdb=" O PHE L1023 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL L1025 " --> pdb=" O VAL L1003 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N MET L1040 " --> pdb=" O VAL L1026 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ASP L1028 " --> pdb=" O MET L1040 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N VAL L1042 " --> pdb=" O ASP L1028 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'L' and resid 865 through 867 removed outlier: 6.292A pdb=" N VAL L 841 " --> pdb=" O VAL L 866 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLY L 964 " --> pdb=" O ILE L 933 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N ILE L 935 " --> pdb=" O GLY L 964 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE L 966 " --> pdb=" O ILE L 935 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'L' and resid 1052 through 1055 Processing sheet with id= BL, first strand: chain 'L' and resid 381 through 387 removed outlier: 3.518A pdb=" N ALA L 382 " --> pdb=" O GLU L 399 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS L 397 " --> pdb=" O VAL L 384 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N VAL L 386 " --> pdb=" O ALA L 395 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA L 395 " --> pdb=" O VAL L 386 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLU L 419 " --> pdb=" O ILE L 400 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ARG L 402 " --> pdb=" O THR L 417 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N THR L 417 " --> pdb=" O ARG L 402 " (cutoff:3.500A) 1837 hydrogen bonds defined for protein. 5127 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.34 Time building geometry restraints manager: 18.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.19: 4 1.19 - 1.46: 31025 1.46 - 1.74: 27058 1.74 - 2.01: 641 2.01 - 2.28: 480 Bond restraints: 59208 Sorted by residual: bond pdb=" C ASN K 181 " pdb=" O ASN K 181 " ideal model delta sigma weight residual 1.233 1.888 -0.655 1.43e-02 4.89e+03 2.10e+03 bond pdb=" N ASN K 181 " pdb=" CA ASN K 181 " ideal model delta sigma weight residual 1.458 1.629 -0.171 1.19e-02 7.06e+03 2.07e+02 bond pdb=" CB PRO C 383 " pdb=" CG PRO C 383 " ideal model delta sigma weight residual 1.492 0.914 0.578 5.00e-02 4.00e+02 1.34e+02 bond pdb=" CB PRO L 383 " pdb=" CG PRO L 383 " ideal model delta sigma weight residual 1.492 0.918 0.574 5.00e-02 4.00e+02 1.32e+02 bond pdb=" C CYS K 180 " pdb=" N ASN K 181 " ideal model delta sigma weight residual 1.333 1.511 -0.178 1.56e-02 4.11e+03 1.31e+02 ... (remaining 59203 not shown) Histogram of bond angle deviations from ideal: 73.53 - 94.82: 465 94.82 - 116.11: 39434 116.11 - 137.40: 40463 137.40 - 158.69: 2 158.69 - 179.98: 4 Bond angle restraints: 80368 Sorted by residual: angle pdb=" CB PRO C 383 " pdb=" CG PRO C 383 " pdb=" CD PRO C 383 " ideal model delta sigma weight residual 106.10 179.98 -73.88 3.20e+00 9.77e-02 5.33e+02 angle pdb=" CB PRO L 383 " pdb=" CG PRO L 383 " pdb=" CD PRO L 383 " ideal model delta sigma weight residual 106.10 178.47 -72.37 3.20e+00 9.77e-02 5.12e+02 angle pdb=" CB PRO F 383 " pdb=" CG PRO F 383 " pdb=" CD PRO F 383 " ideal model delta sigma weight residual 106.10 177.36 -71.26 3.20e+00 9.77e-02 4.96e+02 angle pdb=" CB PRO I 383 " pdb=" CG PRO I 383 " pdb=" CD PRO I 383 " ideal model delta sigma weight residual 106.10 176.79 -70.69 3.20e+00 9.77e-02 4.88e+02 angle pdb=" N PRO C 383 " pdb=" CD PRO C 383 " pdb=" CG PRO C 383 " ideal model delta sigma weight residual 103.20 76.56 26.64 1.50e+00 4.44e-01 3.16e+02 ... (remaining 80363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.53: 34686 33.53 - 67.06: 1061 67.06 - 100.59: 95 100.59 - 134.12: 0 134.12 - 167.64: 2 Dihedral angle restraints: 35844 sinusoidal: 14160 harmonic: 21684 Sorted by residual: dihedral pdb=" CD ARG K 22 " pdb=" NE ARG K 22 " pdb=" CZ ARG K 22 " pdb=" NH1 ARG K 22 " ideal model delta sinusoidal sigma weight residual 0.00 -83.68 83.68 1 1.00e+01 1.00e-02 8.54e+01 dihedral pdb=" C ASP K 183 " pdb=" N ASP K 183 " pdb=" CA ASP K 183 " pdb=" CB ASP K 183 " ideal model delta harmonic sigma weight residual -122.60 -100.16 -22.44 0 2.50e+00 1.60e-01 8.06e+01 dihedral pdb=" CA TYR A 77 " pdb=" C TYR A 77 " pdb=" N SER A 78 " pdb=" CA SER A 78 " ideal model delta harmonic sigma weight residual 180.00 150.25 29.75 0 5.00e+00 4.00e-02 3.54e+01 ... (remaining 35841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 8697 0.102 - 0.205: 531 0.205 - 0.307: 11 0.307 - 0.409: 4 0.409 - 0.512: 1 Chirality restraints: 9244 Sorted by residual: chirality pdb=" CA ASP K 183 " pdb=" N ASP K 183 " pdb=" C ASP K 183 " pdb=" CB ASP K 183 " both_signs ideal model delta sigma weight residual False 2.51 3.02 -0.51 2.00e-01 2.50e+01 6.54e+00 chirality pdb=" CA TYR G 77 " pdb=" N TYR G 77 " pdb=" C TYR G 77 " pdb=" CB TYR G 77 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" CA TYR J 77 " pdb=" N TYR J 77 " pdb=" C TYR J 77 " pdb=" CB TYR J 77 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 ... (remaining 9241 not shown) Planarity restraints: 10304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG K 22 " 1.091 9.50e-02 1.11e+02 4.89e-01 1.44e+02 pdb=" NE ARG K 22 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG K 22 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG K 22 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG K 22 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS K 180 " -0.044 2.00e-02 2.50e+03 7.27e-02 5.29e+01 pdb=" C CYS K 180 " 0.126 2.00e-02 2.50e+03 pdb=" O CYS K 180 " -0.043 2.00e-02 2.50e+03 pdb=" N ASN K 181 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 98 " -0.024 2.00e-02 2.50e+03 4.94e-02 2.44e+01 pdb=" C ILE H 98 " 0.085 2.00e-02 2.50e+03 pdb=" O ILE H 98 " -0.031 2.00e-02 2.50e+03 pdb=" N LEU H 99 " -0.031 2.00e-02 2.50e+03 ... (remaining 10301 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 20 2.25 - 2.91: 23492 2.91 - 3.57: 81343 3.57 - 4.24: 135561 4.24 - 4.90: 231291 Nonbonded interactions: 471707 Sorted by model distance: nonbonded pdb=" CG2 ILE H 42 " pdb=" CE MET H 44 " model vdw 1.586 3.880 nonbonded pdb=" CG2 ILE E 42 " pdb=" CE MET E 44 " model vdw 1.627 3.880 nonbonded pdb=" O ALA K 182 " pdb=" N GLU K 184 " model vdw 1.853 2.520 nonbonded pdb=" O ALA K 182 " pdb=" C ASP K 183 " model vdw 1.910 3.270 nonbonded pdb=" O ILE H 98 " pdb=" N ALA H 100 " model vdw 2.008 2.520 ... (remaining 471702 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: 1.640 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: 0.050 Extract box with map and model: 7.920 Check model and map are aligned: 0.630 Set scattering table: 0.390 Process input model: 139.890 Find NCS groups from input model: 3.270 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 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 : 0.009 0.655 59208 Z= 0.603 Angle : 0.996 73.878 80368 Z= 0.500 Chirality : 0.052 0.512 9244 Planarity : 0.008 0.489 10304 Dihedral : 15.704 167.645 22020 Min Nonbonded Distance : 1.586 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.75 % Favored : 95.88 % Rotamer: Outliers : 0.41 % Allowed : 16.65 % Favored : 82.95 % Cbeta Deviations : 0.04 % 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: -0.54 (0.09), residues: 7600 helix: 0.02 (0.09), residues: 2932 sheet: 0.13 (0.17), residues: 980 loop : -0.72 (0.10), residues: 3688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F1122 HIS 0.005 0.001 HIS C 734 PHE 0.053 0.002 PHE G 76 TYR 0.035 0.002 TYR J 77 ARG 0.015 0.001 ARG J 160 *********************** 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 591 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 566 time to evaluate : 4.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 12 residues processed: 579 average time/residue: 0.5432 time to fit residues: 537.6404 Evaluate side-chains 578 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 566 time to evaluate : 4.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 CYS Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain E residue 45 CYS Chi-restraints excluded: chain H residue 319 ILE Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 989 VAL Chi-restraints excluded: chain K residue 45 CYS Chi-restraints excluded: chain K residue 184 GLU Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain K residue 453 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 641 optimal weight: 0.0000 chunk 576 optimal weight: 9.9990 chunk 319 optimal weight: 0.7980 chunk 196 optimal weight: 9.9990 chunk 388 optimal weight: 7.9990 chunk 307 optimal weight: 0.3980 chunk 595 optimal weight: 40.0000 chunk 230 optimal weight: 30.0000 chunk 362 optimal weight: 4.9990 chunk 443 optimal weight: 0.9980 chunk 690 optimal weight: 0.9980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 GLN C 390 ASN E 102 GLN E 166 ASN ** E 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 390 ASN ** H 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 390 ASN K 166 ASN ** K 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 390 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.0524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 59208 Z= 0.128 Angle : 0.501 11.167 80368 Z= 0.256 Chirality : 0.042 0.295 9244 Planarity : 0.004 0.069 10304 Dihedral : 5.892 153.093 8427 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.76 % Favored : 97.05 % Rotamer: Outliers : 1.40 % Allowed : 15.66 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.10 (0.09), residues: 7600 helix: 0.76 (0.10), residues: 2924 sheet: 0.25 (0.18), residues: 920 loop : -0.46 (0.10), residues: 3756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F1122 HIS 0.002 0.000 HIS L 734 PHE 0.032 0.001 PHE G 76 TYR 0.028 0.001 TYR J 77 ARG 0.006 0.000 ARG J 160 *********************** 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 698 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 612 time to evaluate : 4.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 540 THR cc_start: 0.5735 (OUTLIER) cc_final: 0.5385 (m) REVERT: F 639 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.7051 (m-80) REVERT: G 69 LYS cc_start: 0.8644 (ttmm) cc_final: 0.7971 (mttt) REVERT: H 320 MET cc_start: 0.5846 (tpp) cc_final: 0.5463 (tpp) REVERT: K 252 MET cc_start: 0.6365 (mmm) cc_final: 0.5672 (mtp) outliers start: 86 outliers final: 32 residues processed: 666 average time/residue: 0.5270 time to fit residues: 602.2782 Evaluate side-chains 607 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 573 time to evaluate : 4.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain C residue 595 HIS Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 378 GLN Chi-restraints excluded: chain F residue 595 HIS Chi-restraints excluded: chain F residue 639 PHE Chi-restraints excluded: chain F residue 671 CYS Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 595 HIS Chi-restraints excluded: chain I residue 671 CYS Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 595 HIS Chi-restraints excluded: chain L residue 671 CYS Chi-restraints excluded: chain L residue 681 ILE Chi-restraints excluded: chain L residue 865 SER Chi-restraints excluded: chain L residue 968 VAL Chi-restraints excluded: chain L residue 989 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 383 optimal weight: 7.9990 chunk 214 optimal weight: 8.9990 chunk 574 optimal weight: 5.9990 chunk 469 optimal weight: 0.7980 chunk 190 optimal weight: 8.9990 chunk 691 optimal weight: 4.9990 chunk 746 optimal weight: 10.0000 chunk 615 optimal weight: 8.9990 chunk 685 optimal weight: 2.9990 chunk 235 optimal weight: 40.0000 chunk 554 optimal weight: 0.8980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 GLN B 29 ASN C 390 ASN C 661 GLN C 870 GLN D 57 GLN ** E 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 390 ASN F 870 GLN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 166 ASN ** H 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 390 ASN I 870 GLN J 57 GLN K 166 ASN ** K 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 390 ASN L 870 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 59208 Z= 0.313 Angle : 0.576 16.432 80368 Z= 0.293 Chirality : 0.046 0.316 9244 Planarity : 0.004 0.055 10304 Dihedral : 5.850 151.707 8404 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.63 % Favored : 96.18 % Rotamer: Outliers : 2.66 % Allowed : 15.87 % Favored : 81.47 % 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: 0.18 (0.10), residues: 7600 helix: 0.93 (0.10), residues: 2936 sheet: 0.11 (0.17), residues: 936 loop : -0.46 (0.10), residues: 3728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F1122 HIS 0.004 0.001 HIS L 734 PHE 0.031 0.002 PHE G 76 TYR 0.031 0.001 TYR A 77 ARG 0.026 0.001 ARG A 160 *********************** 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 755 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 591 time to evaluate : 4.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 581 VAL cc_start: 0.3667 (t) cc_final: 0.3370 (m) REVERT: C 22 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8612 (tp) REVERT: C 602 ASN cc_start: 0.7391 (p0) cc_final: 0.7123 (p0) REVERT: C 639 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7513 (m-80) REVERT: D 42 GLN cc_start: 0.7275 (mt0) cc_final: 0.6560 (mt0) REVERT: D 69 LYS cc_start: 0.8655 (ttmm) cc_final: 0.8088 (mttt) REVERT: F 602 ASN cc_start: 0.7276 (p0) cc_final: 0.7037 (p0) REVERT: F 639 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7380 (m-80) REVERT: F 685 MET cc_start: 0.8037 (mtt) cc_final: 0.7767 (mtt) REVERT: H 259 ASP cc_start: 0.6472 (t0) cc_final: 0.6272 (m-30) REVERT: H 320 MET cc_start: 0.5817 (tpp) cc_final: 0.5360 (tpp) REVERT: H 548 VAL cc_start: 0.4456 (OUTLIER) cc_final: 0.4188 (t) REVERT: I 394 LYS cc_start: 0.7693 (ptmt) cc_final: 0.7479 (pttp) REVERT: I 602 ASN cc_start: 0.7077 (p0) cc_final: 0.6846 (p0) REVERT: I 639 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7321 (m-80) REVERT: L 22 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8588 (tp) REVERT: L 394 LYS cc_start: 0.7755 (pttp) cc_final: 0.7504 (pttp) REVERT: L 602 ASN cc_start: 0.7348 (p0) cc_final: 0.7056 (p0) outliers start: 164 outliers final: 96 residues processed: 702 average time/residue: 0.5291 time to fit residues: 633.3804 Evaluate side-chains 647 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 545 time to evaluate : 4.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 595 HIS Chi-restraints excluded: chain C residue 639 PHE Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 714 THR Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain C residue 865 SER Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 1092 ASP Chi-restraints excluded: chain C residue 1093 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 595 HIS Chi-restraints excluded: chain F residue 639 PHE Chi-restraints excluded: chain F residue 671 CYS Chi-restraints excluded: chain F residue 676 VAL Chi-restraints excluded: chain F residue 714 THR Chi-restraints excluded: chain F residue 806 THR Chi-restraints excluded: chain F residue 865 SER Chi-restraints excluded: chain F residue 968 VAL Chi-restraints excluded: chain F residue 989 VAL Chi-restraints excluded: chain F residue 1092 ASP Chi-restraints excluded: chain F residue 1093 THR Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 92 GLN Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 381 VAL Chi-restraints excluded: chain H residue 540 THR Chi-restraints excluded: chain H residue 548 VAL Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 375 VAL Chi-restraints excluded: chain I residue 588 LYS Chi-restraints excluded: chain I residue 595 HIS Chi-restraints excluded: chain I residue 639 PHE Chi-restraints excluded: chain I residue 644 MET Chi-restraints excluded: chain I residue 671 CYS Chi-restraints excluded: chain I residue 676 VAL Chi-restraints excluded: chain I residue 714 THR Chi-restraints excluded: chain I residue 806 THR Chi-restraints excluded: chain I residue 865 SER Chi-restraints excluded: chain I residue 968 VAL Chi-restraints excluded: chain I residue 989 VAL Chi-restraints excluded: chain I residue 1032 THR Chi-restraints excluded: chain I residue 1092 ASP Chi-restraints excluded: chain I residue 1093 THR Chi-restraints excluded: chain J residue 98 CYS Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain K residue 381 VAL Chi-restraints excluded: chain K residue 540 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 139 ILE Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 588 LYS Chi-restraints excluded: chain L residue 595 HIS Chi-restraints excluded: chain L residue 644 MET Chi-restraints excluded: chain L residue 671 CYS Chi-restraints excluded: chain L residue 676 VAL Chi-restraints excluded: chain L residue 714 THR Chi-restraints excluded: chain L residue 806 THR Chi-restraints excluded: chain L residue 865 SER Chi-restraints excluded: chain L residue 968 VAL Chi-restraints excluded: chain L residue 1093 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 683 optimal weight: 30.0000 chunk 519 optimal weight: 0.9990 chunk 358 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 329 optimal weight: 0.8980 chunk 464 optimal weight: 1.9990 chunk 693 optimal weight: 5.9990 chunk 734 optimal weight: 1.9990 chunk 362 optimal weight: 10.0000 chunk 657 optimal weight: 0.4980 chunk 197 optimal weight: 9.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 ASN B 166 ASN B 382 GLN C 390 ASN E 25 GLN E 166 ASN ** E 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 390 ASN G 57 GLN H 166 ASN ** H 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 390 ASN ** J 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 166 ASN ** K 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 390 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 59208 Z= 0.158 Angle : 0.508 13.180 80368 Z= 0.256 Chirality : 0.043 0.296 9244 Planarity : 0.003 0.046 10304 Dihedral : 5.561 148.713 8404 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.89 % Favored : 96.93 % Rotamer: Outliers : 2.32 % Allowed : 16.69 % Favored : 80.99 % 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: 0.42 (0.10), residues: 7600 helix: 1.17 (0.10), residues: 2908 sheet: 0.18 (0.17), residues: 936 loop : -0.34 (0.10), residues: 3756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP F1122 HIS 0.003 0.000 HIS C 734 PHE 0.031 0.001 PHE G 76 TYR 0.028 0.001 TYR G 77 ARG 0.010 0.000 ARG A 160 *********************** 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 738 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 595 time to evaluate : 4.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 TYR cc_start: 0.6275 (OUTLIER) cc_final: 0.5451 (t80) REVERT: C 602 ASN cc_start: 0.7334 (p0) cc_final: 0.7087 (p0) REVERT: C 639 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7505 (m-80) REVERT: D 42 GLN cc_start: 0.7043 (mt0) cc_final: 0.6236 (mt0) REVERT: D 69 LYS cc_start: 0.8663 (ttmm) cc_final: 0.8055 (mttt) REVERT: D 79 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8005 (tm-30) REVERT: E 320 MET cc_start: 0.6659 (tpp) cc_final: 0.6060 (tpp) REVERT: F 22 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8593 (tp) REVERT: F 69 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.8137 (mp-120) REVERT: F 378 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7526 (mm-40) REVERT: F 602 ASN cc_start: 0.7279 (p0) cc_final: 0.6982 (p0) REVERT: F 639 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7395 (m-80) REVERT: F 685 MET cc_start: 0.8006 (mtt) cc_final: 0.7748 (mtt) REVERT: G 69 LYS cc_start: 0.8716 (ttmm) cc_final: 0.8096 (mttt) REVERT: G 79 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8090 (tm-30) REVERT: G 135 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6212 (mm) REVERT: H 259 ASP cc_start: 0.6448 (t0) cc_final: 0.6245 (m-30) REVERT: H 548 VAL cc_start: 0.4544 (OUTLIER) cc_final: 0.4251 (t) REVERT: I 22 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8606 (tp) REVERT: I 394 LYS cc_start: 0.7652 (ptmt) cc_final: 0.7428 (pttp) REVERT: I 602 ASN cc_start: 0.7071 (p0) cc_final: 0.6802 (p0) REVERT: I 639 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7423 (m-80) REVERT: I 685 MET cc_start: 0.8139 (mtt) cc_final: 0.7691 (mtt) REVERT: J 79 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.8111 (tm-30) REVERT: K 581 VAL cc_start: 0.3525 (t) cc_final: 0.3251 (m) REVERT: L 394 LYS cc_start: 0.7681 (pttp) cc_final: 0.7417 (pttp) REVERT: L 401 MET cc_start: 0.8121 (mmm) cc_final: 0.7868 (mmt) REVERT: L 602 ASN cc_start: 0.7297 (p0) cc_final: 0.7042 (p0) outliers start: 143 outliers final: 80 residues processed: 692 average time/residue: 0.5241 time to fit residues: 623.3426 Evaluate side-chains 646 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 553 time to evaluate : 4.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain C residue 595 HIS Chi-restraints excluded: chain C residue 639 PHE Chi-restraints excluded: chain C residue 865 SER Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1068 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 378 GLN Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain F residue 595 HIS Chi-restraints excluded: chain F residue 639 PHE Chi-restraints excluded: chain F residue 671 CYS Chi-restraints excluded: chain F residue 865 SER Chi-restraints excluded: chain F residue 968 VAL Chi-restraints excluded: chain F residue 989 VAL Chi-restraints excluded: chain F residue 1025 VAL Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 92 GLN Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 381 VAL Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain H residue 540 THR Chi-restraints excluded: chain H residue 548 VAL Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 494 ASP Chi-restraints excluded: chain I residue 595 HIS Chi-restraints excluded: chain I residue 639 PHE Chi-restraints excluded: chain I residue 671 CYS Chi-restraints excluded: chain I residue 865 SER Chi-restraints excluded: chain I residue 968 VAL Chi-restraints excluded: chain I residue 989 VAL Chi-restraints excluded: chain I residue 1025 VAL Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 98 CYS Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 381 VAL Chi-restraints excluded: chain K residue 540 THR Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 494 ASP Chi-restraints excluded: chain L residue 595 HIS Chi-restraints excluded: chain L residue 644 MET Chi-restraints excluded: chain L residue 671 CYS Chi-restraints excluded: chain L residue 681 ILE Chi-restraints excluded: chain L residue 865 SER Chi-restraints excluded: chain L residue 968 VAL Chi-restraints excluded: chain L residue 989 VAL Chi-restraints excluded: chain L residue 1025 VAL Chi-restraints excluded: chain L residue 1068 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 611 optimal weight: 20.0000 chunk 417 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 chunk 546 optimal weight: 10.0000 chunk 303 optimal weight: 20.0000 chunk 626 optimal weight: 20.0000 chunk 507 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 375 optimal weight: 3.9990 chunk 659 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 GLN B 166 ASN B 382 GLN C 390 ASN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 390 ASN F 661 GLN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 HIS ** H 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 390 ASN I 661 GLN ** J 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 166 ASN ** K 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 390 ASN L 661 GLN L 680 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 59208 Z= 0.374 Angle : 0.607 15.656 80368 Z= 0.307 Chirality : 0.048 0.325 9244 Planarity : 0.004 0.044 10304 Dihedral : 5.801 150.602 8404 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.04 % Favored : 95.79 % Rotamer: Outliers : 3.05 % Allowed : 16.45 % Favored : 80.50 % 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: 0.22 (0.10), residues: 7600 helix: 1.01 (0.10), residues: 2904 sheet: 0.16 (0.17), residues: 984 loop : -0.50 (0.10), residues: 3712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F1122 HIS 0.006 0.001 HIS F 96 PHE 0.031 0.002 PHE J 76 TYR 0.031 0.002 TYR J 77 ARG 0.010 0.001 ARG H 169 *********************** 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 766 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 578 time to evaluate : 4.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 TYR cc_start: 0.6526 (OUTLIER) cc_final: 0.5832 (t80) REVERT: A 79 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7898 (tm-30) REVERT: C 22 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8596 (tp) REVERT: C 602 ASN cc_start: 0.7415 (p0) cc_final: 0.7184 (p0) REVERT: C 639 PHE cc_start: 0.8321 (OUTLIER) cc_final: 0.7573 (m-80) REVERT: C 672 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8473 (mtp) REVERT: D 79 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8078 (tm-30) REVERT: E 320 MET cc_start: 0.6741 (tpp) cc_final: 0.6170 (tpp) REVERT: F 22 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8730 (tp) REVERT: F 602 ASN cc_start: 0.7364 (p0) cc_final: 0.7090 (p0) REVERT: F 639 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7745 (m-80) REVERT: F 672 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8565 (mtp) REVERT: F 685 MET cc_start: 0.7915 (mtt) cc_final: 0.7670 (mtt) REVERT: G 79 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8084 (tm-30) REVERT: H 320 MET cc_start: 0.6374 (tpp) cc_final: 0.5823 (tpp) REVERT: H 548 VAL cc_start: 0.4629 (OUTLIER) cc_final: 0.4338 (t) REVERT: I 22 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8724 (tp) REVERT: I 401 MET cc_start: 0.8308 (mmm) cc_final: 0.8104 (mmt) REVERT: I 602 ASN cc_start: 0.7203 (p0) cc_final: 0.6962 (p0) REVERT: I 639 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.7589 (m-80) REVERT: I 672 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8558 (mtp) REVERT: J 79 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8084 (tm-30) REVERT: K 581 VAL cc_start: 0.3612 (t) cc_final: 0.3320 (m) REVERT: L 22 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8609 (tp) REVERT: L 357 ILE cc_start: 0.8511 (mp) cc_final: 0.8263 (mm) REVERT: L 394 LYS cc_start: 0.7857 (pttp) cc_final: 0.7542 (pttp) REVERT: L 602 ASN cc_start: 0.7405 (p0) cc_final: 0.7164 (p0) REVERT: L 672 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8508 (mtp) outliers start: 188 outliers final: 122 residues processed: 713 average time/residue: 0.5324 time to fit residues: 653.3349 Evaluate side-chains 673 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 534 time to evaluate : 4.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 62 TYR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 139 ILE 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 253 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 595 HIS Chi-restraints excluded: chain C residue 639 PHE Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 865 SER Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1093 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 139 ILE 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 253 THR Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 595 HIS Chi-restraints excluded: chain F residue 639 PHE Chi-restraints excluded: chain F residue 671 CYS Chi-restraints excluded: chain F residue 672 MET Chi-restraints excluded: chain F residue 676 VAL Chi-restraints excluded: chain F residue 806 THR Chi-restraints excluded: chain F residue 865 SER Chi-restraints excluded: chain F residue 968 VAL Chi-restraints excluded: chain F residue 989 VAL Chi-restraints excluded: chain F residue 1025 VAL Chi-restraints excluded: chain F residue 1092 ASP Chi-restraints excluded: chain F residue 1093 THR Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 92 GLN Chi-restraints excluded: chain G residue 98 CYS Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 381 VAL Chi-restraints excluded: chain H residue 548 VAL Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 139 ILE 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 253 THR Chi-restraints excluded: chain I residue 375 VAL Chi-restraints excluded: chain I residue 437 VAL Chi-restraints excluded: chain I residue 494 ASP Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain I residue 595 HIS Chi-restraints excluded: chain I residue 639 PHE Chi-restraints excluded: chain I residue 644 MET Chi-restraints excluded: chain I residue 671 CYS Chi-restraints excluded: chain I residue 672 MET Chi-restraints excluded: chain I residue 676 VAL Chi-restraints excluded: chain I residue 806 THR Chi-restraints excluded: chain I residue 865 SER Chi-restraints excluded: chain I residue 968 VAL Chi-restraints excluded: chain I residue 989 VAL Chi-restraints excluded: chain I residue 1025 VAL Chi-restraints excluded: chain I residue 1032 THR Chi-restraints excluded: chain I residue 1092 ASP Chi-restraints excluded: chain I residue 1093 THR Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 98 CYS Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 381 VAL Chi-restraints excluded: chain K residue 498 VAL Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 139 ILE 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 246 ASP Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 494 ASP Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 588 LYS Chi-restraints excluded: chain L residue 595 HIS Chi-restraints excluded: chain L residue 644 MET Chi-restraints excluded: chain L residue 671 CYS Chi-restraints excluded: chain L residue 672 MET Chi-restraints excluded: chain L residue 676 VAL Chi-restraints excluded: chain L residue 865 SER Chi-restraints excluded: chain L residue 968 VAL Chi-restraints excluded: chain L residue 989 VAL Chi-restraints excluded: chain L residue 1025 VAL Chi-restraints excluded: chain L residue 1092 ASP Chi-restraints excluded: chain L residue 1093 THR Chi-restraints excluded: chain L residue 1131 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 247 optimal weight: 9.9990 chunk 661 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 431 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 735 optimal weight: 6.9990 chunk 610 optimal weight: 20.0000 chunk 340 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 243 optimal weight: 20.0000 chunk 386 optimal weight: 9.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN B 166 ASN C 390 ASN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 GLN F 390 ASN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 166 ASN ** H 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 390 ASN J 57 GLN K 166 ASN ** K 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN L 390 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 59208 Z= 0.369 Angle : 0.611 19.290 80368 Z= 0.307 Chirality : 0.047 0.327 9244 Planarity : 0.004 0.043 10304 Dihedral : 5.792 152.041 8404 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.91 % Favored : 95.92 % Rotamer: Outliers : 3.08 % Allowed : 17.07 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.10), residues: 7600 helix: 0.93 (0.10), residues: 2900 sheet: -0.06 (0.16), residues: 1064 loop : -0.57 (0.10), residues: 3636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP F1122 HIS 0.004 0.001 HIS C 96 PHE 0.032 0.002 PHE G 76 TYR 0.028 0.002 TYR G 77 ARG 0.006 0.001 ARG H 169 *********************** 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 772 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 582 time to evaluate : 4.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 TYR cc_start: 0.6778 (OUTLIER) cc_final: 0.6041 (t80) REVERT: A 79 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7858 (tm-30) REVERT: B 44 MET cc_start: 0.4087 (tmm) cc_final: 0.3786 (tmm) REVERT: C 22 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8593 (tp) REVERT: C 602 ASN cc_start: 0.7487 (p0) cc_final: 0.7281 (p0) REVERT: C 720 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8105 (t0) REVERT: D 79 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7984 (tm-30) REVERT: E 320 MET cc_start: 0.6644 (tpp) cc_final: 0.6140 (tpp) REVERT: E 333 GLU cc_start: 0.6629 (pm20) cc_final: 0.6196 (mp0) REVERT: E 581 VAL cc_start: 0.3530 (t) cc_final: 0.3268 (m) REVERT: F 22 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8669 (tp) REVERT: F 394 LYS cc_start: 0.7989 (pttp) cc_final: 0.7726 (pttp) REVERT: F 602 ASN cc_start: 0.7400 (p0) cc_final: 0.7129 (p0) REVERT: F 672 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8448 (mtp) REVERT: F 685 MET cc_start: 0.7916 (mtt) cc_final: 0.7701 (mtt) REVERT: F 720 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7987 (t0) REVERT: G 43 LYS cc_start: 0.8387 (mmtm) cc_final: 0.8114 (mmtm) REVERT: G 79 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7986 (tm-30) REVERT: G 94 GLN cc_start: 0.8451 (mm-40) cc_final: 0.8226 (mm-40) REVERT: H 320 MET cc_start: 0.6303 (tpp) cc_final: 0.5784 (tpp) REVERT: H 548 VAL cc_start: 0.4751 (OUTLIER) cc_final: 0.4473 (t) REVERT: I 22 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8671 (tp) REVERT: I 394 LYS cc_start: 0.7841 (pttp) cc_final: 0.7529 (pttp) REVERT: I 602 ASN cc_start: 0.7288 (p0) cc_final: 0.7066 (p0) REVERT: I 639 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.7665 (m-80) REVERT: I 672 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8442 (mtp) REVERT: I 685 MET cc_start: 0.8217 (mtt) cc_final: 0.7913 (mtt) REVERT: J 43 LYS cc_start: 0.8351 (mmtm) cc_final: 0.8085 (mmtm) REVERT: J 79 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8014 (tm-30) REVERT: K 581 VAL cc_start: 0.3799 (t) cc_final: 0.3490 (m) REVERT: L 22 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8622 (tp) REVERT: L 357 ILE cc_start: 0.8551 (mp) cc_final: 0.8293 (mm) REVERT: L 394 LYS cc_start: 0.7987 (pttp) cc_final: 0.7703 (pttp) REVERT: L 602 ASN cc_start: 0.7448 (p0) cc_final: 0.7215 (p0) REVERT: L 672 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8493 (mtp) REVERT: L 720 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.8085 (t0) outliers start: 190 outliers final: 135 residues processed: 720 average time/residue: 0.5323 time to fit residues: 660.1423 Evaluate side-chains 691 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 539 time to evaluate : 4.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 62 TYR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 132 LEU 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 253 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 595 HIS Chi-restraints excluded: chain C residue 639 PHE Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 714 THR Chi-restraints excluded: chain C residue 720 ASP Chi-restraints excluded: chain C residue 865 SER Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1032 THR Chi-restraints excluded: chain C residue 1092 ASP Chi-restraints excluded: chain C residue 1093 THR Chi-restraints excluded: chain C residue 1131 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 132 LEU 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 375 VAL Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 595 HIS Chi-restraints excluded: chain F residue 639 PHE Chi-restraints excluded: chain F residue 671 CYS Chi-restraints excluded: chain F residue 672 MET Chi-restraints excluded: chain F residue 676 VAL Chi-restraints excluded: chain F residue 720 ASP Chi-restraints excluded: chain F residue 806 THR Chi-restraints excluded: chain F residue 865 SER Chi-restraints excluded: chain F residue 968 VAL Chi-restraints excluded: chain F residue 989 VAL Chi-restraints excluded: chain F residue 1022 SER Chi-restraints excluded: chain F residue 1025 VAL Chi-restraints excluded: chain F residue 1093 THR Chi-restraints excluded: chain F residue 1131 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 92 GLN Chi-restraints excluded: chain G residue 98 CYS Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 381 VAL Chi-restraints excluded: chain H residue 498 VAL Chi-restraints excluded: chain H residue 548 VAL Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 132 LEU 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 375 VAL Chi-restraints excluded: chain I residue 494 ASP Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain I residue 595 HIS Chi-restraints excluded: chain I residue 639 PHE Chi-restraints excluded: chain I residue 644 MET Chi-restraints excluded: chain I residue 671 CYS Chi-restraints excluded: chain I residue 672 MET Chi-restraints excluded: chain I residue 676 VAL Chi-restraints excluded: chain I residue 806 THR Chi-restraints excluded: chain I residue 865 SER Chi-restraints excluded: chain I residue 968 VAL Chi-restraints excluded: chain I residue 989 VAL Chi-restraints excluded: chain I residue 1022 SER Chi-restraints excluded: chain I residue 1025 VAL Chi-restraints excluded: chain I residue 1032 THR Chi-restraints excluded: chain I residue 1093 THR Chi-restraints excluded: chain I residue 1131 THR Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 381 VAL Chi-restraints excluded: chain K residue 438 VAL Chi-restraints excluded: chain K residue 498 VAL Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 139 ILE Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain L residue 246 ASP Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 494 ASP Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 588 LYS Chi-restraints excluded: chain L residue 595 HIS Chi-restraints excluded: chain L residue 644 MET Chi-restraints excluded: chain L residue 671 CYS Chi-restraints excluded: chain L residue 672 MET Chi-restraints excluded: chain L residue 676 VAL Chi-restraints excluded: chain L residue 714 THR Chi-restraints excluded: chain L residue 720 ASP Chi-restraints excluded: chain L residue 806 THR Chi-restraints excluded: chain L residue 865 SER Chi-restraints excluded: chain L residue 968 VAL Chi-restraints excluded: chain L residue 989 VAL Chi-restraints excluded: chain L residue 1025 VAL Chi-restraints excluded: chain L residue 1092 ASP Chi-restraints excluded: chain L residue 1093 THR Chi-restraints excluded: chain L residue 1131 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 708 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 418 optimal weight: 0.8980 chunk 536 optimal weight: 0.1980 chunk 416 optimal weight: 40.0000 chunk 618 optimal weight: 10.0000 chunk 410 optimal weight: 6.9990 chunk 732 optimal weight: 9.9990 chunk 458 optimal weight: 5.9990 chunk 446 optimal weight: 20.0000 chunk 338 optimal weight: 0.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 GLN B 29 ASN B 166 ASN B 382 GLN C 390 ASN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 390 ASN G 57 GLN H 166 ASN ** H 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 390 ASN J 94 GLN K 166 ASN ** K 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 390 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 59208 Z= 0.201 Angle : 0.552 17.321 80368 Z= 0.274 Chirality : 0.044 0.304 9244 Planarity : 0.003 0.039 10304 Dihedral : 5.545 152.383 8404 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.66 % Favored : 96.17 % Rotamer: Outliers : 2.42 % Allowed : 18.04 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.34 (0.10), residues: 7600 helix: 1.12 (0.10), residues: 2912 sheet: 0.11 (0.17), residues: 992 loop : -0.39 (0.10), residues: 3696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP F1122 HIS 0.003 0.001 HIS I 96 PHE 0.032 0.001 PHE G 76 TYR 0.029 0.001 TYR H 60 ARG 0.006 0.000 ARG J 160 *********************** 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 727 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 578 time to evaluate : 5.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 TYR cc_start: 0.6829 (OUTLIER) cc_final: 0.5881 (t80) REVERT: A 79 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7882 (tm-30) REVERT: B 44 MET cc_start: 0.4157 (tmm) cc_final: 0.3895 (tmm) REVERT: C 235 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8690 (mm) REVERT: C 602 ASN cc_start: 0.7447 (p0) cc_final: 0.7181 (p0) REVERT: C 672 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8388 (mtp) REVERT: C 685 MET cc_start: 0.8343 (mtm) cc_final: 0.8065 (mtt) REVERT: C 720 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7981 (t0) REVERT: D 79 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7881 (tm-30) REVERT: E 320 MET cc_start: 0.6948 (tpp) cc_final: 0.6477 (tpp) REVERT: E 581 VAL cc_start: 0.3469 (t) cc_final: 0.3210 (m) REVERT: F 22 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8596 (tp) REVERT: F 235 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8529 (mm) REVERT: F 394 LYS cc_start: 0.7943 (pttp) cc_final: 0.7712 (pttp) REVERT: F 602 ASN cc_start: 0.7353 (p0) cc_final: 0.7079 (p0) REVERT: F 639 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7553 (m-80) REVERT: G 79 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7932 (tm-30) REVERT: H 320 MET cc_start: 0.6263 (tpp) cc_final: 0.5680 (tpp) REVERT: H 548 VAL cc_start: 0.4828 (OUTLIER) cc_final: 0.4559 (t) REVERT: I 22 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8601 (tp) REVERT: I 235 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8521 (mm) REVERT: I 394 LYS cc_start: 0.7881 (pttp) cc_final: 0.7545 (pttp) REVERT: I 602 ASN cc_start: 0.7256 (p0) cc_final: 0.7038 (p0) REVERT: I 639 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7654 (m-80) REVERT: I 685 MET cc_start: 0.8170 (mtt) cc_final: 0.7852 (mtt) REVERT: J 43 LYS cc_start: 0.8445 (mmtm) cc_final: 0.8227 (mmtm) REVERT: J 79 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7943 (tm-30) REVERT: K 17 ARG cc_start: 0.6628 (tpt-90) cc_final: 0.6384 (mtp85) REVERT: K 581 VAL cc_start: 0.3797 (t) cc_final: 0.3508 (m) REVERT: L 235 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8573 (mm) REVERT: L 357 ILE cc_start: 0.8442 (mp) cc_final: 0.8183 (mm) REVERT: L 394 LYS cc_start: 0.7959 (pttp) cc_final: 0.7708 (pttp) REVERT: L 588 LYS cc_start: 0.6927 (OUTLIER) cc_final: 0.6578 (mttp) REVERT: L 602 ASN cc_start: 0.7417 (p0) cc_final: 0.7188 (p0) REVERT: L 685 MET cc_start: 0.8239 (mtt) cc_final: 0.7913 (mtt) outliers start: 149 outliers final: 102 residues processed: 691 average time/residue: 0.5288 time to fit residues: 628.4519 Evaluate side-chains 677 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 558 time to evaluate : 4.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 62 TYR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain C residue 595 HIS Chi-restraints excluded: chain C residue 639 PHE Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 720 ASP Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain C residue 865 SER Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 989 VAL Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1093 THR Chi-restraints excluded: chain C residue 1131 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain F residue 595 HIS Chi-restraints excluded: chain F residue 639 PHE Chi-restraints excluded: chain F residue 671 CYS Chi-restraints excluded: chain F residue 714 THR Chi-restraints excluded: chain F residue 865 SER Chi-restraints excluded: chain F residue 968 VAL Chi-restraints excluded: chain F residue 989 VAL Chi-restraints excluded: chain F residue 1025 VAL Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 92 GLN Chi-restraints excluded: chain G residue 98 CYS Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 381 VAL Chi-restraints excluded: chain H residue 548 VAL Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 375 VAL Chi-restraints excluded: chain I residue 494 ASP Chi-restraints excluded: chain I residue 595 HIS Chi-restraints excluded: chain I residue 639 PHE Chi-restraints excluded: chain I residue 671 CYS Chi-restraints excluded: chain I residue 714 THR Chi-restraints excluded: chain I residue 865 SER Chi-restraints excluded: chain I residue 968 VAL Chi-restraints excluded: chain I residue 989 VAL Chi-restraints excluded: chain I residue 1025 VAL Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 381 VAL Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 132 LEU 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 246 ASP Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 494 ASP Chi-restraints excluded: chain L residue 588 LYS Chi-restraints excluded: chain L residue 595 HIS Chi-restraints excluded: chain L residue 671 CYS Chi-restraints excluded: chain L residue 806 THR Chi-restraints excluded: chain L residue 865 SER Chi-restraints excluded: chain L residue 968 VAL Chi-restraints excluded: chain L residue 989 VAL Chi-restraints excluded: chain L residue 1025 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 453 optimal weight: 0.7980 chunk 292 optimal weight: 10.0000 chunk 437 optimal weight: 8.9990 chunk 220 optimal weight: 20.0000 chunk 143 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 465 optimal weight: 2.9990 chunk 499 optimal weight: 2.9990 chunk 362 optimal weight: 10.0000 chunk 68 optimal weight: 30.0000 chunk 575 optimal weight: 6.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 GLN B 29 ASN B 382 GLN C 390 ASN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 390 ASN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 166 ASN ** H 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 390 ASN ** J 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 166 ASN ** K 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 59208 Z= 0.274 Angle : 0.582 18.279 80368 Z= 0.289 Chirality : 0.045 0.310 9244 Planarity : 0.003 0.039 10304 Dihedral : 5.592 153.134 8404 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.96 % Favored : 95.87 % Rotamer: Outliers : 2.51 % Allowed : 18.14 % Favored : 79.35 % 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: 0.32 (0.10), residues: 7600 helix: 1.13 (0.10), residues: 2896 sheet: 0.07 (0.17), residues: 980 loop : -0.43 (0.10), residues: 3724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F1122 HIS 0.003 0.001 HIS I 96 PHE 0.031 0.002 PHE G 76 TYR 0.026 0.001 TYR G 77 ARG 0.006 0.000 ARG J 160 *********************** 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 724 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 569 time to evaluate : 4.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 TYR cc_start: 0.6954 (OUTLIER) cc_final: 0.6062 (t80) REVERT: A 79 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7897 (tm-30) REVERT: B 44 MET cc_start: 0.4049 (tmm) cc_final: 0.3805 (tmm) REVERT: C 22 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8576 (tp) REVERT: C 235 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8686 (mm) REVERT: C 602 ASN cc_start: 0.7472 (p0) cc_final: 0.7208 (p0) REVERT: C 639 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7584 (m-80) REVERT: C 672 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8437 (mtp) REVERT: C 685 MET cc_start: 0.8324 (mtm) cc_final: 0.8029 (mtt) REVERT: C 720 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.8016 (t0) REVERT: D 79 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7947 (tm-30) REVERT: E 320 MET cc_start: 0.6828 (tpp) cc_final: 0.6338 (tpp) REVERT: E 581 VAL cc_start: 0.3578 (t) cc_final: 0.3295 (m) REVERT: F 22 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8665 (tp) REVERT: F 602 ASN cc_start: 0.7395 (p0) cc_final: 0.7111 (p0) REVERT: F 639 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7471 (m-80) REVERT: G 79 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7941 (tm-30) REVERT: H 320 MET cc_start: 0.6355 (tpp) cc_final: 0.6020 (tpp) REVERT: H 548 VAL cc_start: 0.4904 (OUTLIER) cc_final: 0.4627 (t) REVERT: I 22 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8667 (tp) REVERT: I 360 MET cc_start: 0.8117 (mmm) cc_final: 0.7830 (mtp) REVERT: I 394 LYS cc_start: 0.7919 (pttp) cc_final: 0.7637 (pttp) REVERT: I 588 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6901 (mttp) REVERT: I 602 ASN cc_start: 0.7300 (p0) cc_final: 0.7066 (p0) REVERT: I 639 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7644 (m-80) REVERT: I 685 MET cc_start: 0.8147 (mtt) cc_final: 0.7831 (mtt) REVERT: J 79 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7960 (tm-30) REVERT: K 17 ARG cc_start: 0.6819 (tpt-90) cc_final: 0.6524 (mtp85) REVERT: K 581 VAL cc_start: 0.3948 (t) cc_final: 0.3679 (m) REVERT: L 22 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8570 (tp) REVERT: L 357 ILE cc_start: 0.8492 (mp) cc_final: 0.8276 (mm) REVERT: L 394 LYS cc_start: 0.7956 (pttp) cc_final: 0.7712 (pttp) REVERT: L 588 LYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6808 (mttp) REVERT: L 602 ASN cc_start: 0.7430 (p0) cc_final: 0.7194 (p0) REVERT: L 685 MET cc_start: 0.8251 (mtt) cc_final: 0.7918 (mtt) outliers start: 155 outliers final: 123 residues processed: 688 average time/residue: 0.5414 time to fit residues: 641.1510 Evaluate side-chains 692 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 551 time to evaluate : 4.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 62 TYR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain C residue 595 HIS Chi-restraints excluded: chain C residue 639 PHE Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 720 ASP Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain C residue 809 THR Chi-restraints excluded: chain C residue 865 SER Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 989 VAL Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1093 THR Chi-restraints excluded: chain C residue 1131 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain F residue 595 HIS Chi-restraints excluded: chain F residue 639 PHE Chi-restraints excluded: chain F residue 671 CYS Chi-restraints excluded: chain F residue 714 THR Chi-restraints excluded: chain F residue 865 SER Chi-restraints excluded: chain F residue 968 VAL Chi-restraints excluded: chain F residue 989 VAL Chi-restraints excluded: chain F residue 1022 SER Chi-restraints excluded: chain F residue 1025 VAL Chi-restraints excluded: chain F residue 1092 ASP Chi-restraints excluded: chain F residue 1093 THR Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 92 GLN Chi-restraints excluded: chain G residue 98 CYS Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 381 VAL Chi-restraints excluded: chain H residue 548 VAL Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 375 VAL Chi-restraints excluded: chain I residue 494 ASP Chi-restraints excluded: chain I residue 588 LYS Chi-restraints excluded: chain I residue 595 HIS Chi-restraints excluded: chain I residue 639 PHE Chi-restraints excluded: chain I residue 671 CYS Chi-restraints excluded: chain I residue 714 THR Chi-restraints excluded: chain I residue 865 SER Chi-restraints excluded: chain I residue 948 MET Chi-restraints excluded: chain I residue 968 VAL Chi-restraints excluded: chain I residue 989 VAL Chi-restraints excluded: chain I residue 1022 SER Chi-restraints excluded: chain I residue 1025 VAL Chi-restraints excluded: chain I residue 1093 THR Chi-restraints excluded: chain I residue 1131 THR Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain K residue 62 TYR Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 381 VAL Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 139 ILE 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 246 ASP Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 358 ASP Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 494 ASP Chi-restraints excluded: chain L residue 588 LYS Chi-restraints excluded: chain L residue 595 HIS Chi-restraints excluded: chain L residue 671 CYS Chi-restraints excluded: chain L residue 681 ILE Chi-restraints excluded: chain L residue 806 THR Chi-restraints excluded: chain L residue 809 THR Chi-restraints excluded: chain L residue 865 SER Chi-restraints excluded: chain L residue 968 VAL Chi-restraints excluded: chain L residue 989 VAL Chi-restraints excluded: chain L residue 1025 VAL Chi-restraints excluded: chain L residue 1093 THR Chi-restraints excluded: chain L residue 1131 THR 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: 1.9990 chunk 640 optimal weight: 0.0670 chunk 682 optimal weight: 20.0000 chunk 410 optimal weight: 20.0000 chunk 297 optimal weight: 0.9990 chunk 536 optimal weight: 8.9990 chunk 209 optimal weight: 40.0000 chunk 616 optimal weight: 7.9990 chunk 645 optimal weight: 0.0970 chunk 680 optimal weight: 0.5980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 GLN B 29 ASN B 166 ASN B 382 GLN C 390 ASN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 GLN H 166 ASN ** H 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 390 ASN ** J 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 HIS K 166 ASN ** K 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 59208 Z= 0.136 Angle : 0.537 18.974 80368 Z= 0.262 Chirality : 0.042 0.284 9244 Planarity : 0.003 0.037 10304 Dihedral : 5.285 150.784 8404 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.13 % Favored : 96.70 % Rotamer: Outliers : 1.93 % Allowed : 18.88 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.54 (0.10), residues: 7600 helix: 1.29 (0.10), residues: 2896 sheet: 0.20 (0.17), residues: 940 loop : -0.26 (0.10), residues: 3764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F1122 HIS 0.004 0.000 HIS F 392 PHE 0.032 0.001 PHE G 76 TYR 0.021 0.001 TYR J 77 ARG 0.007 0.000 ARG J 160 *********************** 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 720 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 601 time to evaluate : 5.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 TYR cc_start: 0.6940 (OUTLIER) cc_final: 0.5999 (t80) REVERT: A 79 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7805 (tm-30) REVERT: B 44 MET cc_start: 0.3984 (tmm) cc_final: 0.3758 (tmm) REVERT: C 602 ASN cc_start: 0.7433 (p0) cc_final: 0.7173 (p0) REVERT: C 639 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7499 (m-80) REVERT: C 685 MET cc_start: 0.8257 (mtm) cc_final: 0.7976 (mtt) REVERT: D 79 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7585 (tm-30) REVERT: E 1 MET cc_start: 0.4503 (tpp) cc_final: 0.3987 (mmp) REVERT: E 320 MET cc_start: 0.6803 (tpp) cc_final: 0.6409 (tpp) REVERT: E 333 GLU cc_start: 0.6517 (pm20) cc_final: 0.6312 (mp0) REVERT: E 581 VAL cc_start: 0.3583 (t) cc_final: 0.3345 (m) REVERT: F 22 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8602 (tp) REVERT: F 602 ASN cc_start: 0.7337 (p0) cc_final: 0.7053 (p0) REVERT: F 639 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7577 (m-80) REVERT: G 69 LYS cc_start: 0.8720 (ttmm) cc_final: 0.8082 (mttt) REVERT: G 79 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7832 (tm-30) REVERT: H 320 MET cc_start: 0.6424 (tpp) cc_final: 0.6042 (tpp) REVERT: H 548 VAL cc_start: 0.5073 (OUTLIER) cc_final: 0.4678 (t) REVERT: I 22 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8596 (tp) REVERT: I 394 LYS cc_start: 0.7893 (pttp) cc_final: 0.7620 (pttp) REVERT: I 588 LYS cc_start: 0.6669 (OUTLIER) cc_final: 0.6352 (mttp) REVERT: I 602 ASN cc_start: 0.7249 (p0) cc_final: 0.7015 (p0) REVERT: I 685 MET cc_start: 0.8224 (mtt) cc_final: 0.7921 (mtt) REVERT: J 79 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7872 (tm-30) REVERT: K 17 ARG cc_start: 0.6807 (tpt-90) cc_final: 0.6534 (mtp85) REVERT: L 22 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8609 (tp) REVERT: L 394 LYS cc_start: 0.7917 (pttp) cc_final: 0.7658 (pttp) REVERT: L 588 LYS cc_start: 0.6820 (OUTLIER) cc_final: 0.6501 (mttp) REVERT: L 602 ASN cc_start: 0.7395 (p0) cc_final: 0.7155 (p0) REVERT: L 685 MET cc_start: 0.8150 (mtt) cc_final: 0.7776 (mtt) outliers start: 119 outliers final: 90 residues processed: 700 average time/residue: 0.5324 time to fit residues: 637.3693 Evaluate side-chains 670 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 567 time to evaluate : 4.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 62 TYR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 595 HIS Chi-restraints excluded: chain C residue 639 PHE Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain C residue 865 SER Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 989 VAL Chi-restraints excluded: chain C residue 1022 SER Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain F residue 595 HIS Chi-restraints excluded: chain F residue 639 PHE Chi-restraints excluded: chain F residue 671 CYS Chi-restraints excluded: chain F residue 714 THR Chi-restraints excluded: chain F residue 865 SER Chi-restraints excluded: chain F residue 968 VAL Chi-restraints excluded: chain F residue 989 VAL Chi-restraints excluded: chain F residue 1022 SER Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 98 CYS Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 381 VAL Chi-restraints excluded: chain H residue 548 VAL Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 375 VAL Chi-restraints excluded: chain I residue 494 ASP Chi-restraints excluded: chain I residue 588 LYS Chi-restraints excluded: chain I residue 595 HIS Chi-restraints excluded: chain I residue 671 CYS Chi-restraints excluded: chain I residue 714 THR Chi-restraints excluded: chain I residue 809 THR Chi-restraints excluded: chain I residue 865 SER Chi-restraints excluded: chain I residue 948 MET Chi-restraints excluded: chain I residue 968 VAL Chi-restraints excluded: chain I residue 989 VAL Chi-restraints excluded: chain I residue 1022 SER Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain K residue 47 TYR Chi-restraints excluded: chain K residue 62 TYR Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 381 VAL Chi-restraints excluded: chain K residue 438 VAL Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 41 ILE 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 375 VAL Chi-restraints excluded: chain L residue 494 ASP Chi-restraints excluded: chain L residue 588 LYS Chi-restraints excluded: chain L residue 595 HIS Chi-restraints excluded: chain L residue 671 CYS Chi-restraints excluded: chain L residue 865 SER Chi-restraints excluded: chain L residue 989 VAL Chi-restraints excluded: chain L residue 1022 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 448 optimal weight: 6.9990 chunk 721 optimal weight: 9.9990 chunk 440 optimal weight: 5.9990 chunk 342 optimal weight: 1.9990 chunk 501 optimal weight: 0.8980 chunk 757 optimal weight: 5.9990 chunk 696 optimal weight: 9.9990 chunk 602 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 465 optimal weight: 3.9990 chunk 369 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 GLN B 29 ASN B 166 ASN B 382 GLN C 390 ASN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 390 ASN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 166 ASN ** H 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 ASN ** J 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 166 ASN ** K 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 837 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 59208 Z= 0.360 Angle : 0.624 21.778 80368 Z= 0.310 Chirality : 0.047 0.333 9244 Planarity : 0.004 0.040 10304 Dihedral : 5.598 153.270 8404 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.11 % Favored : 95.72 % Rotamer: Outliers : 2.11 % Allowed : 18.75 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.10), residues: 7600 helix: 1.14 (0.10), residues: 2888 sheet: 0.12 (0.18), residues: 932 loop : -0.38 (0.10), residues: 3780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP K 318 HIS 0.006 0.001 HIS F 96 PHE 0.031 0.002 PHE J 76 TYR 0.027 0.002 TYR G 77 ARG 0.009 0.001 ARG I 717 ********************** 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 699 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 569 time to evaluate : 4.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 TYR cc_start: 0.6990 (OUTLIER) cc_final: 0.6033 (t80) REVERT: A 79 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7932 (tm-30) REVERT: A 92 GLN cc_start: 0.7305 (pt0) cc_final: 0.7058 (pt0) REVERT: C 22 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8621 (tp) REVERT: C 421 VAL cc_start: 0.8172 (p) cc_final: 0.7788 (m) REVERT: C 639 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.7574 (m-80) REVERT: C 672 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8461 (mtp) REVERT: C 720 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.8073 (t0) REVERT: D 79 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7974 (tm-30) REVERT: E 1 MET cc_start: 0.4534 (tpp) cc_final: 0.4323 (mmp) REVERT: E 320 MET cc_start: 0.6870 (tpp) cc_final: 0.6422 (tpp) REVERT: E 581 VAL cc_start: 0.3590 (t) cc_final: 0.3329 (m) REVERT: F 22 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8699 (tp) REVERT: F 602 ASN cc_start: 0.7413 (p0) cc_final: 0.7136 (p0) REVERT: G 79 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7963 (tm-30) REVERT: H 320 MET cc_start: 0.6461 (tpp) cc_final: 0.6029 (tpp) REVERT: I 22 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8682 (tp) REVERT: I 360 MET cc_start: 0.8121 (mmm) cc_final: 0.7899 (mtp) REVERT: I 394 LYS cc_start: 0.7972 (pttp) cc_final: 0.7743 (pttp) REVERT: I 588 LYS cc_start: 0.7081 (OUTLIER) cc_final: 0.6875 (mttp) REVERT: I 602 ASN cc_start: 0.7333 (p0) cc_final: 0.7091 (p0) REVERT: J 79 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7968 (tm-30) REVERT: K 1 MET cc_start: 0.3992 (mmm) cc_final: 0.3364 (mmp) REVERT: K 17 ARG cc_start: 0.6794 (tpt-90) cc_final: 0.6517 (mtp85) REVERT: K 581 VAL cc_start: 0.4063 (t) cc_final: 0.3756 (m) REVERT: L 22 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8633 (tp) REVERT: L 394 LYS cc_start: 0.8014 (pttp) cc_final: 0.7773 (pttp) REVERT: L 421 VAL cc_start: 0.8002 (p) cc_final: 0.7760 (m) REVERT: L 588 LYS cc_start: 0.7129 (OUTLIER) cc_final: 0.6781 (mttp) REVERT: L 602 ASN cc_start: 0.7401 (p0) cc_final: 0.7156 (p0) REVERT: L 948 MET cc_start: 0.8780 (mmt) cc_final: 0.8551 (mmt) outliers start: 130 outliers final: 107 residues processed: 674 average time/residue: 0.5482 time to fit residues: 636.8782 Evaluate side-chains 675 residues out of total 6164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 554 time to evaluate : 4.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 62 TYR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 595 HIS Chi-restraints excluded: chain C residue 639 PHE Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 720 ASP Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain C residue 809 THR Chi-restraints excluded: chain C residue 865 SER Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 1022 SER Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 187 MET Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain F residue 595 HIS Chi-restraints excluded: chain F residue 639 PHE Chi-restraints excluded: chain F residue 671 CYS Chi-restraints excluded: chain F residue 714 THR Chi-restraints excluded: chain F residue 809 THR Chi-restraints excluded: chain F residue 865 SER Chi-restraints excluded: chain F residue 968 VAL Chi-restraints excluded: chain F residue 989 VAL Chi-restraints excluded: chain F residue 1022 SER Chi-restraints excluded: chain F residue 1092 ASP Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 98 CYS Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 381 VAL Chi-restraints excluded: chain H residue 548 VAL Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 375 VAL Chi-restraints excluded: chain I residue 494 ASP Chi-restraints excluded: chain I residue 588 LYS Chi-restraints excluded: chain I residue 595 HIS Chi-restraints excluded: chain I residue 671 CYS Chi-restraints excluded: chain I residue 676 VAL Chi-restraints excluded: chain I residue 714 THR Chi-restraints excluded: chain I residue 809 THR Chi-restraints excluded: chain I residue 865 SER Chi-restraints excluded: chain I residue 948 MET Chi-restraints excluded: chain I residue 968 VAL Chi-restraints excluded: chain I residue 989 VAL Chi-restraints excluded: chain I residue 1022 SER Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain K residue 62 TYR Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 381 VAL Chi-restraints excluded: chain K residue 438 VAL Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 187 MET Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 246 ASP Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 494 ASP Chi-restraints excluded: chain L residue 588 LYS Chi-restraints excluded: chain L residue 595 HIS Chi-restraints excluded: chain L residue 671 CYS Chi-restraints excluded: chain L residue 681 ILE Chi-restraints excluded: chain L residue 806 THR Chi-restraints excluded: chain L residue 865 SER Chi-restraints excluded: chain L residue 989 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 478 optimal weight: 1.9990 chunk 642 optimal weight: 9.9990 chunk 184 optimal weight: 8.9990 chunk 555 optimal weight: 2.9990 chunk 89 optimal weight: 0.0570 chunk 167 optimal weight: 0.9980 chunk 603 optimal weight: 40.0000 chunk 252 optimal weight: 7.9990 chunk 620 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 382 GLN C 390 ASN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 390 ASN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 166 ASN ** H 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 540 ASN ** J 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 GLN K 166 ASN ** K 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 559 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.166317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.105553 restraints weight = 77518.172| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.90 r_work: 0.3046 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 59208 Z= 0.202 Angle : 0.572 20.986 80368 Z= 0.280 Chirality : 0.044 0.316 9244 Planarity : 0.003 0.054 10304 Dihedral : 5.439 153.128 8404 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.29 % Favored : 96.54 % Rotamer: Outliers : 1.96 % Allowed : 19.08 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.46 (0.10), residues: 7600 helix: 1.21 (0.10), residues: 2896 sheet: 0.21 (0.17), residues: 976 loop : -0.31 (0.10), residues: 3728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP F1122 HIS 0.003 0.001 HIS C 96 PHE 0.030 0.001 PHE J 76 TYR 0.022 0.001 TYR G 77 ARG 0.013 0.000 ARG F 717 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12530.93 seconds wall clock time: 221 minutes 36.38 seconds (13296.38 seconds total)