Starting phenix.real_space_refine on Sun Dec 29 17:32:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oh9_16879/12_2024/8oh9_16879.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oh9_16879/12_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/cci-nas-00/data/ceres_data/8oh9_16879/12_2024/8oh9_16879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oh9_16879/12_2024/8oh9_16879.map" model { file = "/net/cci-nas-00/data/ceres_data/8oh9_16879/12_2024/8oh9_16879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oh9_16879/12_2024/8oh9_16879.cif" } 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. Time to flip 96 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 24.90, per 1000 atoms: 0.43 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 - 3.00 Amino acid : True - 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: 12.74 Conformation dependent library (CDL) restraints added in 6.0 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... Secondary structure from input PDB file: 342 helices and 72 sheets defined 44.8% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.33 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 Proline residue: A 25 - end of helix Processing helix chain 'A' and resid 36 through 49 Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 67 through 76 Processing helix chain 'A' and resid 95 through 101 Processing helix chain 'A' and resid 102 through 115 removed outlier: 3.643A pdb=" N ILE A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'A' and resid 155 through 167 Processing helix chain 'B' and resid 10 through 15 removed outlier: 3.561A pdb=" N ALA B 14 " --> pdb=" O CYS B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 31 Processing helix chain 'B' and resid 44 through 48 Processing helix chain 'B' and resid 66 through 77 Processing helix chain 'B' and resid 96 through 101 removed outlier: 4.129A pdb=" N LYS B 101 " --> pdb=" O THR B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 removed outlier: 4.182A pdb=" N TYR B 121 " --> pdb=" O ASN B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 137 removed outlier: 3.662A pdb=" N MET B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 160 through 171 Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 199 through 215 removed outlier: 4.013A pdb=" N LEU B 203 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 244 Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 269 through 272 Processing helix chain 'B' and resid 273 through 282 Processing helix chain 'B' and resid 299 through 303 Processing helix chain 'B' and resid 310 through 323 Proline residue: B 317 - end of helix Processing helix chain 'B' and resid 323 through 329 Processing helix chain 'B' and resid 360 through 367 Processing helix chain 'B' and resid 372 through 376 Processing helix chain 'B' and resid 385 through 388 Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 401 through 408 Processing helix chain 'B' and resid 425 through 440 Processing helix chain 'B' and resid 445 through 464 removed outlier: 3.639A pdb=" N ARG B 449 " --> pdb=" O CYS B 445 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR B 452 " --> pdb=" O CYS B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 486 Processing helix chain 'B' and resid 488 through 493 Processing helix chain 'B' and resid 495 through 514 removed outlier: 7.661A pdb=" N ASP B 507 " --> pdb=" O ARG B 503 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLU B 508 " --> pdb=" O TYR B 504 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR B 509 " --> pdb=" O PHE B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 Processing helix chain 'B' and resid 540 through 545 removed outlier: 3.574A pdb=" N LYS B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 575 removed outlier: 3.877A pdb=" N VAL B 575 " --> pdb=" O ASN B 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 28 Processing helix chain 'C' and resid 78 through 93 Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 113 through 123 Processing helix chain 'C' and resid 125 through 134 Processing helix chain 'C' and resid 139 through 147 Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 165 through 180 Processing helix chain 'C' and resid 201 through 213 Processing helix chain 'C' and resid 229 through 234 Processing helix chain 'C' and resid 241 through 254 removed outlier: 3.609A pdb=" N LEU C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 278 removed outlier: 3.740A pdb=" N LEU C 274 " --> pdb=" O SER C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 315 Processing helix chain 'C' and resid 331 through 344 Processing helix chain 'C' and resid 356 through 360 Processing helix chain 'C' and resid 363 through 374 Processing helix chain 'C' and resid 470 through 475 Processing helix chain 'C' and resid 478 through 498 removed outlier: 3.537A pdb=" N ALA C 482 " --> pdb=" O ILE C 478 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN C 498 " --> pdb=" O ASP C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 521 removed outlier: 4.025A pdb=" N ALA C 521 " --> pdb=" O ALA C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 540 removed outlier: 3.692A pdb=" N ASN C 540 " --> pdb=" O ALA C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 560 Processing helix chain 'C' and resid 573 through 582 removed outlier: 3.815A pdb=" N LYS C 577 " --> pdb=" O CYS C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 613 Processing helix chain 'C' and resid 617 through 626 Processing helix chain 'C' and resid 637 through 641 Processing helix chain 'C' and resid 647 through 649 No H-bonds generated for 'chain 'C' and resid 647 through 649' Processing helix chain 'C' and resid 660 through 666 Processing helix chain 'C' and resid 725 through 731 Processing helix chain 'C' and resid 732 through 737 removed outlier: 3.620A pdb=" N ASN C 736 " --> pdb=" O GLY C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 776 Processing helix chain 'C' and resid 789 through 803 Processing helix chain 'C' and resid 819 through 824 Processing helix chain 'C' and resid 831 through 835 Processing helix chain 'C' and resid 846 through 851 Processing helix chain 'C' and resid 851 through 862 removed outlier: 3.576A pdb=" N ASP C 855 " --> pdb=" O HIS C 851 " (cutoff:3.500A) Processing helix chain 'C' and resid 874 through 888 removed outlier: 4.025A pdb=" N MET C 878 " --> pdb=" O ASN C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 891 through 898 removed outlier: 3.672A pdb=" N VAL C 895 " --> pdb=" O ASP C 891 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 909 Processing helix chain 'C' and resid 915 through 928 removed outlier: 3.551A pdb=" N ALA C 928 " --> pdb=" O LYS C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 955 Processing helix chain 'C' and resid 973 through 980 Processing helix chain 'C' and resid 985 through 995 removed outlier: 3.964A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1007 through 1010 removed outlier: 3.791A pdb=" N ALA C1010 " --> pdb=" O ASP C1007 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1007 through 1010' Processing helix chain 'C' and resid 1011 through 1019 Processing helix chain 'C' and resid 1032 through 1037 removed outlier: 3.805A pdb=" N ALA C1037 " --> pdb=" O LYS C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1075 through 1088 Processing helix chain 'C' and resid 1093 through 1105 Processing helix chain 'C' and resid 1159 through 1170 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) Processing helix chain 'D' and resid 19 through 31 Proline residue: D 25 - end of helix Processing helix chain 'D' and resid 36 through 49 Processing helix chain 'D' and resid 52 through 61 Processing helix chain 'D' and resid 66 through 76 removed outlier: 3.791A pdb=" N ILE D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 101 Processing helix chain 'D' and resid 102 through 115 removed outlier: 3.706A pdb=" N ILE D 106 " --> pdb=" O GLY D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 141 Processing helix chain 'D' and resid 155 through 167 Processing helix chain 'E' and resid 10 through 15 removed outlier: 3.546A pdb=" N ALA E 14 " --> pdb=" O CYS E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 31 removed outlier: 4.389A pdb=" N ARG E 22 " --> pdb=" O LYS E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 77 Processing helix chain 'E' and resid 117 through 124 removed outlier: 4.145A pdb=" N TYR E 121 " --> pdb=" O ASN E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 137 removed outlier: 3.777A pdb=" N MET E 137 " --> pdb=" O ALA E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 150 Processing helix chain 'E' and resid 160 through 171 Processing helix chain 'E' and resid 190 through 199 removed outlier: 3.605A pdb=" N SER E 194 " --> pdb=" O PHE E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 215 removed outlier: 3.954A pdb=" N LEU E 203 " --> pdb=" O ASP E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 244 Processing helix chain 'E' and resid 250 through 254 removed outlier: 3.509A pdb=" N GLY E 253 " --> pdb=" O ASN E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 272 Processing helix chain 'E' and resid 273 through 282 Processing helix chain 'E' and resid 299 through 303 Processing helix chain 'E' and resid 310 through 323 Proline residue: E 317 - end of helix Processing helix chain 'E' and resid 323 through 329 removed outlier: 3.525A pdb=" N TYR E 327 " --> pdb=" O GLY E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 367 Processing helix chain 'E' and resid 372 through 376 Processing helix chain 'E' and resid 385 through 388 Processing helix chain 'E' and resid 394 through 396 No H-bonds generated for 'chain 'E' and resid 394 through 396' Processing helix chain 'E' and resid 401 through 408 Processing helix chain 'E' and resid 425 through 440 Processing helix chain 'E' and resid 445 through 464 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 470 through 486 Processing helix chain 'E' and resid 488 through 493 Processing helix chain 'E' and resid 495 through 514 removed outlier: 7.648A pdb=" N ASP E 507 " --> pdb=" O ARG E 503 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLU E 508 " --> pdb=" O TYR E 504 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR E 509 " --> pdb=" O PHE E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 527 Processing helix chain 'E' and resid 540 through 545 removed outlier: 3.603A pdb=" N LYS E 545 " --> pdb=" O LEU E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 575 removed outlier: 3.865A pdb=" N VAL E 575 " --> pdb=" O ASN E 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 28 Processing helix chain 'F' and resid 78 through 93 Processing helix chain 'F' and resid 102 through 108 Processing helix chain 'F' and resid 113 through 123 Processing helix chain 'F' and resid 125 through 134 Processing helix chain 'F' and resid 139 through 147 Processing helix chain 'F' and resid 155 through 160 Processing helix chain 'F' and resid 165 through 180 Processing helix chain 'F' and resid 201 through 213 Processing helix chain 'F' and resid 229 through 234 Processing helix chain 'F' and resid 241 through 254 removed outlier: 3.570A pdb=" N LEU F 245 " --> pdb=" O ASP F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 278 removed outlier: 3.740A pdb=" N LEU F 274 " --> pdb=" O SER F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 315 Processing helix chain 'F' and resid 331 through 344 Processing helix chain 'F' and resid 356 through 360 Processing helix chain 'F' and resid 363 through 374 Processing helix chain 'F' and resid 470 through 475 Processing helix chain 'F' and resid 478 through 498 removed outlier: 3.538A pdb=" N ALA F 482 " --> pdb=" O ILE F 478 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN F 498 " --> pdb=" O ASP F 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 516 through 521 removed outlier: 4.021A pdb=" N ALA F 521 " --> pdb=" O ALA F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 535 through 540 removed outlier: 3.680A pdb=" N ASN F 540 " --> pdb=" O ALA F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 551 through 560 Processing helix chain 'F' and resid 573 through 582 removed outlier: 3.787A pdb=" N LYS F 577 " --> pdb=" O CYS F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 610 through 613 Processing helix chain 'F' and resid 617 through 626 Processing helix chain 'F' and resid 637 through 641 Processing helix chain 'F' and resid 647 through 649 No H-bonds generated for 'chain 'F' and resid 647 through 649' Processing helix chain 'F' and resid 660 through 666 Processing helix chain 'F' and resid 725 through 731 Processing helix chain 'F' and resid 732 through 737 removed outlier: 3.617A pdb=" N ASN F 736 " --> pdb=" O GLY F 733 " (cutoff:3.500A) Processing helix chain 'F' and resid 756 through 776 Processing helix chain 'F' and resid 789 through 803 Processing helix chain 'F' and resid 819 through 824 Processing helix chain 'F' and resid 831 through 835 Processing helix chain 'F' and resid 846 through 851 Processing helix chain 'F' and resid 851 through 862 removed outlier: 3.581A pdb=" N ASP F 855 " --> pdb=" O HIS F 851 " (cutoff:3.500A) Processing helix chain 'F' and resid 874 through 888 removed outlier: 4.023A pdb=" N MET F 878 " --> pdb=" O ASN F 874 " (cutoff:3.500A) Processing helix chain 'F' and resid 891 through 898 removed outlier: 3.676A pdb=" N VAL F 895 " --> pdb=" O ASP F 891 " (cutoff:3.500A) Processing helix chain 'F' and resid 901 through 909 Processing helix chain 'F' and resid 915 through 928 Processing helix chain 'F' and resid 941 through 955 Processing helix chain 'F' and resid 973 through 980 Processing helix chain 'F' and resid 985 through 995 removed outlier: 3.923A pdb=" N VAL F 989 " --> pdb=" O PRO F 985 " (cutoff:3.500A) Processing helix chain 'F' and resid 1007 through 1010 removed outlier: 4.174A pdb=" N ALA F1010 " --> pdb=" O ASP F1007 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1007 through 1010' Processing helix chain 'F' and resid 1011 through 1019 Processing helix chain 'F' and resid 1032 through 1037 removed outlier: 3.831A pdb=" N ALA F1037 " --> pdb=" O LYS F1033 " (cutoff:3.500A) Processing helix chain 'F' and resid 1075 through 1088 Processing helix chain 'F' and resid 1093 through 1105 Processing helix chain 'F' and resid 1159 through 1170 removed outlier: 3.800A pdb=" N GLN F1170 " --> pdb=" O VAL F1166 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 31 Proline residue: G 25 - end of helix Processing helix chain 'G' and resid 36 through 49 Processing helix chain 'G' and resid 52 through 61 Processing helix chain 'G' and resid 66 through 76 removed outlier: 3.787A pdb=" N ILE G 70 " --> pdb=" O LYS G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 101 Processing helix chain 'G' and resid 102 through 115 removed outlier: 3.719A pdb=" N ILE G 106 " --> pdb=" O GLY G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 141 Processing helix chain 'G' and resid 155 through 167 Processing helix chain 'H' and resid 10 through 15 removed outlier: 3.639A pdb=" N ALA H 14 " --> pdb=" O CYS H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 31 removed outlier: 4.395A pdb=" N ARG H 22 " --> pdb=" O LYS H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 77 Processing helix chain 'H' and resid 98 through 102 Processing helix chain 'H' and resid 117 through 124 removed outlier: 4.176A pdb=" N TYR H 121 " --> pdb=" O ASN H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 137 removed outlier: 3.744A pdb=" N MET H 137 " --> pdb=" O ALA H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 149 Processing helix chain 'H' and resid 160 through 171 Processing helix chain 'H' and resid 190 through 197 removed outlier: 3.576A pdb=" N SER H 194 " --> pdb=" O PHE H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 215 Processing helix chain 'H' and resid 227 through 244 Processing helix chain 'H' and resid 250 through 254 removed outlier: 3.535A pdb=" N GLY H 253 " --> pdb=" O ASN H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 272 Processing helix chain 'H' and resid 273 through 282 Processing helix chain 'H' and resid 299 through 303 Processing helix chain 'H' and resid 310 through 323 Proline residue: H 317 - end of helix Processing helix chain 'H' and resid 323 through 329 removed outlier: 3.600A pdb=" N TYR H 327 " --> pdb=" O GLY H 323 " (cutoff:3.500A) Processing helix chain 'H' and resid 360 through 367 Processing helix chain 'H' and resid 372 through 376 Processing helix chain 'H' and resid 384 through 388 removed outlier: 3.878A pdb=" N SER H 387 " --> pdb=" O GLY H 384 " (cutoff:3.500A) Processing helix chain 'H' and resid 394 through 396 No H-bonds generated for 'chain 'H' and resid 394 through 396' Processing helix chain 'H' and resid 401 through 408 Processing helix chain 'H' and resid 425 through 440 Processing helix chain 'H' and resid 445 through 464 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 470 through 486 Processing helix chain 'H' and resid 488 through 493 Processing helix chain 'H' and resid 495 through 514 removed outlier: 7.632A pdb=" N ASP H 507 " --> pdb=" O ARG H 503 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLU H 508 " --> pdb=" O TYR H 504 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR H 509 " --> pdb=" O PHE H 505 " (cutoff:3.500A) Processing helix chain 'H' and resid 523 through 527 Processing helix chain 'H' and resid 540 through 545 removed outlier: 3.583A pdb=" N LYS H 545 " --> pdb=" O LEU H 541 " (cutoff:3.500A) Processing helix chain 'H' and resid 570 through 575 removed outlier: 3.845A pdb=" N VAL H 575 " --> pdb=" O ASN H 571 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 28 Processing helix chain 'I' and resid 78 through 93 Processing helix chain 'I' and resid 102 through 108 Processing helix chain 'I' and resid 113 through 123 Processing helix chain 'I' and resid 125 through 134 Processing helix chain 'I' and resid 139 through 147 Processing helix chain 'I' and resid 155 through 160 Processing helix chain 'I' and resid 165 through 180 Processing helix chain 'I' and resid 201 through 213 Processing helix chain 'I' and resid 229 through 234 Processing helix chain 'I' and resid 241 through 254 removed outlier: 3.569A pdb=" N LEU I 245 " --> pdb=" O ASP I 241 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 278 removed outlier: 3.738A pdb=" N LEU I 274 " --> pdb=" O SER I 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 306 through 315 Processing helix chain 'I' and resid 331 through 344 Processing helix chain 'I' and resid 356 through 360 Processing helix chain 'I' and resid 363 through 374 Processing helix chain 'I' and resid 470 through 475 Processing helix chain 'I' and resid 478 through 498 removed outlier: 3.584A pdb=" N ALA I 482 " --> pdb=" O ILE I 478 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN I 498 " --> pdb=" O ASP I 494 " (cutoff:3.500A) Processing helix chain 'I' and resid 516 through 521 removed outlier: 4.019A pdb=" N ALA I 521 " --> pdb=" O ALA I 518 " (cutoff:3.500A) Processing helix chain 'I' and resid 535 through 540 removed outlier: 3.684A pdb=" N ASN I 540 " --> pdb=" O ALA I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 560 Processing helix chain 'I' and resid 573 through 582 removed outlier: 3.790A pdb=" N LYS I 577 " --> pdb=" O CYS I 573 " (cutoff:3.500A) Processing helix chain 'I' and resid 610 through 613 Processing helix chain 'I' and resid 617 through 626 Processing helix chain 'I' and resid 637 through 641 Processing helix chain 'I' and resid 647 through 649 No H-bonds generated for 'chain 'I' and resid 647 through 649' Processing helix chain 'I' and resid 660 through 666 Processing helix chain 'I' and resid 725 through 731 Processing helix chain 'I' and resid 732 through 737 removed outlier: 3.618A pdb=" N ASN I 736 " --> pdb=" O GLY I 733 " (cutoff:3.500A) Processing helix chain 'I' and resid 756 through 776 Processing helix chain 'I' and resid 789 through 803 Processing helix chain 'I' and resid 819 through 824 Processing helix chain 'I' and resid 831 through 835 Processing helix chain 'I' and resid 846 through 851 Processing helix chain 'I' and resid 851 through 862 removed outlier: 3.585A pdb=" N ASP I 855 " --> pdb=" O HIS I 851 " (cutoff:3.500A) Processing helix chain 'I' and resid 874 through 888 removed outlier: 4.011A pdb=" N MET I 878 " --> pdb=" O ASN I 874 " (cutoff:3.500A) Processing helix chain 'I' and resid 891 through 898 removed outlier: 3.676A pdb=" N VAL I 895 " --> pdb=" O ASP I 891 " (cutoff:3.500A) Processing helix chain 'I' and resid 901 through 909 Processing helix chain 'I' and resid 915 through 928 Processing helix chain 'I' and resid 941 through 956 Processing helix chain 'I' and resid 973 through 980 Processing helix chain 'I' and resid 985 through 995 removed outlier: 3.922A pdb=" N VAL I 989 " --> pdb=" O PRO I 985 " (cutoff:3.500A) Processing helix chain 'I' and resid 1011 through 1019 Processing helix chain 'I' and resid 1032 through 1037 removed outlier: 3.819A pdb=" N ALA I1037 " --> pdb=" O LYS I1033 " (cutoff:3.500A) Processing helix chain 'I' and resid 1075 through 1088 Processing helix chain 'I' and resid 1093 through 1105 Processing helix chain 'I' and resid 1159 through 1170 removed outlier: 3.771A pdb=" N GLN I1170 " --> pdb=" O VAL I1166 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 31 Proline residue: J 25 - end of helix Processing helix chain 'J' and resid 36 through 49 Processing helix chain 'J' and resid 52 through 61 Processing helix chain 'J' and resid 67 through 76 Processing helix chain 'J' and resid 95 through 101 Processing helix chain 'J' and resid 102 through 115 removed outlier: 3.651A pdb=" N ILE J 106 " --> pdb=" O GLY J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 141 Processing helix chain 'J' and resid 155 through 167 Processing helix chain 'K' and resid 10 through 15 Processing helix chain 'K' and resid 15 through 31 Processing helix chain 'K' and resid 66 through 77 Processing helix chain 'K' and resid 96 through 101 removed outlier: 4.150A pdb=" N LYS K 101 " --> pdb=" O THR K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 124 removed outlier: 4.125A pdb=" N TYR K 121 " --> pdb=" O ASN K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 137 removed outlier: 3.755A pdb=" N MET K 137 " --> pdb=" O ALA K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 150 Processing helix chain 'K' and resid 160 through 171 Processing helix chain 'K' and resid 190 through 199 Processing helix chain 'K' and resid 199 through 215 removed outlier: 3.935A pdb=" N LEU K 203 " --> pdb=" O ASP K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 244 Processing helix chain 'K' and resid 250 through 254 removed outlier: 3.543A pdb=" N GLY K 253 " --> pdb=" O ASN K 250 " (cutoff:3.500A) Processing helix chain 'K' and resid 269 through 272 Processing helix chain 'K' and resid 273 through 282 Processing helix chain 'K' and resid 299 through 303 Processing helix chain 'K' and resid 309 through 323 removed outlier: 3.712A pdb=" N PHE K 313 " --> pdb=" O ASN K 309 " (cutoff:3.500A) Proline residue: K 317 - end of helix Processing helix chain 'K' and resid 323 through 330 removed outlier: 3.663A pdb=" N TYR K 327 " --> pdb=" O GLY K 323 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR K 330 " --> pdb=" O ALA K 326 " (cutoff:3.500A) Processing helix chain 'K' and resid 360 through 367 Processing helix chain 'K' and resid 372 through 376 Processing helix chain 'K' and resid 384 through 388 removed outlier: 3.874A pdb=" N SER K 387 " --> pdb=" O GLY K 384 " (cutoff:3.500A) Processing helix chain 'K' and resid 394 through 396 No H-bonds generated for 'chain 'K' and resid 394 through 396' Processing helix chain 'K' and resid 401 through 408 Processing helix chain 'K' and resid 425 through 440 Processing helix chain 'K' and resid 445 through 464 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 470 through 486 Processing helix chain 'K' and resid 488 through 493 Processing helix chain 'K' and resid 495 through 514 removed outlier: 7.664A pdb=" N ASP K 507 " --> pdb=" O ARG K 503 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLU K 508 " --> pdb=" O TYR K 504 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR K 509 " --> pdb=" O PHE K 505 " (cutoff:3.500A) Processing helix chain 'K' and resid 523 through 527 Processing helix chain 'K' and resid 540 through 545 removed outlier: 3.611A pdb=" N LYS K 545 " --> pdb=" O LEU K 541 " (cutoff:3.500A) Processing helix chain 'K' and resid 570 through 575 removed outlier: 3.872A pdb=" N VAL K 575 " --> pdb=" O ASN K 571 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 28 Processing helix chain 'L' and resid 78 through 93 Processing helix chain 'L' and resid 102 through 108 Processing helix chain 'L' and resid 113 through 123 Processing helix chain 'L' and resid 125 through 134 Processing helix chain 'L' and resid 139 through 147 Processing helix chain 'L' and resid 155 through 160 Processing helix chain 'L' and resid 165 through 180 Processing helix chain 'L' and resid 201 through 213 Processing helix chain 'L' and resid 229 through 234 Processing helix chain 'L' and resid 241 through 254 removed outlier: 3.565A pdb=" N LEU L 245 " --> pdb=" O ASP L 241 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 278 removed outlier: 3.744A pdb=" N LEU L 274 " --> pdb=" O SER L 270 " (cutoff:3.500A) Processing helix chain 'L' and resid 306 through 315 Processing helix chain 'L' and resid 331 through 344 Processing helix chain 'L' and resid 356 through 360 Processing helix chain 'L' and resid 363 through 374 Processing helix chain 'L' and resid 470 through 475 Processing helix chain 'L' and resid 478 through 498 removed outlier: 3.586A pdb=" N ALA L 482 " --> pdb=" O ILE L 478 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN L 498 " --> pdb=" O ASP L 494 " (cutoff:3.500A) Processing helix chain 'L' and resid 516 through 521 removed outlier: 4.023A pdb=" N ALA L 521 " --> pdb=" O ALA L 518 " (cutoff:3.500A) Processing helix chain 'L' and resid 535 through 540 removed outlier: 3.690A pdb=" N ASN L 540 " --> pdb=" O ALA L 536 " (cutoff:3.500A) Processing helix chain 'L' and resid 551 through 560 Processing helix chain 'L' and resid 573 through 582 removed outlier: 3.821A pdb=" N LYS L 577 " --> pdb=" O CYS L 573 " (cutoff:3.500A) Processing helix chain 'L' and resid 610 through 613 Processing helix chain 'L' and resid 617 through 626 Processing helix chain 'L' and resid 647 through 649 No H-bonds generated for 'chain 'L' and resid 647 through 649' Processing helix chain 'L' and resid 660 through 666 Processing helix chain 'L' and resid 725 through 731 Processing helix chain 'L' and resid 732 through 737 removed outlier: 3.618A pdb=" N ASN L 736 " --> pdb=" O GLY L 733 " (cutoff:3.500A) Processing helix chain 'L' and resid 756 through 776 Processing helix chain 'L' and resid 789 through 803 Processing helix chain 'L' and resid 819 through 824 Processing helix chain 'L' and resid 831 through 835 Processing helix chain 'L' and resid 846 through 851 Processing helix chain 'L' and resid 851 through 862 removed outlier: 3.568A pdb=" N ASP L 855 " --> pdb=" O HIS L 851 " (cutoff:3.500A) Processing helix chain 'L' and resid 874 through 888 removed outlier: 3.987A pdb=" N MET L 878 " --> pdb=" O ASN L 874 " (cutoff:3.500A) Processing helix chain 'L' and resid 891 through 898 removed outlier: 3.677A pdb=" N VAL L 895 " --> pdb=" O ASP L 891 " (cutoff:3.500A) Processing helix chain 'L' and resid 901 through 909 Processing helix chain 'L' and resid 915 through 928 removed outlier: 3.531A pdb=" N ALA L 928 " --> pdb=" O LYS L 924 " (cutoff:3.500A) Processing helix chain 'L' and resid 941 through 955 Processing helix chain 'L' and resid 973 through 980 Processing helix chain 'L' and resid 985 through 995 removed outlier: 3.917A pdb=" N VAL L 989 " --> pdb=" O PRO L 985 " (cutoff:3.500A) Processing helix chain 'L' and resid 1007 through 1010 removed outlier: 4.097A pdb=" N ALA L1010 " --> pdb=" O ASP L1007 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1007 through 1010' Processing helix chain 'L' and resid 1011 through 1019 Processing helix chain 'L' and resid 1032 through 1037 removed outlier: 3.829A pdb=" N ALA L1037 " --> pdb=" O LYS L1033 " (cutoff:3.500A) Processing helix chain 'L' and resid 1075 through 1088 Processing helix chain 'L' and resid 1093 through 1105 Processing helix chain 'L' and resid 1159 through 1170 removed outlier: 3.789A pdb=" N GLN L1170 " --> pdb=" O VAL L1166 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 127 through 132 removed outlier: 3.533A pdb=" N GLN A 92 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 132 " --> pdb=" O GLN A 92 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL A 143 " --> pdb=" O CYS A 93 " (cutoff:3.500A) Processing sheet with id=AA2, 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) removed outlier: 3.776A pdb=" N SER B 90 " --> pdb=" O SER B 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 259 through 265 removed outlier: 6.296A pdb=" N GLY B 219 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LYS B 263 " --> pdb=" O GLY B 219 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ILE B 221 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY B 265 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N CYS B 223 " --> pdb=" O GLY B 265 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL B 178 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N TYR B 222 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N CYS B 180 " --> pdb=" O TYR B 222 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ARG B 224 " --> pdb=" O CYS B 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 351 through 356 Processing sheet with id=AA5, first strand: chain 'B' and resid 528 through 531 Processing sheet with id=AA6, first strand: chain 'B' and resid 551 through 552 Processing sheet with id=AA7, first strand: chain 'C' and resid 11 through 14 removed outlier: 9.517A pdb=" N ILE C 74 " --> pdb=" O SER C 5 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN C 7 " --> pdb=" O ILE C 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 258 through 260 removed outlier: 6.847A pdb=" N VAL C 218 " --> pdb=" O GLU C 258 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ILE C 260 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE C 220 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 289 through 290 Processing sheet with id=AB1, first strand: chain 'C' and resid 303 through 305 removed outlier: 6.783A pdb=" N LEU C 304 " --> pdb=" O ALA C 430 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS C 324 " --> pdb=" O ARG C 427 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ILE C 429 " --> pdb=" O LYS C 324 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU C 326 " --> pdb=" O ILE C 429 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL C 349 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLN C 378 " --> pdb=" O VAL C 349 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE C 351 " --> pdb=" O GLN C 378 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 381 through 389 removed outlier: 6.414A pdb=" N VAL C 381 " --> pdb=" O MET C 401 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N MET C 401 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLU C 399 " --> pdb=" O PRO C 383 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLU C 389 " --> pdb=" O ALA C 393 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ALA C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ALA C 395 " --> pdb=" O TYR C 423 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N TYR C 423 " --> pdb=" O ALA C 395 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LYS C 397 " --> pdb=" O VAL C 421 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL C 421 " --> pdb=" O LYS C 397 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLU C 399 " --> pdb=" O GLU C 419 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLU C 419 " --> pdb=" O GLU C 399 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N MET C 401 " --> pdb=" O THR C 417 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N THR C 417 " --> pdb=" O MET C 401 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU C 403 " --> pdb=" O GLU C 415 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N GLU C 415 " --> pdb=" O LEU C 403 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU C 405 " --> pdb=" O LYS C 413 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 606 through 608 Processing sheet with id=AB4, first strand: chain 'C' and resid 632 through 635 Processing sheet with id=AB5, first strand: chain 'C' and resid 686 through 691 Processing sheet with id=AB6, first strand: chain 'C' and resid 751 through 754 removed outlier: 6.814A pdb=" N LEU C1024 " --> pdb=" O MET C1040 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N VAL C1042 " --> pdb=" O LEU C1024 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL C1026 " --> pdb=" O VAL C1042 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE C 780 " --> pdb=" O ILE C 807 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N THR C 809 " --> pdb=" O ILE C 780 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL C 782 " --> pdb=" O THR C 809 " (cutoff:3.500A) Processing sheet with id=AB7, 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: 6.462A pdb=" N PHE C 840 " --> pdb=" O LEU C 932 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL C 934 " --> pdb=" O PHE C 840 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU C 842 " --> pdb=" O VAL C 934 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ASP C 936 " --> pdb=" O LEU C 842 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU C 844 " --> pdb=" O ASP C 936 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE C 966 " --> pdb=" O PRO C 931 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ILE C 933 " --> pdb=" O ILE C 966 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N VAL C 968 " --> pdb=" O ILE C 933 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE C 935 " --> pdb=" O VAL C 968 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 899 through 900 Processing sheet with id=AB9, first strand: chain 'C' and resid 1052 through 1055 Processing sheet with id=AC1, first strand: chain 'D' and resid 127 through 132 removed outlier: 3.560A pdb=" N VAL D 132 " --> pdb=" O GLN D 92 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N VAL D 143 " --> pdb=" O CYS D 93 " (cutoff:3.500A) Processing sheet with id=AC2, 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=AC3, first strand: chain 'E' and resid 259 through 265 removed outlier: 6.465A pdb=" N GLY E 219 " --> pdb=" O LYS E 261 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LYS E 263 " --> pdb=" O GLY E 219 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE E 221 " --> pdb=" O LYS E 263 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLY E 265 " --> pdb=" O ILE E 221 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N CYS E 223 " --> pdb=" O GLY E 265 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 351 through 356 removed outlier: 7.716A pdb=" N MET E 417 " --> pdb=" O VAL E 340 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ALA E 342 " --> pdb=" O MET E 417 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL E 419 " --> pdb=" O ALA E 342 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ALA E 344 " --> pdb=" O VAL E 419 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N ASP E 421 " --> pdb=" O ALA E 344 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 528 through 531 Processing sheet with id=AC6, first strand: chain 'E' and resid 551 through 552 Processing sheet with id=AC7, first strand: chain 'F' and resid 11 through 14 removed outlier: 9.366A pdb=" N ILE F 74 " --> pdb=" O SER F 5 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN F 7 " --> pdb=" O ILE F 74 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 258 through 260 removed outlier: 6.825A pdb=" N VAL F 218 " --> pdb=" O GLU F 258 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ILE F 260 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE F 220 " --> pdb=" O ILE F 260 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 289 through 290 Processing sheet with id=AD1, first strand: chain 'F' and resid 303 through 305 removed outlier: 6.774A pdb=" N LEU F 304 " --> pdb=" O ALA F 430 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LYS F 324 " --> pdb=" O ARG F 427 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE F 429 " --> pdb=" O LYS F 324 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU F 326 " --> pdb=" O ILE F 429 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL F 349 " --> pdb=" O LYS F 376 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLN F 378 " --> pdb=" O VAL F 349 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ILE F 351 " --> pdb=" O GLN F 378 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 381 through 389 removed outlier: 6.251A pdb=" N VAL F 381 " --> pdb=" O MET F 401 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N MET F 401 " --> pdb=" O VAL F 381 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLU F 399 " --> pdb=" O PRO F 383 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLU F 389 " --> pdb=" O ALA F 393 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ALA F 393 " --> pdb=" O GLU F 389 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA F 395 " --> pdb=" O TYR F 423 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR F 423 " --> pdb=" O ALA F 395 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LYS F 397 " --> pdb=" O VAL F 421 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL F 421 " --> pdb=" O LYS F 397 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU F 399 " --> pdb=" O GLU F 419 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLU F 419 " --> pdb=" O GLU F 399 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N MET F 401 " --> pdb=" O THR F 417 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N THR F 417 " --> pdb=" O MET F 401 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LEU F 403 " --> pdb=" O GLU F 415 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N GLU F 415 " --> pdb=" O LEU F 403 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU F 405 " --> pdb=" O LYS F 413 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 606 through 608 Processing sheet with id=AD4, first strand: chain 'F' and resid 632 through 635 Processing sheet with id=AD5, first strand: chain 'F' and resid 686 through 691 Processing sheet with id=AD6, first strand: chain 'F' and resid 751 through 754 removed outlier: 6.816A pdb=" N LEU F1024 " --> pdb=" O MET F1040 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N VAL F1042 " --> pdb=" O LEU F1024 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL F1026 " --> pdb=" O VAL F1042 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE F 780 " --> pdb=" O ILE F 807 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N THR F 809 " --> pdb=" O ILE F 780 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL F 782 " --> pdb=" O THR F 809 " (cutoff:3.500A) Processing sheet with id=AD7, 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: 6.460A pdb=" N PHE F 840 " --> pdb=" O LEU F 932 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL F 934 " --> pdb=" O PHE F 840 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU F 842 " --> pdb=" O VAL F 934 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ASP F 936 " --> pdb=" O LEU F 842 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU F 844 " --> pdb=" O ASP F 936 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILE F 966 " --> pdb=" O PRO F 931 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ILE F 933 " --> pdb=" O ILE F 966 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL F 968 " --> pdb=" O ILE F 933 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE F 935 " --> pdb=" O VAL F 968 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'F' and resid 899 through 900 Processing sheet with id=AD9, first strand: chain 'F' and resid 1052 through 1055 Processing sheet with id=AE1, first strand: chain 'G' and resid 127 through 132 removed outlier: 3.533A pdb=" N VAL G 132 " --> pdb=" O GLN G 92 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N VAL G 143 " --> pdb=" O CYS G 93 " (cutoff:3.500A) Processing sheet with id=AE2, 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) removed outlier: 3.731A pdb=" N SER H 90 " --> pdb=" O SER H 61 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 259 through 265 removed outlier: 6.262A pdb=" N GLY H 219 " --> pdb=" O LYS H 261 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LYS H 263 " --> pdb=" O GLY H 219 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE H 221 " --> pdb=" O LYS H 263 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLY H 265 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N CYS H 223 " --> pdb=" O GLY H 265 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL H 178 " --> pdb=" O HIS H 220 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N TYR H 222 " --> pdb=" O VAL H 178 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N CYS H 180 " --> pdb=" O TYR H 222 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ARG H 224 " --> pdb=" O CYS H 180 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 351 through 356 removed outlier: 7.588A pdb=" N MET H 417 " --> pdb=" O VAL H 340 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ALA H 342 " --> pdb=" O MET H 417 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL H 419 " --> pdb=" O ALA H 342 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ALA H 344 " --> pdb=" O VAL H 419 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N ASP H 421 " --> pdb=" O ALA H 344 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA H 380 " --> pdb=" O MET H 420 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 528 through 531 Processing sheet with id=AE6, first strand: chain 'H' and resid 551 through 552 Processing sheet with id=AE7, first strand: chain 'I' and resid 11 through 14 removed outlier: 9.575A pdb=" N ILE I 74 " --> pdb=" O SER I 5 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASN I 7 " --> pdb=" O ILE I 74 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 258 through 260 removed outlier: 6.834A pdb=" N VAL I 218 " --> pdb=" O GLU I 258 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ILE I 260 " --> pdb=" O VAL I 218 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE I 220 " --> pdb=" O ILE I 260 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 289 through 290 Processing sheet with id=AF1, first strand: chain 'I' and resid 303 through 305 removed outlier: 6.779A pdb=" N LEU I 304 " --> pdb=" O ALA I 430 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS I 324 " --> pdb=" O ARG I 427 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ILE I 429 " --> pdb=" O LYS I 324 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU I 326 " --> pdb=" O ILE I 429 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL I 349 " --> pdb=" O LYS I 376 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLN I 378 " --> pdb=" O VAL I 349 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ILE I 351 " --> pdb=" O GLN I 378 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 381 through 389 removed outlier: 6.308A pdb=" N VAL I 381 " --> pdb=" O MET I 401 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N MET I 401 " --> pdb=" O VAL I 381 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N GLU I 399 " --> pdb=" O PRO I 383 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLU I 389 " --> pdb=" O ALA I 393 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ALA I 393 " --> pdb=" O GLU I 389 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ALA I 395 " --> pdb=" O TYR I 423 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TYR I 423 " --> pdb=" O ALA I 395 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LYS I 397 " --> pdb=" O VAL I 421 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL I 421 " --> pdb=" O LYS I 397 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU I 399 " --> pdb=" O GLU I 419 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLU I 419 " --> pdb=" O GLU I 399 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N MET I 401 " --> pdb=" O THR I 417 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N THR I 417 " --> pdb=" O MET I 401 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LEU I 403 " --> pdb=" O GLU I 415 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N GLU I 415 " --> pdb=" O LEU I 403 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU I 405 " --> pdb=" O LYS I 413 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 606 through 608 Processing sheet with id=AF4, first strand: chain 'I' and resid 632 through 635 Processing sheet with id=AF5, first strand: chain 'I' and resid 686 through 691 Processing sheet with id=AF6, first strand: chain 'I' and resid 751 through 754 removed outlier: 6.811A pdb=" N LEU I1024 " --> pdb=" O MET I1040 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N VAL I1042 " --> pdb=" O LEU I1024 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL I1026 " --> pdb=" O VAL I1042 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE I 780 " --> pdb=" O ILE I 807 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N THR I 809 " --> pdb=" O ILE I 780 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL I 782 " --> pdb=" O THR I 809 " (cutoff:3.500A) Processing sheet with id=AF7, 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: 6.458A pdb=" N PHE I 840 " --> pdb=" O LEU I 932 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N VAL I 934 " --> pdb=" O PHE I 840 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU I 842 " --> pdb=" O VAL I 934 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ASP I 936 " --> pdb=" O LEU I 842 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU I 844 " --> pdb=" O ASP I 936 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE I 966 " --> pdb=" O PRO I 931 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE I 933 " --> pdb=" O ILE I 966 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VAL I 968 " --> pdb=" O ILE I 933 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE I 935 " --> pdb=" O VAL I 968 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'I' and resid 899 through 900 Processing sheet with id=AF9, first strand: chain 'I' and resid 1052 through 1055 Processing sheet with id=AG1, first strand: chain 'J' and resid 127 through 132 Processing sheet with id=AG2, first strand: chain 'K' and resid 35 through 39 removed outlier: 6.759A pdb=" N VAL K 3 " --> pdb=" O LEU K 37 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N THR K 39 " --> pdb=" O VAL K 3 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N VAL K 5 " --> pdb=" O THR K 39 " (cutoff:3.500A) 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) removed outlier: 3.694A pdb=" N SER K 90 " --> pdb=" O SER K 61 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 259 through 265 removed outlier: 6.307A pdb=" N GLY K 219 " --> pdb=" O LYS K 261 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LYS K 263 " --> pdb=" O GLY K 219 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE K 221 " --> pdb=" O LYS K 263 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLY K 265 " --> pdb=" O ILE K 221 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N CYS K 223 " --> pdb=" O GLY K 265 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 351 through 356 removed outlier: 7.595A pdb=" N MET K 417 " --> pdb=" O VAL K 340 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ALA K 342 " --> pdb=" O MET K 417 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL K 419 " --> pdb=" O ALA K 342 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ALA K 344 " --> pdb=" O VAL K 419 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N ASP K 421 " --> pdb=" O ALA K 344 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA K 380 " --> pdb=" O MET K 420 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 528 through 531 Processing sheet with id=AG6, first strand: chain 'K' and resid 551 through 552 Processing sheet with id=AG7, first strand: chain 'L' and resid 11 through 15 removed outlier: 4.125A pdb=" N ILE L 4 " --> pdb=" O VAL L 15 " (cutoff:3.500A) removed outlier: 9.351A pdb=" N ILE L 74 " --> pdb=" O SER L 5 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASN L 7 " --> pdb=" O ILE L 74 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 258 through 260 removed outlier: 6.847A pdb=" N VAL L 218 " --> pdb=" O GLU L 258 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ILE L 260 " --> pdb=" O VAL L 218 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE L 220 " --> pdb=" O ILE L 260 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 289 through 290 Processing sheet with id=AH1, first strand: chain 'L' and resid 303 through 305 removed outlier: 6.776A pdb=" N LEU L 304 " --> pdb=" O ALA L 430 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LYS L 324 " --> pdb=" O ARG L 427 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ILE L 429 " --> pdb=" O LYS L 324 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU L 326 " --> pdb=" O ILE L 429 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL L 349 " --> pdb=" O LYS L 376 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLN L 378 " --> pdb=" O VAL L 349 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ILE L 351 " --> pdb=" O GLN L 378 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 381 through 389 removed outlier: 6.282A pdb=" N VAL L 381 " --> pdb=" O MET L 401 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N MET L 401 " --> pdb=" O VAL L 381 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLU L 399 " --> pdb=" O PRO L 383 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLU L 389 " --> pdb=" O ALA L 393 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ALA L 393 " --> pdb=" O GLU L 389 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ALA L 395 " --> pdb=" O TYR L 423 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR L 423 " --> pdb=" O ALA L 395 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LYS L 397 " --> pdb=" O VAL L 421 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL L 421 " --> pdb=" O LYS L 397 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLU L 399 " --> pdb=" O GLU L 419 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLU L 419 " --> pdb=" O GLU L 399 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N MET L 401 " --> pdb=" O THR L 417 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N THR L 417 " --> pdb=" O MET L 401 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU L 403 " --> pdb=" O GLU L 415 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N GLU L 415 " --> pdb=" O LEU L 403 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU L 405 " --> pdb=" O LYS L 413 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 606 through 608 Processing sheet with id=AH4, first strand: chain 'L' and resid 632 through 635 Processing sheet with id=AH5, first strand: chain 'L' and resid 686 through 691 Processing sheet with id=AH6, first strand: chain 'L' and resid 751 through 754 removed outlier: 6.824A pdb=" N LEU L1024 " --> pdb=" O MET L1040 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N VAL L1042 " --> pdb=" O LEU L1024 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL L1026 " --> pdb=" O VAL L1042 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE L 780 " --> pdb=" O ILE L 807 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N THR L 809 " --> pdb=" O ILE L 780 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL L 782 " --> pdb=" O THR L 809 " (cutoff:3.500A) Processing sheet with id=AH7, 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: 6.465A pdb=" N PHE L 840 " --> pdb=" O LEU L 932 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL L 934 " --> pdb=" O PHE L 840 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU L 842 " --> pdb=" O VAL L 934 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ASP L 936 " --> pdb=" O LEU L 842 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU L 844 " --> pdb=" O ASP L 936 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ILE L 966 " --> pdb=" O PRO L 931 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ILE L 933 " --> pdb=" O ILE L 966 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL L 968 " --> pdb=" O ILE L 933 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE L 935 " --> pdb=" O VAL L 968 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'L' and resid 899 through 900 Processing sheet with id=AH9, first strand: chain 'L' and resid 1052 through 1055 2416 hydrogen bonds defined for protein. 6756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 30.64 Time building geometry restraints manager: 14.68 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: 0.00 - 14.78: 80345 14.78 - 29.55: 19 29.55 - 44.33: 0 44.33 - 59.10: 0 59.10 - 73.88: 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: 23360 2.91 - 3.57: 80774 3.57 - 4.24: 134379 4.24 - 4.90: 230858 Nonbonded interactions: 469391 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 3.120 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 3.120 ... (remaining 469386 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 1.650 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: 0.090 Extract box with map and model: 2.070 Check model and map are aligned: 0.380 Set scattering table: 0.410 Process input model: 129.880 Find NCS groups from input model: 2.080 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.620 ------------------------------------------------------------------------------- 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= 0.531 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 to be fit. rotamer outliers: 25 poor density : 566 time to evaluate : 4.947 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: 0.5898 time to fit residues: 586.2718 Evaluate side-chains 578 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 566 time to evaluate : 4.928 ------------------------------------------------------------------------------- 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: 9.9990 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: 0.9990 chunk 595 optimal weight: 30.0000 chunk 230 optimal weight: 9.9990 chunk 362 optimal weight: 3.9990 chunk 443 optimal weight: 7.9990 chunk 690 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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 C 661 GLN ** C 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 734 HIS C 870 GLN D 57 GLN E 102 GLN F 390 ASN F 661 GLN ** F 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 734 HIS F 870 GLN H 166 ASN H 382 GLN I 390 ASN I 661 GLN ** I 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 734 HIS I 870 GLN J 57 GLN K 382 GLN L 390 ASN L 661 GLN ** L 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 734 HIS L 870 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 59208 Z= 0.403 Angle : 0.652 12.526 80368 Z= 0.340 Chirality : 0.049 0.398 9244 Planarity : 0.005 0.071 10304 Dihedral : 6.454 152.241 8427 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.05 % Favored : 95.74 % Rotamer: Outliers : 2.74 % Allowed : 15.20 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.09), residues: 7600 helix: 0.60 (0.09), residues: 3004 sheet: -0.01 (0.18), residues: 904 loop : -0.70 (0.10), residues: 3692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F1122 HIS 0.004 0.001 HIS C 734 PHE 0.030 0.002 PHE G 76 TYR 0.030 0.002 TYR E 96 ARG 0.010 0.001 ARG K 449 *********************** 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 765 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 596 time to evaluate : 5.034 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: 0.5651 (OUTLIER) cc_final: 0.5298 (m) REVERT: B 581 VAL cc_start: 0.3970 (t) cc_final: 0.3666 (m) REVERT: C 22 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8612 (tp) REVERT: C 494 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.8055 (t0) REVERT: C 672 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8448 (mtp) REVERT: E 320 MET cc_start: 0.6795 (tpp) cc_final: 0.6151 (tpp) REVERT: E 429 MET cc_start: 0.6425 (mmm) cc_final: 0.6192 (mmm) REVERT: F 22 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8539 (tp) REVERT: F 494 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.8090 (t0) REVERT: F 602 ASN cc_start: 0.7079 (p0) cc_final: 0.6820 (p0) REVERT: F 639 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.7543 (m-80) REVERT: H 320 MET cc_start: 0.5870 (tpp) cc_final: 0.5484 (tpp) REVERT: H 429 MET cc_start: 0.6460 (mmm) cc_final: 0.6252 (mmm) REVERT: I 22 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8534 (tp) REVERT: I 494 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.8083 (t0) REVERT: I 602 ASN cc_start: 0.7098 (p0) cc_final: 0.6842 (p0) REVERT: I 639 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7412 (m-80) REVERT: I 672 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8541 (mtp) REVERT: K 252 MET cc_start: 0.6122 (mmm) cc_final: 0.5811 (mtm) REVERT: K 429 MET cc_start: 0.6515 (mmm) cc_final: 0.6313 (mmm) REVERT: L 22 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8586 (tp) REVERT: L 357 ILE cc_start: 0.8455 (mp) cc_final: 0.8206 (mm) REVERT: L 394 LYS cc_start: 0.7904 (pttp) cc_final: 0.7681 (pttp) REVERT: L 494 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.8074 (t0) REVERT: L 602 ASN cc_start: 0.7040 (p0) cc_final: 0.6810 (p0) REVERT: L 672 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8480 (mtp) outliers start: 169 outliers final: 88 residues processed: 717 average time/residue: 0.5447 time to fit residues: 668.1879 Evaluate side-chains 640 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 538 time to evaluate : 5.000 ------------------------------------------------------------------------------- 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 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 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 139 ILE 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 671 CYS Chi-restraints excluded: chain C residue 672 MET 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 D residue 70 ILE Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 139 ILE 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 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 948 MET Chi-restraints excluded: chain F residue 968 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 132 VAL 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 498 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 139 ILE 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 494 ASP Chi-restraints excluded: chain I residue 538 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 671 CYS Chi-restraints excluded: chain I residue 672 MET 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 948 MET Chi-restraints excluded: chain I residue 968 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain K residue 316 VAL 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 139 ILE Chi-restraints excluded: chain L residue 235 ILE 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 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 806 THR Chi-restraints excluded: chain L residue 865 SER Chi-restraints excluded: chain L residue 948 MET 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: 5.9990 chunk 214 optimal weight: 5.9990 chunk 574 optimal weight: 10.0000 chunk 469 optimal weight: 0.9980 chunk 190 optimal weight: 20.0000 chunk 691 optimal weight: 1.9990 chunk 746 optimal weight: 3.9990 chunk 615 optimal weight: 1.9990 chunk 685 optimal weight: 3.9990 chunk 235 optimal weight: 9.9990 chunk 554 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 390 ASN C 680 GLN E 382 GLN F 390 ASN F 680 GLN I 390 ASN I 680 GLN J 94 GLN K 559 HIS L 390 ASN L 680 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 59208 Z= 0.263 Angle : 0.579 12.713 80368 Z= 0.300 Chirality : 0.046 0.374 9244 Planarity : 0.004 0.052 10304 Dihedral : 6.012 153.789 8404 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.04 % Favored : 95.78 % Rotamer: Outliers : 2.40 % Allowed : 16.21 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 (0.10), residues: 7600 helix: 1.02 (0.10), residues: 2984 sheet: -0.14 (0.17), residues: 988 loop : -0.61 (0.10), residues: 3628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP L1122 HIS 0.003 0.001 HIS C 96 PHE 0.030 0.001 PHE G 76 TYR 0.027 0.001 TYR A 77 ARG 0.010 0.000 ARG E 22 *********************** 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 734 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 586 time to evaluate : 5.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7162 (tm-30) cc_final: 0.6877 (tm-30) REVERT: B 62 TYR cc_start: 0.3938 (p90) cc_final: 0.3723 (p90) REVERT: B 540 THR cc_start: 0.5729 (OUTLIER) cc_final: 0.5343 (m) REVERT: B 581 VAL cc_start: 0.3731 (t) cc_final: 0.3420 (m) REVERT: C 602 ASN cc_start: 0.7165 (p0) cc_final: 0.6899 (p0) REVERT: D 42 GLN cc_start: 0.7217 (mt0) cc_final: 0.6198 (mt0) REVERT: E 320 MET cc_start: 0.6845 (tpp) cc_final: 0.6247 (tpp) REVERT: E 429 MET cc_start: 0.6420 (mmm) cc_final: 0.6180 (mmm) REVERT: F 394 LYS cc_start: 0.7938 (pttp) cc_final: 0.7624 (pttp) REVERT: F 602 ASN cc_start: 0.7169 (p0) cc_final: 0.6888 (p0) REVERT: F 639 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7612 (m-80) REVERT: F 672 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8595 (mtp) REVERT: F 685 MET cc_start: 0.7909 (mtt) cc_final: 0.7704 (mtt) REVERT: G 42 GLN cc_start: 0.7139 (mt0) cc_final: 0.5865 (mt0) REVERT: H 320 MET cc_start: 0.5864 (tpp) cc_final: 0.5387 (tpp) REVERT: H 429 MET cc_start: 0.6586 (mmm) cc_final: 0.6328 (mmm) REVERT: H 548 VAL cc_start: 0.4616 (OUTLIER) cc_final: 0.4326 (t) REVERT: I 602 ASN cc_start: 0.7182 (p0) cc_final: 0.6908 (p0) REVERT: I 639 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7597 (m-80) REVERT: K 429 MET cc_start: 0.6574 (mmm) cc_final: 0.6370 (mmm) REVERT: K 581 VAL cc_start: 0.3647 (t) cc_final: 0.3367 (m) REVERT: L 394 LYS cc_start: 0.7964 (pttp) cc_final: 0.7651 (pttp) REVERT: L 602 ASN cc_start: 0.7120 (p0) cc_final: 0.6893 (p0) outliers start: 148 outliers final: 85 residues processed: 691 average time/residue: 0.5311 time to fit residues: 632.4227 Evaluate side-chains 637 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 547 time to evaluate : 4.854 ------------------------------------------------------------------------------- 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 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 130 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 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 253 THR 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 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 70 ILE 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 319 ILE Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 540 THR 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 253 THR Chi-restraints excluded: chain F residue 378 GLN 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 865 SER Chi-restraints excluded: chain F residue 948 MET 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 132 VAL Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 130 LEU 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 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 253 THR 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 671 CYS 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 132 VAL Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 47 TYR Chi-restraints excluded: chain K residue 540 THR 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 246 ASP Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 538 VAL 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 Chi-restraints excluded: chain L residue 1022 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 683 optimal weight: 7.9990 chunk 519 optimal weight: 0.9980 chunk 358 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 329 optimal weight: 0.3980 chunk 464 optimal weight: 0.6980 chunk 693 optimal weight: 5.9990 chunk 734 optimal weight: 5.9990 chunk 362 optimal weight: 4.9990 chunk 657 optimal weight: 0.9990 chunk 197 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 390 ASN F 390 ASN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 390 ASN J 57 GLN L 390 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 59208 Z= 0.143 Angle : 0.531 12.783 80368 Z= 0.271 Chirality : 0.043 0.351 9244 Planarity : 0.004 0.044 10304 Dihedral : 5.626 152.380 8404 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.39 % Favored : 96.42 % Rotamer: Outliers : 2.47 % Allowed : 16.84 % Favored : 80.69 % 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: 0.39 (0.10), residues: 7600 helix: 1.32 (0.10), residues: 2960 sheet: -0.01 (0.17), residues: 920 loop : -0.49 (0.10), residues: 3720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP F1122 HIS 0.002 0.000 HIS L 734 PHE 0.030 0.001 PHE J 76 TYR 0.026 0.001 TYR E 96 ARG 0.006 0.000 ARG J 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 749 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 597 time to evaluate : 4.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 GLN cc_start: 0.8632 (tp40) cc_final: 0.8416 (tp40) REVERT: A 79 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7686 (tm-30) REVERT: A 160 ARG cc_start: 0.5153 (ptp-110) cc_final: 0.4883 (ptp90) REVERT: B 540 THR cc_start: 0.5728 (OUTLIER) cc_final: 0.5322 (m) REVERT: C 602 ASN cc_start: 0.7137 (p0) cc_final: 0.6793 (p0) REVERT: C 685 MET cc_start: 0.8289 (mtt) cc_final: 0.7929 (mtt) REVERT: C 720 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7839 (t0) REVERT: D 79 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7512 (tm-30) REVERT: F 602 ASN cc_start: 0.7134 (p0) cc_final: 0.6837 (p0) REVERT: F 720 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7769 (t0) REVERT: G 79 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: H 320 MET cc_start: 0.5858 (tpp) cc_final: 0.5375 (tpp) REVERT: H 359 MET cc_start: 0.6658 (mmp) cc_final: 0.6407 (mmm) REVERT: H 548 VAL cc_start: 0.4573 (OUTLIER) cc_final: 0.4249 (t) REVERT: I 355 ARG cc_start: 0.7527 (mmt90) cc_final: 0.7295 (mpt-90) REVERT: I 394 LYS cc_start: 0.7881 (pttp) cc_final: 0.7550 (pttp) REVERT: I 602 ASN cc_start: 0.7157 (p0) cc_final: 0.6862 (p0) REVERT: I 720 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7890 (t0) REVERT: J 79 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7717 (tm-30) REVERT: K 252 MET cc_start: 0.6032 (mmm) cc_final: 0.5667 (mtm) REVERT: K 581 VAL cc_start: 0.3715 (t) cc_final: 0.3460 (m) REVERT: L 394 LYS cc_start: 0.7935 (pttp) cc_final: 0.7621 (pttp) REVERT: L 602 ASN cc_start: 0.7176 (p0) cc_final: 0.6863 (p0) REVERT: L 685 MET cc_start: 0.8204 (mtt) cc_final: 0.7762 (mtt) REVERT: L 720 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7846 (t0) outliers start: 152 outliers final: 81 residues processed: 711 average time/residue: 0.5253 time to fit residues: 649.0612 Evaluate side-chains 644 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 553 time to evaluate : 4.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL 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 130 LEU Chi-restraints excluded: chain B residue 203 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 41 ILE 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 320 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 671 CYS Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 720 ASP Chi-restraints excluded: chain C residue 865 SER Chi-restraints excluded: chain C residue 989 VAL Chi-restraints excluded: chain C residue 1022 SER Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain D residue 70 ILE 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 135 LEU Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 130 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 139 ILE Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 595 HIS Chi-restraints excluded: chain F residue 671 CYS Chi-restraints excluded: chain F residue 676 VAL Chi-restraints excluded: chain F residue 720 ASP Chi-restraints excluded: chain F residue 865 SER 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 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 130 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 4 ILE Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 41 ILE 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 320 THR 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 720 ASP Chi-restraints excluded: chain I residue 865 SER 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 J residue 79 GLN Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 381 VAL Chi-restraints excluded: chain K residue 540 THR Chi-restraints excluded: chain L residue 41 ILE 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 320 THR Chi-restraints excluded: chain L residue 494 ASP Chi-restraints excluded: chain L residue 595 HIS Chi-restraints excluded: chain L residue 671 CYS Chi-restraints excluded: chain L residue 676 VAL Chi-restraints excluded: chain L residue 720 ASP Chi-restraints excluded: chain L residue 865 SER Chi-restraints excluded: chain L residue 989 VAL Chi-restraints excluded: chain L residue 1022 SER Chi-restraints excluded: chain L residue 1025 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 611 optimal weight: 0.1980 chunk 417 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 546 optimal weight: 0.7980 chunk 303 optimal weight: 40.0000 chunk 626 optimal weight: 30.0000 chunk 507 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 375 optimal weight: 5.9990 chunk 659 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 390 ASN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 390 ASN G 57 GLN I 390 ASN L 390 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 59208 Z= 0.254 Angle : 0.573 15.351 80368 Z= 0.292 Chirality : 0.046 0.388 9244 Planarity : 0.004 0.044 10304 Dihedral : 5.682 152.250 8404 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.92 % Favored : 95.91 % Rotamer: Outliers : 2.48 % Allowed : 17.25 % Favored : 80.27 % 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: 0.36 (0.10), residues: 7600 helix: 1.32 (0.10), residues: 2992 sheet: -0.15 (0.17), residues: 940 loop : -0.51 (0.10), residues: 3668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP F1122 HIS 0.003 0.001 HIS C 96 PHE 0.025 0.001 PHE J 76 TYR 0.032 0.001 TYR A 77 ARG 0.005 0.000 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 736 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 583 time to evaluate : 4.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 540 THR cc_start: 0.5982 (OUTLIER) cc_final: 0.5582 (m) REVERT: C 22 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8461 (tp) REVERT: C 602 ASN cc_start: 0.7154 (p0) cc_final: 0.6853 (p0) REVERT: C 720 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7939 (t0) REVERT: D 79 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8037 (tm-30) REVERT: E 320 MET cc_start: 0.6878 (tpp) cc_final: 0.6332 (tpp) REVERT: F 602 ASN cc_start: 0.7210 (p0) cc_final: 0.6921 (p0) REVERT: F 672 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8348 (mtp) REVERT: G 79 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8041 (tm-30) REVERT: H 320 MET cc_start: 0.5886 (tpp) cc_final: 0.5405 (tpp) REVERT: H 548 VAL cc_start: 0.4417 (OUTLIER) cc_final: 0.4132 (t) REVERT: I 235 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8709 (mm) REVERT: I 355 ARG cc_start: 0.7561 (mmt90) cc_final: 0.7354 (mpt-90) REVERT: I 602 ASN cc_start: 0.7230 (p0) cc_final: 0.6944 (p0) REVERT: I 720 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7803 (t0) REVERT: J 79 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8059 (tm-30) REVERT: K 581 VAL cc_start: 0.3763 (t) cc_final: 0.3504 (m) REVERT: L 22 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8446 (tp) REVERT: L 357 ILE cc_start: 0.8444 (mp) cc_final: 0.8115 (mm) REVERT: L 360 MET cc_start: 0.7812 (mmm) cc_final: 0.7566 (mtp) REVERT: L 394 LYS cc_start: 0.8036 (pttp) cc_final: 0.7684 (pttp) REVERT: L 602 ASN cc_start: 0.7201 (p0) cc_final: 0.6907 (p0) REVERT: L 720 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7927 (t0) outliers start: 153 outliers final: 116 residues processed: 698 average time/residue: 0.5223 time to fit residues: 634.1519 Evaluate side-chains 668 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 540 time to evaluate : 4.873 ------------------------------------------------------------------------------- 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 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 130 LEU Chi-restraints excluded: chain B residue 203 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 22 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 76 THR 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 253 THR Chi-restraints excluded: chain C residue 320 THR 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 681 ILE 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 989 VAL Chi-restraints excluded: chain C residue 1022 SER Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1131 THR Chi-restraints excluded: chain D residue 70 ILE 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 E residue 62 TYR Chi-restraints excluded: chain E residue 130 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 41 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 76 THR 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 253 THR Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 595 HIS Chi-restraints excluded: chain F residue 644 MET 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 1022 SER 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 98 CYS Chi-restraints excluded: chain G residue 106 ILE 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 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 14 VAL Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 76 THR 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 320 THR Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain I residue 588 LYS Chi-restraints excluded: chain I residue 595 HIS 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 681 ILE Chi-restraints excluded: chain I residue 720 ASP 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 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 352 LEU Chi-restraints excluded: chain K residue 381 VAL Chi-restraints excluded: chain K residue 498 VAL Chi-restraints excluded: chain K residue 540 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 54 VAL 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 246 ASP Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 320 THR Chi-restraints excluded: chain L residue 494 ASP Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 595 HIS Chi-restraints excluded: chain L residue 671 CYS Chi-restraints excluded: chain L residue 676 VAL Chi-restraints excluded: chain L residue 681 ILE Chi-restraints excluded: chain L residue 720 ASP 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 1022 SER Chi-restraints excluded: chain L residue 1025 VAL 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: 6.9990 chunk 661 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 431 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 735 optimal weight: 0.0670 chunk 610 optimal weight: 20.0000 chunk 340 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 243 optimal weight: 6.9990 chunk 386 optimal weight: 0.5980 overall best weight: 1.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN C 390 ASN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN F 390 ASN G 92 GLN G 94 GLN I 390 ASN L 390 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 59208 Z= 0.213 Angle : 0.566 17.826 80368 Z= 0.285 Chirality : 0.045 0.380 9244 Planarity : 0.004 0.041 10304 Dihedral : 5.601 152.102 8404 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.67 % Favored : 96.16 % Rotamer: Outliers : 2.76 % Allowed : 17.31 % Favored : 79.93 % 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: 0.40 (0.10), residues: 7600 helix: 1.36 (0.10), residues: 3012 sheet: -0.21 (0.17), residues: 948 loop : -0.48 (0.10), residues: 3640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP F1122 HIS 0.005 0.001 HIS E 77 PHE 0.029 0.001 PHE J 76 TYR 0.033 0.001 TYR E 60 ARG 0.012 0.000 ARG A 160 *********************** 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 747 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 577 time to evaluate : 4.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLN cc_start: 0.8694 (tp40) cc_final: 0.8493 (tp40) REVERT: A 79 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7703 (tm-30) REVERT: B 359 MET cc_start: 0.6583 (mmm) cc_final: 0.6247 (mmm) REVERT: C 602 ASN cc_start: 0.7213 (p0) cc_final: 0.6908 (p0) REVERT: C 685 MET cc_start: 0.8288 (mtt) cc_final: 0.7967 (mtt) REVERT: D 79 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7981 (tm-30) REVERT: E 98 ILE cc_start: 0.5235 (OUTLIER) cc_final: 0.4973 (tt) REVERT: E 320 MET cc_start: 0.6851 (tpp) cc_final: 0.6368 (tpp) REVERT: E 359 MET cc_start: 0.5985 (mmm) cc_final: 0.5433 (mmp) REVERT: E 568 LYS cc_start: 0.7208 (OUTLIER) cc_final: 0.6999 (mmtt) REVERT: F 355 ARG cc_start: 0.7563 (mpt-90) cc_final: 0.7315 (mtt-85) REVERT: F 602 ASN cc_start: 0.7220 (p0) cc_final: 0.6926 (p0) REVERT: F 672 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8282 (mtp) REVERT: G 79 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7999 (tm-30) REVERT: H 320 MET cc_start: 0.5970 (tpp) cc_final: 0.5498 (tpp) REVERT: H 548 VAL cc_start: 0.4498 (OUTLIER) cc_final: 0.4191 (t) REVERT: I 602 ASN cc_start: 0.7237 (p0) cc_final: 0.6947 (p0) REVERT: I 720 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7784 (t0) REVERT: J 79 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7747 (tm-30) REVERT: K 581 VAL cc_start: 0.3914 (t) cc_final: 0.3649 (m) REVERT: L 22 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8445 (tp) REVERT: L 357 ILE cc_start: 0.8454 (mp) cc_final: 0.8141 (mm) REVERT: L 360 MET cc_start: 0.7899 (mmm) cc_final: 0.7610 (mtp) REVERT: L 394 LYS cc_start: 0.7972 (pttp) cc_final: 0.7687 (pttp) REVERT: L 602 ASN cc_start: 0.7216 (p0) cc_final: 0.6919 (p0) REVERT: L 685 MET cc_start: 0.8233 (mtt) cc_final: 0.7899 (mtt) REVERT: L 720 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7919 (t0) outliers start: 170 outliers final: 119 residues processed: 706 average time/residue: 0.5173 time to fit residues: 634.0795 Evaluate side-chains 682 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 552 time to evaluate : 6.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL 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 B residue 5 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 203 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 54 VAL Chi-restraints excluded: chain C residue 76 THR 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 253 THR Chi-restraints excluded: chain C residue 320 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 671 CYS Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 681 ILE 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 983 VAL Chi-restraints excluded: chain C residue 989 VAL Chi-restraints excluded: chain C residue 1022 SER Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1131 THR Chi-restraints excluded: chain D residue 70 ILE 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 E residue 62 TYR Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 130 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 E residue 568 LYS Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 54 VAL 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 253 THR Chi-restraints excluded: chain F residue 320 THR 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 681 ILE 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 1131 THR 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 130 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 14 VAL Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 54 VAL 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 320 THR Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain I residue 588 LYS Chi-restraints excluded: chain I residue 595 HIS 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 681 ILE Chi-restraints excluded: chain I residue 720 ASP 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 1131 THR 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 42 ILE Chi-restraints excluded: chain K residue 352 LEU 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 41 ILE Chi-restraints excluded: chain L residue 54 VAL 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 246 ASP Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 320 THR Chi-restraints excluded: chain L residue 494 ASP Chi-restraints excluded: chain L residue 595 HIS Chi-restraints excluded: chain L residue 671 CYS Chi-restraints excluded: chain L residue 676 VAL Chi-restraints excluded: chain L residue 681 ILE 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 983 VAL Chi-restraints excluded: chain L residue 989 VAL Chi-restraints excluded: chain L residue 1022 SER Chi-restraints excluded: chain L residue 1025 VAL 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: 7.9990 chunk 82 optimal weight: 6.9990 chunk 418 optimal weight: 9.9990 chunk 536 optimal weight: 0.0770 chunk 416 optimal weight: 8.9990 chunk 618 optimal weight: 4.9990 chunk 410 optimal weight: 10.0000 chunk 732 optimal weight: 10.0000 chunk 458 optimal weight: 6.9990 chunk 446 optimal weight: 3.9990 chunk 338 optimal weight: 0.8980 overall best weight: 3.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 390 ASN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN F 390 ASN I 390 ASN L 390 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 59208 Z= 0.335 Angle : 0.630 21.413 80368 Z= 0.316 Chirality : 0.048 0.396 9244 Planarity : 0.004 0.040 10304 Dihedral : 5.729 152.388 8404 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.38 % Favored : 95.45 % Rotamer: Outliers : 2.74 % Allowed : 17.59 % Favored : 79.67 % 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: 0.29 (0.10), residues: 7600 helix: 1.24 (0.10), residues: 3016 sheet: -0.17 (0.17), residues: 992 loop : -0.55 (0.10), residues: 3592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F1122 HIS 0.004 0.001 HIS C 96 PHE 0.029 0.002 PHE J 76 TYR 0.029 0.002 TYR A 77 ARG 0.008 0.000 ARG A 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 744 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 575 time to evaluate : 4.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8000 (tm-30) REVERT: C 22 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8505 (tp) REVERT: C 602 ASN cc_start: 0.7309 (p0) cc_final: 0.7080 (p0) REVERT: C 672 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8375 (mtp) REVERT: D 79 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7981 (tm-30) REVERT: E 98 ILE cc_start: 0.5206 (OUTLIER) cc_final: 0.4964 (tt) REVERT: E 320 MET cc_start: 0.6887 (tpp) cc_final: 0.6436 (tpp) REVERT: F 22 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8462 (tp) REVERT: F 355 ARG cc_start: 0.7622 (mpt-90) cc_final: 0.7413 (mtt-85) REVERT: F 394 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.7194 (pttp) REVERT: F 602 ASN cc_start: 0.7283 (p0) cc_final: 0.6995 (p0) REVERT: F 639 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7691 (m-80) REVERT: F 672 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8482 (mtp) REVERT: G 79 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7985 (tm-30) REVERT: H 320 MET cc_start: 0.6105 (tpp) cc_final: 0.5643 (tpp) REVERT: H 548 VAL cc_start: 0.4588 (OUTLIER) cc_final: 0.4302 (t) REVERT: I 22 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8470 (tp) REVERT: I 602 ASN cc_start: 0.7300 (p0) cc_final: 0.7018 (p0) REVERT: I 672 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8374 (mtp) REVERT: J 79 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8031 (tm-30) REVERT: K 359 MET cc_start: 0.6506 (mmm) cc_final: 0.6234 (mmm) REVERT: K 581 VAL cc_start: 0.3905 (t) cc_final: 0.3638 (m) REVERT: L 22 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8519 (tp) REVERT: L 357 ILE cc_start: 0.8572 (mp) cc_final: 0.8242 (mm) REVERT: L 394 LYS cc_start: 0.7979 (pttp) cc_final: 0.7740 (pttp) REVERT: L 602 ASN cc_start: 0.7304 (p0) cc_final: 0.7024 (p0) REVERT: L 672 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8411 (mtp) outliers start: 169 outliers final: 133 residues processed: 703 average time/residue: 0.5117 time to fit residues: 622.8726 Evaluate side-chains 686 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 537 time to evaluate : 4.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL 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 62 TYR Chi-restraints excluded: chain B residue 130 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 498 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 54 VAL Chi-restraints excluded: chain C residue 76 THR 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 320 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 644 MET 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 714 THR Chi-restraints excluded: chain C residue 799 LEU 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 C residue 1025 VAL Chi-restraints excluded: chain C residue 1131 THR Chi-restraints excluded: chain D residue 70 ILE 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 42 ILE Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 130 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 E residue 568 LYS 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 54 VAL Chi-restraints excluded: chain F residue 76 THR 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 253 THR Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 394 LYS 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 681 ILE Chi-restraints excluded: chain F residue 714 THR Chi-restraints excluded: chain F residue 799 LEU 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 1131 THR 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 130 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 22 LEU Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 76 THR 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 320 THR Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain I residue 588 LYS Chi-restraints excluded: chain I residue 595 HIS 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 681 ILE Chi-restraints excluded: chain I residue 714 THR Chi-restraints excluded: chain I residue 799 LEU 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 1131 THR 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 42 ILE 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 498 VAL Chi-restraints excluded: chain K residue 540 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 54 VAL 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 246 ASP Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 320 THR Chi-restraints excluded: chain L residue 494 ASP Chi-restraints excluded: chain L residue 595 HIS 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 681 ILE Chi-restraints excluded: chain L residue 714 THR Chi-restraints excluded: chain L residue 799 LEU 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 1022 SER Chi-restraints excluded: chain L residue 1025 VAL Chi-restraints excluded: chain L residue 1131 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 453 optimal weight: 0.9980 chunk 292 optimal weight: 0.2980 chunk 437 optimal weight: 9.9990 chunk 220 optimal weight: 20.0000 chunk 143 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 465 optimal weight: 1.9990 chunk 499 optimal weight: 3.9990 chunk 362 optimal weight: 8.9990 chunk 68 optimal weight: 30.0000 chunk 575 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 390 ASN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 GLN F 390 ASN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 390 ASN L 390 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 59208 Z= 0.210 Angle : 0.586 19.024 80368 Z= 0.292 Chirality : 0.045 0.375 9244 Planarity : 0.004 0.039 10304 Dihedral : 5.516 152.667 8404 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.50 % Favored : 96.33 % Rotamer: Outliers : 2.32 % Allowed : 18.23 % Favored : 79.45 % 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: 0.40 (0.10), residues: 7600 helix: 1.35 (0.10), residues: 3016 sheet: -0.23 (0.17), residues: 944 loop : -0.47 (0.10), residues: 3640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP F1122 HIS 0.003 0.001 HIS C 96 PHE 0.030 0.001 PHE J 76 TYR 0.026 0.001 TYR A 77 ARG 0.008 0.000 ARG A 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 722 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 579 time to evaluate : 4.995 Fit side-chains revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7943 (tm-30) REVERT: A 149 GLU cc_start: 0.3505 (pp20) cc_final: 0.3001 (tm-30) REVERT: B 359 MET cc_start: 0.6194 (mmm) cc_final: 0.5991 (mmm) REVERT: C 22 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8453 (tp) REVERT: C 602 ASN cc_start: 0.7283 (p0) cc_final: 0.6979 (p0) REVERT: C 672 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8280 (mtp) REVERT: C 685 MET cc_start: 0.8263 (mtt) cc_final: 0.7948 (mtt) REVERT: D 79 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7917 (tm-30) REVERT: E 320 MET cc_start: 0.6921 (tpp) cc_final: 0.6527 (tpp) REVERT: F 394 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7246 (pttp) REVERT: F 602 ASN cc_start: 0.7289 (p0) cc_final: 0.7002 (p0) REVERT: F 672 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8272 (mtp) REVERT: G 46 GLU cc_start: 0.7573 (pp20) cc_final: 0.7366 (pp20) REVERT: G 79 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7929 (tm-30) REVERT: H 320 MET cc_start: 0.6117 (tpp) cc_final: 0.5669 (tpp) REVERT: H 548 VAL cc_start: 0.4713 (OUTLIER) cc_final: 0.4434 (t) REVERT: I 394 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7172 (pttp) REVERT: I 602 ASN cc_start: 0.7310 (p0) cc_final: 0.7027 (p0) REVERT: I 672 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8233 (mtp) REVERT: J 79 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7773 (tm-30) REVERT: K 581 VAL cc_start: 0.3859 (t) cc_final: 0.3604 (m) REVERT: L 22 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8441 (tp) REVERT: L 357 ILE cc_start: 0.8480 (mp) cc_final: 0.8177 (mm) REVERT: L 394 LYS cc_start: 0.7975 (pttp) cc_final: 0.7737 (pttp) REVERT: L 602 ASN cc_start: 0.7293 (p0) cc_final: 0.6998 (p0) REVERT: L 672 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8294 (mtp) REVERT: L 685 MET cc_start: 0.8217 (mtt) cc_final: 0.7867 (mtt) outliers start: 143 outliers final: 117 residues processed: 682 average time/residue: 0.5323 time to fit residues: 630.6714 Evaluate side-chains 676 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 546 time to evaluate : 4.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL 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 62 TYR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 203 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 22 LEU Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 76 THR 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 320 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 644 MET Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 672 MET 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 989 VAL Chi-restraints excluded: chain C residue 1022 SER Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1131 THR Chi-restraints excluded: chain D residue 70 ILE 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 E residue 62 TYR Chi-restraints excluded: chain E residue 130 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 41 ILE Chi-restraints excluded: chain F residue 54 VAL 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 253 THR Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain F residue 595 HIS Chi-restraints excluded: chain F residue 671 CYS Chi-restraints excluded: chain F residue 672 MET Chi-restraints excluded: chain F residue 681 ILE 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 1131 THR 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 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 41 ILE Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 76 THR 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 320 THR Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain I residue 394 LYS 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 672 MET Chi-restraints excluded: chain I residue 681 ILE 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 1022 SER Chi-restraints excluded: chain I residue 1025 VAL 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 155 THR 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 540 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 54 VAL 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 246 ASP Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 320 THR Chi-restraints excluded: chain L residue 494 ASP Chi-restraints excluded: chain L residue 595 HIS Chi-restraints excluded: chain L residue 671 CYS Chi-restraints excluded: chain L residue 672 MET Chi-restraints excluded: chain L residue 681 ILE 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 989 VAL Chi-restraints excluded: chain L residue 1022 SER Chi-restraints excluded: chain L residue 1025 VAL Chi-restraints excluded: chain L residue 1068 ILE 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: 3.9990 chunk 701 optimal weight: 0.0170 chunk 640 optimal weight: 1.9990 chunk 682 optimal weight: 0.0770 chunk 410 optimal weight: 10.0000 chunk 297 optimal weight: 1.9990 chunk 536 optimal weight: 0.2980 chunk 209 optimal weight: 0.9990 chunk 616 optimal weight: 4.9990 chunk 645 optimal weight: 1.9990 chunk 680 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 390 ASN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN F 390 ASN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 GLN I 390 ASN ** K 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 390 ASN L 919 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 59208 Z= 0.141 Angle : 0.560 19.084 80368 Z= 0.278 Chirality : 0.044 0.360 9244 Planarity : 0.003 0.039 10304 Dihedral : 5.255 147.727 8404 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.37 % Favored : 96.46 % Rotamer: Outliers : 1.93 % Allowed : 18.59 % Favored : 79.48 % 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: 0.56 (0.10), residues: 7600 helix: 1.49 (0.10), residues: 2988 sheet: -0.13 (0.18), residues: 940 loop : -0.38 (0.10), residues: 3672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F1122 HIS 0.002 0.000 HIS F 734 PHE 0.029 0.001 PHE J 76 TYR 0.021 0.001 TYR A 77 ARG 0.017 0.000 ARG G 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 723 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 604 time to evaluate : 4.981 Fit side-chains revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7660 (tm-30) REVERT: A 149 GLU cc_start: 0.3554 (pp20) cc_final: 0.3013 (tm-30) REVERT: B 252 MET cc_start: 0.6156 (mmm) cc_final: 0.5110 (mtp) REVERT: C 357 ILE cc_start: 0.8401 (mp) cc_final: 0.8054 (mm) REVERT: C 602 ASN cc_start: 0.7271 (p0) cc_final: 0.6965 (p0) REVERT: C 639 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7454 (m-80) REVERT: C 685 MET cc_start: 0.8230 (mtt) cc_final: 0.7879 (mtt) REVERT: D 46 GLU cc_start: 0.7570 (pp20) cc_final: 0.7356 (pp20) REVERT: D 79 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7455 (tm-30) REVERT: E 320 MET cc_start: 0.6938 (tpp) cc_final: 0.6474 (tpp) REVERT: E 359 MET cc_start: 0.5346 (mmm) cc_final: 0.5138 (mmp) REVERT: F 22 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8366 (tp) REVERT: F 602 ASN cc_start: 0.7257 (p0) cc_final: 0.6952 (p0) REVERT: G 79 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7421 (tm-30) REVERT: H 320 MET cc_start: 0.5941 (tpp) cc_final: 0.5501 (tpp) REVERT: H 548 VAL cc_start: 0.4720 (OUTLIER) cc_final: 0.4410 (t) REVERT: I 22 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8390 (tp) REVERT: I 394 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7216 (pttp) REVERT: I 588 LYS cc_start: 0.6938 (OUTLIER) cc_final: 0.6696 (mttp) REVERT: I 602 ASN cc_start: 0.7271 (p0) cc_final: 0.6970 (p0) REVERT: J 79 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7673 (tm-30) REVERT: K 359 MET cc_start: 0.6006 (mmm) cc_final: 0.5724 (mmm) REVERT: K 581 VAL cc_start: 0.3835 (t) cc_final: 0.3551 (m) REVERT: L 357 ILE cc_start: 0.8401 (mp) cc_final: 0.8069 (mm) REVERT: L 394 LYS cc_start: 0.7991 (pttp) cc_final: 0.7730 (pttp) REVERT: L 602 ASN cc_start: 0.7274 (p0) cc_final: 0.6967 (p0) REVERT: L 685 MET cc_start: 0.8191 (mtt) cc_final: 0.7830 (mtt) outliers start: 119 outliers final: 89 residues processed: 693 average time/residue: 0.5254 time to fit residues: 627.6970 Evaluate side-chains 664 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 565 time to evaluate : 4.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 98 CYS 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 203 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 41 ILE Chi-restraints excluded: chain C residue 54 VAL 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 320 THR 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 968 VAL Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain C residue 989 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 155 THR Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 130 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 54 VAL Chi-restraints excluded: chain F residue 76 THR 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 320 THR Chi-restraints excluded: chain F residue 595 HIS Chi-restraints excluded: chain F residue 671 CYS Chi-restraints excluded: chain F residue 681 ILE Chi-restraints excluded: chain F residue 806 THR 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 1131 THR 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 8 ILE Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 54 VAL 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 320 THR Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain I residue 394 LYS 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 681 ILE Chi-restraints excluded: chain I residue 806 THR 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 1131 THR 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 234 LEU Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 381 VAL Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 54 VAL 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 320 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 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 1022 SER Chi-restraints excluded: chain L residue 1025 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 448 optimal weight: 40.0000 chunk 721 optimal weight: 0.1980 chunk 440 optimal weight: 5.9990 chunk 342 optimal weight: 0.9990 chunk 501 optimal weight: 4.9990 chunk 757 optimal weight: 5.9990 chunk 696 optimal weight: 8.9990 chunk 602 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 465 optimal weight: 2.9990 chunk 369 optimal weight: 5.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 92 GLN D 92 GLN F 390 ASN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 390 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 59208 Z= 0.300 Angle : 0.628 20.147 80368 Z= 0.313 Chirality : 0.047 0.412 9244 Planarity : 0.004 0.042 10304 Dihedral : 5.466 149.039 8404 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.08 % Favored : 95.75 % Rotamer: Outliers : 1.87 % Allowed : 18.79 % Favored : 79.35 % 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: 0.42 (0.10), residues: 7600 helix: 1.36 (0.10), residues: 3012 sheet: -0.18 (0.18), residues: 940 loop : -0.47 (0.10), residues: 3648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F1122 HIS 0.004 0.001 HIS I 734 PHE 0.027 0.002 PHE A 127 TYR 0.027 0.001 TYR A 77 ARG 0.017 0.000 ARG G 160 ********************** 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 670 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 555 time to evaluate : 5.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7494 (tm-30) REVERT: A 149 GLU cc_start: 0.3644 (pp20) cc_final: 0.3144 (tm-30) REVERT: C 22 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8454 (tp) REVERT: C 357 ILE cc_start: 0.8586 (mp) cc_final: 0.8290 (mm) REVERT: C 602 ASN cc_start: 0.7313 (p0) cc_final: 0.7072 (p0) REVERT: C 639 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7494 (m-80) REVERT: C 685 MET cc_start: 0.8239 (mtt) cc_final: 0.7914 (mtt) REVERT: D 79 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7913 (tm-30) REVERT: E 1 MET cc_start: 0.4250 (tpp) cc_final: 0.3906 (mmp) REVERT: E 320 MET cc_start: 0.6948 (tpp) cc_final: 0.6565 (tpp) REVERT: F 22 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8440 (tp) REVERT: F 602 ASN cc_start: 0.7294 (p0) cc_final: 0.6992 (p0) REVERT: G 79 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7958 (tm-30) REVERT: H 320 MET cc_start: 0.6139 (tpp) cc_final: 0.5734 (tpp) REVERT: I 22 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8416 (tp) REVERT: I 394 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7296 (pttp) REVERT: I 602 ASN cc_start: 0.7283 (p0) cc_final: 0.6979 (p0) REVERT: J 79 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7728 (tm-30) REVERT: K 359 MET cc_start: 0.6066 (mmm) cc_final: 0.5743 (mmm) REVERT: K 581 VAL cc_start: 0.3880 (t) cc_final: 0.3587 (m) REVERT: L 357 ILE cc_start: 0.8531 (mp) cc_final: 0.8278 (mm) REVERT: L 394 LYS cc_start: 0.8031 (pttp) cc_final: 0.7757 (pttp) REVERT: L 588 LYS cc_start: 0.7324 (OUTLIER) cc_final: 0.7105 (mttp) REVERT: L 602 ASN cc_start: 0.7294 (p0) cc_final: 0.7049 (p0) REVERT: L 685 MET cc_start: 0.8193 (mtt) cc_final: 0.7857 (mtt) outliers start: 115 outliers final: 97 residues processed: 649 average time/residue: 0.5442 time to fit residues: 609.9402 Evaluate side-chains 650 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 543 time to evaluate : 4.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 98 CYS 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 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 41 ILE Chi-restraints excluded: chain C residue 54 VAL 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 320 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 671 CYS 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 986 VAL Chi-restraints excluded: chain C residue 989 VAL 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 155 THR Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 130 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 54 VAL Chi-restraints excluded: chain F residue 76 THR 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 320 THR Chi-restraints excluded: chain F residue 595 HIS Chi-restraints excluded: chain F residue 671 CYS Chi-restraints excluded: chain F residue 681 ILE Chi-restraints excluded: chain F residue 714 THR Chi-restraints excluded: chain F residue 806 THR 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 1131 THR 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 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 54 VAL 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 320 THR Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain I residue 394 LYS Chi-restraints excluded: chain I residue 595 HIS Chi-restraints excluded: chain I residue 671 CYS Chi-restraints excluded: chain I residue 681 ILE Chi-restraints excluded: chain I residue 806 THR Chi-restraints excluded: chain I residue 968 VAL Chi-restraints excluded: chain I residue 986 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 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 234 LEU Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 381 VAL Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 54 VAL 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 246 ASP Chi-restraints excluded: chain L residue 320 THR 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 968 VAL Chi-restraints excluded: chain L residue 986 VAL Chi-restraints excluded: chain L residue 989 VAL Chi-restraints excluded: chain L residue 1025 VAL Chi-restraints excluded: chain L residue 1131 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 478 optimal weight: 4.9990 chunk 642 optimal weight: 0.1980 chunk 184 optimal weight: 0.0370 chunk 555 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 603 optimal weight: 6.9990 chunk 252 optimal weight: 0.9990 chunk 620 optimal weight: 20.0000 chunk 76 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.6462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 GLN F 390 ASN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 GLN ** H 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 390 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.170391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.106859 restraints weight = 76913.558| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.18 r_work: 0.3099 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 59208 Z= 0.145 Angle : 0.578 18.917 80368 Z= 0.285 Chirality : 0.044 0.395 9244 Planarity : 0.003 0.056 10304 Dihedral : 5.131 146.123 8404 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.97 % Favored : 96.86 % Rotamer: Outliers : 1.52 % Allowed : 19.21 % Favored : 79.27 % 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: 0.57 (0.10), residues: 7600 helix: 1.47 (0.10), residues: 2992 sheet: -0.14 (0.18), residues: 940 loop : -0.34 (0.10), residues: 3668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP L1122 HIS 0.002 0.000 HIS C 734 PHE 0.027 0.001 PHE J 76 TYR 0.037 0.001 TYR H 60 ARG 0.013 0.000 ARG I 717 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11722.37 seconds wall clock time: 207 minutes 9.80 seconds (12429.80 seconds total)