Starting phenix.real_space_refine on Sat Feb 7 15:17:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mp0_48496/02_2026/9mp0_48496.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mp0_48496/02_2026/9mp0_48496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mp0_48496/02_2026/9mp0_48496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mp0_48496/02_2026/9mp0_48496.map" model { file = "/net/cci-nas-00/data/ceres_data/9mp0_48496/02_2026/9mp0_48496.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mp0_48496/02_2026/9mp0_48496.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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: 5 Type Number sf(0) Gaussians Zn 30 6.06 5 S 330 5.16 5 C 21093 2.51 5 N 5894 2.21 5 O 5984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33331 Number of models: 1 Model: "" Number of chains: 20 Chain: "L" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3464 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 22, 'TRANS': 408} Chain breaks: 1 Chain: "M" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3430 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 1 Chain: "N" Number of atoms: 3438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3438 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 22, 'TRANS': 405} Chain breaks: 1 Chain: "O" Number of atoms: 3438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3438 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 22, 'TRANS': 405} Chain breaks: 1 Chain: "R" Number of atoms: 3438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3438 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 22, 'TRANS': 405} Chain breaks: 1 Chain: "S" Number of atoms: 3438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3438 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 22, 'TRANS': 405} Chain breaks: 1 Chain: "T" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3430 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 1 Chain: "U" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3447 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 22, 'TRANS': 406} Chain breaks: 1 Chain: "P" Number of atoms: 2785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2785 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 23, 'TRANS': 323} Chain: "Q" Number of atoms: 2785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2785 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 23, 'TRANS': 323} Chain: "L" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "M" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "N" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "O" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "S" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "T" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "U" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "P" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 202 SG CYS L 494 56.085 214.470 67.833 1.00260.11 S ATOM 222 SG CYS L 497 55.865 212.292 71.590 1.00245.18 S ATOM 344 SG CYS L 514 57.381 216.175 71.223 1.00259.72 S ATOM 367 SG CYS L 517 58.982 213.196 70.142 1.00300.00 S ATOM 535 SG CYS L 537 62.221 204.617 63.477 1.00140.50 S ATOM 556 SG CYS L 540 60.654 205.741 67.271 1.00132.02 S ATOM 693 SG CYS L 559 59.996 202.343 65.458 1.00300.00 S ATOM 715 SG CYS L 562 58.008 205.113 64.485 1.00300.00 S ATOM 619 SG CYS L 549 67.608 200.555 52.933 1.00274.36 S ATOM 653 SG CYS L 554 69.564 203.724 53.928 1.00255.83 S ATOM 866 SG CYS L 583 65.867 203.667 53.789 1.00275.20 S ATOM 892 SG CYS L 586 67.970 204.733 50.878 1.00262.50 S ATOM 3649 SG CYS M 494 148.061 180.586 62.716 1.00300.00 S ATOM 3669 SG CYS M 497 146.407 177.041 64.791 1.00300.00 S ATOM 3791 SG CYS M 514 146.488 177.584 60.746 1.00300.00 S ATOM 3814 SG CYS M 517 144.276 179.256 62.982 1.00300.00 S ATOM 3982 SG CYS M 537 140.231 186.644 70.624 1.00300.00 S ATOM 4003 SG CYS M 540 141.122 182.627 69.580 1.00300.00 S ATOM 4140 SG CYS M 559 140.876 184.140 73.298 1.00300.00 S ATOM 4162 SG CYS M 562 143.914 184.610 71.299 1.00300.00 S ATOM 4066 SG CYS M 549 136.852 198.536 73.005 1.00300.00 S ATOM 4100 SG CYS M 554 135.995 198.051 69.243 1.00300.00 S ATOM 4313 SG CYS M 583 139.254 197.046 70.721 1.00300.00 S ATOM 4339 SG CYS M 586 138.580 200.497 69.098 1.00300.00 S ATOM 7079 SG CYS N 494 94.388 158.740 54.279 1.00152.00 S ATOM 7099 SG CYS N 497 95.737 161.124 57.718 1.00242.55 S ATOM 7221 SG CYS N 514 96.228 162.254 53.811 1.00112.69 S ATOM 7244 SG CYS N 517 98.018 159.659 55.415 1.00300.00 S ATOM 7412 SG CYS N 537 101.235 149.598 60.104 1.00164.62 S ATOM 7433 SG CYS N 540 100.385 153.775 60.489 1.00111.64 S ATOM 7570 SG CYS N 559 100.171 151.005 63.291 1.00115.78 S ATOM 7592 SG CYS N 562 97.464 151.444 60.928 1.00178.37 S ATOM 7496 SG CYS N 549 104.270 137.732 57.843 1.00257.82 S ATOM 7530 SG CYS N 554 105.604 139.476 54.885 1.00280.05 S ATOM 7743 SG CYS N 583 102.046 140.056 56.103 1.00175.22 S ATOM 7769 SG CYS N 586 103.078 137.474 53.348 1.00181.34 S ATOM 10517 SG CYS O 494 185.544 119.211 51.524 1.00300.00 S ATOM 10537 SG CYS O 497 185.600 119.793 55.909 1.00300.00 S ATOM 10659 SG CYS O 514 184.027 116.548 54.023 1.00300.00 S ATOM 10682 SG CYS O 517 182.556 119.789 54.100 1.00300.00 S ATOM 10850 SG CYS O 537 180.152 130.483 51.681 1.00300.00 S ATOM 10871 SG CYS O 540 181.469 127.721 54.631 1.00224.91 S ATOM 11008 SG CYS O 559 182.265 131.648 54.533 1.00300.00 S ATOM 11030 SG CYS O 562 184.160 129.423 52.427 1.00300.00 S ATOM 10934 SG CYS O 549 175.449 138.775 43.421 1.00300.00 S ATOM 10968 SG CYS O 554 173.263 135.498 42.854 1.00300.00 S ATOM 11181 SG CYS O 583 176.985 135.513 43.075 1.00300.00 S ATOM 11207 SG CYS O 586 174.959 135.876 39.762 1.00300.00 S ATOM 13955 SG CYS R 494 24.712 137.340 51.289 1.00300.00 S ATOM 13975 SG CYS R 497 24.634 136.843 55.672 1.00300.00 S ATOM 14097 SG CYS R 514 26.203 140.036 53.805 1.00293.53 S ATOM 14120 SG CYS R 517 27.689 136.796 53.889 1.00300.00 S ATOM 14288 SG CYS R 537 30.121 126.131 51.515 1.00300.00 S ATOM 14309 SG CYS R 540 28.805 128.858 54.463 1.00205.00 S ATOM 14446 SG CYS R 559 28.026 124.940 54.398 1.00300.00 S ATOM 14468 SG CYS R 562 26.126 127.147 52.235 1.00300.00 S ATOM 14372 SG CYS R 549 34.857 117.817 43.284 1.00300.00 S ATOM 14406 SG CYS R 554 37.078 121.061 42.728 1.00300.00 S ATOM 14619 SG CYS R 583 33.346 121.096 42.916 1.00300.00 S ATOM 14645 SG CYS R 586 35.394 120.735 39.630 1.00300.00 S ATOM 17393 SG CYS S 494 115.956 97.862 54.220 1.00164.73 S ATOM 17413 SG CYS S 497 114.575 95.482 57.668 1.00257.17 S ATOM 17535 SG CYS S 514 114.094 94.378 53.754 1.00124.07 S ATOM 17558 SG CYS S 517 112.311 96.971 55.366 1.00300.00 S ATOM 17726 SG CYS S 537 109.173 107.038 60.008 1.00166.51 S ATOM 17747 SG CYS S 540 109.957 102.866 60.444 1.00111.86 S ATOM 17884 SG CYS S 559 110.215 105.630 63.237 1.00116.45 S ATOM 17906 SG CYS S 562 112.919 105.178 60.888 1.00196.11 S ATOM 17810 SG CYS S 549 106.234 118.938 57.821 1.00252.22 S ATOM 17844 SG CYS S 554 104.876 117.193 54.833 1.00290.32 S ATOM 18057 SG CYS S 583 108.419 116.592 56.065 1.00171.46 S ATOM 18083 SG CYS S 586 107.425 119.198 53.331 1.00199.42 S ATOM 20831 SG CYS T 494 61.528 76.799 60.774 1.00289.26 S ATOM 20851 SG CYS T 497 63.180 80.457 62.763 1.00300.00 S ATOM 20973 SG CYS T 514 63.169 79.699 58.800 1.00300.00 S ATOM 20996 SG CYS T 517 65.307 78.125 61.167 1.00300.00 S ATOM 21164 SG CYS T 537 69.074 71.042 69.250 1.00300.00 S ATOM 21185 SG CYS T 540 68.188 75.029 68.014 1.00300.00 S ATOM 21322 SG CYS T 559 68.331 73.669 71.787 1.00300.00 S ATOM 21344 SG CYS T 562 65.372 73.116 69.717 1.00300.00 S ATOM 21248 SG CYS T 549 72.347 59.292 72.231 1.00300.00 S ATOM 21282 SG CYS T 554 73.348 59.618 68.482 1.00300.00 S ATOM 21495 SG CYS T 583 70.026 60.683 69.803 1.00300.00 S ATOM 21521 SG CYS T 586 70.766 57.170 68.353 1.00300.00 S ATOM 24261 SG CYS U 494 154.276 42.537 67.981 1.00268.62 S ATOM 24281 SG CYS U 497 154.492 44.745 71.747 1.00246.51 S ATOM 24403 SG CYS U 514 153.014 40.865 71.389 1.00300.00 S ATOM 24426 SG CYS U 517 151.377 43.801 70.275 1.00300.00 S ATOM 24594 SG CYS U 537 148.145 52.278 63.613 1.00160.02 S ATOM 24615 SG CYS U 540 149.832 51.109 67.434 1.00146.84 S ATOM 24752 SG CYS U 559 150.307 54.637 65.477 1.00300.00 S ATOM 24774 SG CYS U 562 152.195 51.982 64.186 1.00300.00 S ATOM 24678 SG CYS U 549 142.715 56.286 52.958 1.00282.24 S ATOM 24712 SG CYS U 554 140.782 53.091 53.958 1.00269.25 S ATOM 24925 SG CYS U 583 144.469 53.191 53.815 1.00277.70 S ATOM 24951 SG CYS U 586 142.381 52.061 50.929 1.00265.59 S ATOM 27684 SG CYS P 53 129.164 71.138 80.736 1.00116.79 S ATOM 27704 SG CYS P 56 128.294 71.796 84.360 1.00120.44 S ATOM 27831 SG CYS P 73 127.765 74.689 81.534 1.00142.88 S ATOM 27849 SG CYS P 76 131.073 74.338 82.770 1.00185.81 S ATOM 28019 SG CYS P 96 141.026 69.256 84.205 1.00 84.10 S ATOM 28039 SG CYS P 99 137.566 70.657 85.158 1.00116.69 S ATOM 28176 SG CYS P 118 139.482 68.130 87.250 1.00137.83 S ATOM 28202 SG CYS P 121 137.190 67.028 84.687 1.00177.27 S ATOM 28101 SG CYS P 108 150.966 63.488 79.474 1.00243.59 S ATOM 28134 SG CYS P 113 150.515 66.783 77.017 1.00191.23 S ATOM 28350 SG CYS P 142 147.587 64.217 77.758 1.00190.84 S ATOM 28376 SG CYS P 145 150.942 63.138 75.883 1.00300.00 S ATOM 30469 SG CYS Q 53 81.117 185.463 80.946 1.00127.43 S ATOM 30489 SG CYS Q 56 81.955 184.798 84.515 1.00142.59 S ATOM 30616 SG CYS Q 73 82.508 181.848 81.716 1.00147.44 S ATOM 30634 SG CYS Q 76 79.190 182.251 82.934 1.00186.82 S ATOM 30804 SG CYS Q 96 69.242 187.411 84.290 1.00 78.41 S ATOM 30824 SG CYS Q 99 72.697 186.013 85.284 1.00119.60 S ATOM 30961 SG CYS Q 118 70.791 188.528 87.318 1.00138.37 S ATOM 30987 SG CYS Q 121 73.124 189.614 84.791 1.00168.53 S ATOM 30886 SG CYS Q 108 59.443 193.263 79.519 1.00236.01 S ATOM 30919 SG CYS Q 113 59.842 189.985 77.069 1.00179.05 S ATOM 31135 SG CYS Q 142 62.749 192.497 77.826 1.00183.61 S ATOM 31161 SG CYS Q 145 59.355 193.667 75.930 1.00300.00 S Residues with excluded nonbonded symmetry interactions: 6 residue: pdb="ZN ZN P1001 " occ=0.85 residue: pdb="ZN ZN P1002 " occ=0.41 residue: pdb="ZN ZN P1003 " occ=0.92 residue: pdb="ZN ZN Q1001 " occ=0.85 residue: pdb="ZN ZN Q1002 " occ=0.41 residue: pdb="ZN ZN Q1003 " occ=0.92 Time building chain proxies: 8.99, per 1000 atoms: 0.27 Number of scatterers: 33331 At special positions: 0 Unit cell: (211.14, 257.508, 105.156, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 30 29.99 S 330 16.00 O 5984 8.00 N 5894 7.00 C 21093 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: 2.85 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 497 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 494 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 514 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 517 " pdb=" ZN L1002 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 537 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 540 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 562 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 559 " pdb=" ZN L1003 " pdb="ZN ZN L1003 " - pdb=" SG CYS L 549 " pdb="ZN ZN L1003 " - pdb=" SG CYS L 583 " pdb="ZN ZN L1003 " - pdb=" SG CYS L 586 " pdb="ZN ZN L1003 " - pdb=" SG CYS L 554 " pdb=" ZN M1001 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 494 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 514 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 497 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 517 " pdb=" ZN M1002 " pdb="ZN ZN M1002 " - pdb=" SG CYS M 559 " pdb="ZN ZN M1002 " - pdb=" SG CYS M 540 " pdb="ZN ZN M1002 " - pdb=" SG CYS M 562 " pdb="ZN ZN M1002 " - pdb=" SG CYS M 537 " pdb=" ZN M1003 " pdb="ZN ZN M1003 " - pdb=" SG CYS M 583 " pdb="ZN ZN M1003 " - pdb=" SG CYS M 549 " pdb="ZN ZN M1003 " - pdb=" SG CYS M 554 " pdb="ZN ZN M1003 " - pdb=" SG CYS M 586 " pdb=" ZN N1001 " pdb="ZN ZN N1001 " - pdb=" SG CYS N 494 " pdb="ZN ZN N1001 " - pdb=" SG CYS N 497 " pdb="ZN ZN N1001 " - pdb=" SG CYS N 514 " pdb="ZN ZN N1001 " - pdb=" SG CYS N 517 " pdb=" ZN N1002 " pdb="ZN ZN N1002 " - pdb=" SG CYS N 559 " pdb="ZN ZN N1002 " - pdb=" SG CYS N 540 " pdb="ZN ZN N1002 " - pdb=" SG CYS N 537 " pdb="ZN ZN N1002 " - pdb=" SG CYS N 562 " pdb=" ZN N1003 " pdb="ZN ZN N1003 " - pdb=" SG CYS N 583 " pdb="ZN ZN N1003 " - pdb=" SG CYS N 549 " pdb="ZN ZN N1003 " - pdb=" SG CYS N 586 " pdb="ZN ZN N1003 " - pdb=" SG CYS N 554 " pdb=" ZN O1001 " pdb="ZN ZN O1001 " - pdb=" SG CYS O 494 " pdb="ZN ZN O1001 " - pdb=" SG CYS O 514 " pdb="ZN ZN O1001 " - pdb=" SG CYS O 497 " pdb="ZN ZN O1001 " - pdb=" SG CYS O 517 " pdb=" ZN O1002 " pdb="ZN ZN O1002 " - pdb=" SG CYS O 540 " pdb="ZN ZN O1002 " - pdb=" SG CYS O 559 " pdb="ZN ZN O1002 " - pdb=" SG CYS O 537 " pdb="ZN ZN O1002 " - pdb=" SG CYS O 562 " pdb=" ZN O1003 " pdb="ZN ZN O1003 " - pdb=" SG CYS O 583 " pdb="ZN ZN O1003 " - pdb=" SG CYS O 549 " pdb="ZN ZN O1003 " - pdb=" SG CYS O 554 " pdb="ZN ZN O1003 " - pdb=" SG CYS O 586 " pdb=" ZN P1001 " pdb="ZN ZN P1001 " - pdb=" SG CYS P 53 " pdb="ZN ZN P1001 " - pdb=" SG CYS P 56 " pdb="ZN ZN P1001 " - pdb=" SG CYS P 73 " pdb="ZN ZN P1001 " - pdb=" SG CYS P 76 " pdb=" ZN P1002 " pdb="ZN ZN P1002 " - pdb=" SG CYS P 96 " pdb="ZN ZN P1002 " - pdb=" SG CYS P 121 " pdb="ZN ZN P1002 " - pdb=" SG CYS P 99 " pdb="ZN ZN P1002 " - pdb=" SG CYS P 118 " pdb=" ZN P1003 " pdb="ZN ZN P1003 " - pdb=" SG CYS P 113 " pdb="ZN ZN P1003 " - pdb=" SG CYS P 142 " pdb="ZN ZN P1003 " - pdb=" SG CYS P 145 " pdb="ZN ZN P1003 " - pdb=" SG CYS P 108 " pdb=" ZN Q1001 " pdb="ZN ZN Q1001 " - pdb=" SG CYS Q 53 " pdb="ZN ZN Q1001 " - pdb=" SG CYS Q 56 " pdb="ZN ZN Q1001 " - pdb=" SG CYS Q 73 " pdb="ZN ZN Q1001 " - pdb=" SG CYS Q 76 " pdb=" ZN Q1002 " pdb="ZN ZN Q1002 " - pdb=" SG CYS Q 96 " pdb="ZN ZN Q1002 " - pdb=" SG CYS Q 121 " pdb="ZN ZN Q1002 " - pdb=" SG CYS Q 99 " pdb="ZN ZN Q1002 " - pdb=" SG CYS Q 118 " pdb=" ZN Q1003 " pdb="ZN ZN Q1003 " - pdb=" SG CYS Q 142 " pdb="ZN ZN Q1003 " - pdb=" SG CYS Q 113 " pdb="ZN ZN Q1003 " - pdb=" SG CYS Q 145 " pdb="ZN ZN Q1003 " - pdb=" SG CYS Q 108 " pdb=" ZN R1001 " pdb="ZN ZN R1001 " - pdb=" SG CYS R 494 " pdb="ZN ZN R1001 " - pdb=" SG CYS R 497 " pdb="ZN ZN R1001 " - pdb=" SG CYS R 514 " pdb="ZN ZN R1001 " - pdb=" SG CYS R 517 " pdb=" ZN R1002 " pdb="ZN ZN R1002 " - pdb=" SG CYS R 540 " pdb="ZN ZN R1002 " - pdb=" SG CYS R 537 " pdb="ZN ZN R1002 " - pdb=" SG CYS R 559 " pdb="ZN ZN R1002 " - pdb=" SG CYS R 562 " pdb=" ZN R1003 " pdb="ZN ZN R1003 " - pdb=" SG CYS R 583 " pdb="ZN ZN R1003 " - pdb=" SG CYS R 549 " pdb="ZN ZN R1003 " - pdb=" SG CYS R 554 " pdb="ZN ZN R1003 " - pdb=" SG CYS R 586 " pdb=" ZN S1001 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 494 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 497 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 514 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 517 " pdb=" ZN S1002 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 559 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 540 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 537 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 562 " pdb=" ZN S1003 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 583 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 549 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 586 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 554 " pdb=" ZN T1001 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 494 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 514 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 497 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 517 " pdb=" ZN T1002 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 559 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 562 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 540 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 537 " pdb=" ZN T1003 " pdb="ZN ZN T1003 " - pdb=" SG CYS T 583 " pdb="ZN ZN T1003 " - pdb=" SG CYS T 549 " pdb="ZN ZN T1003 " - pdb=" SG CYS T 554 " pdb="ZN ZN T1003 " - pdb=" SG CYS T 586 " pdb=" ZN U1001 " pdb="ZN ZN U1001 " - pdb=" SG CYS U 497 " pdb="ZN ZN U1001 " - pdb=" SG CYS U 494 " pdb="ZN ZN U1001 " - pdb=" SG CYS U 514 " pdb="ZN ZN U1001 " - pdb=" SG CYS U 517 " pdb=" ZN U1002 " pdb="ZN ZN U1002 " - pdb=" SG CYS U 537 " pdb="ZN ZN U1002 " - pdb=" SG CYS U 540 " pdb="ZN ZN U1002 " - pdb=" SG CYS U 562 " pdb="ZN ZN U1002 " - pdb=" SG CYS U 559 " pdb=" ZN U1003 " pdb="ZN ZN U1003 " - pdb=" SG CYS U 549 " pdb="ZN ZN U1003 " - pdb=" SG CYS U 583 " pdb="ZN ZN U1003 " - pdb=" SG CYS U 554 " pdb="ZN ZN U1003 " - pdb=" SG CYS U 586 " Number of angles added : 180 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7676 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 38 sheets defined 38.5% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'L' and resid 472 through 485 Processing helix chain 'L' and resid 489 through 493 Processing helix chain 'L' and resid 514 through 525 Processing helix chain 'L' and resid 560 through 567 removed outlier: 3.586A pdb=" N LEU L 565 " --> pdb=" O GLU L 561 " (cutoff:3.500A) Processing helix chain 'L' and resid 570 through 578 removed outlier: 3.604A pdb=" N ALA L 574 " --> pdb=" O GLY L 570 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS L 577 " --> pdb=" O GLN L 573 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU L 578 " --> pdb=" O ALA L 574 " (cutoff:3.500A) Processing helix chain 'L' and resid 600 through 611 removed outlier: 3.860A pdb=" N PHE L 609 " --> pdb=" O LEU L 605 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA L 610 " --> pdb=" O GLN L 606 " (cutoff:3.500A) Processing helix chain 'L' and resid 644 through 654 Processing helix chain 'L' and resid 666 through 677 Processing helix chain 'L' and resid 691 through 698 Processing helix chain 'L' and resid 726 through 742 Processing helix chain 'L' and resid 762 through 773 Processing helix chain 'L' and resid 783 through 785 No H-bonds generated for 'chain 'L' and resid 783 through 785' Processing helix chain 'L' and resid 814 through 819 removed outlier: 3.927A pdb=" N CYS L 818 " --> pdb=" O GLU L 814 " (cutoff:3.500A) Processing helix chain 'L' and resid 860 through 869 Processing helix chain 'L' and resid 881 through 891 removed outlier: 3.520A pdb=" N ARG L 891 " --> pdb=" O ARG L 887 " (cutoff:3.500A) Processing helix chain 'L' and resid 894 through 903 Processing helix chain 'L' and resid 904 through 908 Processing helix chain 'M' and resid 475 through 485 removed outlier: 3.884A pdb=" N GLU M 482 " --> pdb=" O ARG M 478 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL M 483 " --> pdb=" O LEU M 479 " (cutoff:3.500A) Processing helix chain 'M' and resid 514 through 525 Processing helix chain 'M' and resid 560 through 567 removed outlier: 3.980A pdb=" N LEU M 565 " --> pdb=" O GLU M 561 " (cutoff:3.500A) Processing helix chain 'M' and resid 570 through 578 removed outlier: 3.562A pdb=" N ALA M 574 " --> pdb=" O GLY M 570 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS M 577 " --> pdb=" O GLN M 573 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU M 578 " --> pdb=" O ALA M 574 " (cutoff:3.500A) Processing helix chain 'M' and resid 600 through 608 Processing helix chain 'M' and resid 644 through 654 Processing helix chain 'M' and resid 666 through 677 Processing helix chain 'M' and resid 691 through 698 Processing helix chain 'M' and resid 726 through 742 Processing helix chain 'M' and resid 762 through 774 Processing helix chain 'M' and resid 783 through 785 No H-bonds generated for 'chain 'M' and resid 783 through 785' Processing helix chain 'M' and resid 814 through 819 removed outlier: 3.829A pdb=" N CYS M 818 " --> pdb=" O GLU M 814 " (cutoff:3.500A) Processing helix chain 'M' and resid 860 through 869 Processing helix chain 'M' and resid 881 through 891 removed outlier: 3.676A pdb=" N ARG M 891 " --> pdb=" O ARG M 887 " (cutoff:3.500A) Processing helix chain 'M' and resid 894 through 903 Processing helix chain 'M' and resid 904 through 908 Processing helix chain 'N' and resid 475 through 485 Processing helix chain 'N' and resid 489 through 493 removed outlier: 3.512A pdb=" N ASP N 492 " --> pdb=" O ASN N 489 " (cutoff:3.500A) Processing helix chain 'N' and resid 514 through 525 Processing helix chain 'N' and resid 560 through 567 removed outlier: 3.686A pdb=" N LEU N 565 " --> pdb=" O GLU N 561 " (cutoff:3.500A) Processing helix chain 'N' and resid 570 through 578 removed outlier: 3.613A pdb=" N ALA N 574 " --> pdb=" O GLY N 570 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS N 577 " --> pdb=" O GLN N 573 " (cutoff:3.500A) Processing helix chain 'N' and resid 600 through 611 removed outlier: 4.050A pdb=" N PHE N 609 " --> pdb=" O LEU N 605 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA N 610 " --> pdb=" O GLN N 606 " (cutoff:3.500A) Processing helix chain 'N' and resid 627 through 631 removed outlier: 3.689A pdb=" N ARG N 631 " --> pdb=" O ALA N 628 " (cutoff:3.500A) Processing helix chain 'N' and resid 644 through 654 Processing helix chain 'N' and resid 666 through 677 Processing helix chain 'N' and resid 686 through 690 Processing helix chain 'N' and resid 691 through 698 Processing helix chain 'N' and resid 726 through 742 Processing helix chain 'N' and resid 762 through 774 Processing helix chain 'N' and resid 783 through 785 No H-bonds generated for 'chain 'N' and resid 783 through 785' Processing helix chain 'N' and resid 815 through 819 Processing helix chain 'N' and resid 860 through 868 Processing helix chain 'N' and resid 881 through 891 removed outlier: 3.715A pdb=" N ARG N 891 " --> pdb=" O ARG N 887 " (cutoff:3.500A) Processing helix chain 'N' and resid 894 through 903 Processing helix chain 'N' and resid 904 through 908 Processing helix chain 'O' and resid 475 through 484 Processing helix chain 'O' and resid 489 through 493 Processing helix chain 'O' and resid 514 through 525 Processing helix chain 'O' and resid 560 through 567 removed outlier: 3.791A pdb=" N LEU O 565 " --> pdb=" O GLU O 561 " (cutoff:3.500A) Processing helix chain 'O' and resid 570 through 578 removed outlier: 3.578A pdb=" N ALA O 574 " --> pdb=" O GLY O 570 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS O 577 " --> pdb=" O GLN O 573 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU O 578 " --> pdb=" O ALA O 574 " (cutoff:3.500A) Processing helix chain 'O' and resid 600 through 608 Processing helix chain 'O' and resid 644 through 653 Processing helix chain 'O' and resid 666 through 677 Processing helix chain 'O' and resid 691 through 698 Processing helix chain 'O' and resid 726 through 742 removed outlier: 3.603A pdb=" N LEU O 730 " --> pdb=" O GLY O 726 " (cutoff:3.500A) Processing helix chain 'O' and resid 762 through 774 Processing helix chain 'O' and resid 783 through 785 No H-bonds generated for 'chain 'O' and resid 783 through 785' Processing helix chain 'O' and resid 814 through 819 removed outlier: 3.965A pdb=" N CYS O 818 " --> pdb=" O GLU O 814 " (cutoff:3.500A) Processing helix chain 'O' and resid 860 through 868 Processing helix chain 'O' and resid 881 through 891 removed outlier: 3.760A pdb=" N ARG O 891 " --> pdb=" O ARG O 887 " (cutoff:3.500A) Processing helix chain 'O' and resid 894 through 903 Processing helix chain 'O' and resid 904 through 906 No H-bonds generated for 'chain 'O' and resid 904 through 906' Processing helix chain 'R' and resid 475 through 484 Processing helix chain 'R' and resid 489 through 493 Processing helix chain 'R' and resid 514 through 525 Processing helix chain 'R' and resid 560 through 567 removed outlier: 3.779A pdb=" N LEU R 565 " --> pdb=" O GLU R 561 " (cutoff:3.500A) Processing helix chain 'R' and resid 570 through 578 removed outlier: 3.581A pdb=" N ALA R 574 " --> pdb=" O GLY R 570 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS R 577 " --> pdb=" O GLN R 573 " (cutoff:3.500A) Processing helix chain 'R' and resid 600 through 608 Processing helix chain 'R' and resid 644 through 653 Processing helix chain 'R' and resid 666 through 677 Processing helix chain 'R' and resid 686 through 690 Processing helix chain 'R' and resid 691 through 698 Processing helix chain 'R' and resid 726 through 742 removed outlier: 3.597A pdb=" N LEU R 730 " --> pdb=" O GLY R 726 " (cutoff:3.500A) Processing helix chain 'R' and resid 762 through 774 Processing helix chain 'R' and resid 783 through 785 No H-bonds generated for 'chain 'R' and resid 783 through 785' Processing helix chain 'R' and resid 814 through 819 removed outlier: 3.998A pdb=" N CYS R 818 " --> pdb=" O GLU R 814 " (cutoff:3.500A) Processing helix chain 'R' and resid 860 through 868 Processing helix chain 'R' and resid 881 through 891 removed outlier: 3.762A pdb=" N ARG R 891 " --> pdb=" O ARG R 887 " (cutoff:3.500A) Processing helix chain 'R' and resid 894 through 903 Processing helix chain 'R' and resid 904 through 906 No H-bonds generated for 'chain 'R' and resid 904 through 906' Processing helix chain 'S' and resid 475 through 485 Processing helix chain 'S' and resid 489 through 493 removed outlier: 3.513A pdb=" N ASP S 492 " --> pdb=" O ASN S 489 " (cutoff:3.500A) Processing helix chain 'S' and resid 514 through 525 Processing helix chain 'S' and resid 560 through 567 removed outlier: 3.687A pdb=" N LEU S 565 " --> pdb=" O GLU S 561 " (cutoff:3.500A) Processing helix chain 'S' and resid 570 through 578 removed outlier: 3.632A pdb=" N ALA S 574 " --> pdb=" O GLY S 570 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS S 577 " --> pdb=" O GLN S 573 " (cutoff:3.500A) Processing helix chain 'S' and resid 600 through 611 removed outlier: 4.018A pdb=" N PHE S 609 " --> pdb=" O LEU S 605 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA S 610 " --> pdb=" O GLN S 606 " (cutoff:3.500A) Processing helix chain 'S' and resid 627 through 631 removed outlier: 3.679A pdb=" N ARG S 631 " --> pdb=" O ALA S 628 " (cutoff:3.500A) Processing helix chain 'S' and resid 644 through 654 Processing helix chain 'S' and resid 666 through 677 Processing helix chain 'S' and resid 686 through 690 Processing helix chain 'S' and resid 691 through 698 Processing helix chain 'S' and resid 726 through 742 Processing helix chain 'S' and resid 762 through 774 Processing helix chain 'S' and resid 783 through 785 No H-bonds generated for 'chain 'S' and resid 783 through 785' Processing helix chain 'S' and resid 815 through 819 Processing helix chain 'S' and resid 860 through 868 Processing helix chain 'S' and resid 881 through 891 removed outlier: 3.740A pdb=" N ARG S 891 " --> pdb=" O ARG S 887 " (cutoff:3.500A) Processing helix chain 'S' and resid 894 through 903 Processing helix chain 'S' and resid 904 through 908 Processing helix chain 'T' and resid 475 through 484 Processing helix chain 'T' and resid 489 through 493 Processing helix chain 'T' and resid 514 through 525 Processing helix chain 'T' and resid 560 through 567 removed outlier: 3.821A pdb=" N LEU T 565 " --> pdb=" O GLU T 561 " (cutoff:3.500A) Processing helix chain 'T' and resid 570 through 578 removed outlier: 3.617A pdb=" N ALA T 574 " --> pdb=" O GLY T 570 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS T 577 " --> pdb=" O GLN T 573 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU T 578 " --> pdb=" O ALA T 574 " (cutoff:3.500A) Processing helix chain 'T' and resid 600 through 608 Processing helix chain 'T' and resid 644 through 653 Processing helix chain 'T' and resid 666 through 677 Processing helix chain 'T' and resid 691 through 698 Processing helix chain 'T' and resid 726 through 742 Processing helix chain 'T' and resid 762 through 773 Processing helix chain 'T' and resid 783 through 785 No H-bonds generated for 'chain 'T' and resid 783 through 785' Processing helix chain 'T' and resid 814 through 819 removed outlier: 3.819A pdb=" N CYS T 818 " --> pdb=" O GLU T 814 " (cutoff:3.500A) Processing helix chain 'T' and resid 860 through 869 Processing helix chain 'T' and resid 881 through 891 removed outlier: 3.792A pdb=" N ARG T 891 " --> pdb=" O ARG T 887 " (cutoff:3.500A) Processing helix chain 'T' and resid 894 through 903 Processing helix chain 'T' and resid 904 through 908 Processing helix chain 'U' and resid 475 through 485 Processing helix chain 'U' and resid 489 through 493 Processing helix chain 'U' and resid 514 through 525 Processing helix chain 'U' and resid 560 through 567 Processing helix chain 'U' and resid 570 through 578 removed outlier: 3.588A pdb=" N ALA U 574 " --> pdb=" O GLY U 570 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS U 577 " --> pdb=" O GLN U 573 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU U 578 " --> pdb=" O ALA U 574 " (cutoff:3.500A) Processing helix chain 'U' and resid 600 through 611 removed outlier: 3.871A pdb=" N PHE U 609 " --> pdb=" O LEU U 605 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA U 610 " --> pdb=" O GLN U 606 " (cutoff:3.500A) Processing helix chain 'U' and resid 644 through 654 Processing helix chain 'U' and resid 666 through 677 Processing helix chain 'U' and resid 686 through 690 Processing helix chain 'U' and resid 691 through 698 Processing helix chain 'U' and resid 726 through 741 Processing helix chain 'U' and resid 762 through 773 Processing helix chain 'U' and resid 783 through 785 No H-bonds generated for 'chain 'U' and resid 783 through 785' Processing helix chain 'U' and resid 814 through 819 removed outlier: 3.942A pdb=" N CYS U 818 " --> pdb=" O GLU U 814 " (cutoff:3.500A) Processing helix chain 'U' and resid 860 through 869 Processing helix chain 'U' and resid 881 through 891 removed outlier: 3.549A pdb=" N ARG U 891 " --> pdb=" O ARG U 887 " (cutoff:3.500A) Processing helix chain 'U' and resid 894 through 903 Processing helix chain 'U' and resid 904 through 908 Processing helix chain 'P' and resid 37 through 44 Processing helix chain 'P' and resid 48 through 52 Processing helix chain 'P' and resid 73 through 84 Processing helix chain 'P' and resid 118 through 127 Processing helix chain 'P' and resid 129 through 138 removed outlier: 4.091A pdb=" N LYS P 133 " --> pdb=" O GLY P 129 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER P 138 " --> pdb=" O VAL P 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 172 removed outlier: 3.631A pdb=" N GLN P 163 " --> pdb=" O LYS P 159 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 187 Processing helix chain 'P' and resid 199 through 206 Processing helix chain 'P' and resid 228 through 235 Processing helix chain 'P' and resid 255 through 271 removed outlier: 3.880A pdb=" N TYR P 259 " --> pdb=" O PRO P 255 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU P 260 " --> pdb=" O PRO P 256 " (cutoff:3.500A) Processing helix chain 'P' and resid 291 through 303 Processing helix chain 'P' and resid 330 through 334 removed outlier: 3.531A pdb=" N ARG P 333 " --> pdb=" O ILE P 330 " (cutoff:3.500A) Processing helix chain 'P' and resid 339 through 352 Processing helix chain 'P' and resid 360 through 366 removed outlier: 4.034A pdb=" N VAL P 364 " --> pdb=" O PRO P 360 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASN P 366 " --> pdb=" O LYS P 362 " (cutoff:3.500A) Processing helix chain 'P' and resid 367 through 374 Proline residue: P 370 - end of helix Processing helix chain 'Q' and resid 37 through 44 removed outlier: 3.614A pdb=" N LYS Q 43 " --> pdb=" O ALA Q 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 52 Processing helix chain 'Q' and resid 73 through 84 Processing helix chain 'Q' and resid 118 through 127 Processing helix chain 'Q' and resid 129 through 138 removed outlier: 4.079A pdb=" N LYS Q 133 " --> pdb=" O GLY Q 129 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER Q 138 " --> pdb=" O VAL Q 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 159 through 172 removed outlier: 3.702A pdb=" N GLN Q 163 " --> pdb=" O LYS Q 159 " (cutoff:3.500A) Processing helix chain 'Q' and resid 183 through 187 Processing helix chain 'Q' and resid 199 through 206 Processing helix chain 'Q' and resid 228 through 235 Processing helix chain 'Q' and resid 255 through 271 removed outlier: 3.875A pdb=" N TYR Q 259 " --> pdb=" O PRO Q 255 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU Q 260 " --> pdb=" O PRO Q 256 " (cutoff:3.500A) Processing helix chain 'Q' and resid 291 through 303 Processing helix chain 'Q' and resid 330 through 334 removed outlier: 3.503A pdb=" N ARG Q 333 " --> pdb=" O ILE Q 330 " (cutoff:3.500A) Processing helix chain 'Q' and resid 339 through 352 Processing helix chain 'Q' and resid 360 through 366 removed outlier: 4.045A pdb=" N VAL Q 364 " --> pdb=" O PRO Q 360 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASN Q 366 " --> pdb=" O LYS Q 362 " (cutoff:3.500A) Processing helix chain 'Q' and resid 367 through 374 Proline residue: Q 370 - end of helix Processing sheet with id=AA1, first strand: chain 'L' and resid 504 through 505 Processing sheet with id=AA2, first strand: chain 'L' and resid 546 through 548 Processing sheet with id=AA3, first strand: chain 'L' and resid 681 through 683 removed outlier: 7.299A pdb=" N ILE L 634 " --> pdb=" O ASP L 658 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N TYR L 660 " --> pdb=" O ILE L 634 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL L 636 " --> pdb=" O TYR L 660 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ALA L 662 " --> pdb=" O VAL L 636 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N SER L 638 " --> pdb=" O ALA L 662 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG L 635 " --> pdb=" O LEU L 703 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE L 705 " --> pdb=" O ARG L 635 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU L 637 " --> pdb=" O ILE L 705 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N GLY L 707 " --> pdb=" O LEU L 637 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LEU L 639 " --> pdb=" O GLY L 707 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 824 through 825 removed outlier: 4.081A pdb=" N ILE L 824 " --> pdb=" O PHE L 851 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE L 851 " --> pdb=" O ILE L 824 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 504 through 505 Processing sheet with id=AA6, first strand: chain 'M' and resid 546 through 548 Processing sheet with id=AA7, first strand: chain 'M' and resid 682 through 684 removed outlier: 5.953A pdb=" N ILE M 634 " --> pdb=" O VAL M 657 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG M 659 " --> pdb=" O ILE M 634 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 824 through 825 removed outlier: 4.002A pdb=" N ILE M 824 " --> pdb=" O PHE M 851 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 504 through 505 Processing sheet with id=AB1, first strand: chain 'N' and resid 546 through 548 Processing sheet with id=AB2, first strand: chain 'N' and resid 681 through 684 removed outlier: 5.886A pdb=" N ILE N 634 " --> pdb=" O VAL N 657 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG N 659 " --> pdb=" O ILE N 634 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY N 707 " --> pdb=" O LEU N 639 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 824 through 825 removed outlier: 3.824A pdb=" N ILE N 824 " --> pdb=" O PHE N 851 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'O' and resid 504 through 505 Processing sheet with id=AB5, first strand: chain 'O' and resid 546 through 548 Processing sheet with id=AB6, first strand: chain 'O' and resid 682 through 684 removed outlier: 8.511A pdb=" N MET O 682 " --> pdb=" O ASP O 658 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TYR O 660 " --> pdb=" O MET O 682 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL O 684 " --> pdb=" O TYR O 660 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ALA O 662 " --> pdb=" O VAL O 684 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ILE O 634 " --> pdb=" O VAL O 657 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG O 659 " --> pdb=" O ILE O 634 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY O 707 " --> pdb=" O LEU O 639 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'O' and resid 824 through 825 removed outlier: 3.995A pdb=" N ILE O 824 " --> pdb=" O PHE O 851 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE O 851 " --> pdb=" O ILE O 824 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'R' and resid 504 through 505 Processing sheet with id=AB9, first strand: chain 'R' and resid 546 through 548 Processing sheet with id=AC1, first strand: chain 'R' and resid 682 through 684 removed outlier: 5.886A pdb=" N ILE R 634 " --> pdb=" O VAL R 657 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG R 659 " --> pdb=" O ILE R 634 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY R 707 " --> pdb=" O LEU R 639 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 824 through 825 removed outlier: 3.710A pdb=" N ILE R 824 " --> pdb=" O PHE R 851 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE R 851 " --> pdb=" O ILE R 824 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'S' and resid 504 through 505 Processing sheet with id=AC4, first strand: chain 'S' and resid 546 through 548 Processing sheet with id=AC5, first strand: chain 'S' and resid 681 through 684 removed outlier: 8.769A pdb=" N MET S 682 " --> pdb=" O ASP S 658 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TYR S 660 " --> pdb=" O MET S 682 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL S 684 " --> pdb=" O TYR S 660 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA S 662 " --> pdb=" O VAL S 684 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE S 634 " --> pdb=" O ASP S 658 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N TYR S 660 " --> pdb=" O ILE S 634 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL S 636 " --> pdb=" O TYR S 660 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ALA S 662 " --> pdb=" O VAL S 636 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N SER S 638 " --> pdb=" O ALA S 662 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY S 707 " --> pdb=" O LEU S 639 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'S' and resid 824 through 825 removed outlier: 3.639A pdb=" N ILE S 824 " --> pdb=" O PHE S 851 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'T' and resid 504 through 505 Processing sheet with id=AC8, first strand: chain 'T' and resid 546 through 548 Processing sheet with id=AC9, first strand: chain 'T' and resid 682 through 684 removed outlier: 3.500A pdb=" N MET T 682 " --> pdb=" O TYR T 660 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ILE T 634 " --> pdb=" O VAL T 657 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG T 659 " --> pdb=" O ILE T 634 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'T' and resid 824 through 825 removed outlier: 3.764A pdb=" N ILE T 824 " --> pdb=" O PHE T 851 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'U' and resid 504 through 505 Processing sheet with id=AD3, first strand: chain 'U' and resid 546 through 548 Processing sheet with id=AD4, first strand: chain 'U' and resid 682 through 684 removed outlier: 5.796A pdb=" N ILE U 634 " --> pdb=" O VAL U 657 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG U 659 " --> pdb=" O ILE U 634 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ARG U 635 " --> pdb=" O LEU U 703 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE U 705 " --> pdb=" O ARG U 635 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU U 637 " --> pdb=" O ILE U 705 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N GLY U 707 " --> pdb=" O LEU U 637 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N LEU U 639 " --> pdb=" O GLY U 707 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'U' and resid 850 through 851 Processing sheet with id=AD6, first strand: chain 'P' and resid 63 through 64 Processing sheet with id=AD7, first strand: chain 'P' and resid 218 through 221 removed outlier: 7.217A pdb=" N VAL P 192 " --> pdb=" O LYS P 219 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL P 221 " --> pdb=" O VAL P 192 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER P 194 " --> pdb=" O VAL P 221 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL P 241 " --> pdb=" O MET P 283 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N VAL P 285 " --> pdb=" O VAL P 241 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLY P 243 " --> pdb=" O VAL P 285 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 311 through 313 removed outlier: 6.653A pdb=" N HIS P 313 " --> pdb=" O LEU P 317 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU P 317 " --> pdb=" O HIS P 313 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Q' and resid 63 through 64 Processing sheet with id=AE1, first strand: chain 'Q' and resid 218 through 221 removed outlier: 7.202A pdb=" N VAL Q 192 " --> pdb=" O LYS Q 219 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N VAL Q 221 " --> pdb=" O VAL Q 192 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER Q 194 " --> pdb=" O VAL Q 221 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL Q 241 " --> pdb=" O MET Q 283 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N VAL Q 285 " --> pdb=" O VAL Q 241 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY Q 243 " --> pdb=" O VAL Q 285 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Q' and resid 311 through 313 removed outlier: 6.648A pdb=" N ASP Q 311 " --> pdb=" O GLN Q 318 " (cutoff:3.500A) 1101 hydrogen bonds defined for protein. 3024 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: 7.18 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10266 1.34 - 1.46: 7100 1.46 - 1.58: 16329 1.58 - 1.70: 0 1.70 - 1.82: 442 Bond restraints: 34137 Sorted by residual: bond pdb=" N VAL Q 126 " pdb=" CA VAL Q 126 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.08e-02 8.57e+03 1.24e+01 bond pdb=" N ILE Q 199 " pdb=" CA ILE Q 199 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.68e+00 bond pdb=" N ILE P 199 " pdb=" CA ILE P 199 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.96e+00 bond pdb=" N LEU R 889 " pdb=" CA LEU R 889 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.33e-02 5.65e+03 7.45e+00 bond pdb=" CZ ARG N 604 " pdb=" NH1 ARG N 604 " ideal model delta sigma weight residual 1.323 1.289 0.034 1.40e-02 5.10e+03 6.00e+00 ... (remaining 34132 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 43446 2.04 - 4.07: 2377 4.07 - 6.11: 270 6.11 - 8.14: 78 8.14 - 10.18: 12 Bond angle restraints: 46183 Sorted by residual: angle pdb=" C ASP R 530 " pdb=" N ASP R 531 " pdb=" CA ASP R 531 " ideal model delta sigma weight residual 120.38 128.18 -7.80 1.37e+00 5.33e-01 3.24e+01 angle pdb=" C ASP N 530 " pdb=" N ASP N 531 " pdb=" CA ASP N 531 " ideal model delta sigma weight residual 120.38 128.11 -7.73 1.37e+00 5.33e-01 3.18e+01 angle pdb=" C ASP O 530 " pdb=" N ASP O 531 " pdb=" CA ASP O 531 " ideal model delta sigma weight residual 120.38 128.00 -7.62 1.37e+00 5.33e-01 3.09e+01 angle pdb=" C ASP T 876 " pdb=" N VAL T 877 " pdb=" CA VAL T 877 " ideal model delta sigma weight residual 123.08 117.77 5.31 1.01e+00 9.80e-01 2.77e+01 angle pdb=" C SER U 894 " pdb=" N VAL U 895 " pdb=" CA VAL U 895 " ideal model delta sigma weight residual 120.24 123.32 -3.08 6.30e-01 2.52e+00 2.39e+01 ... (remaining 46178 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.45: 19612 16.45 - 32.90: 626 32.90 - 49.34: 112 49.34 - 65.79: 17 65.79 - 82.24: 4 Dihedral angle restraints: 20371 sinusoidal: 8449 harmonic: 11922 Sorted by residual: dihedral pdb=" CA HIS O 677 " pdb=" C HIS O 677 " pdb=" N GLN O 678 " pdb=" CA GLN O 678 " ideal model delta harmonic sigma weight residual 180.00 150.97 29.03 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA GLY Q 127 " pdb=" C GLY Q 127 " pdb=" N PRO Q 128 " pdb=" CA PRO Q 128 " ideal model delta harmonic sigma weight residual -180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA HIS R 677 " pdb=" C HIS R 677 " pdb=" N GLN R 678 " pdb=" CA GLN R 678 " ideal model delta harmonic sigma weight residual 180.00 151.65 28.35 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 20368 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3531 0.054 - 0.108: 1065 0.108 - 0.161: 228 0.161 - 0.215: 42 0.215 - 0.269: 4 Chirality restraints: 4870 Sorted by residual: chirality pdb=" CB VAL S 758 " pdb=" CA VAL S 758 " pdb=" CG1 VAL S 758 " pdb=" CG2 VAL S 758 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB VAL N 758 " pdb=" CA VAL N 758 " pdb=" CG1 VAL N 758 " pdb=" CG2 VAL N 758 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA TRP N 601 " pdb=" N TRP N 601 " pdb=" C TRP N 601 " pdb=" CB TRP N 601 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 4867 not shown) Planarity restraints: 6024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE N 851 " 0.033 2.00e-02 2.50e+03 3.60e-02 2.27e+01 pdb=" CG PHE N 851 " -0.083 2.00e-02 2.50e+03 pdb=" CD1 PHE N 851 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE N 851 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE N 851 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE N 851 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE N 851 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR P 225 " -0.017 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C THR P 225 " 0.059 2.00e-02 2.50e+03 pdb=" O THR P 225 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP P 226 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE U 851 " 0.023 2.00e-02 2.50e+03 2.23e-02 8.74e+00 pdb=" CG PHE U 851 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE U 851 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE U 851 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE U 851 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE U 851 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE U 851 " 0.004 2.00e-02 2.50e+03 ... (remaining 6021 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 8044 2.81 - 3.33: 30119 3.33 - 3.86: 54146 3.86 - 4.38: 64991 4.38 - 4.90: 106852 Nonbonded interactions: 264152 Sorted by model distance: nonbonded pdb=" NH1 ARG M 476 " pdb=" O SER M 496 " model vdw 2.288 3.120 nonbonded pdb=" O GLU Q 202 " pdb=" OG SER Q 205 " model vdw 2.289 3.040 nonbonded pdb=" O GLU P 202 " pdb=" OG SER P 205 " model vdw 2.305 3.040 nonbonded pdb=" O SER L 786 " pdb=" NZ LYS L 829 " model vdw 2.307 3.120 nonbonded pdb=" O SER U 786 " pdb=" NZ LYS U 829 " model vdw 2.315 3.120 ... (remaining 264147 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 'L' and (resid 474 through 833 or resid 846 through 1004)) selection = chain 'M' selection = (chain 'N' and (resid 474 through 833 or resid 846 through 1004)) selection = (chain 'O' and (resid 474 through 833 or resid 846 through 1004)) selection = (chain 'R' and (resid 474 through 833 or resid 846 through 1004)) selection = (chain 'S' and (resid 474 through 833 or resid 846 through 1004)) selection = chain 'T' selection = (chain 'U' and (resid 474 through 833 or resid 846 through 1004)) } ncs_group { reference = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.41 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.500 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: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 36.630 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 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 0.175 34257 Z= 0.371 Angle : 1.343 40.819 46363 Z= 0.617 Chirality : 0.054 0.269 4870 Planarity : 0.008 0.069 6024 Dihedral : 9.148 82.240 12695 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.47 % Allowed : 1.49 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.11), residues: 4084 helix: -1.46 (0.12), residues: 1325 sheet: -1.58 (0.27), residues: 276 loop : -1.50 (0.11), residues: 2483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.048 0.002 ARG M 476 TYR 0.026 0.003 TYR S 592 PHE 0.083 0.005 PHE N 851 TRP 0.027 0.003 TRP M 860 HIS 0.015 0.003 HIS L 789 Details of bonding type rmsd covalent geometry : bond 0.00596 (34137) covalent geometry : angle 1.03183 (46183) hydrogen bonds : bond 0.17877 ( 1101) hydrogen bonds : angle 7.88502 ( 3024) metal coordination : bond 0.10400 ( 120) metal coordination : angle 13.82404 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 844 time to evaluate : 1.294 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 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 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: L 478 ARG cc_start: 0.9079 (ttt90) cc_final: 0.8496 (ttp80) REVERT: L 482 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8422 (mp0) REVERT: L 647 LEU cc_start: 0.9304 (tp) cc_final: 0.8974 (tp) REVERT: L 648 LEU cc_start: 0.8971 (tp) cc_final: 0.8753 (tp) REVERT: L 651 LYS cc_start: 0.9201 (mttt) cc_final: 0.8944 (mttt) REVERT: L 656 GLN cc_start: 0.7940 (mt0) cc_final: 0.7685 (mm110) REVERT: L 667 GLU cc_start: 0.8151 (mp0) cc_final: 0.7834 (mp0) REVERT: L 668 ASP cc_start: 0.8010 (m-30) cc_final: 0.7786 (m-30) REVERT: L 674 MET cc_start: 0.9042 (mtp) cc_final: 0.8808 (mtp) REVERT: L 682 MET cc_start: 0.8422 (ttm) cc_final: 0.8117 (tmm) REVERT: L 742 ARG cc_start: 0.8022 (tpp80) cc_final: 0.7604 (ptp-110) REVERT: L 772 PHE cc_start: 0.7642 (m-10) cc_final: 0.7083 (m-10) REVERT: L 781 ASP cc_start: 0.8223 (t0) cc_final: 0.7805 (t0) REVERT: L 790 ARG cc_start: 0.8674 (tpp80) cc_final: 0.8442 (tpp80) REVERT: L 797 ASN cc_start: 0.7266 (p0) cc_final: 0.6881 (p0) REVERT: L 847 HIS cc_start: 0.6375 (m90) cc_final: 0.5725 (m90) REVERT: L 850 VAL cc_start: 0.6898 (t) cc_final: 0.6207 (t) REVERT: L 858 ILE cc_start: 0.8605 (mt) cc_final: 0.8354 (mt) REVERT: L 899 ARG cc_start: 0.7480 (ttt90) cc_final: 0.7195 (mtm-85) REVERT: M 548 MET cc_start: -0.1686 (mtt) cc_final: -0.2028 (mtt) REVERT: M 677 HIS cc_start: 0.7571 (m-70) cc_final: 0.7210 (m-70) REVERT: M 705 ILE cc_start: 0.7474 (pt) cc_final: 0.7172 (tt) REVERT: M 737 LEU cc_start: 0.8078 (mt) cc_final: 0.7827 (mt) REVERT: M 771 ARG cc_start: 0.8336 (mtt180) cc_final: 0.7995 (ttp-110) REVERT: M 852 MET cc_start: 0.7268 (ttt) cc_final: 0.6951 (ttt) REVERT: M 899 ARG cc_start: 0.6867 (ttt90) cc_final: 0.6564 (ttt90) REVERT: N 477 GLU cc_start: 0.8225 (mt-10) cc_final: 0.8017 (mt-10) REVERT: N 478 ARG cc_start: 0.8578 (ttt90) cc_final: 0.8138 (ttt90) REVERT: N 481 TYR cc_start: 0.8507 (t80) cc_final: 0.8169 (t80) REVERT: N 597 ARG cc_start: 0.8342 (ttp-110) cc_final: 0.7914 (ttp-110) REVERT: N 607 MET cc_start: 0.7698 (mtp) cc_final: 0.7450 (mtp) REVERT: N 668 ASP cc_start: 0.6739 (m-30) cc_final: 0.6389 (m-30) REVERT: N 733 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7239 (mm-30) REVERT: N 756 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7229 (tm-30) REVERT: N 797 ASN cc_start: 0.7346 (p0) cc_final: 0.6350 (p0) REVERT: N 814 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7415 (mt-10) REVERT: N 852 MET cc_start: 0.7717 (ttt) cc_final: 0.7436 (tpt) REVERT: N 868 PHE cc_start: 0.7010 (m-10) cc_final: 0.6706 (m-10) REVERT: N 907 GLU cc_start: 0.8594 (tt0) cc_final: 0.8381 (tt0) REVERT: O 607 MET cc_start: 0.4999 (mtp) cc_final: 0.4578 (mtp) REVERT: O 647 LEU cc_start: 0.7887 (tp) cc_final: 0.7399 (tt) REVERT: O 651 LYS cc_start: 0.8643 (mttt) cc_final: 0.8203 (mttt) REVERT: O 669 SER cc_start: 0.8168 (m) cc_final: 0.7963 (p) REVERT: O 681 ILE cc_start: 0.6310 (mt) cc_final: 0.5951 (mt) REVERT: O 733 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7102 (mm-30) REVERT: O 790 ARG cc_start: 0.7127 (tpp80) cc_final: 0.6819 (mmm160) REVERT: O 817 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7631 (mt-10) REVERT: O 906 LYS cc_start: 0.8619 (mtpp) cc_final: 0.8401 (mttm) REVERT: R 607 MET cc_start: 0.5069 (mtp) cc_final: 0.4775 (mtp) REVERT: R 647 LEU cc_start: 0.7619 (tp) cc_final: 0.7336 (tt) REVERT: R 653 LEU cc_start: 0.6747 (mt) cc_final: 0.6540 (mt) REVERT: R 733 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7262 (mm-30) REVERT: R 886 GLN cc_start: 0.8271 (mt0) cc_final: 0.8018 (mt0) REVERT: S 513 MET cc_start: 0.7376 (ttt) cc_final: 0.6854 (ttt) REVERT: S 528 TYR cc_start: 0.5179 (m-80) cc_final: 0.4286 (m-80) REVERT: S 597 ARG cc_start: 0.7741 (ttp-110) cc_final: 0.7455 (ttp80) REVERT: S 607 MET cc_start: 0.7630 (mtp) cc_final: 0.7109 (mtp) REVERT: S 647 LEU cc_start: 0.6880 (tp) cc_final: 0.6218 (tt) REVERT: S 797 ASN cc_start: 0.7345 (p0) cc_final: 0.6661 (p0) REVERT: S 852 MET cc_start: 0.7463 (ttt) cc_final: 0.7125 (tpt) REVERT: S 868 PHE cc_start: 0.7400 (m-10) cc_final: 0.7091 (m-80) REVERT: S 885 ARG cc_start: 0.5221 (ttt180) cc_final: 0.3921 (ttp-110) REVERT: S 907 GLU cc_start: 0.8668 (tt0) cc_final: 0.8174 (tt0) REVERT: T 677 HIS cc_start: 0.7782 (m-70) cc_final: 0.7379 (m-70) REVERT: T 682 MET cc_start: 0.7813 (ttm) cc_final: 0.7499 (ttm) REVERT: T 763 VAL cc_start: 0.8234 (t) cc_final: 0.7676 (t) REVERT: T 767 ARG cc_start: 0.8846 (mtt180) cc_final: 0.8546 (mtt180) REVERT: T 771 ARG cc_start: 0.8022 (mtt180) cc_final: 0.7725 (mtm110) REVERT: T 805 LEU cc_start: 0.6903 (mp) cc_final: 0.6492 (tt) REVERT: T 860 TRP cc_start: 0.8112 (m-10) cc_final: 0.7643 (m-10) REVERT: T 885 ARG cc_start: 0.7144 (ttt180) cc_final: 0.6273 (ptm160) REVERT: T 889 LEU cc_start: 0.7520 (mt) cc_final: 0.7087 (mt) REVERT: T 907 GLU cc_start: 0.7582 (tt0) cc_final: 0.7255 (tt0) REVERT: U 648 LEU cc_start: 0.9007 (tp) cc_final: 0.8771 (tp) REVERT: U 652 ASP cc_start: 0.8800 (m-30) cc_final: 0.8528 (t0) REVERT: U 696 GLN cc_start: 0.8854 (mt0) cc_final: 0.8487 (mt0) REVERT: U 697 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8603 (mm-30) REVERT: U 772 PHE cc_start: 0.7387 (m-10) cc_final: 0.6825 (m-10) REVERT: U 826 LYS cc_start: 0.8601 (tttt) cc_final: 0.8167 (tptp) REVERT: U 852 MET cc_start: 0.7803 (ttt) cc_final: 0.7349 (ttt) REVERT: U 860 TRP cc_start: 0.6844 (m-10) cc_final: 0.6498 (m-10) REVERT: U 899 ARG cc_start: 0.7220 (ttt90) cc_final: 0.6967 (mtm-85) REVERT: U 911 CYS cc_start: 0.8747 (m) cc_final: 0.8531 (m) REVERT: P 141 VAL cc_start: 0.8390 (m) cc_final: 0.8161 (m) REVERT: P 158 ARG cc_start: 0.8908 (pmt170) cc_final: 0.8526 (pmt170) REVERT: P 163 GLN cc_start: 0.8220 (tp40) cc_final: 0.7758 (tp40) REVERT: P 242 TYR cc_start: 0.4837 (t80) cc_final: 0.4064 (t80) REVERT: P 283 MET cc_start: 0.7285 (ttt) cc_final: 0.6456 (ttt) REVERT: P 305 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8289 (mm-30) REVERT: P 324 TRP cc_start: 0.4185 (m-90) cc_final: 0.3564 (m-90) REVERT: P 335 TRP cc_start: 0.6354 (m100) cc_final: 0.6105 (m100) REVERT: P 368 PHE cc_start: 0.6125 (m-80) cc_final: 0.5885 (m-80) REVERT: Q 158 ARG cc_start: 0.8870 (pmt170) cc_final: 0.8581 (pmt170) REVERT: Q 234 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7610 (mm-30) REVERT: Q 308 THR cc_start: 0.7787 (p) cc_final: 0.7491 (p) outliers start: 17 outliers final: 4 residues processed: 852 average time/residue: 0.2513 time to fit residues: 326.7801 Evaluate side-chains 722 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 718 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 831 ARG Chi-restraints excluded: chain O residue 684 VAL Chi-restraints excluded: chain O residue 851 PHE Chi-restraints excluded: chain R residue 831 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.6980 chunk 401 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 612 ASN L 847 HIS L 886 GLN L 900 HIS M 516 ASN M 612 ASN M 615 GLN ** M 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 900 HIS N 516 ASN N 611 ASN ** N 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 900 HIS O 516 ASN ** O 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 816 GLN O 847 HIS O 873 HIS R 516 ASN ** R 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 816 GLN R 873 HIS S 515 GLN S 516 ASN ** S 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 900 HIS T 516 ASN T 612 ASN T 900 HIS U 516 ASN U 612 ASN U 656 GLN U 816 GLN ** U 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 900 HIS ** P 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 264 HIS Q 268 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.231416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.194022 restraints weight = 61950.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.200530 restraints weight = 35185.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.205020 restraints weight = 23154.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.207855 restraints weight = 17008.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.210245 restraints weight = 13608.335| |-----------------------------------------------------------------------------| r_work (final): 0.4609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4612 r_free = 0.4612 target_work(ls_wunit_k1) = 0.210 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4611 r_free = 0.4611 target_work(ls_wunit_k1) = 0.210 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5329 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 34257 Z= 0.187 Angle : 0.737 11.870 46363 Z= 0.359 Chirality : 0.043 0.225 4870 Planarity : 0.006 0.059 6024 Dihedral : 5.710 57.086 4587 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.95 % Allowed : 7.43 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.12), residues: 4084 helix: -0.24 (0.14), residues: 1356 sheet: -1.12 (0.25), residues: 344 loop : -0.79 (0.12), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG U 484 TYR 0.025 0.002 TYR R 793 PHE 0.041 0.003 PHE M 902 TRP 0.031 0.003 TRP U 753 HIS 0.010 0.001 HIS N 789 Details of bonding type rmsd covalent geometry : bond 0.00394 (34137) covalent geometry : angle 0.67815 (46183) hydrogen bonds : bond 0.04401 ( 1101) hydrogen bonds : angle 5.95233 ( 3024) metal coordination : bond 0.00891 ( 120) metal coordination : angle 4.69106 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 774 time to evaluate : 1.385 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 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 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: L 476 ARG cc_start: 0.7232 (ttt-90) cc_final: 0.7019 (ttt-90) REVERT: L 478 ARG cc_start: 0.8628 (ttt90) cc_final: 0.8106 (ttp80) REVERT: L 482 GLU cc_start: 0.8554 (mt-10) cc_final: 0.7968 (mt-10) REVERT: L 561 GLU cc_start: 0.6907 (mt-10) cc_final: 0.6672 (mp0) REVERT: L 651 LYS cc_start: 0.8871 (mttt) cc_final: 0.8490 (mttt) REVERT: L 671 THR cc_start: 0.8785 (m) cc_final: 0.8312 (m) REVERT: L 674 MET cc_start: 0.8259 (mtp) cc_final: 0.7908 (mtp) REVERT: L 738 LEU cc_start: 0.6819 (tp) cc_final: 0.6419 (tp) REVERT: L 772 PHE cc_start: 0.7790 (m-10) cc_final: 0.7193 (m-10) REVERT: L 780 ILE cc_start: 0.6821 (mp) cc_final: 0.6552 (mp) REVERT: L 781 ASP cc_start: 0.7708 (t0) cc_final: 0.7414 (t0) REVERT: L 868 PHE cc_start: 0.3804 (m-10) cc_final: 0.2359 (m-80) REVERT: L 878 SER cc_start: 0.7934 (OUTLIER) cc_final: 0.7536 (p) REVERT: M 548 MET cc_start: -0.0832 (mtt) cc_final: -0.1072 (mtt) REVERT: M 671 THR cc_start: 0.7806 (m) cc_final: 0.7354 (t) REVERT: M 677 HIS cc_start: 0.7242 (m-70) cc_final: 0.7033 (m-70) REVERT: M 737 LEU cc_start: 0.7501 (mt) cc_final: 0.7269 (mt) REVERT: M 767 ARG cc_start: 0.8130 (mtt180) cc_final: 0.7558 (mtt180) REVERT: M 771 ARG cc_start: 0.7295 (mtt180) cc_final: 0.7085 (mtt180) REVERT: M 899 ARG cc_start: 0.6309 (ttt90) cc_final: 0.5833 (ttt90) REVERT: N 566 LEU cc_start: 0.6612 (mt) cc_final: 0.6346 (mm) REVERT: N 584 TYR cc_start: 0.7611 (m-80) cc_final: 0.7213 (m-80) REVERT: N 595 LEU cc_start: 0.6994 (pp) cc_final: 0.6426 (tp) REVERT: N 597 ARG cc_start: 0.7486 (ttp-110) cc_final: 0.7252 (ttm170) REVERT: N 607 MET cc_start: 0.7233 (mtp) cc_final: 0.6860 (mtp) REVERT: N 639 LEU cc_start: 0.7362 (mp) cc_final: 0.7106 (mt) REVERT: N 647 LEU cc_start: 0.6461 (tp) cc_final: 0.5844 (tp) REVERT: N 668 ASP cc_start: 0.6617 (m-30) cc_final: 0.6351 (m-30) REVERT: N 669 SER cc_start: 0.8134 (m) cc_final: 0.7650 (p) REVERT: N 703 LEU cc_start: 0.7366 (tp) cc_final: 0.6784 (mp) REVERT: N 733 GLU cc_start: 0.6760 (mm-30) cc_final: 0.6290 (mm-30) REVERT: N 801 MET cc_start: 0.6016 (mtp) cc_final: 0.5567 (mtt) REVERT: N 823 ARG cc_start: 0.5989 (mtp85) cc_final: 0.5503 (mtp-110) REVERT: N 861 CYS cc_start: 0.7339 (m) cc_final: 0.7081 (m) REVERT: N 878 SER cc_start: 0.7909 (p) cc_final: 0.7704 (t) REVERT: O 513 MET cc_start: 0.7452 (ppp) cc_final: 0.4555 (pmm) REVERT: O 607 MET cc_start: 0.5185 (mtp) cc_final: 0.4766 (mtp) REVERT: O 667 GLU cc_start: 0.6729 (mp0) cc_final: 0.6367 (mp0) REVERT: O 669 SER cc_start: 0.8582 (m) cc_final: 0.8297 (p) REVERT: O 678 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.7352 (mp10) REVERT: O 680 LYS cc_start: 0.6843 (OUTLIER) cc_final: 0.6451 (ptpp) REVERT: O 733 GLU cc_start: 0.6021 (mm-30) cc_final: 0.5783 (mm-30) REVERT: O 738 LEU cc_start: 0.6051 (OUTLIER) cc_final: 0.5676 (tt) REVERT: O 790 ARG cc_start: 0.6933 (tpp80) cc_final: 0.6675 (ttp80) REVERT: O 801 MET cc_start: 0.6620 (mtp) cc_final: 0.6416 (mtp) REVERT: R 513 MET cc_start: 0.6579 (ppp) cc_final: 0.3798 (pmm) REVERT: R 607 MET cc_start: 0.5275 (mtp) cc_final: 0.4977 (mtp) REVERT: R 682 MET cc_start: 0.6546 (ttm) cc_final: 0.6304 (ttm) REVERT: R 866 ARG cc_start: 0.7123 (ttm110) cc_final: 0.6820 (ttm110) REVERT: S 513 MET cc_start: 0.7208 (ttt) cc_final: 0.6455 (ttt) REVERT: S 566 LEU cc_start: 0.7132 (mt) cc_final: 0.6880 (mm) REVERT: S 595 LEU cc_start: 0.7681 (pp) cc_final: 0.7458 (tt) REVERT: S 597 ARG cc_start: 0.7442 (ttp-110) cc_final: 0.7008 (ttm170) REVERT: S 607 MET cc_start: 0.7254 (mtp) cc_final: 0.6660 (mtp) REVERT: S 647 LEU cc_start: 0.6515 (tp) cc_final: 0.6260 (tt) REVERT: S 733 GLU cc_start: 0.6885 (mm-30) cc_final: 0.6572 (mm-30) REVERT: S 767 ARG cc_start: 0.7246 (mtt180) cc_final: 0.6923 (mtt180) REVERT: S 769 ILE cc_start: 0.7255 (mt) cc_final: 0.7039 (mt) REVERT: S 772 PHE cc_start: 0.7773 (m-80) cc_final: 0.7546 (m-80) REVERT: S 792 ARG cc_start: 0.6269 (mtt180) cc_final: 0.5549 (mtt180) REVERT: S 801 MET cc_start: 0.5372 (mtp) cc_final: 0.4911 (mtt) REVERT: S 823 ARG cc_start: 0.6387 (mtp85) cc_final: 0.5950 (mtp180) REVERT: S 878 SER cc_start: 0.7900 (p) cc_final: 0.7674 (m) REVERT: S 891 ARG cc_start: 0.7197 (ttp80) cc_final: 0.6921 (tmm-80) REVERT: S 907 GLU cc_start: 0.8075 (tt0) cc_final: 0.7609 (tt0) REVERT: T 513 MET cc_start: 0.5388 (ttt) cc_final: 0.5094 (ttt) REVERT: T 607 MET cc_start: 0.2856 (mtp) cc_final: 0.2630 (mpp) REVERT: T 640 PHE cc_start: 0.5937 (m-80) cc_final: 0.4470 (m-80) REVERT: T 676 ARG cc_start: 0.5946 (mmt180) cc_final: 0.5565 (mmm-85) REVERT: T 677 HIS cc_start: 0.6799 (m-70) cc_final: 0.6535 (m-70) REVERT: T 682 MET cc_start: 0.6585 (ttm) cc_final: 0.6366 (ttm) REVERT: T 688 ARG cc_start: 0.7629 (mtm180) cc_final: 0.6810 (ttm110) REVERT: T 872 VAL cc_start: 0.5605 (m) cc_final: 0.5393 (t) REVERT: U 552 ASN cc_start: 0.7583 (p0) cc_final: 0.6998 (p0) REVERT: U 651 LYS cc_start: 0.8845 (mttt) cc_final: 0.8563 (mttt) REVERT: U 694 HIS cc_start: 0.7314 (m170) cc_final: 0.6791 (m170) REVERT: U 696 GLN cc_start: 0.8325 (mt0) cc_final: 0.7734 (mt0) REVERT: U 697 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7672 (mm-30) REVERT: U 761 MET cc_start: 0.4382 (ptm) cc_final: 0.3686 (tmm) REVERT: U 772 PHE cc_start: 0.7561 (m-10) cc_final: 0.6945 (m-10) REVERT: U 797 ASN cc_start: 0.7968 (p0) cc_final: 0.7731 (p0) REVERT: U 826 LYS cc_start: 0.8265 (tttt) cc_final: 0.7774 (tptp) REVERT: U 852 MET cc_start: 0.6845 (ttt) cc_final: 0.6617 (ttt) REVERT: U 855 LYS cc_start: 0.7591 (ttmm) cc_final: 0.7317 (ttmm) REVERT: U 868 PHE cc_start: 0.3359 (m-10) cc_final: 0.2925 (m-80) REVERT: P 45 ASN cc_start: 0.8544 (t0) cc_final: 0.7852 (t0) REVERT: P 144 LEU cc_start: 0.8704 (mp) cc_final: 0.8116 (mp) REVERT: P 156 ARG cc_start: 0.8089 (ttm170) cc_final: 0.7603 (tmm160) REVERT: P 242 TYR cc_start: 0.5737 (t80) cc_final: 0.4584 (t80) REVERT: P 282 TRP cc_start: 0.5744 (p-90) cc_final: 0.5428 (p90) REVERT: P 283 MET cc_start: 0.6858 (ttt) cc_final: 0.5957 (ttt) REVERT: P 290 LEU cc_start: 0.5816 (pt) cc_final: 0.5190 (mm) REVERT: P 294 ASP cc_start: 0.8005 (m-30) cc_final: 0.7653 (m-30) REVERT: P 300 ARG cc_start: 0.6920 (mtm110) cc_final: 0.6453 (mtm110) REVERT: P 305 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7695 (mm-30) REVERT: P 368 PHE cc_start: 0.6753 (m-80) cc_final: 0.5475 (m-80) REVERT: Q 117 TYR cc_start: 0.7287 (m-10) cc_final: 0.7029 (m-10) REVERT: Q 155 GLN cc_start: 0.8185 (tm-30) cc_final: 0.7846 (tm-30) REVERT: Q 161 ARG cc_start: 0.7877 (ptm-80) cc_final: 0.7463 (ptm-80) REVERT: Q 163 GLN cc_start: 0.8080 (tp40) cc_final: 0.7507 (tp40) REVERT: Q 180 GLU cc_start: 0.7083 (pp20) cc_final: 0.6594 (pp20) REVERT: Q 283 MET cc_start: 0.7038 (ttt) cc_final: 0.6483 (ttt) REVERT: Q 293 GLU cc_start: 0.8662 (tt0) cc_final: 0.8433 (tt0) REVERT: Q 294 ASP cc_start: 0.8041 (m-30) cc_final: 0.7753 (m-30) REVERT: Q 297 VAL cc_start: 0.7503 (t) cc_final: 0.7294 (p) outliers start: 71 outliers final: 35 residues processed: 803 average time/residue: 0.2429 time to fit residues: 302.5756 Evaluate side-chains 764 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 725 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 481 TYR Chi-restraints excluded: chain L residue 504 LEU Chi-restraints excluded: chain L residue 516 ASN Chi-restraints excluded: chain L residue 675 VAL Chi-restraints excluded: chain L residue 681 ILE Chi-restraints excluded: chain L residue 852 MET Chi-restraints excluded: chain L residue 878 SER Chi-restraints excluded: chain L residue 880 MET Chi-restraints excluded: chain M residue 684 VAL Chi-restraints excluded: chain M residue 875 THR Chi-restraints excluded: chain N residue 504 LEU Chi-restraints excluded: chain N residue 855 LYS Chi-restraints excluded: chain N residue 858 ILE Chi-restraints excluded: chain N residue 872 VAL Chi-restraints excluded: chain N residue 875 THR Chi-restraints excluded: chain O residue 653 LEU Chi-restraints excluded: chain O residue 678 GLN Chi-restraints excluded: chain O residue 680 LYS Chi-restraints excluded: chain O residue 684 VAL Chi-restraints excluded: chain O residue 738 LEU Chi-restraints excluded: chain O residue 826 LYS Chi-restraints excluded: chain O residue 851 PHE Chi-restraints excluded: chain O residue 867 VAL Chi-restraints excluded: chain R residue 669 SER Chi-restraints excluded: chain R residue 678 GLN Chi-restraints excluded: chain R residue 862 THR Chi-restraints excluded: chain R residue 867 VAL Chi-restraints excluded: chain S residue 591 THR Chi-restraints excluded: chain S residue 855 LYS Chi-restraints excluded: chain S residue 858 ILE Chi-restraints excluded: chain T residue 687 VAL Chi-restraints excluded: chain T residue 705 ILE Chi-restraints excluded: chain T residue 779 MET Chi-restraints excluded: chain T residue 875 THR Chi-restraints excluded: chain T residue 878 SER Chi-restraints excluded: chain U residue 667 GLU Chi-restraints excluded: chain P residue 226 ASP Chi-restraints excluded: chain P residue 266 LEU Chi-restraints excluded: chain Q residue 292 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 272 optimal weight: 1.9990 chunk 258 optimal weight: 5.9990 chunk 260 optimal weight: 0.2980 chunk 73 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 227 optimal weight: 0.9990 chunk 350 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 356 optimal weight: 0.0980 chunk 400 optimal weight: 0.0770 overall best weight: 0.4942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 656 GLN ** L 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 873 HIS ** N 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 615 GLN O 757 ASN R 615 GLN R 692 GLN ** R 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 611 ASN T 873 HIS U 873 HIS ** P 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.231959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.194386 restraints weight = 61965.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.200991 restraints weight = 34971.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.205822 restraints weight = 22949.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.208140 restraints weight = 16579.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.210925 restraints weight = 13474.389| |-----------------------------------------------------------------------------| r_work (final): 0.4653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4653 r_free = 0.4653 target_work(ls_wunit_k1) = 0.222 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4653 r_free = 0.4653 target_work(ls_wunit_k1) = 0.221 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5340 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34257 Z= 0.120 Angle : 0.634 9.845 46363 Z= 0.304 Chirality : 0.041 0.160 4870 Planarity : 0.005 0.063 6024 Dihedral : 5.159 59.574 4579 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.20 % Allowed : 9.11 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.13), residues: 4084 helix: 0.43 (0.14), residues: 1358 sheet: -0.76 (0.25), residues: 350 loop : -0.51 (0.12), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 866 TYR 0.014 0.001 TYR Q 269 PHE 0.028 0.002 PHE N 772 TRP 0.034 0.002 TRP L 698 HIS 0.008 0.001 HIS O 739 Details of bonding type rmsd covalent geometry : bond 0.00256 (34137) covalent geometry : angle 0.58268 (46183) hydrogen bonds : bond 0.03576 ( 1101) hydrogen bonds : angle 5.41749 ( 3024) metal coordination : bond 0.00513 ( 120) metal coordination : angle 4.04304 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 772 time to evaluate : 1.114 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 477 GLU cc_start: 0.7900 (tp30) cc_final: 0.7617 (tp30) REVERT: L 478 ARG cc_start: 0.8614 (ttt90) cc_final: 0.7952 (ttp80) REVERT: L 482 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8144 (mp0) REVERT: L 561 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6486 (mp0) REVERT: L 603 SER cc_start: 0.8777 (m) cc_final: 0.8470 (m) REVERT: L 651 LYS cc_start: 0.8878 (mttt) cc_final: 0.8457 (mttt) REVERT: L 671 THR cc_start: 0.8788 (m) cc_final: 0.8308 (m) REVERT: L 674 MET cc_start: 0.8371 (mtp) cc_final: 0.7962 (mtp) REVERT: L 683 TYR cc_start: 0.7194 (m-80) cc_final: 0.6985 (m-80) REVERT: L 772 PHE cc_start: 0.7820 (m-10) cc_final: 0.7196 (m-10) REVERT: L 781 ASP cc_start: 0.7714 (t0) cc_final: 0.7400 (t0) REVERT: L 790 ARG cc_start: 0.7075 (tpp80) cc_final: 0.6508 (mmm160) REVERT: L 860 TRP cc_start: 0.6680 (m-10) cc_final: 0.6473 (m-10) REVERT: L 878 SER cc_start: 0.7890 (OUTLIER) cc_final: 0.7588 (p) REVERT: M 640 PHE cc_start: 0.5820 (m-80) cc_final: 0.4361 (m-80) REVERT: M 671 THR cc_start: 0.7787 (m) cc_final: 0.7447 (p) REVERT: M 677 HIS cc_start: 0.7367 (m-70) cc_final: 0.7093 (m-70) REVERT: M 682 MET cc_start: 0.6341 (ttm) cc_final: 0.6049 (ptp) REVERT: M 737 LEU cc_start: 0.7593 (mt) cc_final: 0.7353 (mt) REVERT: M 767 ARG cc_start: 0.8216 (mtt180) cc_final: 0.7525 (mtt180) REVERT: M 771 ARG cc_start: 0.7307 (mtt180) cc_final: 0.7048 (mtt180) REVERT: M 897 VAL cc_start: 0.6569 (t) cc_final: 0.6336 (t) REVERT: M 899 ARG cc_start: 0.6425 (ttt90) cc_final: 0.6124 (ttt90) REVERT: N 581 TRP cc_start: 0.4723 (t60) cc_final: 0.4397 (t60) REVERT: N 584 TYR cc_start: 0.7531 (m-80) cc_final: 0.7069 (m-80) REVERT: N 597 ARG cc_start: 0.7459 (ttp-110) cc_final: 0.7155 (ttm170) REVERT: N 607 MET cc_start: 0.7231 (mtp) cc_final: 0.6872 (mtp) REVERT: N 639 LEU cc_start: 0.7296 (mp) cc_final: 0.6891 (mt) REVERT: N 647 LEU cc_start: 0.6206 (tp) cc_final: 0.5825 (tt) REVERT: N 669 SER cc_start: 0.8032 (m) cc_final: 0.7611 (p) REVERT: N 733 GLU cc_start: 0.6802 (mm-30) cc_final: 0.6515 (mm-30) REVERT: N 801 MET cc_start: 0.6135 (mtp) cc_final: 0.5671 (mtt) REVERT: N 880 MET cc_start: 0.7113 (pmm) cc_final: 0.6904 (pmm) REVERT: O 585 MET cc_start: 0.4899 (mmm) cc_final: 0.4535 (mmm) REVERT: O 607 MET cc_start: 0.5254 (mtp) cc_final: 0.4835 (mtp) REVERT: O 667 GLU cc_start: 0.6867 (mp0) cc_final: 0.6535 (mp0) REVERT: O 669 SER cc_start: 0.8541 (m) cc_final: 0.8196 (p) REVERT: O 676 ARG cc_start: 0.7941 (mmm160) cc_final: 0.7458 (mmm-85) REVERT: O 680 LYS cc_start: 0.6520 (OUTLIER) cc_final: 0.6283 (ptpp) REVERT: O 733 GLU cc_start: 0.5852 (mm-30) cc_final: 0.5482 (mm-30) REVERT: O 780 ILE cc_start: 0.3807 (mm) cc_final: 0.3474 (mt) REVERT: O 790 ARG cc_start: 0.7014 (tpp80) cc_final: 0.6648 (ttp80) REVERT: O 801 MET cc_start: 0.6769 (mtp) cc_final: 0.6558 (mtp) REVERT: O 907 GLU cc_start: 0.8212 (tt0) cc_final: 0.7918 (tp30) REVERT: R 607 MET cc_start: 0.5255 (mtp) cc_final: 0.4960 (mtp) REVERT: R 676 ARG cc_start: 0.7981 (mmm160) cc_final: 0.7482 (tpp80) REVERT: R 738 LEU cc_start: 0.6142 (tp) cc_final: 0.5783 (tt) REVERT: R 757 ASN cc_start: 0.7072 (m-40) cc_final: 0.6824 (m-40) REVERT: R 801 MET cc_start: 0.6442 (mtp) cc_final: 0.6208 (mtp) REVERT: R 866 ARG cc_start: 0.7153 (ttm110) cc_final: 0.6850 (ttm110) REVERT: R 887 ARG cc_start: 0.7408 (tmm-80) cc_final: 0.6822 (tmm-80) REVERT: S 513 MET cc_start: 0.7194 (ttt) cc_final: 0.6414 (ttt) REVERT: S 595 LEU cc_start: 0.7757 (pp) cc_final: 0.7422 (tt) REVERT: S 597 ARG cc_start: 0.7398 (ttp-110) cc_final: 0.7156 (ttp80) REVERT: S 607 MET cc_start: 0.7248 (mtp) cc_final: 0.6918 (mtp) REVERT: S 669 SER cc_start: 0.8207 (m) cc_final: 0.7809 (p) REVERT: S 733 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6859 (mm-30) REVERT: S 735 TYR cc_start: 0.7523 (t80) cc_final: 0.7215 (t80) REVERT: S 756 GLU cc_start: 0.6038 (tm-30) cc_final: 0.5835 (tm-30) REVERT: S 769 ILE cc_start: 0.7430 (mt) cc_final: 0.7161 (mt) REVERT: S 772 PHE cc_start: 0.7676 (m-80) cc_final: 0.7402 (m-80) REVERT: S 801 MET cc_start: 0.5414 (mtp) cc_final: 0.4889 (mtt) REVERT: S 823 ARG cc_start: 0.6790 (mtp85) cc_final: 0.6332 (mtp85) REVERT: T 513 MET cc_start: 0.5596 (ttt) cc_final: 0.5277 (ttt) REVERT: T 640 PHE cc_start: 0.6178 (m-80) cc_final: 0.4592 (m-80) REVERT: T 659 ARG cc_start: 0.5635 (ptp90) cc_final: 0.5330 (ptp90) REVERT: T 676 ARG cc_start: 0.6033 (mmt180) cc_final: 0.4982 (mmm-85) REVERT: T 677 HIS cc_start: 0.6902 (m-70) cc_final: 0.6621 (m-70) REVERT: T 688 ARG cc_start: 0.7709 (mtm180) cc_final: 0.6893 (mtm180) REVERT: T 756 GLU cc_start: 0.5604 (tm-30) cc_final: 0.5202 (tm-30) REVERT: T 885 ARG cc_start: 0.7076 (ttt180) cc_final: 0.6717 (mtp-110) REVERT: U 481 TYR cc_start: 0.8127 (t80) cc_final: 0.7619 (t80) REVERT: U 648 LEU cc_start: 0.8508 (tp) cc_final: 0.8204 (tp) REVERT: U 651 LYS cc_start: 0.8829 (mttt) cc_final: 0.8513 (mttt) REVERT: U 682 MET cc_start: 0.7008 (tmm) cc_final: 0.6805 (tmm) REVERT: U 683 TYR cc_start: 0.7716 (m-80) cc_final: 0.7407 (m-80) REVERT: U 694 HIS cc_start: 0.7496 (m170) cc_final: 0.6928 (m170) REVERT: U 696 GLN cc_start: 0.8328 (mt0) cc_final: 0.8057 (mt0) REVERT: U 761 MET cc_start: 0.4682 (ptm) cc_final: 0.4443 (ppp) REVERT: U 772 PHE cc_start: 0.7573 (m-10) cc_final: 0.6921 (m-10) REVERT: U 781 ASP cc_start: 0.7741 (t0) cc_final: 0.7434 (t0) REVERT: U 826 LYS cc_start: 0.8297 (tttt) cc_final: 0.7826 (tptp) REVERT: U 852 MET cc_start: 0.6828 (ttt) cc_final: 0.6600 (ttt) REVERT: U 855 LYS cc_start: 0.7570 (ttmm) cc_final: 0.7284 (ttmm) REVERT: U 868 PHE cc_start: 0.2985 (m-10) cc_final: 0.2532 (m-10) REVERT: P 45 ASN cc_start: 0.8433 (t0) cc_final: 0.8151 (t0) REVERT: P 47 ARG cc_start: 0.8180 (mmp80) cc_final: 0.7936 (mmp80) REVERT: P 144 LEU cc_start: 0.8658 (mp) cc_final: 0.8197 (mp) REVERT: P 156 ARG cc_start: 0.8104 (ttm170) cc_final: 0.7845 (tmm160) REVERT: P 242 TYR cc_start: 0.5608 (t80) cc_final: 0.4488 (t80) REVERT: P 266 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8452 (mt) REVERT: P 283 MET cc_start: 0.6916 (ttt) cc_final: 0.5878 (ttt) REVERT: P 300 ARG cc_start: 0.6833 (mtm110) cc_final: 0.6543 (mtm110) REVERT: P 303 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8259 (mp0) REVERT: P 305 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7819 (mm-30) REVERT: P 368 PHE cc_start: 0.6891 (m-80) cc_final: 0.5351 (m-80) REVERT: Q 117 TYR cc_start: 0.7370 (m-10) cc_final: 0.7160 (m-10) REVERT: Q 155 GLN cc_start: 0.8165 (tm-30) cc_final: 0.7835 (tm-30) REVERT: Q 161 ARG cc_start: 0.7947 (ptm-80) cc_final: 0.7389 (ptm-80) REVERT: Q 163 GLN cc_start: 0.8173 (tp40) cc_final: 0.7511 (tp40) REVERT: Q 165 LYS cc_start: 0.7529 (tptt) cc_final: 0.7060 (tptt) REVERT: Q 180 GLU cc_start: 0.7250 (pp20) cc_final: 0.6361 (pp20) REVERT: Q 283 MET cc_start: 0.7165 (ttt) cc_final: 0.6691 (ttt) REVERT: Q 290 LEU cc_start: 0.5143 (pt) cc_final: 0.4343 (mm) REVERT: Q 294 ASP cc_start: 0.8054 (m-30) cc_final: 0.7712 (m-30) REVERT: Q 297 VAL cc_start: 0.7520 (t) cc_final: 0.7306 (p) REVERT: Q 300 ARG cc_start: 0.7460 (ttm170) cc_final: 0.6958 (ttp80) outliers start: 80 outliers final: 44 residues processed: 804 average time/residue: 0.2316 time to fit residues: 290.9637 Evaluate side-chains 783 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 736 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 481 TYR Chi-restraints excluded: chain L residue 606 GLN Chi-restraints excluded: chain L residue 675 VAL Chi-restraints excluded: chain L residue 681 ILE Chi-restraints excluded: chain L residue 878 SER Chi-restraints excluded: chain L residue 880 MET Chi-restraints excluded: chain M residue 684 VAL Chi-restraints excluded: chain M residue 875 THR Chi-restraints excluded: chain N residue 475 THR Chi-restraints excluded: chain N residue 500 LEU Chi-restraints excluded: chain N residue 504 LEU Chi-restraints excluded: chain N residue 689 SER Chi-restraints excluded: chain N residue 737 LEU Chi-restraints excluded: chain N residue 761 MET Chi-restraints excluded: chain N residue 858 ILE Chi-restraints excluded: chain N residue 875 THR Chi-restraints excluded: chain O residue 657 VAL Chi-restraints excluded: chain O residue 680 LYS Chi-restraints excluded: chain O residue 757 ASN Chi-restraints excluded: chain O residue 826 LYS Chi-restraints excluded: chain O residue 830 VAL Chi-restraints excluded: chain O residue 851 PHE Chi-restraints excluded: chain O residue 867 VAL Chi-restraints excluded: chain R residue 538 THR Chi-restraints excluded: chain R residue 669 SER Chi-restraints excluded: chain R residue 680 LYS Chi-restraints excluded: chain R residue 710 CYS Chi-restraints excluded: chain R residue 723 LEU Chi-restraints excluded: chain R residue 862 THR Chi-restraints excluded: chain R residue 867 VAL Chi-restraints excluded: chain S residue 591 THR Chi-restraints excluded: chain S residue 650 LEU Chi-restraints excluded: chain S residue 713 LEU Chi-restraints excluded: chain S residue 855 LYS Chi-restraints excluded: chain S residue 858 ILE Chi-restraints excluded: chain S residue 875 THR Chi-restraints excluded: chain S residue 889 LEU Chi-restraints excluded: chain T residue 687 VAL Chi-restraints excluded: chain T residue 779 MET Chi-restraints excluded: chain U residue 641 ASP Chi-restraints excluded: chain U residue 738 LEU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain P residue 165 LYS Chi-restraints excluded: chain P residue 266 LEU Chi-restraints excluded: chain Q residue 62 HIS Chi-restraints excluded: chain Q residue 266 LEU Chi-restraints excluded: chain Q residue 292 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 57 optimal weight: 0.0050 chunk 300 optimal weight: 3.9990 chunk 232 optimal weight: 0.1980 chunk 253 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 260 optimal weight: 50.0000 chunk 85 optimal weight: 0.3980 chunk 230 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.231248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.192480 restraints weight = 61989.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.199212 restraints weight = 35397.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.203978 restraints weight = 23353.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.206376 restraints weight = 17052.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.209195 restraints weight = 13902.538| |-----------------------------------------------------------------------------| r_work (final): 0.4638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4638 r_free = 0.4638 target_work(ls_wunit_k1) = 0.225 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4637 r_free = 0.4637 target_work(ls_wunit_k1) = 0.225 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.4637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5398 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34257 Z= 0.114 Angle : 0.621 12.297 46363 Z= 0.298 Chirality : 0.041 0.159 4870 Planarity : 0.005 0.075 6024 Dihedral : 4.919 59.412 4578 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.20 % Allowed : 10.24 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.13), residues: 4084 helix: 0.69 (0.15), residues: 1359 sheet: -0.61 (0.26), residues: 350 loop : -0.34 (0.13), residues: 2375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG U 742 TYR 0.015 0.001 TYR U 735 PHE 0.027 0.002 PHE R 751 TRP 0.052 0.002 TRP L 698 HIS 0.007 0.001 HIS R 900 Details of bonding type rmsd covalent geometry : bond 0.00251 (34137) covalent geometry : angle 0.57966 (46183) hydrogen bonds : bond 0.03299 ( 1101) hydrogen bonds : angle 5.20743 ( 3024) metal coordination : bond 0.00467 ( 120) metal coordination : angle 3.63602 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 761 time to evaluate : 1.231 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 476 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.6788 (ptt-90) REVERT: L 478 ARG cc_start: 0.8576 (ttt90) cc_final: 0.7886 (ttp80) REVERT: L 482 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8118 (mp0) REVERT: L 561 GLU cc_start: 0.6867 (mt-10) cc_final: 0.6564 (mp0) REVERT: L 603 SER cc_start: 0.8774 (m) cc_final: 0.8501 (m) REVERT: L 640 PHE cc_start: 0.6803 (m-80) cc_final: 0.6560 (m-80) REVERT: L 647 LEU cc_start: 0.8748 (tp) cc_final: 0.8429 (tp) REVERT: L 651 LYS cc_start: 0.8839 (mttt) cc_final: 0.8418 (mttt) REVERT: L 671 THR cc_start: 0.8784 (m) cc_final: 0.8278 (m) REVERT: L 674 MET cc_start: 0.8384 (mtp) cc_final: 0.7986 (mtp) REVERT: L 761 MET cc_start: 0.4138 (ppp) cc_final: 0.3891 (tmm) REVERT: L 781 ASP cc_start: 0.7765 (t0) cc_final: 0.7479 (t0) REVERT: L 860 TRP cc_start: 0.6860 (m-10) cc_final: 0.6589 (m-10) REVERT: L 864 MET cc_start: 0.7130 (OUTLIER) cc_final: 0.6856 (ptp) REVERT: L 868 PHE cc_start: 0.3828 (m-10) cc_final: 0.2675 (m-80) REVERT: L 878 SER cc_start: 0.8009 (OUTLIER) cc_final: 0.7795 (p) REVERT: M 585 MET cc_start: -0.2643 (mmm) cc_final: -0.3109 (mmm) REVERT: M 671 THR cc_start: 0.7712 (m) cc_final: 0.7400 (t) REVERT: M 682 MET cc_start: 0.6296 (ttm) cc_final: 0.6050 (ttp) REVERT: M 767 ARG cc_start: 0.8230 (mtt180) cc_final: 0.7430 (mtt180) REVERT: M 771 ARG cc_start: 0.7277 (mtt180) cc_final: 0.6985 (mtt180) REVERT: M 852 MET cc_start: 0.6385 (ttt) cc_final: 0.6092 (ttt) REVERT: M 868 PHE cc_start: 0.7334 (OUTLIER) cc_final: 0.6989 (t80) REVERT: M 897 VAL cc_start: 0.6632 (t) cc_final: 0.6385 (t) REVERT: M 899 ARG cc_start: 0.6509 (ttt90) cc_final: 0.6176 (ttt90) REVERT: N 584 TYR cc_start: 0.7639 (m-80) cc_final: 0.7032 (m-80) REVERT: N 597 ARG cc_start: 0.7539 (ttp-110) cc_final: 0.7191 (ttm170) REVERT: N 607 MET cc_start: 0.7202 (mtp) cc_final: 0.6905 (mtp) REVERT: N 611 ASN cc_start: 0.5926 (OUTLIER) cc_final: 0.5688 (t0) REVERT: N 639 LEU cc_start: 0.7288 (mp) cc_final: 0.6927 (mt) REVERT: N 682 MET cc_start: 0.7130 (tmm) cc_final: 0.6591 (tmm) REVERT: N 733 GLU cc_start: 0.6827 (mm-30) cc_final: 0.6577 (mm-30) REVERT: N 757 ASN cc_start: 0.7287 (t0) cc_final: 0.7006 (m-40) REVERT: N 801 MET cc_start: 0.6143 (mtp) cc_final: 0.5662 (mtp) REVERT: N 823 ARG cc_start: 0.6521 (mtp85) cc_final: 0.6072 (mtp-110) REVERT: N 878 SER cc_start: 0.8045 (t) cc_final: 0.7448 (m) REVERT: N 880 MET cc_start: 0.7152 (pmm) cc_final: 0.6872 (pmm) REVERT: O 513 MET cc_start: 0.6962 (ppp) cc_final: 0.4428 (pmm) REVERT: O 607 MET cc_start: 0.5270 (mtp) cc_final: 0.4842 (mtp) REVERT: O 651 LYS cc_start: 0.8403 (mttt) cc_final: 0.8096 (mttt) REVERT: O 667 GLU cc_start: 0.6926 (mp0) cc_final: 0.6610 (mp0) REVERT: O 669 SER cc_start: 0.8526 (m) cc_final: 0.7982 (p) REVERT: O 676 ARG cc_start: 0.7930 (mmm160) cc_final: 0.7421 (mmm-85) REVERT: O 680 LYS cc_start: 0.6608 (OUTLIER) cc_final: 0.6383 (ptpp) REVERT: O 684 VAL cc_start: 0.8477 (OUTLIER) cc_final: 0.8226 (m) REVERT: O 733 GLU cc_start: 0.5901 (mm-30) cc_final: 0.5431 (mm-30) REVERT: O 738 LEU cc_start: 0.6153 (tp) cc_final: 0.5796 (tt) REVERT: O 768 ASP cc_start: 0.7189 (m-30) cc_final: 0.6918 (m-30) REVERT: O 790 ARG cc_start: 0.7078 (tpp80) cc_final: 0.6875 (mmm160) REVERT: O 907 GLU cc_start: 0.8200 (tt0) cc_final: 0.7863 (tp30) REVERT: R 607 MET cc_start: 0.5272 (mtp) cc_final: 0.4994 (mtp) REVERT: R 757 ASN cc_start: 0.7084 (m-40) cc_final: 0.6831 (m-40) REVERT: R 866 ARG cc_start: 0.7199 (ttm110) cc_final: 0.6881 (ttm110) REVERT: R 887 ARG cc_start: 0.7408 (tmm-80) cc_final: 0.6779 (tmm-80) REVERT: S 479 LEU cc_start: 0.8354 (tt) cc_final: 0.8025 (tt) REVERT: S 482 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7216 (mt-10) REVERT: S 513 MET cc_start: 0.7132 (ttt) cc_final: 0.6399 (ttt) REVERT: S 595 LEU cc_start: 0.7802 (pp) cc_final: 0.7444 (tp) REVERT: S 597 ARG cc_start: 0.7398 (ttp-110) cc_final: 0.7118 (ttm170) REVERT: S 607 MET cc_start: 0.7278 (mtp) cc_final: 0.6954 (mtp) REVERT: S 639 LEU cc_start: 0.7378 (mt) cc_final: 0.7007 (mt) REVERT: S 647 LEU cc_start: 0.6267 (tp) cc_final: 0.6051 (tt) REVERT: S 733 GLU cc_start: 0.7081 (mm-30) cc_final: 0.6832 (mm-30) REVERT: S 769 ILE cc_start: 0.7420 (mt) cc_final: 0.7154 (mt) REVERT: S 801 MET cc_start: 0.5553 (mtp) cc_final: 0.5024 (mtt) REVERT: S 823 ARG cc_start: 0.6787 (mtp85) cc_final: 0.6389 (mtp85) REVERT: S 878 SER cc_start: 0.8195 (OUTLIER) cc_final: 0.7489 (m) REVERT: T 513 MET cc_start: 0.5658 (ttt) cc_final: 0.5318 (ttt) REVERT: T 676 ARG cc_start: 0.6067 (mmt180) cc_final: 0.5748 (mmm-85) REVERT: T 677 HIS cc_start: 0.6996 (m-70) cc_final: 0.6639 (m-70) REVERT: T 688 ARG cc_start: 0.7560 (mtm180) cc_final: 0.7090 (mtm-85) REVERT: T 756 GLU cc_start: 0.5746 (tm-30) cc_final: 0.5319 (tm-30) REVERT: T 765 ASP cc_start: 0.6991 (t0) cc_final: 0.6525 (t0) REVERT: T 885 ARG cc_start: 0.7050 (ttt180) cc_final: 0.6690 (mtp-110) REVERT: T 899 ARG cc_start: 0.7348 (ttm110) cc_final: 0.6865 (ttm-80) REVERT: U 481 TYR cc_start: 0.8062 (t80) cc_final: 0.7700 (t80) REVERT: U 482 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8375 (mp0) REVERT: U 548 MET cc_start: 0.6387 (mtt) cc_final: 0.5974 (mtm) REVERT: U 607 MET cc_start: 0.8205 (mmp) cc_final: 0.7991 (mmt) REVERT: U 648 LEU cc_start: 0.8540 (tp) cc_final: 0.7566 (tp) REVERT: U 651 LYS cc_start: 0.8831 (mttt) cc_final: 0.8482 (mttt) REVERT: U 694 HIS cc_start: 0.7526 (m170) cc_final: 0.6962 (m170) REVERT: U 696 GLN cc_start: 0.8286 (mt0) cc_final: 0.8033 (mt0) REVERT: U 761 MET cc_start: 0.4678 (ptm) cc_final: 0.4295 (ppp) REVERT: U 772 PHE cc_start: 0.7561 (m-10) cc_final: 0.6930 (m-10) REVERT: U 781 ASP cc_start: 0.7813 (t0) cc_final: 0.7503 (t0) REVERT: U 826 LYS cc_start: 0.8377 (tttt) cc_final: 0.7912 (tptp) REVERT: U 855 LYS cc_start: 0.7613 (ttmm) cc_final: 0.7357 (ttmm) REVERT: U 874 TYR cc_start: 0.7105 (t80) cc_final: 0.6430 (t80) REVERT: P 45 ASN cc_start: 0.8468 (t0) cc_final: 0.8145 (t0) REVERT: P 47 ARG cc_start: 0.8119 (mmp80) cc_final: 0.7900 (mmp80) REVERT: P 158 ARG cc_start: 0.7242 (pmt170) cc_final: 0.6855 (pmt170) REVERT: P 159 LYS cc_start: 0.7340 (mptt) cc_final: 0.6844 (mptt) REVERT: P 242 TYR cc_start: 0.5627 (t80) cc_final: 0.4505 (t80) REVERT: P 282 TRP cc_start: 0.5337 (p-90) cc_final: 0.3911 (p-90) REVERT: P 283 MET cc_start: 0.6917 (ttt) cc_final: 0.5636 (ttt) REVERT: P 290 LEU cc_start: 0.5742 (pt) cc_final: 0.4181 (mt) REVERT: P 300 ARG cc_start: 0.6925 (mtm110) cc_final: 0.6561 (mtm110) REVERT: P 303 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8315 (mp0) REVERT: P 368 PHE cc_start: 0.6934 (m-80) cc_final: 0.5366 (m-80) REVERT: Q 155 GLN cc_start: 0.8195 (tm-30) cc_final: 0.7864 (tm-30) REVERT: Q 161 ARG cc_start: 0.7991 (ptm-80) cc_final: 0.7027 (mtp180) REVERT: Q 163 GLN cc_start: 0.8199 (tp40) cc_final: 0.7527 (tp40) REVERT: Q 283 MET cc_start: 0.7203 (ttt) cc_final: 0.6758 (ttt) REVERT: Q 290 LEU cc_start: 0.4989 (pt) cc_final: 0.3931 (mm) REVERT: Q 294 ASP cc_start: 0.8159 (m-30) cc_final: 0.7789 (m-30) REVERT: Q 300 ARG cc_start: 0.7536 (ttm170) cc_final: 0.7331 (ttp-110) REVERT: Q 302 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7375 (mm) outliers start: 80 outliers final: 49 residues processed: 790 average time/residue: 0.2379 time to fit residues: 294.4291 Evaluate side-chains 794 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 735 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 481 TYR Chi-restraints excluded: chain L residue 606 GLN Chi-restraints excluded: chain L residue 667 GLU Chi-restraints excluded: chain L residue 681 ILE Chi-restraints excluded: chain L residue 801 MET Chi-restraints excluded: chain L residue 864 MET Chi-restraints excluded: chain L residue 878 SER Chi-restraints excluded: chain L residue 880 MET Chi-restraints excluded: chain M residue 684 VAL Chi-restraints excluded: chain M residue 868 PHE Chi-restraints excluded: chain M residue 875 THR Chi-restraints excluded: chain N residue 500 LEU Chi-restraints excluded: chain N residue 504 LEU Chi-restraints excluded: chain N residue 611 ASN Chi-restraints excluded: chain N residue 650 LEU Chi-restraints excluded: chain N residue 737 LEU Chi-restraints excluded: chain N residue 761 MET Chi-restraints excluded: chain N residue 858 ILE Chi-restraints excluded: chain N residue 875 THR Chi-restraints excluded: chain O residue 657 VAL Chi-restraints excluded: chain O residue 680 LYS Chi-restraints excluded: chain O residue 684 VAL Chi-restraints excluded: chain O residue 826 LYS Chi-restraints excluded: chain O residue 830 VAL Chi-restraints excluded: chain O residue 851 PHE Chi-restraints excluded: chain R residue 538 THR Chi-restraints excluded: chain R residue 669 SER Chi-restraints excluded: chain R residue 678 GLN Chi-restraints excluded: chain R residue 710 CYS Chi-restraints excluded: chain R residue 723 LEU Chi-restraints excluded: chain R residue 819 LEU Chi-restraints excluded: chain R residue 862 THR Chi-restraints excluded: chain S residue 504 LEU Chi-restraints excluded: chain S residue 591 THR Chi-restraints excluded: chain S residue 855 LYS Chi-restraints excluded: chain S residue 858 ILE Chi-restraints excluded: chain S residue 875 THR Chi-restraints excluded: chain S residue 878 SER Chi-restraints excluded: chain S residue 889 LEU Chi-restraints excluded: chain T residue 687 VAL Chi-restraints excluded: chain T residue 779 MET Chi-restraints excluded: chain T residue 875 THR Chi-restraints excluded: chain T residue 878 SER Chi-restraints excluded: chain U residue 475 THR Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 641 ASP Chi-restraints excluded: chain U residue 738 LEU Chi-restraints excluded: chain U residue 878 SER Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain P residue 165 LYS Chi-restraints excluded: chain P residue 266 LEU Chi-restraints excluded: chain P residue 309 ILE Chi-restraints excluded: chain Q residue 62 HIS Chi-restraints excluded: chain Q residue 146 LEU Chi-restraints excluded: chain Q residue 266 LEU Chi-restraints excluded: chain Q residue 267 LEU Chi-restraints excluded: chain Q residue 292 LYS Chi-restraints excluded: chain Q residue 302 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 222 optimal weight: 0.8980 chunk 197 optimal weight: 0.9980 chunk 340 optimal weight: 0.9980 chunk 346 optimal weight: 6.9990 chunk 201 optimal weight: 0.7980 chunk 332 optimal weight: 0.9980 chunk 160 optimal weight: 0.5980 chunk 190 optimal weight: 0.1980 chunk 82 optimal weight: 0.2980 chunk 171 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 615 GLN O 739 HIS O 757 ASN ** R 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 886 GLN P 264 HIS Q 62 HIS Q 220 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4878 r_free = 0.4878 target = 0.231507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.194023 restraints weight = 61546.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.200417 restraints weight = 35057.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.204903 restraints weight = 23243.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.207520 restraints weight = 16979.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.210286 restraints weight = 13697.110| |-----------------------------------------------------------------------------| r_work (final): 0.4642 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4642 r_free = 0.4642 target_work(ls_wunit_k1) = 0.225 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4642 r_free = 0.4642 target_work(ls_wunit_k1) = 0.225 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.4642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5412 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34257 Z= 0.117 Angle : 0.615 13.633 46363 Z= 0.295 Chirality : 0.041 0.217 4870 Planarity : 0.004 0.059 6024 Dihedral : 4.756 56.240 4578 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.26 % Allowed : 12.20 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.13), residues: 4084 helix: 0.80 (0.15), residues: 1362 sheet: -0.50 (0.26), residues: 350 loop : -0.25 (0.13), residues: 2372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 882 TYR 0.015 0.001 TYR U 735 PHE 0.026 0.002 PHE O 755 TRP 0.060 0.002 TRP L 698 HIS 0.008 0.001 HIS L 694 Details of bonding type rmsd covalent geometry : bond 0.00257 (34137) covalent geometry : angle 0.57711 (46183) hydrogen bonds : bond 0.03206 ( 1101) hydrogen bonds : angle 5.10449 ( 3024) metal coordination : bond 0.00461 ( 120) metal coordination : angle 3.44453 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 771 time to evaluate : 1.231 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 476 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6878 (ptt-90) REVERT: L 482 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8155 (mp0) REVERT: L 505 GLU cc_start: 0.6260 (pp20) cc_final: 0.6001 (pp20) REVERT: L 561 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6590 (mp0) REVERT: L 640 PHE cc_start: 0.6804 (m-80) cc_final: 0.6518 (m-80) REVERT: L 647 LEU cc_start: 0.8700 (tp) cc_final: 0.8300 (tp) REVERT: L 651 LYS cc_start: 0.8816 (mttt) cc_final: 0.8381 (mttt) REVERT: L 671 THR cc_start: 0.8683 (m) cc_final: 0.8170 (m) REVERT: L 674 MET cc_start: 0.8331 (mtp) cc_final: 0.7962 (mtp) REVERT: L 761 MET cc_start: 0.4311 (ppp) cc_final: 0.3682 (tmm) REVERT: L 781 ASP cc_start: 0.7729 (t0) cc_final: 0.7334 (t0) REVERT: L 790 ARG cc_start: 0.6846 (tpp80) cc_final: 0.6534 (tpp80) REVERT: L 847 HIS cc_start: 0.6217 (m-70) cc_final: 0.5654 (m-70) REVERT: L 864 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6977 (ptp) REVERT: L 868 PHE cc_start: 0.4081 (m-10) cc_final: 0.2761 (m-10) REVERT: L 878 SER cc_start: 0.7982 (OUTLIER) cc_final: 0.7607 (p) REVERT: M 585 MET cc_start: -0.2617 (mmm) cc_final: -0.3070 (mmm) REVERT: M 671 THR cc_start: 0.7747 (m) cc_final: 0.7466 (t) REVERT: M 682 MET cc_start: 0.6240 (ttm) cc_final: 0.6020 (ttm) REVERT: M 767 ARG cc_start: 0.8174 (mtt180) cc_final: 0.7376 (mtt180) REVERT: M 771 ARG cc_start: 0.7231 (mtt180) cc_final: 0.6928 (mtt180) REVERT: M 852 MET cc_start: 0.6397 (ttt) cc_final: 0.6099 (ttt) REVERT: M 868 PHE cc_start: 0.7562 (OUTLIER) cc_final: 0.7056 (t80) REVERT: M 897 VAL cc_start: 0.6656 (t) cc_final: 0.6421 (t) REVERT: M 899 ARG cc_start: 0.6542 (ttt90) cc_final: 0.6200 (ttt90) REVERT: N 584 TYR cc_start: 0.7691 (m-80) cc_final: 0.7146 (m-80) REVERT: N 596 ARG cc_start: 0.7385 (ptt-90) cc_final: 0.6955 (ptt-90) REVERT: N 597 ARG cc_start: 0.7604 (ttp-110) cc_final: 0.7219 (ttm170) REVERT: N 611 ASN cc_start: 0.5907 (OUTLIER) cc_final: 0.5688 (t0) REVERT: N 639 LEU cc_start: 0.7282 (mp) cc_final: 0.6913 (mt) REVERT: N 647 LEU cc_start: 0.5887 (tp) cc_final: 0.5211 (tt) REVERT: N 669 SER cc_start: 0.8026 (m) cc_final: 0.7598 (p) REVERT: N 682 MET cc_start: 0.7090 (tmm) cc_final: 0.6623 (tmm) REVERT: N 756 GLU cc_start: 0.6432 (tm-30) cc_final: 0.6169 (tm-30) REVERT: N 757 ASN cc_start: 0.7465 (t0) cc_final: 0.7052 (m-40) REVERT: N 801 MET cc_start: 0.6200 (mtp) cc_final: 0.5697 (mtt) REVERT: N 878 SER cc_start: 0.8065 (t) cc_final: 0.7438 (m) REVERT: N 880 MET cc_start: 0.7283 (pmm) cc_final: 0.6936 (pmm) REVERT: O 513 MET cc_start: 0.7150 (ppp) cc_final: 0.6934 (tmm) REVERT: O 607 MET cc_start: 0.5277 (mtp) cc_final: 0.4870 (mtp) REVERT: O 651 LYS cc_start: 0.8383 (mttt) cc_final: 0.8104 (mmtt) REVERT: O 667 GLU cc_start: 0.6994 (mp0) cc_final: 0.6713 (mp0) REVERT: O 669 SER cc_start: 0.8593 (m) cc_final: 0.8023 (p) REVERT: O 676 ARG cc_start: 0.7947 (mmm160) cc_final: 0.7503 (mmm-85) REVERT: O 680 LYS cc_start: 0.6483 (OUTLIER) cc_final: 0.6252 (ptpp) REVERT: O 684 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8270 (m) REVERT: O 698 TRP cc_start: 0.6574 (m-10) cc_final: 0.6289 (m-10) REVERT: O 738 LEU cc_start: 0.6173 (tp) cc_final: 0.5859 (tt) REVERT: O 768 ASP cc_start: 0.7207 (m-30) cc_final: 0.6941 (m-30) REVERT: O 780 ILE cc_start: 0.4384 (mm) cc_final: 0.4052 (mt) REVERT: O 801 MET cc_start: 0.6762 (mtp) cc_final: 0.6530 (mtp) REVERT: O 907 GLU cc_start: 0.8207 (tt0) cc_final: 0.7775 (tp30) REVERT: R 513 MET cc_start: 0.6213 (ppp) cc_final: 0.3535 (pmm) REVERT: R 607 MET cc_start: 0.5244 (mtp) cc_final: 0.4993 (mtp) REVERT: R 676 ARG cc_start: 0.8073 (mmm160) cc_final: 0.7732 (mmm160) REVERT: R 708 SER cc_start: 0.7975 (t) cc_final: 0.7705 (p) REVERT: R 757 ASN cc_start: 0.7246 (m-40) cc_final: 0.6796 (m-40) REVERT: R 866 ARG cc_start: 0.7332 (ttm110) cc_final: 0.7001 (ttm110) REVERT: R 887 ARG cc_start: 0.7449 (tmm-80) cc_final: 0.6907 (tmm-80) REVERT: S 513 MET cc_start: 0.7066 (ttt) cc_final: 0.6430 (ttt) REVERT: S 595 LEU cc_start: 0.7823 (pp) cc_final: 0.7475 (tp) REVERT: S 597 ARG cc_start: 0.7420 (ttp-110) cc_final: 0.7185 (ttm170) REVERT: S 606 GLN cc_start: 0.7811 (tp40) cc_final: 0.7567 (tp40) REVERT: S 639 LEU cc_start: 0.7431 (mt) cc_final: 0.6972 (mt) REVERT: S 647 LEU cc_start: 0.6234 (tp) cc_final: 0.6023 (tt) REVERT: S 669 SER cc_start: 0.8174 (m) cc_final: 0.7845 (p) REVERT: S 733 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6893 (mm-30) REVERT: S 769 ILE cc_start: 0.7493 (mt) cc_final: 0.7238 (mt) REVERT: S 801 MET cc_start: 0.5814 (mtp) cc_final: 0.5288 (mtt) REVERT: S 831 ARG cc_start: 0.5942 (ptp-170) cc_final: 0.5709 (ptp-170) REVERT: S 878 SER cc_start: 0.8196 (t) cc_final: 0.7646 (m) REVERT: S 891 ARG cc_start: 0.7179 (ttp80) cc_final: 0.6971 (tmm160) REVERT: T 513 MET cc_start: 0.5627 (ttt) cc_final: 0.5276 (ttt) REVERT: T 661 ILE cc_start: 0.7653 (mm) cc_final: 0.7182 (mm) REVERT: T 676 ARG cc_start: 0.6221 (mmt180) cc_final: 0.5628 (mmm-85) REVERT: T 677 HIS cc_start: 0.7118 (m-70) cc_final: 0.6764 (m-70) REVERT: T 688 ARG cc_start: 0.7624 (mtm180) cc_final: 0.7155 (mtm180) REVERT: T 756 GLU cc_start: 0.5833 (tm-30) cc_final: 0.4050 (tm-30) REVERT: T 765 ASP cc_start: 0.6937 (t0) cc_final: 0.6424 (t0) REVERT: T 899 ARG cc_start: 0.7355 (ttm110) cc_final: 0.6938 (ttm-80) REVERT: U 478 ARG cc_start: 0.8807 (ptt90) cc_final: 0.8565 (ptt-90) REVERT: U 481 TYR cc_start: 0.8037 (t80) cc_final: 0.7727 (t80) REVERT: U 482 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8374 (mp0) REVERT: U 607 MET cc_start: 0.8214 (mmp) cc_final: 0.8010 (mmt) REVERT: U 648 LEU cc_start: 0.8554 (tp) cc_final: 0.8295 (tp) REVERT: U 651 LYS cc_start: 0.8801 (mttt) cc_final: 0.8435 (mttt) REVERT: U 682 MET cc_start: 0.7001 (tmm) cc_final: 0.6741 (tmm) REVERT: U 694 HIS cc_start: 0.7539 (m170) cc_final: 0.7013 (m170) REVERT: U 696 GLN cc_start: 0.8249 (mt0) cc_final: 0.7986 (mt0) REVERT: U 772 PHE cc_start: 0.7560 (m-10) cc_final: 0.6936 (m-10) REVERT: U 781 ASP cc_start: 0.7786 (t0) cc_final: 0.7461 (t0) REVERT: U 797 ASN cc_start: 0.8340 (p0) cc_final: 0.8135 (p0) REVERT: U 826 LYS cc_start: 0.8430 (tttt) cc_final: 0.7995 (tptp) REVERT: U 855 LYS cc_start: 0.7651 (ttmm) cc_final: 0.7373 (ttmm) REVERT: P 45 ASN cc_start: 0.8437 (t0) cc_final: 0.8129 (t0) REVERT: P 47 ARG cc_start: 0.8080 (mmp80) cc_final: 0.7866 (mmp80) REVERT: P 79 LYS cc_start: 0.8831 (ptmm) cc_final: 0.8576 (ptpp) REVERT: P 158 ARG cc_start: 0.7249 (pmt170) cc_final: 0.6820 (pmt170) REVERT: P 159 LYS cc_start: 0.7325 (mptt) cc_final: 0.6734 (mptt) REVERT: P 179 PHE cc_start: 0.8228 (m-80) cc_final: 0.7799 (m-80) REVERT: P 242 TYR cc_start: 0.5566 (t80) cc_final: 0.4392 (t80) REVERT: P 266 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8487 (mt) REVERT: P 283 MET cc_start: 0.6902 (ttt) cc_final: 0.5840 (ttt) REVERT: P 290 LEU cc_start: 0.5434 (pt) cc_final: 0.4267 (mm) REVERT: P 368 PHE cc_start: 0.6948 (m-80) cc_final: 0.5407 (m-80) REVERT: Q 121 CYS cc_start: 0.6204 (OUTLIER) cc_final: 0.5891 (m) REVERT: Q 155 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7911 (tm-30) REVERT: Q 163 GLN cc_start: 0.8202 (tp40) cc_final: 0.7533 (tp40) REVERT: Q 180 GLU cc_start: 0.7424 (pp20) cc_final: 0.6753 (pp20) REVERT: Q 283 MET cc_start: 0.7140 (ttt) cc_final: 0.6759 (ttt) REVERT: Q 290 LEU cc_start: 0.5219 (pt) cc_final: 0.4203 (mm) REVERT: Q 294 ASP cc_start: 0.8102 (m-30) cc_final: 0.7827 (m-30) REVERT: Q 300 ARG cc_start: 0.7585 (ttm170) cc_final: 0.7287 (ttp-110) REVERT: Q 302 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7505 (mm) outliers start: 82 outliers final: 47 residues processed: 803 average time/residue: 0.2200 time to fit residues: 276.9912 Evaluate side-chains 793 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 735 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 481 TYR Chi-restraints excluded: chain L residue 606 GLN Chi-restraints excluded: chain L residue 608 PHE Chi-restraints excluded: chain L residue 641 ASP Chi-restraints excluded: chain L residue 667 GLU Chi-restraints excluded: chain L residue 681 ILE Chi-restraints excluded: chain L residue 801 MET Chi-restraints excluded: chain L residue 864 MET Chi-restraints excluded: chain L residue 878 SER Chi-restraints excluded: chain L residue 880 MET Chi-restraints excluded: chain M residue 684 VAL Chi-restraints excluded: chain M residue 868 PHE Chi-restraints excluded: chain M residue 875 THR Chi-restraints excluded: chain N residue 475 THR Chi-restraints excluded: chain N residue 500 LEU Chi-restraints excluded: chain N residue 504 LEU Chi-restraints excluded: chain N residue 611 ASN Chi-restraints excluded: chain N residue 678 GLN Chi-restraints excluded: chain N residue 737 LEU Chi-restraints excluded: chain N residue 761 MET Chi-restraints excluded: chain N residue 858 ILE Chi-restraints excluded: chain O residue 657 VAL Chi-restraints excluded: chain O residue 678 GLN Chi-restraints excluded: chain O residue 680 LYS Chi-restraints excluded: chain O residue 684 VAL Chi-restraints excluded: chain O residue 826 LYS Chi-restraints excluded: chain O residue 830 VAL Chi-restraints excluded: chain R residue 538 THR Chi-restraints excluded: chain R residue 669 SER Chi-restraints excluded: chain R residue 710 CYS Chi-restraints excluded: chain R residue 723 LEU Chi-restraints excluded: chain R residue 862 THR Chi-restraints excluded: chain S residue 504 LEU Chi-restraints excluded: chain S residue 548 MET Chi-restraints excluded: chain S residue 761 MET Chi-restraints excluded: chain S residue 855 LYS Chi-restraints excluded: chain S residue 858 ILE Chi-restraints excluded: chain S residue 875 THR Chi-restraints excluded: chain T residue 687 VAL Chi-restraints excluded: chain T residue 868 PHE Chi-restraints excluded: chain T residue 872 VAL Chi-restraints excluded: chain T residue 875 THR Chi-restraints excluded: chain T residue 878 SER Chi-restraints excluded: chain U residue 475 THR Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 641 ASP Chi-restraints excluded: chain U residue 852 MET Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain P residue 165 LYS Chi-restraints excluded: chain P residue 266 LEU Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain Q residue 62 HIS Chi-restraints excluded: chain Q residue 121 CYS Chi-restraints excluded: chain Q residue 146 LEU Chi-restraints excluded: chain Q residue 266 LEU Chi-restraints excluded: chain Q residue 292 LYS Chi-restraints excluded: chain Q residue 302 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 149 optimal weight: 0.5980 chunk 379 optimal weight: 8.9990 chunk 258 optimal weight: 4.9990 chunk 295 optimal weight: 0.7980 chunk 307 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 223 optimal weight: 3.9990 chunk 336 optimal weight: 0.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 776 ASN M 694 HIS N 611 ASN O 612 ASN R 612 ASN R 739 HIS ** R 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 678 GLN S 821 HIS ** P 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 268 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.226638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.181857 restraints weight = 61381.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.187935 restraints weight = 36983.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.192229 restraints weight = 25855.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.195253 restraints weight = 19861.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.196916 restraints weight = 16443.283| |-----------------------------------------------------------------------------| r_work (final): 0.4465 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4463 r_free = 0.4463 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4463 r_free = 0.4463 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.4463 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5830 moved from start: 0.5447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 34257 Z= 0.237 Angle : 0.764 13.251 46363 Z= 0.373 Chirality : 0.044 0.185 4870 Planarity : 0.006 0.116 6024 Dihedral : 5.180 49.878 4576 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.64 % Allowed : 13.71 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.13), residues: 4084 helix: 0.29 (0.14), residues: 1380 sheet: -0.74 (0.26), residues: 352 loop : -0.36 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Q 322 TYR 0.032 0.002 TYR M 683 PHE 0.038 0.003 PHE O 755 TRP 0.045 0.003 TRP P 335 HIS 0.057 0.002 HIS Q 62 Details of bonding type rmsd covalent geometry : bond 0.00501 (34137) covalent geometry : angle 0.70615 (46183) hydrogen bonds : bond 0.04532 ( 1101) hydrogen bonds : angle 5.84251 ( 3024) metal coordination : bond 0.00798 ( 120) metal coordination : angle 4.73826 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 788 time to evaluate : 0.879 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 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 REVERT: L 476 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6952 (ptt-90) REVERT: L 479 LEU cc_start: 0.8840 (mt) cc_final: 0.8036 (mt) REVERT: L 482 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8331 (mp0) REVERT: L 556 ARG cc_start: 0.7066 (mtt-85) cc_final: 0.6454 (mtt-85) REVERT: L 561 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6830 (mp0) REVERT: L 585 MET cc_start: 0.6775 (tpt) cc_final: 0.6399 (tmm) REVERT: L 606 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7810 (pm20) REVERT: L 607 MET cc_start: 0.8599 (mmt) cc_final: 0.8241 (mmt) REVERT: L 640 PHE cc_start: 0.7522 (m-80) cc_final: 0.7166 (m-80) REVERT: L 651 LYS cc_start: 0.8752 (mttt) cc_final: 0.8257 (mttt) REVERT: L 671 THR cc_start: 0.8632 (m) cc_final: 0.8084 (m) REVERT: L 674 MET cc_start: 0.8379 (mtp) cc_final: 0.7973 (mtp) REVERT: L 761 MET cc_start: 0.4465 (ppp) cc_final: 0.3587 (tmm) REVERT: L 765 ASP cc_start: 0.6679 (t70) cc_final: 0.6071 (t0) REVERT: L 776 ASN cc_start: 0.7577 (OUTLIER) cc_final: 0.7355 (p0) REVERT: L 790 ARG cc_start: 0.6985 (tpp80) cc_final: 0.6750 (mmm160) REVERT: L 868 PHE cc_start: 0.4718 (m-10) cc_final: 0.3232 (m-10) REVERT: L 882 ARG cc_start: 0.6928 (ptt90) cc_final: 0.6689 (ttt90) REVERT: L 886 GLN cc_start: 0.7679 (mt0) cc_final: 0.7229 (mt0) REVERT: M 585 MET cc_start: -0.2941 (mmm) cc_final: -0.3305 (mmm) REVERT: M 852 MET cc_start: 0.6647 (ttt) cc_final: 0.6274 (ttt) REVERT: M 882 ARG cc_start: 0.7621 (tpp-160) cc_final: 0.7272 (mmm-85) REVERT: M 889 LEU cc_start: 0.7808 (mt) cc_final: 0.7521 (mt) REVERT: M 899 ARG cc_start: 0.6731 (ttt90) cc_final: 0.6276 (ttt90) REVERT: N 477 GLU cc_start: 0.8266 (mt-10) cc_final: 0.8054 (mt-10) REVERT: N 584 TYR cc_start: 0.8025 (m-80) cc_final: 0.7745 (m-80) REVERT: N 596 ARG cc_start: 0.7530 (ptt-90) cc_final: 0.7208 (ptt-90) REVERT: N 597 ARG cc_start: 0.7650 (ttp-110) cc_final: 0.7210 (ttm170) REVERT: N 647 LEU cc_start: 0.5940 (tp) cc_final: 0.5374 (tp) REVERT: N 669 SER cc_start: 0.8115 (m) cc_final: 0.7798 (p) REVERT: N 682 MET cc_start: 0.7374 (tmm) cc_final: 0.6969 (tmm) REVERT: N 684 VAL cc_start: 0.7481 (OUTLIER) cc_final: 0.6595 (p) REVERT: N 733 GLU cc_start: 0.6628 (mm-30) cc_final: 0.6323 (mm-30) REVERT: N 757 ASN cc_start: 0.7547 (t0) cc_final: 0.7239 (m-40) REVERT: N 801 MET cc_start: 0.6706 (mtp) cc_final: 0.6235 (mtp) REVERT: N 823 ARG cc_start: 0.6853 (mtp-110) cc_final: 0.6356 (ptm-80) REVERT: O 513 MET cc_start: 0.7421 (ppp) cc_final: 0.6809 (ppp) REVERT: O 585 MET cc_start: 0.5227 (mmm) cc_final: 0.4908 (mmm) REVERT: O 607 MET cc_start: 0.5262 (mtp) cc_final: 0.4883 (mtp) REVERT: O 675 VAL cc_start: 0.8500 (t) cc_final: 0.8226 (p) REVERT: O 676 ARG cc_start: 0.8195 (mmm160) cc_final: 0.7735 (tpp80) REVERT: O 684 VAL cc_start: 0.8709 (OUTLIER) cc_final: 0.8426 (m) REVERT: O 729 ARG cc_start: 0.5794 (OUTLIER) cc_final: 0.5420 (mmt180) REVERT: O 733 GLU cc_start: 0.6267 (mm-30) cc_final: 0.5945 (mm-30) REVERT: O 738 LEU cc_start: 0.6238 (tp) cc_final: 0.5795 (tt) REVERT: O 864 MET cc_start: 0.6876 (mtt) cc_final: 0.6328 (mtt) REVERT: R 513 MET cc_start: 0.6386 (ppp) cc_final: 0.4011 (pmm) REVERT: R 607 MET cc_start: 0.5314 (mtp) cc_final: 0.5047 (mtp) REVERT: R 667 GLU cc_start: 0.7014 (mp0) cc_final: 0.6808 (mp0) REVERT: R 676 ARG cc_start: 0.8179 (mmm160) cc_final: 0.7574 (tpp80) REVERT: R 708 SER cc_start: 0.8205 (t) cc_final: 0.7921 (p) REVERT: R 846 GLN cc_start: 0.6560 (tm-30) cc_final: 0.6173 (tm-30) REVERT: R 887 ARG cc_start: 0.7422 (tmm-80) cc_final: 0.7098 (tmm-80) REVERT: R 888 LEU cc_start: 0.8493 (tt) cc_final: 0.8058 (tp) REVERT: S 482 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7514 (mt-10) REVERT: S 513 MET cc_start: 0.7107 (ttt) cc_final: 0.6495 (ttt) REVERT: S 597 ARG cc_start: 0.7587 (ttp-110) cc_final: 0.7179 (ttm170) REVERT: S 606 GLN cc_start: 0.7812 (tp40) cc_final: 0.7609 (tp40) REVERT: S 647 LEU cc_start: 0.6279 (tp) cc_final: 0.6066 (tt) REVERT: S 684 VAL cc_start: 0.8084 (OUTLIER) cc_final: 0.7489 (p) REVERT: S 688 ARG cc_start: 0.7697 (mtm180) cc_final: 0.7460 (mtm180) REVERT: S 733 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6916 (mm-30) REVERT: S 769 ILE cc_start: 0.7689 (mt) cc_final: 0.7484 (mt) REVERT: S 801 MET cc_start: 0.6297 (mtp) cc_final: 0.5644 (mtt) REVERT: T 513 MET cc_start: 0.6085 (ttt) cc_final: 0.5799 (ttt) REVERT: T 671 THR cc_start: 0.7478 (m) cc_final: 0.7259 (t) REVERT: T 677 HIS cc_start: 0.7311 (m-70) cc_final: 0.6939 (m-70) REVERT: T 682 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.6858 (ppp) REVERT: T 761 MET cc_start: 0.4429 (ptm) cc_final: 0.3874 (ptm) REVERT: T 765 ASP cc_start: 0.7124 (t0) cc_final: 0.6614 (t0) REVERT: T 880 MET cc_start: 0.7333 (mtp) cc_final: 0.7068 (mtt) REVERT: T 891 ARG cc_start: 0.6643 (ttp80) cc_final: 0.6200 (tmm-80) REVERT: U 478 ARG cc_start: 0.8791 (ptt90) cc_final: 0.8476 (ptt-90) REVERT: U 481 TYR cc_start: 0.8082 (t80) cc_final: 0.7772 (t80) REVERT: U 482 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8399 (mp0) REVERT: U 565 LEU cc_start: 0.8622 (tp) cc_final: 0.8238 (mm) REVERT: U 648 LEU cc_start: 0.8519 (tp) cc_final: 0.8270 (tp) REVERT: U 651 LYS cc_start: 0.8698 (mttt) cc_final: 0.8291 (mttt) REVERT: U 693 LYS cc_start: 0.7621 (tttt) cc_final: 0.7347 (tttt) REVERT: U 694 HIS cc_start: 0.7461 (m170) cc_final: 0.6896 (m170) REVERT: U 696 GLN cc_start: 0.8260 (mt0) cc_final: 0.7716 (mt0) REVERT: U 697 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7781 (mm-30) REVERT: U 772 PHE cc_start: 0.7814 (m-10) cc_final: 0.7169 (m-10) REVERT: U 826 LYS cc_start: 0.8535 (tttt) cc_final: 0.8012 (tptp) REVERT: P 79 LYS cc_start: 0.8855 (ptmm) cc_final: 0.8647 (ptpp) REVERT: P 179 PHE cc_start: 0.8199 (m-80) cc_final: 0.7897 (m-80) REVERT: P 206 LEU cc_start: 0.8299 (mp) cc_final: 0.8029 (tp) REVERT: P 242 TYR cc_start: 0.5886 (t80) cc_final: 0.4905 (t80) REVERT: P 282 TRP cc_start: 0.5973 (p-90) cc_final: 0.4870 (p-90) REVERT: P 283 MET cc_start: 0.6975 (ttt) cc_final: 0.5827 (ttt) REVERT: P 303 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8305 (mp0) REVERT: P 368 PHE cc_start: 0.7057 (m-80) cc_final: 0.5519 (m-80) REVERT: Q 121 CYS cc_start: 0.6270 (OUTLIER) cc_final: 0.5954 (m) REVERT: Q 161 ARG cc_start: 0.8122 (ptm-80) cc_final: 0.7315 (mtm-85) REVERT: Q 180 GLU cc_start: 0.7503 (pp20) cc_final: 0.6955 (pp20) REVERT: Q 290 LEU cc_start: 0.6052 (pt) cc_final: 0.5024 (mt) REVERT: Q 293 GLU cc_start: 0.8667 (tt0) cc_final: 0.8398 (tm-30) REVERT: Q 368 PHE cc_start: 0.7288 (m-80) cc_final: 0.6701 (m-80) outliers start: 96 outliers final: 58 residues processed: 829 average time/residue: 0.2133 time to fit residues: 278.5387 Evaluate side-chains 823 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 755 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 481 TYR Chi-restraints excluded: chain L residue 510 VAL Chi-restraints excluded: chain L residue 603 SER Chi-restraints excluded: chain L residue 606 GLN Chi-restraints excluded: chain L residue 641 ASP Chi-restraints excluded: chain L residue 667 GLU Chi-restraints excluded: chain L residue 681 ILE Chi-restraints excluded: chain L residue 776 ASN Chi-restraints excluded: chain L residue 801 MET Chi-restraints excluded: chain L residue 852 MET Chi-restraints excluded: chain L residue 880 MET Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 684 VAL Chi-restraints excluded: chain M residue 737 LEU Chi-restraints excluded: chain M residue 875 THR Chi-restraints excluded: chain M residue 905 LEU Chi-restraints excluded: chain N residue 475 THR Chi-restraints excluded: chain N residue 504 LEU Chi-restraints excluded: chain N residue 585 MET Chi-restraints excluded: chain N residue 595 LEU Chi-restraints excluded: chain N residue 607 MET Chi-restraints excluded: chain N residue 643 ILE Chi-restraints excluded: chain N residue 678 GLN Chi-restraints excluded: chain N residue 684 VAL Chi-restraints excluded: chain N residue 713 LEU Chi-restraints excluded: chain N residue 737 LEU Chi-restraints excluded: chain N residue 855 LYS Chi-restraints excluded: chain N residue 858 ILE Chi-restraints excluded: chain O residue 678 GLN Chi-restraints excluded: chain O residue 684 VAL Chi-restraints excluded: chain O residue 729 ARG Chi-restraints excluded: chain O residue 826 LYS Chi-restraints excluded: chain O residue 905 LEU Chi-restraints excluded: chain R residue 538 THR Chi-restraints excluded: chain R residue 657 VAL Chi-restraints excluded: chain R residue 669 SER Chi-restraints excluded: chain S residue 504 LEU Chi-restraints excluded: chain S residue 684 VAL Chi-restraints excluded: chain S residue 761 MET Chi-restraints excluded: chain S residue 824 ILE Chi-restraints excluded: chain S residue 855 LYS Chi-restraints excluded: chain S residue 858 ILE Chi-restraints excluded: chain S residue 875 THR Chi-restraints excluded: chain S residue 880 MET Chi-restraints excluded: chain T residue 607 MET Chi-restraints excluded: chain T residue 682 MET Chi-restraints excluded: chain T residue 875 THR Chi-restraints excluded: chain T residue 878 SER Chi-restraints excluded: chain T residue 907 GLU Chi-restraints excluded: chain U residue 475 THR Chi-restraints excluded: chain U residue 482 GLU Chi-restraints excluded: chain U residue 641 ASP Chi-restraints excluded: chain U residue 684 VAL Chi-restraints excluded: chain U residue 852 MET Chi-restraints excluded: chain P residue 62 HIS Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 309 ILE Chi-restraints excluded: chain Q residue 62 HIS Chi-restraints excluded: chain Q residue 121 CYS Chi-restraints excluded: chain Q residue 122 VAL Chi-restraints excluded: chain Q residue 146 LEU Chi-restraints excluded: chain Q residue 266 LEU Chi-restraints excluded: chain Q residue 292 LYS Chi-restraints excluded: chain Q residue 312 VAL Chi-restraints excluded: chain Q residue 361 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 114 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 183 optimal weight: 0.2980 chunk 347 optimal weight: 7.9990 chunk 243 optimal weight: 0.9980 chunk 336 optimal weight: 0.6980 chunk 378 optimal weight: 3.9990 chunk 391 optimal weight: 2.9990 chunk 242 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 846 GLN ** R 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 678 GLN P 45 ASN P 220 HIS ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 62 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.229432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.190613 restraints weight = 61738.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.196983 restraints weight = 35696.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.201678 restraints weight = 24026.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.204274 restraints weight = 17612.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.206473 restraints weight = 14352.807| |-----------------------------------------------------------------------------| r_work (final): 0.4545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4546 r_free = 0.4546 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4546 r_free = 0.4546 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.4546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5627 moved from start: 0.5672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34257 Z= 0.133 Angle : 0.662 16.032 46363 Z= 0.315 Chirality : 0.042 0.260 4870 Planarity : 0.005 0.086 6024 Dihedral : 4.819 51.899 4576 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.20 % Allowed : 15.86 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.13), residues: 4084 helix: 0.64 (0.15), residues: 1367 sheet: -0.66 (0.26), residues: 368 loop : -0.22 (0.13), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 300 TYR 0.020 0.001 TYR N 683 PHE 0.030 0.002 PHE R 751 TRP 0.048 0.002 TRP M 860 HIS 0.013 0.001 HIS Q 62 Details of bonding type rmsd covalent geometry : bond 0.00295 (34137) covalent geometry : angle 0.62032 (46183) hydrogen bonds : bond 0.03413 ( 1101) hydrogen bonds : angle 5.34603 ( 3024) metal coordination : bond 0.00506 ( 120) metal coordination : angle 3.74673 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 774 time to evaluate : 1.208 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 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 revert: symmetry clash revert: symmetry clash REVERT: L 476 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.6837 (ptt-90) REVERT: L 482 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8235 (mp0) REVERT: L 533 TYR cc_start: 0.8284 (m-10) cc_final: 0.7886 (m-10) REVERT: L 548 MET cc_start: 0.5716 (tmm) cc_final: 0.5460 (tmm) REVERT: L 556 ARG cc_start: 0.6926 (mtt-85) cc_final: 0.6272 (mtt-85) REVERT: L 561 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6984 (mp0) REVERT: L 585 MET cc_start: 0.6767 (tpt) cc_final: 0.6469 (tmm) REVERT: L 640 PHE cc_start: 0.7275 (m-80) cc_final: 0.6924 (m-80) REVERT: L 671 THR cc_start: 0.8596 (m) cc_final: 0.8318 (p) REVERT: L 674 MET cc_start: 0.8334 (mtp) cc_final: 0.7885 (mtp) REVERT: L 761 MET cc_start: 0.4545 (ppp) cc_final: 0.3500 (tmm) REVERT: L 765 ASP cc_start: 0.6641 (t70) cc_final: 0.6048 (t0) REVERT: L 847 HIS cc_start: 0.6316 (m-70) cc_final: 0.5691 (m-70) REVERT: L 864 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7331 (ptp) REVERT: L 868 PHE cc_start: 0.4672 (OUTLIER) cc_final: 0.3762 (m-10) REVERT: L 886 GLN cc_start: 0.7620 (mt0) cc_final: 0.7067 (mt0) REVERT: M 585 MET cc_start: -0.2823 (mmm) cc_final: -0.3191 (mmm) REVERT: M 682 MET cc_start: 0.6218 (ttm) cc_final: 0.6011 (ttm) REVERT: M 793 TYR cc_start: 0.5656 (m-80) cc_final: 0.5312 (m-80) REVERT: M 852 MET cc_start: 0.6288 (ttt) cc_final: 0.5979 (ttt) REVERT: M 865 GLU cc_start: 0.6537 (mt-10) cc_final: 0.6023 (mt-10) REVERT: M 889 LEU cc_start: 0.7741 (mt) cc_final: 0.7428 (mt) REVERT: M 899 ARG cc_start: 0.6610 (ttt90) cc_final: 0.6205 (ttt90) REVERT: N 477 GLU cc_start: 0.8281 (mt-10) cc_final: 0.8063 (mt-10) REVERT: N 584 TYR cc_start: 0.8010 (m-80) cc_final: 0.7749 (m-80) REVERT: N 596 ARG cc_start: 0.7494 (ptt-90) cc_final: 0.7149 (ptt-90) REVERT: N 597 ARG cc_start: 0.7711 (ttp-110) cc_final: 0.7138 (ttm170) REVERT: N 647 LEU cc_start: 0.5890 (tp) cc_final: 0.5648 (tt) REVERT: N 669 SER cc_start: 0.8062 (m) cc_final: 0.7732 (p) REVERT: N 682 MET cc_start: 0.7192 (tmm) cc_final: 0.6899 (tmm) REVERT: N 684 VAL cc_start: 0.7275 (OUTLIER) cc_final: 0.6577 (p) REVERT: N 733 GLU cc_start: 0.6694 (mm-30) cc_final: 0.6454 (mm-30) REVERT: N 751 PHE cc_start: 0.7102 (t80) cc_final: 0.5452 (t80) REVERT: N 753 TRP cc_start: 0.6653 (p90) cc_final: 0.5671 (p90) REVERT: N 757 ASN cc_start: 0.7447 (t0) cc_final: 0.6971 (m-40) REVERT: N 801 MET cc_start: 0.6515 (mtp) cc_final: 0.6293 (mtp) REVERT: N 823 ARG cc_start: 0.6864 (mtp-110) cc_final: 0.6119 (ptm-80) REVERT: N 868 PHE cc_start: 0.6982 (m-10) cc_final: 0.6775 (m-10) REVERT: N 878 SER cc_start: 0.8081 (t) cc_final: 0.7565 (m) REVERT: O 513 MET cc_start: 0.7351 (ppp) cc_final: 0.6813 (ppp) REVERT: O 585 MET cc_start: 0.5110 (mmm) cc_final: 0.4697 (mmm) REVERT: O 607 MET cc_start: 0.5224 (mtp) cc_final: 0.4844 (mtp) REVERT: O 669 SER cc_start: 0.8645 (m) cc_final: 0.8301 (p) REVERT: O 675 VAL cc_start: 0.8403 (t) cc_final: 0.8123 (p) REVERT: O 676 ARG cc_start: 0.8177 (mmm160) cc_final: 0.7728 (tpp80) REVERT: O 684 VAL cc_start: 0.8680 (OUTLIER) cc_final: 0.8452 (m) REVERT: O 729 ARG cc_start: 0.5340 (OUTLIER) cc_final: 0.3414 (mtt90) REVERT: R 513 MET cc_start: 0.6271 (ppp) cc_final: 0.4044 (pmm) REVERT: R 607 MET cc_start: 0.5305 (mtp) cc_final: 0.5019 (mtp) REVERT: R 708 SER cc_start: 0.8162 (t) cc_final: 0.7843 (p) REVERT: R 846 GLN cc_start: 0.6670 (OUTLIER) cc_final: 0.6468 (tm-30) REVERT: R 887 ARG cc_start: 0.7330 (tmm-80) cc_final: 0.7082 (tmm-80) REVERT: R 888 LEU cc_start: 0.8450 (tt) cc_final: 0.8080 (tt) REVERT: S 479 LEU cc_start: 0.8358 (tt) cc_final: 0.7565 (pp) REVERT: S 495 ILE cc_start: 0.6562 (pt) cc_final: 0.6308 (mt) REVERT: S 513 MET cc_start: 0.6900 (ttt) cc_final: 0.6394 (ttt) REVERT: S 597 ARG cc_start: 0.7602 (ttp-110) cc_final: 0.7066 (ttm170) REVERT: S 606 GLN cc_start: 0.7806 (tp40) cc_final: 0.7579 (tp40) REVERT: S 647 LEU cc_start: 0.6199 (tp) cc_final: 0.5993 (tt) REVERT: S 733 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6856 (mm-30) REVERT: S 769 ILE cc_start: 0.7702 (mt) cc_final: 0.7478 (tp) REVERT: S 801 MET cc_start: 0.6240 (mtp) cc_final: 0.5711 (mtt) REVERT: S 878 SER cc_start: 0.8055 (t) cc_final: 0.7512 (m) REVERT: T 513 MET cc_start: 0.5605 (ttt) cc_final: 0.5334 (ttt) REVERT: T 607 MET cc_start: 0.2971 (OUTLIER) cc_final: 0.2732 (mpp) REVERT: T 671 THR cc_start: 0.7503 (m) cc_final: 0.7263 (t) REVERT: T 677 HIS cc_start: 0.7194 (m-70) cc_final: 0.6869 (m-70) REVERT: T 765 ASP cc_start: 0.6987 (t0) cc_final: 0.6542 (t0) REVERT: T 880 MET cc_start: 0.7162 (mtp) cc_final: 0.6917 (mtt) REVERT: U 481 TYR cc_start: 0.8130 (t80) cc_final: 0.7776 (t80) REVERT: U 545 GLU cc_start: 0.6770 (mt-10) cc_final: 0.6531 (mm-30) REVERT: U 552 ASN cc_start: 0.7792 (p0) cc_final: 0.7250 (p0) REVERT: U 640 PHE cc_start: 0.7202 (m-80) cc_final: 0.6985 (m-80) REVERT: U 648 LEU cc_start: 0.8481 (tp) cc_final: 0.8223 (tp) REVERT: U 651 LYS cc_start: 0.8653 (mttt) cc_final: 0.8220 (mttt) REVERT: U 693 LYS cc_start: 0.7531 (tttt) cc_final: 0.7068 (tttt) REVERT: U 694 HIS cc_start: 0.7327 (m170) cc_final: 0.6817 (m170) REVERT: U 696 GLN cc_start: 0.8219 (mt0) cc_final: 0.8003 (mt0) REVERT: U 761 MET cc_start: 0.3724 (ppp) cc_final: 0.2401 (tmm) REVERT: U 772 PHE cc_start: 0.7650 (m-10) cc_final: 0.7015 (m-10) REVERT: U 781 ASP cc_start: 0.7790 (t0) cc_final: 0.7418 (t0) REVERT: U 826 LYS cc_start: 0.8536 (tttt) cc_final: 0.7997 (tptp) REVERT: P 46 GLN cc_start: 0.9073 (mt0) cc_final: 0.8796 (mp10) REVERT: P 64 GLN cc_start: 0.8147 (pt0) cc_final: 0.7888 (pt0) REVERT: P 121 CYS cc_start: 0.7119 (OUTLIER) cc_final: 0.6918 (m) REVERT: P 156 ARG cc_start: 0.8493 (tmm160) cc_final: 0.7404 (ttp-170) REVERT: P 159 LYS cc_start: 0.7482 (mptt) cc_final: 0.7143 (mptt) REVERT: P 161 ARG cc_start: 0.8515 (ptm160) cc_final: 0.7837 (mtp-110) REVERT: P 179 PHE cc_start: 0.8221 (m-80) cc_final: 0.7967 (m-80) REVERT: P 218 LEU cc_start: 0.7400 (tt) cc_final: 0.6943 (tt) REVERT: P 242 TYR cc_start: 0.5789 (t80) cc_final: 0.4720 (t80) REVERT: P 283 MET cc_start: 0.6880 (ttt) cc_final: 0.5815 (ttt) REVERT: P 303 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8351 (mp0) REVERT: P 368 PHE cc_start: 0.7034 (m-80) cc_final: 0.5442 (m-80) REVERT: Q 121 CYS cc_start: 0.6324 (OUTLIER) cc_final: 0.6006 (m) REVERT: Q 159 LYS cc_start: 0.6872 (mttt) cc_final: 0.6521 (mttt) REVERT: Q 160 TRP cc_start: 0.8012 (p-90) cc_final: 0.7695 (p-90) REVERT: Q 180 GLU cc_start: 0.7538 (pp20) cc_final: 0.6865 (pp20) REVERT: Q 303 GLU cc_start: 0.8337 (mp0) cc_final: 0.7864 (mp0) outliers start: 80 outliers final: 51 residues processed: 806 average time/residue: 0.2365 time to fit residues: 298.1833 Evaluate side-chains 814 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 753 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 481 TYR Chi-restraints excluded: chain L residue 603 SER Chi-restraints excluded: chain L residue 641 ASP Chi-restraints excluded: chain L residue 667 GLU Chi-restraints excluded: chain L residue 852 MET Chi-restraints excluded: chain L residue 864 MET Chi-restraints excluded: chain L residue 868 PHE Chi-restraints excluded: chain L residue 878 SER Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 684 VAL Chi-restraints excluded: chain M residue 737 LEU Chi-restraints excluded: chain M residue 875 THR Chi-restraints excluded: chain N residue 475 THR Chi-restraints excluded: chain N residue 500 LEU Chi-restraints excluded: chain N residue 504 LEU Chi-restraints excluded: chain N residue 643 ILE Chi-restraints excluded: chain N residue 684 VAL Chi-restraints excluded: chain N residue 737 LEU Chi-restraints excluded: chain N residue 858 ILE Chi-restraints excluded: chain N residue 875 THR Chi-restraints excluded: chain O residue 657 VAL Chi-restraints excluded: chain O residue 678 GLN Chi-restraints excluded: chain O residue 684 VAL Chi-restraints excluded: chain O residue 705 ILE Chi-restraints excluded: chain O residue 729 ARG Chi-restraints excluded: chain O residue 739 HIS Chi-restraints excluded: chain O residue 826 LYS Chi-restraints excluded: chain O residue 905 LEU Chi-restraints excluded: chain R residue 657 VAL Chi-restraints excluded: chain R residue 665 VAL Chi-restraints excluded: chain R residue 669 SER Chi-restraints excluded: chain R residue 710 CYS Chi-restraints excluded: chain R residue 846 GLN Chi-restraints excluded: chain S residue 504 LEU Chi-restraints excluded: chain S residue 548 MET Chi-restraints excluded: chain S residue 643 ILE Chi-restraints excluded: chain S residue 663 SER Chi-restraints excluded: chain S residue 678 GLN Chi-restraints excluded: chain S residue 761 MET Chi-restraints excluded: chain S residue 855 LYS Chi-restraints excluded: chain S residue 858 ILE Chi-restraints excluded: chain T residue 607 MET Chi-restraints excluded: chain T residue 872 VAL Chi-restraints excluded: chain T residue 875 THR Chi-restraints excluded: chain T residue 878 SER Chi-restraints excluded: chain T residue 907 GLU Chi-restraints excluded: chain U residue 852 MET Chi-restraints excluded: chain P residue 45 ASN Chi-restraints excluded: chain P residue 121 CYS Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 361 THR Chi-restraints excluded: chain Q residue 62 HIS Chi-restraints excluded: chain Q residue 121 CYS Chi-restraints excluded: chain Q residue 146 LEU Chi-restraints excluded: chain Q residue 266 LEU Chi-restraints excluded: chain Q residue 286 ASP Chi-restraints excluded: chain Q residue 292 LYS Chi-restraints excluded: chain Q residue 361 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 124 optimal weight: 0.9980 chunk 219 optimal weight: 0.7980 chunk 389 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 194 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 372 optimal weight: 7.9990 chunk 146 optimal weight: 0.0670 chunk 154 optimal weight: 0.3980 chunk 170 optimal weight: 2.9990 chunk 224 optimal weight: 0.1980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 873 HIS ** R 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 62 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4871 r_free = 0.4871 target = 0.231518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.193148 restraints weight = 61516.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.199506 restraints weight = 35623.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.204167 restraints weight = 23963.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.206677 restraints weight = 17650.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.209265 restraints weight = 14375.310| |-----------------------------------------------------------------------------| r_work (final): 0.4605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4606 r_free = 0.4606 target_work(ls_wunit_k1) = 0.222 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4605 r_free = 0.4605 target_work(ls_wunit_k1) = 0.222 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.4605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5588 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34257 Z= 0.119 Angle : 0.658 12.913 46363 Z= 0.316 Chirality : 0.042 0.272 4870 Planarity : 0.005 0.103 6024 Dihedral : 4.671 47.606 4576 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.18 % Allowed : 16.19 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.13), residues: 4084 helix: 0.72 (0.15), residues: 1369 sheet: -0.71 (0.26), residues: 348 loop : -0.15 (0.13), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG M 823 TYR 0.020 0.001 TYR N 481 PHE 0.035 0.002 PHE P 263 TRP 0.054 0.002 TRP L 753 HIS 0.023 0.001 HIS Q 62 Details of bonding type rmsd covalent geometry : bond 0.00263 (34137) covalent geometry : angle 0.62234 (46183) hydrogen bonds : bond 0.03349 ( 1101) hydrogen bonds : angle 5.25560 ( 3024) metal coordination : bond 0.00434 ( 120) metal coordination : angle 3.49177 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 764 time to evaluate : 1.168 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 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 revert: symmetry clash revert: symmetry clash REVERT: L 476 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6939 (ptt-90) REVERT: L 479 LEU cc_start: 0.8800 (mt) cc_final: 0.7979 (mt) REVERT: L 482 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8223 (mp0) REVERT: L 484 ARG cc_start: 0.8318 (mmm160) cc_final: 0.8037 (mtm180) REVERT: L 533 TYR cc_start: 0.8327 (m-10) cc_final: 0.8032 (m-10) REVERT: L 556 ARG cc_start: 0.6977 (mtt-85) cc_final: 0.6336 (mtt-85) REVERT: L 561 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6877 (mp0) REVERT: L 585 MET cc_start: 0.6740 (tpt) cc_final: 0.6458 (tmm) REVERT: L 607 MET cc_start: 0.8325 (mmt) cc_final: 0.8018 (mmt) REVERT: L 640 PHE cc_start: 0.7257 (m-80) cc_final: 0.6820 (m-80) REVERT: L 671 THR cc_start: 0.8602 (m) cc_final: 0.8298 (p) REVERT: L 674 MET cc_start: 0.8415 (mtp) cc_final: 0.7908 (mtp) REVERT: L 761 MET cc_start: 0.4442 (ppp) cc_final: 0.3212 (tmm) REVERT: L 765 ASP cc_start: 0.6741 (t70) cc_final: 0.6123 (t0) REVERT: L 847 HIS cc_start: 0.6343 (m-70) cc_final: 0.5675 (m-70) REVERT: L 868 PHE cc_start: 0.4633 (m-10) cc_final: 0.3246 (m-10) REVERT: M 585 MET cc_start: -0.2878 (mmm) cc_final: -0.3241 (mmm) REVERT: M 682 MET cc_start: 0.6178 (ttm) cc_final: 0.5927 (ttm) REVERT: M 793 TYR cc_start: 0.5554 (m-80) cc_final: 0.5186 (m-80) REVERT: M 852 MET cc_start: 0.6356 (ttt) cc_final: 0.6023 (ttt) REVERT: M 865 GLU cc_start: 0.6513 (mt-10) cc_final: 0.6014 (mt-10) REVERT: M 889 LEU cc_start: 0.7652 (mt) cc_final: 0.7313 (mt) REVERT: N 477 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8078 (mt-10) REVERT: N 584 TYR cc_start: 0.7970 (m-80) cc_final: 0.7721 (m-80) REVERT: N 596 ARG cc_start: 0.7526 (ptt-90) cc_final: 0.7197 (ptt-90) REVERT: N 597 ARG cc_start: 0.7769 (ttp-110) cc_final: 0.7075 (ttm170) REVERT: N 647 LEU cc_start: 0.5720 (tp) cc_final: 0.5478 (tt) REVERT: N 669 SER cc_start: 0.7891 (m) cc_final: 0.7586 (p) REVERT: N 682 MET cc_start: 0.7085 (tmm) cc_final: 0.6779 (tmm) REVERT: N 684 VAL cc_start: 0.7120 (OUTLIER) cc_final: 0.6469 (p) REVERT: N 751 PHE cc_start: 0.7154 (t80) cc_final: 0.5373 (t80) REVERT: N 753 TRP cc_start: 0.6608 (p90) cc_final: 0.5541 (p90) REVERT: N 757 ASN cc_start: 0.7385 (t0) cc_final: 0.7006 (m-40) REVERT: N 801 MET cc_start: 0.6498 (mtp) cc_final: 0.6247 (mtp) REVERT: O 651 LYS cc_start: 0.8528 (mmtt) cc_final: 0.8279 (mmtt) REVERT: O 669 SER cc_start: 0.8683 (m) cc_final: 0.8317 (p) REVERT: O 676 ARG cc_start: 0.8130 (mmm160) cc_final: 0.7746 (tpp80) REVERT: O 680 LYS cc_start: 0.6662 (ptpp) cc_final: 0.6259 (ptpp) REVERT: O 684 VAL cc_start: 0.8663 (OUTLIER) cc_final: 0.8420 (m) REVERT: O 731 PHE cc_start: 0.6927 (t80) cc_final: 0.6718 (t80) REVERT: O 907 GLU cc_start: 0.8007 (tt0) cc_final: 0.7243 (tp30) REVERT: R 680 LYS cc_start: 0.7244 (ttpp) cc_final: 0.6406 (ptpp) REVERT: R 708 SER cc_start: 0.8134 (t) cc_final: 0.7772 (p) REVERT: R 846 GLN cc_start: 0.6889 (tm-30) cc_final: 0.6615 (tm-30) REVERT: R 887 ARG cc_start: 0.7462 (tmm-80) cc_final: 0.7105 (tmm-80) REVERT: R 888 LEU cc_start: 0.8426 (tt) cc_final: 0.8021 (tt) REVERT: S 495 ILE cc_start: 0.6603 (pt) cc_final: 0.6372 (mt) REVERT: S 513 MET cc_start: 0.6985 (ttt) cc_final: 0.6436 (ttt) REVERT: S 561 GLU cc_start: 0.7777 (tt0) cc_final: 0.7490 (tt0) REVERT: S 597 ARG cc_start: 0.7585 (ttp-110) cc_final: 0.7004 (ttm170) REVERT: S 606 GLN cc_start: 0.7779 (tp40) cc_final: 0.7554 (tp40) REVERT: S 643 ILE cc_start: 0.7290 (OUTLIER) cc_final: 0.6733 (mp) REVERT: S 684 VAL cc_start: 0.7843 (OUTLIER) cc_final: 0.7294 (p) REVERT: S 733 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6978 (mm-30) REVERT: S 801 MET cc_start: 0.6328 (mtp) cc_final: 0.5751 (mtt) REVERT: S 817 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7431 (mt-10) REVERT: S 878 SER cc_start: 0.8185 (t) cc_final: 0.7642 (m) REVERT: S 888 LEU cc_start: 0.7628 (tt) cc_final: 0.7242 (tp) REVERT: T 513 MET cc_start: 0.5659 (ttt) cc_final: 0.5378 (ttt) REVERT: T 607 MET cc_start: 0.3018 (OUTLIER) cc_final: 0.2771 (mpp) REVERT: T 671 THR cc_start: 0.7522 (m) cc_final: 0.7266 (t) REVERT: T 677 HIS cc_start: 0.7339 (m-70) cc_final: 0.6978 (m-70) REVERT: T 682 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.6851 (ppp) REVERT: T 688 ARG cc_start: 0.7400 (mtt180) cc_final: 0.6917 (mtm180) REVERT: T 756 GLU cc_start: 0.5631 (tm-30) cc_final: 0.5216 (tm-30) REVERT: T 765 ASP cc_start: 0.6963 (t0) cc_final: 0.6407 (t0) REVERT: T 792 ARG cc_start: 0.6347 (ttm170) cc_final: 0.5685 (mmm-85) REVERT: T 860 TRP cc_start: 0.6718 (m-10) cc_final: 0.6480 (m-10) REVERT: T 880 MET cc_start: 0.7077 (mtp) cc_final: 0.6811 (mtt) REVERT: U 481 TYR cc_start: 0.8178 (t80) cc_final: 0.7780 (t80) REVERT: U 545 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6695 (mm-30) REVERT: U 552 ASN cc_start: 0.7865 (p0) cc_final: 0.7321 (p0) REVERT: U 648 LEU cc_start: 0.8505 (tp) cc_final: 0.8221 (tp) REVERT: U 651 LYS cc_start: 0.8709 (mttt) cc_final: 0.8245 (mttt) REVERT: U 693 LYS cc_start: 0.7674 (tttt) cc_final: 0.7275 (tttt) REVERT: U 696 GLN cc_start: 0.8307 (mt0) cc_final: 0.8086 (mt0) REVERT: U 761 MET cc_start: 0.3743 (ppp) cc_final: 0.2354 (tmm) REVERT: U 772 PHE cc_start: 0.7642 (m-10) cc_final: 0.7022 (m-10) REVERT: U 776 ASN cc_start: 0.8111 (p0) cc_final: 0.7901 (p0) REVERT: U 781 ASP cc_start: 0.7840 (t0) cc_final: 0.7478 (t0) REVERT: U 826 LYS cc_start: 0.8598 (tttt) cc_final: 0.8012 (tptp) REVERT: U 864 MET cc_start: 0.5951 (ptm) cc_final: 0.5722 (ppp) REVERT: P 64 GLN cc_start: 0.8089 (pt0) cc_final: 0.7883 (pt0) REVERT: P 121 CYS cc_start: 0.7270 (OUTLIER) cc_final: 0.7041 (m) REVERT: P 161 ARG cc_start: 0.8544 (ptm160) cc_final: 0.7802 (mtp-110) REVERT: P 179 PHE cc_start: 0.8288 (m-80) cc_final: 0.7995 (m-80) REVERT: P 218 LEU cc_start: 0.7406 (tt) cc_final: 0.6994 (tt) REVERT: P 242 TYR cc_start: 0.5795 (t80) cc_final: 0.4714 (t80) REVERT: P 283 MET cc_start: 0.6907 (ttt) cc_final: 0.5729 (ttt) REVERT: P 290 LEU cc_start: 0.6307 (pt) cc_final: 0.5257 (mm) REVERT: P 303 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8322 (mp0) REVERT: P 368 PHE cc_start: 0.7082 (m-80) cc_final: 0.5520 (m-80) REVERT: Q 121 CYS cc_start: 0.6353 (OUTLIER) cc_final: 0.6028 (m) REVERT: Q 155 GLN cc_start: 0.8050 (tm-30) cc_final: 0.7718 (tm-30) REVERT: Q 158 ARG cc_start: 0.7184 (pmt170) cc_final: 0.6734 (pmt170) REVERT: Q 159 LYS cc_start: 0.6887 (mttt) cc_final: 0.6603 (mptt) REVERT: Q 160 TRP cc_start: 0.8115 (p-90) cc_final: 0.7768 (p-90) REVERT: Q 180 GLU cc_start: 0.7475 (pp20) cc_final: 0.6788 (pp20) REVERT: Q 283 MET cc_start: 0.7209 (ttt) cc_final: 0.6839 (ttt) REVERT: Q 290 LEU cc_start: 0.6263 (pp) cc_final: 0.5533 (mm) REVERT: Q 302 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8086 (mm) REVERT: Q 303 GLU cc_start: 0.8366 (mp0) cc_final: 0.7807 (mp0) REVERT: Q 368 PHE cc_start: 0.7577 (m-80) cc_final: 0.6824 (m-80) outliers start: 79 outliers final: 57 residues processed: 797 average time/residue: 0.2303 time to fit residues: 287.3809 Evaluate side-chains 811 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 744 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 481 TYR Chi-restraints excluded: chain L residue 510 VAL Chi-restraints excluded: chain L residue 608 PHE Chi-restraints excluded: chain L residue 641 ASP Chi-restraints excluded: chain L residue 667 GLU Chi-restraints excluded: chain L residue 852 MET Chi-restraints excluded: chain L residue 878 SER Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 684 VAL Chi-restraints excluded: chain M residue 737 LEU Chi-restraints excluded: chain M residue 858 ILE Chi-restraints excluded: chain M residue 875 THR Chi-restraints excluded: chain N residue 475 THR Chi-restraints excluded: chain N residue 504 LEU Chi-restraints excluded: chain N residue 548 MET Chi-restraints excluded: chain N residue 585 MET Chi-restraints excluded: chain N residue 674 MET Chi-restraints excluded: chain N residue 684 VAL Chi-restraints excluded: chain N residue 713 LEU Chi-restraints excluded: chain N residue 737 LEU Chi-restraints excluded: chain N residue 855 LYS Chi-restraints excluded: chain N residue 858 ILE Chi-restraints excluded: chain N residue 875 THR Chi-restraints excluded: chain O residue 657 VAL Chi-restraints excluded: chain O residue 684 VAL Chi-restraints excluded: chain O residue 739 HIS Chi-restraints excluded: chain O residue 826 LYS Chi-restraints excluded: chain R residue 657 VAL Chi-restraints excluded: chain R residue 669 SER Chi-restraints excluded: chain R residue 710 CYS Chi-restraints excluded: chain R residue 739 HIS Chi-restraints excluded: chain R residue 858 ILE Chi-restraints excluded: chain S residue 643 ILE Chi-restraints excluded: chain S residue 684 VAL Chi-restraints excluded: chain S residue 761 MET Chi-restraints excluded: chain S residue 855 LYS Chi-restraints excluded: chain S residue 858 ILE Chi-restraints excluded: chain T residue 607 MET Chi-restraints excluded: chain T residue 682 MET Chi-restraints excluded: chain T residue 713 LEU Chi-restraints excluded: chain T residue 742 ARG Chi-restraints excluded: chain T residue 868 PHE Chi-restraints excluded: chain T residue 872 VAL Chi-restraints excluded: chain T residue 875 THR Chi-restraints excluded: chain T residue 878 SER Chi-restraints excluded: chain T residue 907 GLU Chi-restraints excluded: chain U residue 681 ILE Chi-restraints excluded: chain U residue 684 VAL Chi-restraints excluded: chain U residue 855 LYS Chi-restraints excluded: chain P residue 121 CYS Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain P residue 158 ARG Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 230 LYS Chi-restraints excluded: chain P residue 361 THR Chi-restraints excluded: chain Q residue 62 HIS Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 121 CYS Chi-restraints excluded: chain Q residue 146 LEU Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain Q residue 266 LEU Chi-restraints excluded: chain Q residue 286 ASP Chi-restraints excluded: chain Q residue 292 LYS Chi-restraints excluded: chain Q residue 302 LEU Chi-restraints excluded: chain Q residue 312 VAL Chi-restraints excluded: chain Q residue 361 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 257 optimal weight: 10.0000 chunk 168 optimal weight: 0.6980 chunk 285 optimal weight: 0.5980 chunk 202 optimal weight: 2.9990 chunk 253 optimal weight: 40.0000 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 20.0000 chunk 276 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 327 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 789 HIS L 847 HIS M 612 ASN O 757 ASN O 776 ASN ** O 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 873 HIS S 678 GLN U 694 HIS ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.223674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.179370 restraints weight = 61455.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.185150 restraints weight = 37879.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.189049 restraints weight = 26862.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.192060 restraints weight = 21038.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.193780 restraints weight = 17517.412| |-----------------------------------------------------------------------------| r_work (final): 0.4434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4432 r_free = 0.4432 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4432 r_free = 0.4432 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.4432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5932 moved from start: 0.6577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 34257 Z= 0.254 Angle : 0.814 18.836 46363 Z= 0.390 Chirality : 0.045 0.276 4870 Planarity : 0.006 0.091 6024 Dihedral : 5.231 52.172 4576 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.41 % Favored : 95.54 % Rotamer: Outliers : 2.56 % Allowed : 16.33 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.13), residues: 4084 helix: 0.27 (0.14), residues: 1375 sheet: -0.83 (0.27), residues: 321 loop : -0.32 (0.13), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG P 47 TYR 0.030 0.002 TYR T 683 PHE 0.044 0.003 PHE P 263 TRP 0.057 0.004 TRP L 753 HIS 0.034 0.002 HIS Q 62 Details of bonding type rmsd covalent geometry : bond 0.00542 (34137) covalent geometry : angle 0.74712 (46183) hydrogen bonds : bond 0.04697 ( 1101) hydrogen bonds : angle 5.93516 ( 3024) metal coordination : bond 0.00834 ( 120) metal coordination : angle 5.22888 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 776 time to evaluate : 1.231 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 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: L 476 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6984 (ptt-90) REVERT: L 479 LEU cc_start: 0.8938 (mt) cc_final: 0.8072 (mt) REVERT: L 482 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8337 (mp0) REVERT: L 548 MET cc_start: 0.6056 (tmm) cc_final: 0.5610 (tmm) REVERT: L 556 ARG cc_start: 0.6933 (mtt-85) cc_final: 0.6373 (mtt-85) REVERT: L 561 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6896 (mp0) REVERT: L 606 GLN cc_start: 0.8086 (pp30) cc_final: 0.7617 (pp30) REVERT: L 607 MET cc_start: 0.8341 (mmt) cc_final: 0.7708 (mmt) REVERT: L 640 PHE cc_start: 0.7741 (m-80) cc_final: 0.7354 (m-80) REVERT: L 671 THR cc_start: 0.8521 (m) cc_final: 0.7949 (m) REVERT: L 674 MET cc_start: 0.8401 (mtp) cc_final: 0.7897 (mtp) REVERT: L 761 MET cc_start: 0.4474 (ppp) cc_final: 0.3266 (tmm) REVERT: L 765 ASP cc_start: 0.6921 (t70) cc_final: 0.6059 (t0) REVERT: L 772 PHE cc_start: 0.8098 (m-10) cc_final: 0.7480 (m-10) REVERT: L 868 PHE cc_start: 0.4845 (OUTLIER) cc_final: 0.3986 (m-80) REVERT: M 585 MET cc_start: -0.3123 (mmm) cc_final: -0.3432 (mmm) REVERT: M 652 ASP cc_start: 0.6955 (t0) cc_final: 0.6706 (t0) REVERT: M 660 TYR cc_start: 0.6426 (t80) cc_final: 0.4589 (t80) REVERT: M 852 MET cc_start: 0.6821 (ttt) cc_final: 0.6555 (ttp) REVERT: M 864 MET cc_start: 0.7851 (ttm) cc_final: 0.7459 (mtm) REVERT: M 889 LEU cc_start: 0.8038 (mt) cc_final: 0.7712 (mt) REVERT: N 495 ILE cc_start: 0.7036 (pt) cc_final: 0.6756 (mt) REVERT: N 558 PHE cc_start: 0.8302 (m-10) cc_final: 0.8101 (m-10) REVERT: N 596 ARG cc_start: 0.7574 (ptt-90) cc_final: 0.7320 (ptt-90) REVERT: N 597 ARG cc_start: 0.7596 (ttp-110) cc_final: 0.7365 (ttp-110) REVERT: N 647 LEU cc_start: 0.6053 (tp) cc_final: 0.5842 (tt) REVERT: N 669 SER cc_start: 0.8026 (m) cc_final: 0.7658 (p) REVERT: N 682 MET cc_start: 0.7339 (tmm) cc_final: 0.7025 (tmm) REVERT: N 733 GLU cc_start: 0.6628 (mm-30) cc_final: 0.6351 (mm-30) REVERT: N 753 TRP cc_start: 0.6597 (p90) cc_final: 0.5442 (p90) REVERT: N 757 ASN cc_start: 0.7486 (t0) cc_final: 0.7157 (m-40) REVERT: N 801 MET cc_start: 0.6817 (mtp) cc_final: 0.6268 (mtt) REVERT: N 823 ARG cc_start: 0.6909 (OUTLIER) cc_final: 0.6502 (mtm110) REVERT: N 831 ARG cc_start: 0.6147 (ptp-170) cc_final: 0.5623 (ptp-170) REVERT: O 513 MET cc_start: 0.7223 (ppp) cc_final: 0.4564 (pmm) REVERT: O 674 MET cc_start: 0.6926 (mtp) cc_final: 0.6726 (mtt) REVERT: O 675 VAL cc_start: 0.8546 (t) cc_final: 0.8266 (p) REVERT: O 684 VAL cc_start: 0.8790 (OUTLIER) cc_final: 0.8532 (m) REVERT: O 729 ARG cc_start: 0.5780 (OUTLIER) cc_final: 0.5294 (mmt180) REVERT: O 819 LEU cc_start: 0.5737 (OUTLIER) cc_final: 0.5140 (mm) REVERT: O 863 GLU cc_start: 0.6554 (mt-10) cc_final: 0.6187 (mt-10) REVERT: R 651 LYS cc_start: 0.8470 (mttt) cc_final: 0.8227 (mttt) REVERT: R 667 GLU cc_start: 0.7178 (mp0) cc_final: 0.6961 (mp0) REVERT: R 688 ARG cc_start: 0.6875 (mtm180) cc_final: 0.6560 (mtm180) REVERT: R 708 SER cc_start: 0.8240 (t) cc_final: 0.7851 (p) REVERT: R 768 ASP cc_start: 0.7314 (m-30) cc_final: 0.7064 (m-30) REVERT: R 866 ARG cc_start: 0.7639 (ttm110) cc_final: 0.7058 (ttm110) REVERT: S 513 MET cc_start: 0.7157 (ttt) cc_final: 0.6673 (ttt) REVERT: S 733 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6883 (mm-30) REVERT: S 801 MET cc_start: 0.6621 (mtp) cc_final: 0.6117 (mtt) REVERT: S 878 SER cc_start: 0.8022 (t) cc_final: 0.7783 (t) REVERT: T 513 MET cc_start: 0.6129 (ttt) cc_final: 0.5844 (ttt) REVERT: T 607 MET cc_start: 0.3165 (OUTLIER) cc_final: 0.2902 (mpp) REVERT: T 677 HIS cc_start: 0.7360 (m-70) cc_final: 0.7035 (m-70) REVERT: T 682 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.6924 (ppp) REVERT: T 756 GLU cc_start: 0.5868 (tm-30) cc_final: 0.5290 (tm-30) REVERT: T 761 MET cc_start: 0.4847 (ptm) cc_final: 0.4383 (ptm) REVERT: T 765 ASP cc_start: 0.7136 (t0) cc_final: 0.6630 (t0) REVERT: T 792 ARG cc_start: 0.6464 (ttm170) cc_final: 0.5991 (tpp80) REVERT: T 860 TRP cc_start: 0.6944 (m-10) cc_final: 0.6739 (m-10) REVERT: T 873 HIS cc_start: 0.5607 (m90) cc_final: 0.5349 (m90) REVERT: T 883 LEU cc_start: 0.8669 (mt) cc_final: 0.8449 (mt) REVERT: T 891 ARG cc_start: 0.6711 (ttp80) cc_final: 0.6161 (tmm-80) REVERT: U 478 ARG cc_start: 0.8736 (ptt90) cc_final: 0.8533 (ptt90) REVERT: U 481 TYR cc_start: 0.8191 (t80) cc_final: 0.7772 (t80) REVERT: U 545 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6465 (mm-30) REVERT: U 552 ASN cc_start: 0.7363 (p0) cc_final: 0.6917 (p0) REVERT: U 607 MET cc_start: 0.8449 (mmt) cc_final: 0.8118 (mpp) REVERT: U 640 PHE cc_start: 0.7620 (m-80) cc_final: 0.7343 (m-80) REVERT: U 647 LEU cc_start: 0.8812 (tp) cc_final: 0.8516 (tp) REVERT: U 648 LEU cc_start: 0.8510 (tp) cc_final: 0.8233 (tp) REVERT: U 651 LYS cc_start: 0.8656 (mttt) cc_final: 0.8264 (mttt) REVERT: U 674 MET cc_start: 0.7987 (mpp) cc_final: 0.7595 (mpp) REVERT: U 684 VAL cc_start: 0.8381 (OUTLIER) cc_final: 0.7956 (m) REVERT: U 696 GLN cc_start: 0.8234 (mt0) cc_final: 0.7713 (mt0) REVERT: U 755 PHE cc_start: 0.4912 (t80) cc_final: 0.4698 (t80) REVERT: U 761 MET cc_start: 0.4154 (ppp) cc_final: 0.3827 (ppp) REVERT: U 765 ASP cc_start: 0.6621 (m-30) cc_final: 0.6225 (m-30) REVERT: U 772 PHE cc_start: 0.7930 (m-10) cc_final: 0.7412 (m-10) REVERT: U 826 LYS cc_start: 0.8674 (tttt) cc_final: 0.8184 (tptp) REVERT: P 64 GLN cc_start: 0.8251 (pt0) cc_final: 0.7958 (pt0) REVERT: P 121 CYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6876 (m) REVERT: P 156 ARG cc_start: 0.8387 (tmm160) cc_final: 0.7765 (ptt180) REVERT: P 160 TRP cc_start: 0.7740 (p-90) cc_final: 0.7496 (p-90) REVERT: P 161 ARG cc_start: 0.8557 (ptm160) cc_final: 0.7898 (mtp-110) REVERT: P 179 PHE cc_start: 0.8259 (m-80) cc_final: 0.7992 (m-80) REVERT: P 192 VAL cc_start: 0.7928 (t) cc_final: 0.7516 (p) REVERT: P 242 TYR cc_start: 0.5975 (t80) cc_final: 0.4861 (t80) REVERT: P 283 MET cc_start: 0.7012 (ttt) cc_final: 0.5932 (ttt) REVERT: P 293 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8513 (mt-10) REVERT: P 303 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8246 (mp0) REVERT: Q 159 LYS cc_start: 0.7101 (mttt) cc_final: 0.6630 (mttt) REVERT: Q 160 TRP cc_start: 0.8154 (p-90) cc_final: 0.7825 (p-90) REVERT: Q 161 ARG cc_start: 0.8170 (ptm-80) cc_final: 0.7140 (mtm-85) REVERT: Q 180 GLU cc_start: 0.7547 (pp20) cc_final: 0.6616 (pp20) REVERT: Q 242 TYR cc_start: 0.6190 (t80) cc_final: 0.5821 (t80) REVERT: Q 283 MET cc_start: 0.7078 (ttt) cc_final: 0.5954 (ttt) REVERT: Q 293 GLU cc_start: 0.8656 (tt0) cc_final: 0.8425 (tm-30) REVERT: Q 303 GLU cc_start: 0.8486 (mp0) cc_final: 0.7714 (mp0) REVERT: Q 368 PHE cc_start: 0.7465 (m-80) cc_final: 0.6552 (m-80) outliers start: 93 outliers final: 63 residues processed: 815 average time/residue: 0.2350 time to fit residues: 298.2845 Evaluate side-chains 822 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 749 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 481 TYR Chi-restraints excluded: chain L residue 608 PHE Chi-restraints excluded: chain L residue 641 ASP Chi-restraints excluded: chain L residue 667 GLU Chi-restraints excluded: chain L residue 780 ILE Chi-restraints excluded: chain L residue 868 PHE Chi-restraints excluded: chain L residue 880 MET Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 684 VAL Chi-restraints excluded: chain M residue 737 LEU Chi-restraints excluded: chain M residue 819 LEU Chi-restraints excluded: chain M residue 858 ILE Chi-restraints excluded: chain M residue 875 THR Chi-restraints excluded: chain M residue 905 LEU Chi-restraints excluded: chain N residue 475 THR Chi-restraints excluded: chain N residue 504 LEU Chi-restraints excluded: chain N residue 585 MET Chi-restraints excluded: chain N residue 607 MET Chi-restraints excluded: chain N residue 643 ILE Chi-restraints excluded: chain N residue 668 ASP Chi-restraints excluded: chain N residue 674 MET Chi-restraints excluded: chain N residue 684 VAL Chi-restraints excluded: chain N residue 713 LEU Chi-restraints excluded: chain N residue 737 LEU Chi-restraints excluded: chain N residue 823 ARG Chi-restraints excluded: chain N residue 858 ILE Chi-restraints excluded: chain N residue 875 THR Chi-restraints excluded: chain O residue 678 GLN Chi-restraints excluded: chain O residue 684 VAL Chi-restraints excluded: chain O residue 729 ARG Chi-restraints excluded: chain O residue 738 LEU Chi-restraints excluded: chain O residue 739 HIS Chi-restraints excluded: chain O residue 776 ASN Chi-restraints excluded: chain O residue 797 ASN Chi-restraints excluded: chain O residue 819 LEU Chi-restraints excluded: chain O residue 905 LEU Chi-restraints excluded: chain R residue 669 SER Chi-restraints excluded: chain R residue 705 ILE Chi-restraints excluded: chain S residue 504 LEU Chi-restraints excluded: chain S residue 643 ILE Chi-restraints excluded: chain S residue 647 LEU Chi-restraints excluded: chain S residue 650 LEU Chi-restraints excluded: chain S residue 678 GLN Chi-restraints excluded: chain S residue 761 MET Chi-restraints excluded: chain S residue 831 ARG Chi-restraints excluded: chain S residue 855 LYS Chi-restraints excluded: chain S residue 858 ILE Chi-restraints excluded: chain T residue 607 MET Chi-restraints excluded: chain T residue 682 MET Chi-restraints excluded: chain T residue 713 LEU Chi-restraints excluded: chain T residue 878 SER Chi-restraints excluded: chain T residue 907 GLU Chi-restraints excluded: chain U residue 681 ILE Chi-restraints excluded: chain U residue 684 VAL Chi-restraints excluded: chain U residue 694 HIS Chi-restraints excluded: chain U residue 855 LYS Chi-restraints excluded: chain P residue 121 CYS Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 230 LYS Chi-restraints excluded: chain P residue 292 LYS Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 361 THR Chi-restraints excluded: chain Q residue 62 HIS Chi-restraints excluded: chain Q residue 146 LEU Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain Q residue 292 LYS Chi-restraints excluded: chain Q residue 302 LEU Chi-restraints excluded: chain Q residue 312 VAL Chi-restraints excluded: chain Q residue 361 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 244 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 312 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 337 optimal weight: 1.9990 chunk 218 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 303 optimal weight: 0.6980 chunk 142 optimal weight: 0.0270 chunk 66 optimal weight: 0.2980 chunk 22 optimal weight: 0.9980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 694 HIS ** O 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 776 ASN R 846 GLN S 678 GLN U 694 HIS ** P 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.237149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.193834 restraints weight = 59510.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.200050 restraints weight = 35564.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.204359 restraints weight = 24732.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.207364 restraints weight = 18919.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.209181 restraints weight = 15524.777| |-----------------------------------------------------------------------------| r_work (final): 0.4513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4511 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4511 r_free = 0.4511 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4511 r_free = 0.4511 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.4511 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5762 moved from start: 0.6650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34257 Z= 0.129 Angle : 0.718 16.545 46363 Z= 0.340 Chirality : 0.043 0.277 4870 Planarity : 0.005 0.052 6024 Dihedral : 4.914 56.201 4576 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.93 % Allowed : 17.90 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.13), residues: 4084 helix: 0.57 (0.15), residues: 1367 sheet: -0.84 (0.26), residues: 349 loop : -0.19 (0.13), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 676 TYR 0.020 0.001 TYR N 683 PHE 0.040 0.002 PHE P 263 TRP 0.063 0.003 TRP U 698 HIS 0.011 0.001 HIS U 694 Details of bonding type rmsd covalent geometry : bond 0.00290 (34137) covalent geometry : angle 0.67418 (46183) hydrogen bonds : bond 0.03519 ( 1101) hydrogen bonds : angle 5.48774 ( 3024) metal coordination : bond 0.00531 ( 120) metal coordination : angle 3.99932 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 756 time to evaluate : 1.199 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 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: L 476 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.6979 (ptt-90) REVERT: L 479 LEU cc_start: 0.8860 (mt) cc_final: 0.7970 (mt) REVERT: L 482 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8272 (mp0) REVERT: L 548 MET cc_start: 0.5959 (tmm) cc_final: 0.5453 (tmm) REVERT: L 556 ARG cc_start: 0.6829 (mtt-85) cc_final: 0.6164 (mtt-85) REVERT: L 561 GLU cc_start: 0.7257 (mt-10) cc_final: 0.7006 (mp0) REVERT: L 606 GLN cc_start: 0.8027 (pp30) cc_final: 0.7608 (pp30) REVERT: L 607 MET cc_start: 0.8327 (mmt) cc_final: 0.7674 (mmt) REVERT: L 640 PHE cc_start: 0.7330 (m-80) cc_final: 0.6939 (m-80) REVERT: L 671 THR cc_start: 0.8428 (m) cc_final: 0.8194 (p) REVERT: L 674 MET cc_start: 0.8331 (mtp) cc_final: 0.7872 (mtp) REVERT: L 761 MET cc_start: 0.4248 (ppp) cc_final: 0.3127 (tmm) REVERT: L 765 ASP cc_start: 0.6724 (t70) cc_final: 0.6059 (t0) REVERT: L 790 ARG cc_start: 0.7000 (tpp80) cc_final: 0.6629 (tpp80) REVERT: L 847 HIS cc_start: 0.6275 (m90) cc_final: 0.5602 (m90) REVERT: L 868 PHE cc_start: 0.4756 (OUTLIER) cc_final: 0.4019 (m-80) REVERT: L 887 ARG cc_start: 0.7974 (ttm-80) cc_final: 0.7729 (ttm-80) REVERT: M 585 MET cc_start: -0.3024 (mmm) cc_final: -0.3339 (mmm) REVERT: M 682 MET cc_start: 0.6274 (ttm) cc_final: 0.6044 (ttm) REVERT: M 793 TYR cc_start: 0.5559 (m-80) cc_final: 0.4873 (m-80) REVERT: M 852 MET cc_start: 0.6605 (ttt) cc_final: 0.6372 (ttt) REVERT: M 864 MET cc_start: 0.7784 (ttm) cc_final: 0.7375 (mtm) REVERT: M 889 LEU cc_start: 0.7980 (mt) cc_final: 0.7635 (mt) REVERT: M 899 ARG cc_start: 0.6632 (ptm160) cc_final: 0.6380 (ptp-170) REVERT: N 495 ILE cc_start: 0.6864 (pt) cc_final: 0.6547 (mt) REVERT: N 558 PHE cc_start: 0.8196 (m-10) cc_final: 0.7947 (m-10) REVERT: N 595 LEU cc_start: 0.7859 (pp) cc_final: 0.7199 (tt) REVERT: N 596 ARG cc_start: 0.7579 (ptt-90) cc_final: 0.7353 (ptt-90) REVERT: N 597 ARG cc_start: 0.7601 (ttp-110) cc_final: 0.7267 (mtm-85) REVERT: N 598 ARG cc_start: 0.7063 (mmt180) cc_final: 0.6770 (mmt90) REVERT: N 647 LEU cc_start: 0.5924 (tp) cc_final: 0.5664 (tt) REVERT: N 682 MET cc_start: 0.7088 (tmm) cc_final: 0.6881 (tmm) REVERT: N 684 VAL cc_start: 0.7349 (OUTLIER) cc_final: 0.6695 (p) REVERT: N 733 GLU cc_start: 0.6552 (mm-30) cc_final: 0.6322 (mm-30) REVERT: N 757 ASN cc_start: 0.7507 (t0) cc_final: 0.7125 (m-40) REVERT: N 801 MET cc_start: 0.6661 (mtp) cc_final: 0.6387 (mtp) REVERT: N 831 ARG cc_start: 0.5798 (ptp-170) cc_final: 0.5253 (ptp-170) REVERT: N 855 LYS cc_start: 0.7293 (ttmm) cc_final: 0.7046 (ttmm) REVERT: O 513 MET cc_start: 0.7177 (ppp) cc_final: 0.4531 (pmm) REVERT: O 585 MET cc_start: 0.5385 (mmm) cc_final: 0.5074 (mmm) REVERT: O 607 MET cc_start: 0.5224 (mtp) cc_final: 0.5007 (mtp) REVERT: O 684 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8501 (m) REVERT: O 729 ARG cc_start: 0.5385 (OUTLIER) cc_final: 0.2717 (tpp80) REVERT: O 863 GLU cc_start: 0.6522 (mt-10) cc_final: 0.6044 (mt-10) REVERT: O 885 ARG cc_start: 0.7452 (ttt180) cc_final: 0.7069 (ttt90) REVERT: R 513 MET cc_start: 0.7381 (tmm) cc_final: 0.6755 (tmm) REVERT: R 667 GLU cc_start: 0.7209 (mp0) cc_final: 0.6977 (mp0) REVERT: R 733 GLU cc_start: 0.6619 (tp30) cc_final: 0.6329 (tp30) REVERT: R 846 GLN cc_start: 0.6823 (OUTLIER) cc_final: 0.6521 (tm-30) REVERT: S 513 MET cc_start: 0.7017 (ttt) cc_final: 0.6550 (ttt) REVERT: S 597 ARG cc_start: 0.7552 (ttp-110) cc_final: 0.7168 (ttm170) REVERT: S 733 GLU cc_start: 0.7106 (mm-30) cc_final: 0.6815 (mm-30) REVERT: S 801 MET cc_start: 0.6485 (mtp) cc_final: 0.6006 (mtt) REVERT: S 823 ARG cc_start: 0.6604 (mtp85) cc_final: 0.6159 (mtm110) REVERT: S 878 SER cc_start: 0.8053 (t) cc_final: 0.7835 (t) REVERT: T 513 MET cc_start: 0.5995 (ttt) cc_final: 0.5699 (ttt) REVERT: T 607 MET cc_start: 0.3184 (OUTLIER) cc_final: 0.2912 (mpp) REVERT: T 677 HIS cc_start: 0.7241 (m-70) cc_final: 0.6932 (m-70) REVERT: T 682 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.6833 (ppp) REVERT: T 761 MET cc_start: 0.4712 (ptm) cc_final: 0.4176 (ptm) REVERT: T 765 ASP cc_start: 0.6994 (t0) cc_final: 0.6568 (t0) REVERT: T 860 TRP cc_start: 0.6711 (m-10) cc_final: 0.6486 (m-10) REVERT: T 889 LEU cc_start: 0.7754 (mt) cc_final: 0.7358 (mt) REVERT: U 481 TYR cc_start: 0.8123 (t80) cc_final: 0.7693 (t80) REVERT: U 545 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6618 (mm-30) REVERT: U 552 ASN cc_start: 0.7697 (p0) cc_final: 0.7269 (p0) REVERT: U 607 MET cc_start: 0.8380 (mmt) cc_final: 0.8076 (mpp) REVERT: U 640 PHE cc_start: 0.7128 (m-80) cc_final: 0.6873 (m-80) REVERT: U 647 LEU cc_start: 0.8672 (tp) cc_final: 0.8283 (tp) REVERT: U 648 LEU cc_start: 0.8400 (tp) cc_final: 0.8114 (tp) REVERT: U 651 LYS cc_start: 0.8496 (mttt) cc_final: 0.8065 (mttt) REVERT: U 674 MET cc_start: 0.7920 (mpp) cc_final: 0.7489 (mpp) REVERT: U 684 VAL cc_start: 0.8227 (OUTLIER) cc_final: 0.7869 (m) REVERT: U 693 LYS cc_start: 0.7550 (tttt) cc_final: 0.7280 (tttt) REVERT: U 761 MET cc_start: 0.3817 (ppp) cc_final: 0.3550 (ppp) REVERT: U 772 PHE cc_start: 0.7710 (m-10) cc_final: 0.7089 (m-10) REVERT: U 781 ASP cc_start: 0.7778 (t0) cc_final: 0.7410 (t0) REVERT: U 826 LYS cc_start: 0.8668 (tttt) cc_final: 0.8167 (tptp) REVERT: P 64 GLN cc_start: 0.8158 (pt0) cc_final: 0.7847 (pt0) REVERT: P 121 CYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6968 (m) REVERT: P 156 ARG cc_start: 0.8401 (tmm160) cc_final: 0.7756 (ptt180) REVERT: P 159 LYS cc_start: 0.7404 (mttt) cc_final: 0.7151 (mttt) REVERT: P 160 TRP cc_start: 0.7659 (p-90) cc_final: 0.7428 (p-90) REVERT: P 161 ARG cc_start: 0.8643 (ptm160) cc_final: 0.7323 (mtp-110) REVERT: P 179 PHE cc_start: 0.8287 (m-80) cc_final: 0.7988 (m-80) REVERT: P 180 GLU cc_start: 0.8226 (pm20) cc_final: 0.7549 (pp20) REVERT: P 242 TYR cc_start: 0.5807 (t80) cc_final: 0.4711 (t80) REVERT: P 283 MET cc_start: 0.6798 (ttt) cc_final: 0.5766 (ttt) REVERT: P 293 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8390 (mt-10) REVERT: P 368 PHE cc_start: 0.7156 (m-80) cc_final: 0.5822 (m-80) REVERT: Q 143 TYR cc_start: 0.8642 (m-80) cc_final: 0.8077 (m-80) REVERT: Q 155 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7597 (tm-30) REVERT: Q 159 LYS cc_start: 0.6975 (mttt) cc_final: 0.6237 (mptt) REVERT: Q 160 TRP cc_start: 0.8146 (p-90) cc_final: 0.7788 (p-90) REVERT: Q 161 ARG cc_start: 0.8248 (ptm-80) cc_final: 0.7717 (mtm-85) REVERT: Q 163 GLN cc_start: 0.8441 (tp40) cc_final: 0.7205 (tp40) REVERT: Q 200 LYS cc_start: 0.5557 (pptt) cc_final: 0.5324 (pptt) REVERT: Q 302 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7910 (mm) REVERT: Q 303 GLU cc_start: 0.8328 (mp0) cc_final: 0.7688 (mp0) REVERT: Q 368 PHE cc_start: 0.7441 (m-80) cc_final: 0.7162 (m-80) outliers start: 70 outliers final: 51 residues processed: 787 average time/residue: 0.2368 time to fit residues: 291.2299 Evaluate side-chains 816 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 754 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 481 TYR Chi-restraints excluded: chain L residue 608 PHE Chi-restraints excluded: chain L residue 641 ASP Chi-restraints excluded: chain L residue 667 GLU Chi-restraints excluded: chain L residue 694 HIS Chi-restraints excluded: chain L residue 858 ILE Chi-restraints excluded: chain L residue 868 PHE Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 684 VAL Chi-restraints excluded: chain M residue 737 LEU Chi-restraints excluded: chain M residue 819 LEU Chi-restraints excluded: chain M residue 858 ILE Chi-restraints excluded: chain M residue 875 THR Chi-restraints excluded: chain N residue 475 THR Chi-restraints excluded: chain N residue 504 LEU Chi-restraints excluded: chain N residue 548 MET Chi-restraints excluded: chain N residue 585 MET Chi-restraints excluded: chain N residue 607 MET Chi-restraints excluded: chain N residue 643 ILE Chi-restraints excluded: chain N residue 684 VAL Chi-restraints excluded: chain N residue 737 LEU Chi-restraints excluded: chain N residue 858 ILE Chi-restraints excluded: chain N residue 875 THR Chi-restraints excluded: chain O residue 684 VAL Chi-restraints excluded: chain O residue 729 ARG Chi-restraints excluded: chain O residue 738 LEU Chi-restraints excluded: chain O residue 739 HIS Chi-restraints excluded: chain O residue 824 ILE Chi-restraints excluded: chain O residue 905 LEU Chi-restraints excluded: chain R residue 669 SER Chi-restraints excluded: chain R residue 739 HIS Chi-restraints excluded: chain R residue 776 ASN Chi-restraints excluded: chain R residue 846 GLN Chi-restraints excluded: chain S residue 643 ILE Chi-restraints excluded: chain S residue 647 LEU Chi-restraints excluded: chain S residue 761 MET Chi-restraints excluded: chain S residue 855 LYS Chi-restraints excluded: chain S residue 858 ILE Chi-restraints excluded: chain T residue 607 MET Chi-restraints excluded: chain T residue 682 MET Chi-restraints excluded: chain T residue 713 LEU Chi-restraints excluded: chain T residue 878 SER Chi-restraints excluded: chain T residue 907 GLU Chi-restraints excluded: chain U residue 681 ILE Chi-restraints excluded: chain U residue 684 VAL Chi-restraints excluded: chain U residue 694 HIS Chi-restraints excluded: chain U residue 855 LYS Chi-restraints excluded: chain U residue 875 THR Chi-restraints excluded: chain P residue 121 CYS Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain P residue 165 LYS Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 230 LYS Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 361 THR Chi-restraints excluded: chain Q residue 146 LEU Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain Q residue 292 LYS Chi-restraints excluded: chain Q residue 302 LEU Chi-restraints excluded: chain Q residue 312 VAL Chi-restraints excluded: chain Q residue 361 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 76 optimal weight: 30.0000 chunk 364 optimal weight: 0.9980 chunk 236 optimal weight: 0.7980 chunk 264 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 353 optimal weight: 4.9990 chunk 286 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 197 optimal weight: 0.0980 chunk 189 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 694 HIS O 776 ASN ** O 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 776 ASN S 678 GLN ** P 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.226000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.182242 restraints weight = 61898.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.188514 restraints weight = 36743.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.192726 restraints weight = 25454.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.195941 restraints weight = 19531.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.197603 restraints weight = 16070.763| |-----------------------------------------------------------------------------| r_work (final): 0.4488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4490 r_free = 0.4490 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4490 r_free = 0.4490 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5807 moved from start: 0.6677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.282 34257 Z= 0.227 Angle : 0.896 59.200 46363 Z= 0.495 Chirality : 0.046 0.724 4870 Planarity : 0.006 0.214 6024 Dihedral : 4.955 56.143 4576 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.89 % Favored : 97.09 % Rotamer: Outliers : 1.90 % Allowed : 18.17 % Favored : 79.93 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.13), residues: 4084 helix: 0.57 (0.15), residues: 1367 sheet: -0.83 (0.26), residues: 349 loop : -0.18 (0.13), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG Q 157 TYR 0.016 0.001 TYR N 683 PHE 0.037 0.002 PHE P 263 TRP 0.056 0.003 TRP U 698 HIS 0.349 0.004 HIS L 694 Details of bonding type rmsd covalent geometry : bond 0.00485 (34137) covalent geometry : angle 0.86217 (46183) hydrogen bonds : bond 0.03555 ( 1101) hydrogen bonds : angle 5.49420 ( 3024) metal coordination : bond 0.00519 ( 120) metal coordination : angle 3.99350 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11102.41 seconds wall clock time: 190 minutes 7.79 seconds (11407.79 seconds total)