Starting phenix.real_space_refine on Thu Nov 20 21:43:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yfr_39227/11_2025/8yfr_39227.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yfr_39227/11_2025/8yfr_39227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yfr_39227/11_2025/8yfr_39227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yfr_39227/11_2025/8yfr_39227.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yfr_39227/11_2025/8yfr_39227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yfr_39227/11_2025/8yfr_39227.map" } resolution = 3.4 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= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 Mg 1 5.21 5 S 225 5.16 5 C 24932 2.51 5 N 6798 2.21 5 O 7386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39350 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 10920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1384, 10920 Classifications: {'peptide': 1384} Link IDs: {'PCIS': 3, 'PTRANS': 62, 'TRANS': 1318} Chain breaks: 6 Chain: "B" Number of atoms: 9031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1131, 9031 Classifications: {'peptide': 1131} Link IDs: {'PTRANS': 50, 'TRANS': 1080} Chain breaks: 5 Chain: "C" Number of atoms: 2098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2098 Classifications: {'peptide': 263} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 249} Chain: "D" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain breaks: 2 Chain: "E" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1740 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain: "F" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 677 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "G" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1324 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 160} Chain: "H" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1052 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 917 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "J" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 545 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 932 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "R" Number of atoms: 5698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5698 Classifications: {'peptide': 691} Link IDs: {'PTRANS': 46, 'TRANS': 644} Chain breaks: 3 Chain: "S" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3102 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 16, 'TRANS': 361} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 527 SG CYS A 67 55.230 112.614 71.783 1.00260.61 S ATOM 549 SG CYS A 70 55.684 109.036 70.482 1.00251.92 S ATOM 594 SG CYS A 77 56.335 109.841 74.176 1.00254.44 S ATOM 829 SG CYS A 107 97.633 132.278 61.958 1.00303.12 S ATOM 851 SG CYS A 110 96.935 131.090 58.421 1.00296.86 S ATOM 1157 SG CYS A 148 99.951 129.739 60.326 1.00314.32 S ATOM 1172 SG CYS A 168 99.904 133.354 59.112 1.00293.48 S ATOM 19483 SG CYS B1163 69.024 106.962 59.883 1.00201.77 S ATOM 19501 SG CYS B1166 70.131 109.426 62.501 1.00212.83 S ATOM 19624 SG CYS B1182 66.823 109.857 60.654 1.00206.13 S ATOM 19647 SG CYS B1185 70.124 110.564 58.881 1.00210.44 S ATOM 20592 SG CYS C 85 14.119 82.491 108.831 1.00139.56 S ATOM 20605 SG CYS C 87 15.441 86.015 109.310 1.00156.17 S ATOM 20640 SG CYS C 91 13.196 84.530 111.879 1.00123.47 S ATOM 20663 SG CYS C 94 16.691 83.116 111.586 1.00106.63 S ATOM 28381 SG CYS I 75 110.316 56.942 150.889 1.00183.06 S ATOM 28403 SG CYS I 78 109.968 57.010 154.612 1.00184.64 S ATOM 28619 SG CYS I 103 107.770 59.274 152.509 1.00164.31 S ATOM 28641 SG CYS I 106 111.540 59.967 152.665 1.00171.91 S ATOM 27833 SG CYS I 7 136.509 92.696 135.420 1.00188.34 S ATOM 27856 SG CYS I 10 135.872 96.303 134.357 1.00185.37 S ATOM 28019 SG CYS I 29 135.691 93.414 131.689 1.00212.37 S ATOM 28044 SG CYS I 32 138.940 94.392 133.254 1.00208.31 S ATOM 28760 SG CYS J 7 40.520 68.034 127.930 1.00 48.91 S ATOM 28783 SG CYS J 10 37.589 65.796 127.170 1.00 53.66 S ATOM 29059 SG CYS J 44 41.056 64.352 128.190 1.00 50.90 S ATOM 29065 SG CYS J 45 38.710 65.947 130.700 1.00 49.22 S ATOM 30227 SG CYS L 33 44.677 111.728 134.088 1.00115.72 S ATOM 30242 SG CYS L 36 42.235 112.518 136.815 1.00117.57 S ATOM 30352 SG CYS L 50 43.240 115.236 134.365 1.00110.55 S ATOM 30376 SG CYS L 53 45.816 113.964 136.879 1.00121.06 S Time building chain proxies: 8.64, per 1000 atoms: 0.22 Number of scatterers: 39350 At special positions: 0 Unit cell: (183.43, 180.11, 178.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 225 16.00 Mg 1 11.99 O 7386 8.00 N 6798 7.00 C 24932 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: 3.41 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 77 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 168 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 148 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 91 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 85 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 87 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 94 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 103 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 33 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 50 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 53 " Number of angles added : 45 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9248 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 52 sheets defined 41.2% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 130 through 144 removed outlier: 4.421A pdb=" N THR A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 214 Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 231 through 236 removed outlier: 4.040A pdb=" N MET A 235 " --> pdb=" O PRO A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 279 Processing helix chain 'A' and resid 286 through 306 Processing helix chain 'A' and resid 327 through 331 removed outlier: 3.673A pdb=" N LEU A 330 " --> pdb=" O ARG A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 340 removed outlier: 3.570A pdb=" N GLY A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 335 through 340' Processing helix chain 'A' and resid 368 through 375 Processing helix chain 'A' and resid 385 through 396 Processing helix chain 'A' and resid 421 through 425 removed outlier: 3.545A pdb=" N ILE A 425 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 475 through 480 Processing helix chain 'A' and resid 495 through 506 Processing helix chain 'A' and resid 508 through 511 Processing helix chain 'A' and resid 526 through 536 Processing helix chain 'A' and resid 543 through 553 Processing helix chain 'A' and resid 575 through 583 removed outlier: 3.963A pdb=" N ALA A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 629 through 638 Processing helix chain 'A' and resid 639 through 660 removed outlier: 3.602A pdb=" N PHE A 647 " --> pdb=" O CYS A 643 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 Processing helix chain 'A' and resid 673 through 700 Processing helix chain 'A' and resid 710 through 738 Processing helix chain 'A' and resid 742 through 751 Processing helix chain 'A' and resid 755 through 764 Processing helix chain 'A' and resid 810 through 846 removed outlier: 3.773A pdb=" N ALA A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 890 through 899 Processing helix chain 'A' and resid 910 through 914 removed outlier: 3.540A pdb=" N ILE A 914 " --> pdb=" O PRO A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 920 Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 961 through 974 Processing helix chain 'A' and resid 984 through 998 Processing helix chain 'A' and resid 1006 through 1017 removed outlier: 3.548A pdb=" N THR A1017 " --> pdb=" O GLN A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1028 Processing helix chain 'A' and resid 1029 through 1035 Processing helix chain 'A' and resid 1040 through 1058 Processing helix chain 'A' and resid 1065 through 1080 removed outlier: 3.529A pdb=" N ILE A1069 " --> pdb=" O MET A1065 " (cutoff:3.500A) Proline residue: A1077 - end of helix removed outlier: 4.243A pdb=" N GLN A1080 " --> pdb=" O GLU A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1109 removed outlier: 3.914A pdb=" N ARG A1102 " --> pdb=" O LEU A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1128 removed outlier: 3.746A pdb=" N LEU A1128 " --> pdb=" O ARG A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1141 removed outlier: 3.850A pdb=" N ALA A1133 " --> pdb=" O ASP A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1167 No H-bonds generated for 'chain 'A' and resid 1165 through 1167' Processing helix chain 'A' and resid 1168 through 1176 Processing helix chain 'A' and resid 1200 through 1207 removed outlier: 3.668A pdb=" N LYS A1207 " --> pdb=" O ARG A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1222 removed outlier: 3.961A pdb=" N PHE A1222 " --> pdb=" O ILE A1218 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1274 Processing helix chain 'A' and resid 1315 through 1322 Processing helix chain 'A' and resid 1334 through 1342 Processing helix chain 'A' and resid 1343 through 1361 Processing helix chain 'A' and resid 1367 through 1379 removed outlier: 3.919A pdb=" N MET A1371 " --> pdb=" O ASN A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1398 through 1406 Processing helix chain 'A' and resid 1407 through 1419 Processing helix chain 'A' and resid 1426 through 1434 removed outlier: 4.008A pdb=" N ASN A1430 " --> pdb=" O GLY A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1442 Processing helix chain 'A' and resid 1449 through 1456 Processing helix chain 'B' and resid 13 through 28 Processing helix chain 'B' and resid 31 through 44 Processing helix chain 'B' and resid 44 through 52 Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 175 through 183 Processing helix chain 'B' and resid 274 through 282 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 299 through 306 removed outlier: 3.563A pdb=" N LEU B 306 " --> pdb=" O MET B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 313 Processing helix chain 'B' and resid 318 through 329 removed outlier: 3.718A pdb=" N ARG B 329 " --> pdb=" O PHE B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 351 removed outlier: 4.375A pdb=" N LYS B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLN B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 383 Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 401 through 432 removed outlier: 3.503A pdb=" N LEU B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU B 430 " --> pdb=" O GLN B 426 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 457 removed outlier: 3.575A pdb=" N THR B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 465 Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 501 through 506 removed outlier: 3.867A pdb=" N ARG B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 512 Processing helix chain 'B' and resid 544 through 554 Processing helix chain 'B' and resid 585 through 599 removed outlier: 4.136A pdb=" N LEU B 589 " --> pdb=" O ASP B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 658 removed outlier: 3.544A pdb=" N ILE B 652 " --> pdb=" O THR B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 684 Processing helix chain 'B' and resid 693 through 698 removed outlier: 3.511A pdb=" N GLU B 696 " --> pdb=" O GLU B 693 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE B 698 " --> pdb=" O GLU B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 707 Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.606A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 756 Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.508A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 775 removed outlier: 4.315A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 811 Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.229A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.945A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1154 Processing helix chain 'B' and resid 1198 through 1209 Processing helix chain 'C' and resid 25 through 39 Processing helix chain 'C' and resid 58 through 68 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 206 through 210 removed outlier: 3.692A pdb=" N GLU C 210 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 265 Processing helix chain 'D' and resid 52 through 71 Processing helix chain 'D' and resid 85 through 92 removed outlier: 3.646A pdb=" N LEU D 89 " --> pdb=" O ASP D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 112 Processing helix chain 'D' and resid 117 through 129 removed outlier: 3.562A pdb=" N CYS D 121 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 148 removed outlier: 3.546A pdb=" N SER D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 160 removed outlier: 3.688A pdb=" N THR D 158 " --> pdb=" O ASP D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 164 Processing helix chain 'D' and resid 170 through 179 Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 30 through 35 Processing helix chain 'E' and resid 37 through 46 Processing helix chain 'E' and resid 64 through 71 Processing helix chain 'E' and resid 88 through 103 removed outlier: 4.226A pdb=" N MET E 92 " --> pdb=" O GLY E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 123 Processing helix chain 'E' and resid 137 through 140 Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 156 through 168 Processing helix chain 'E' and resid 170 through 174 removed outlier: 4.011A pdb=" N LEU E 174 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 188 Processing helix chain 'F' and resid 75 through 79 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 22 through 35 removed outlier: 3.624A pdb=" N LEU G 26 " --> pdb=" O MET G 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 92 Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 133 through 135 No H-bonds generated for 'chain 'H' and resid 133 through 135' Processing helix chain 'I' and resid 59 through 65 removed outlier: 4.275A pdb=" N GLY I 63 " --> pdb=" O ASP I 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 removed outlier: 3.546A pdb=" N GLU J 27 " --> pdb=" O ARG J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 51 removed outlier: 4.118A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'R' and resid 4 through 14 Processing helix chain 'R' and resid 55 through 57 No H-bonds generated for 'chain 'R' and resid 55 through 57' Processing helix chain 'R' and resid 59 through 63 Processing helix chain 'R' and resid 72 through 92 removed outlier: 3.669A pdb=" N MET R 76 " --> pdb=" O THR R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 121 Processing helix chain 'R' and resid 156 through 160 removed outlier: 3.758A pdb=" N ILE R 160 " --> pdb=" O SER R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 185 removed outlier: 3.616A pdb=" N ASP R 172 " --> pdb=" O HIS R 168 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 189 removed outlier: 3.829A pdb=" N SER R 189 " --> pdb=" O PRO R 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 186 through 189' Processing helix chain 'R' and resid 203 through 218 removed outlier: 3.730A pdb=" N ILE R 208 " --> pdb=" O GLY R 204 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER R 218 " --> pdb=" O SER R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 235 through 244 Processing helix chain 'R' and resid 255 through 258 removed outlier: 3.811A pdb=" N GLN R 258 " --> pdb=" O VAL R 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 255 through 258' Processing helix chain 'R' and resid 266 through 270 Processing helix chain 'R' and resid 291 through 302 Processing helix chain 'R' and resid 312 through 328 removed outlier: 3.537A pdb=" N GLY R 328 " --> pdb=" O CYS R 324 " (cutoff:3.500A) Processing helix chain 'R' and resid 343 through 356 Processing helix chain 'R' and resid 357 through 359 No H-bonds generated for 'chain 'R' and resid 357 through 359' Processing helix chain 'R' and resid 370 through 384 Processing helix chain 'R' and resid 384 through 407 Processing helix chain 'R' and resid 541 through 552 Processing helix chain 'R' and resid 555 through 583 Processing helix chain 'R' and resid 599 through 603 Processing helix chain 'R' and resid 605 through 609 Processing helix chain 'R' and resid 620 through 629 Processing helix chain 'R' and resid 630 through 634 removed outlier: 4.213A pdb=" N SER R 634 " --> pdb=" O ALA R 631 " (cutoff:3.500A) Processing helix chain 'R' and resid 638 through 643 removed outlier: 4.194A pdb=" N SER R 643 " --> pdb=" O ASP R 639 " (cutoff:3.500A) Processing helix chain 'R' and resid 652 through 656 Processing helix chain 'R' and resid 669 through 673 Processing helix chain 'R' and resid 681 through 693 removed outlier: 3.576A pdb=" N LYS R 692 " --> pdb=" O ALA R 688 " (cutoff:3.500A) Processing helix chain 'R' and resid 694 through 696 No H-bonds generated for 'chain 'R' and resid 694 through 696' Processing helix chain 'R' and resid 697 through 704 Processing helix chain 'R' and resid 718 through 731 removed outlier: 4.481A pdb=" N THR R 722 " --> pdb=" O SER R 718 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU R 729 " --> pdb=" O LYS R 725 " (cutoff:3.500A) Processing helix chain 'R' and resid 812 through 819 removed outlier: 3.553A pdb=" N LEU R 818 " --> pdb=" O LYS R 814 " (cutoff:3.500A) Processing helix chain 'R' and resid 838 through 842 removed outlier: 4.118A pdb=" N TYR R 841 " --> pdb=" O PHE R 838 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE R 842 " --> pdb=" O LYS R 839 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 838 through 842' Processing helix chain 'R' and resid 856 through 864 Processing helix chain 'S' and resid 48 through 55 Processing helix chain 'S' and resid 61 through 65 Processing helix chain 'S' and resid 69 through 75 removed outlier: 3.519A pdb=" N LYS S 75 " --> pdb=" O VAL S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 91 Processing helix chain 'S' and resid 102 through 111 Processing helix chain 'S' and resid 135 through 147 Processing helix chain 'S' and resid 150 through 167 Processing helix chain 'S' and resid 172 through 176 Processing helix chain 'S' and resid 178 through 183 Processing helix chain 'S' and resid 184 through 186 No H-bonds generated for 'chain 'S' and resid 184 through 186' Processing helix chain 'S' and resid 225 through 228 Processing helix chain 'S' and resid 241 through 263 removed outlier: 3.585A pdb=" N LEU S 262 " --> pdb=" O GLN S 258 " (cutoff:3.500A) Processing helix chain 'S' and resid 288 through 295 removed outlier: 3.640A pdb=" N LYS S 294 " --> pdb=" O PRO S 290 " (cutoff:3.500A) Processing helix chain 'S' and resid 306 through 326 Processing helix chain 'S' and resid 351 through 363 Processing helix chain 'S' and resid 364 through 378 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 90 removed outlier: 11.295A pdb=" N LEU A 86 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 10.695A pdb=" N LYS A 88 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL A 239 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 178 Processing sheet with id=AA4, first strand: chain 'A' and resid 349 through 356 removed outlier: 8.451A pdb=" N PHE A 469 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL A 353 " --> pdb=" O PHE A 469 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LEU A 471 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N SER A 355 " --> pdb=" O LEU A 471 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 376 through 380 removed outlier: 6.684A pdb=" N LYS A 432 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL A 406 " --> pdb=" O LYS A 432 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLU A 434 " --> pdb=" O LYS A 404 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 513 through 514 removed outlier: 3.830A pdb=" N LYS A 519 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AA8, first strand: chain 'A' and resid 566 through 568 removed outlier: 6.270A pdb=" N VAL H 95 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE H 27 " --> pdb=" O GLN H 13 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N LEU H 121 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER H 116 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N VAL H 100 " --> pdb=" O SER H 116 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 589 through 591 removed outlier: 6.729A pdb=" N LEU A 607 " --> pdb=" O MET A 614 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 767 through 768 Processing sheet with id=AB2, first strand: chain 'A' and resid 850 through 851 removed outlier: 6.812A pdb=" N THR A 857 " --> pdb=" O ILE A 865 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 880 through 883 Processing sheet with id=AB4, first strand: chain 'A' and resid 1285 through 1295 Processing sheet with id=AB5, first strand: chain 'A' and resid 1143 through 1144 removed outlier: 6.718A pdb=" N THR A1143 " --> pdb=" O LEU A1276 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1226 through 1230 removed outlier: 4.909A pdb=" N VAL A1244 " --> pdb=" O TRP A1193 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N TRP A1193 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU A1194 " --> pdb=" O ILE A1154 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE A1154 " --> pdb=" O LEU A1194 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG A1196 " --> pdb=" O THR A1152 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR A1152 " --> pdb=" O ARG A1196 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLU A1198 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A1154 " --> pdb=" O TYR I 44 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR I 44 " --> pdb=" O ILE A1154 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 143 through 147 removed outlier: 5.391A pdb=" N VAL A1446 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY G 59 " --> pdb=" O ILE A1448 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 143 through 147 removed outlier: 5.391A pdb=" N VAL A1446 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY G 59 " --> pdb=" O ILE A1448 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N VAL G 77 " --> pdb=" O VAL G 46 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL G 46 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR G 37 " --> pdb=" O ILE G 45 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 55 through 62 removed outlier: 4.267A pdb=" N ALA B 62 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE B 71 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASP B 118 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE B 82 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TYR B 116 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU B 84 " --> pdb=" O PRO B 114 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY B 159 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU B 117 " --> pdb=" O HIS B 157 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N HIS B 157 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N MET B 119 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS B 155 " --> pdb=" O MET B 119 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 88 through 90 Processing sheet with id=AC2, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC3, first strand: chain 'B' and resid 397 through 400 Processing sheet with id=AC4, first strand: chain 'B' and resid 214 through 218 removed outlier: 3.971A pdb=" N HIS B 227 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU B 235 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU B 241 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 537 through 538 Processing sheet with id=AC6, first strand: chain 'B' and resid 537 through 538 Processing sheet with id=AC7, first strand: chain 'B' and resid 557 through 558 removed outlier: 5.553A pdb=" N TRP B 579 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL B 575 " --> pdb=" O TRP B 579 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY B 581 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.794A pdb=" N PHE B 963 " --> pdb=" O LEU B 954 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY B 947 " --> pdb=" O VAL B 905 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.794A pdb=" N PHE B 963 " --> pdb=" O LEU B 954 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N VAL B 952 " --> pdb=" O LYS L 60 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD2, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.522A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N LEU B1010 " --> pdb=" O ASN B 822 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE B 824 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ILE B1012 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA B 826 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AD4, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.522A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD6, first strand: chain 'B' and resid 1157 through 1163 Processing sheet with id=AD7, first strand: chain 'B' and resid 1171 through 1174 Processing sheet with id=AD8, first strand: chain 'C' and resid 6 through 12 removed outlier: 6.692A pdb=" N GLU C 18 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ALA C 12 " --> pdb=" O GLU C 16 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLU C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU C 233 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 119 through 122 removed outlier: 5.676A pdb=" N LYS C 120 " --> pdb=" O GLU C 99 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLU C 99 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLU C 152 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ASN C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN C 154 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS C 160 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ILE C 45 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY C 162 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LEU C 43 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE L 67 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 71 through 73 removed outlier: 4.650A pdb=" N GLU C 131 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AE3, first strand: chain 'E' and resid 59 through 61 removed outlier: 6.452A pdb=" N TRP E 78 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ILE E 110 " --> pdb=" O TRP E 78 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLU E 80 " --> pdb=" O ILE E 110 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 151 through 154 removed outlier: 4.195A pdb=" N LYS E 151 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE E 198 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 86 through 95 removed outlier: 3.865A pdb=" N ILE G 90 " --> pdb=" O ASP G 102 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N PHE G 100 " --> pdb=" O SER G 92 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N VAL G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLY G 98 " --> pdb=" O VAL G 94 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ALA G 159 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE G 109 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY G 161 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TYR G 158 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N THR G 150 " --> pdb=" O TYR G 158 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE G 160 " --> pdb=" O VAL G 148 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 120 through 122 Processing sheet with id=AE7, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AE8, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AE9, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF1, first strand: chain 'R' and resid 18 through 19 removed outlier: 6.384A pdb=" N HIS R 227 " --> pdb=" O LYS R 249 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU R 251 " --> pdb=" O HIS R 227 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE R 229 " --> pdb=" O LEU R 251 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N GLU R 253 " --> pdb=" O ILE R 229 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP R 53 " --> pdb=" O TYR R 230 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP R 48 " --> pdb=" O ARG R 94 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU R 192 " --> pdb=" O LYS R 95 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE R 97 " --> pdb=" O GLU R 192 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE R 194 " --> pdb=" O ILE R 97 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 27 through 29 Processing sheet with id=AF3, first strand: chain 'R' and resid 364 through 365 Processing sheet with id=AF4, first strand: chain 'R' and resid 759 through 760 Processing sheet with id=AF5, first strand: chain 'S' and resid 4 through 8 removed outlier: 4.386A pdb=" N VAL S 345 " --> pdb=" O SER S 335 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER S 335 " --> pdb=" O VAL S 345 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE S 119 " --> pdb=" O TYR S 336 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TRP S 101 " --> pdb=" O ILE S 132 " (cutoff:3.500A) removed outlier: 9.613A pdb=" N PHE S 134 " --> pdb=" O TRP S 101 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE S 98 " --> pdb=" O LEU S 209 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLY S 211 " --> pdb=" O ILE S 98 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR S 100 " --> pdb=" O GLY S 211 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N ALA S 213 " --> pdb=" O THR S 100 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ARG S 200 " --> pdb=" O GLN S 23 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLN S 23 " --> pdb=" O ARG S 200 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N GLY S 202 " --> pdb=" O PRO S 21 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS S 36 " --> pdb=" O SER S 28 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'S' and resid 44 through 45 Processing sheet with id=AF7, first strand: chain 'S' and resid 216 through 217 removed outlier: 7.271A pdb=" N TYR S 230 " --> pdb=" O LYS S 266 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N ILE S 268 " --> pdb=" O TYR S 230 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU S 232 " --> pdb=" O ILE S 268 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N GLY S 270 " --> pdb=" O GLU S 232 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LYS S 234 " --> pdb=" O GLY S 270 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ARG S 272 " --> pdb=" O LYS S 234 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N THR S 236 " --> pdb=" O ARG S 272 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE S 267 " --> pdb=" O GLU S 283 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU S 283 " --> pdb=" O ILE S 267 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TYR S 269 " --> pdb=" O VAL S 281 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL S 281 " --> pdb=" O TYR S 269 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE S 271 " --> pdb=" O ARG S 279 " (cutoff:3.500A) 1759 hydrogen bonds defined for protein. 4866 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: 11.71 Time building geometry restraints manager: 4.55 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: 12969 1.34 - 1.46: 6454 1.46 - 1.58: 20337 1.58 - 1.70: 0 1.70 - 1.82: 367 Bond restraints: 40127 Sorted by residual: bond pdb=" CG GLU D 177 " pdb=" CD GLU D 177 " ideal model delta sigma weight residual 1.516 1.482 0.034 2.50e-02 1.60e+03 1.85e+00 bond pdb=" CD GLU D 177 " pdb=" OE1 GLU D 177 " ideal model delta sigma weight residual 1.249 1.223 0.026 1.90e-02 2.77e+03 1.81e+00 bond pdb=" CA ILE B1196 " pdb=" CB ILE B1196 " ideal model delta sigma weight residual 1.537 1.551 -0.014 1.29e-02 6.01e+03 1.10e+00 bond pdb=" N LEU B 175 " pdb=" CA LEU B 175 " ideal model delta sigma weight residual 1.456 1.469 -0.013 1.23e-02 6.61e+03 1.04e+00 bond pdb=" N GLN A 526 " pdb=" CA GLN A 526 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 1.01e+00 ... (remaining 40122 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 53258 1.79 - 3.57: 795 3.57 - 5.36: 97 5.36 - 7.14: 33 7.14 - 8.93: 6 Bond angle restraints: 54189 Sorted by residual: angle pdb=" N GLU D 177 " pdb=" CA GLU D 177 " pdb=" CB GLU D 177 " ideal model delta sigma weight residual 110.40 116.68 -6.28 1.63e+00 3.76e-01 1.48e+01 angle pdb=" C GLN R 738 " pdb=" CA GLN R 738 " pdb=" CB GLN R 738 " ideal model delta sigma weight residual 115.79 111.47 4.32 1.19e+00 7.06e-01 1.32e+01 angle pdb=" CA ARG A 231 " pdb=" CB ARG A 231 " pdb=" CG ARG A 231 " ideal model delta sigma weight residual 114.10 121.27 -7.17 2.00e+00 2.50e-01 1.29e+01 angle pdb=" C ASP D 176 " pdb=" N GLU D 177 " pdb=" CA GLU D 177 " ideal model delta sigma weight residual 121.14 114.93 6.21 1.75e+00 3.27e-01 1.26e+01 angle pdb=" N GLU K 88 " pdb=" CA GLU K 88 " pdb=" CB GLU K 88 " ideal model delta sigma weight residual 110.16 115.41 -5.25 1.48e+00 4.57e-01 1.26e+01 ... (remaining 54184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 22316 17.94 - 35.87: 1872 35.87 - 53.81: 278 53.81 - 71.75: 62 71.75 - 89.68: 33 Dihedral angle restraints: 24561 sinusoidal: 10259 harmonic: 14302 Sorted by residual: dihedral pdb=" CA PHE R 737 " pdb=" C PHE R 737 " pdb=" N GLN R 738 " pdb=" CA GLN R 738 " ideal model delta harmonic sigma weight residual -180.00 -155.02 -24.98 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA GLN A 769 " pdb=" C GLN A 769 " pdb=" N MET A 770 " pdb=" CA MET A 770 " ideal model delta harmonic sigma weight residual -180.00 -158.06 -21.94 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ARG I 30 " pdb=" C ARG I 30 " pdb=" N ASN I 31 " pdb=" CA ASN I 31 " ideal model delta harmonic sigma weight residual 180.00 159.94 20.06 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 24558 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 4276 0.041 - 0.081: 1225 0.081 - 0.122: 432 0.122 - 0.163: 45 0.163 - 0.203: 2 Chirality restraints: 5980 Sorted by residual: chirality pdb=" CB ILE G 97 " pdb=" CA ILE G 97 " pdb=" CG1 ILE G 97 " pdb=" CG2 ILE G 97 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ILE B1196 " pdb=" N ILE B1196 " pdb=" C ILE B1196 " pdb=" CB ILE B1196 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.44e-01 chirality pdb=" CA MET E 92 " pdb=" N MET E 92 " pdb=" C MET E 92 " pdb=" CB MET E 92 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 5977 not shown) Planarity restraints: 7014 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 170 " -0.016 2.00e-02 2.50e+03 1.26e-02 3.98e+00 pdb=" CG TRP C 170 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP C 170 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP C 170 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 170 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 170 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 170 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 170 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 170 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 170 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B1196 " -0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO B1197 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B1197 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B1197 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 797 " -0.016 2.00e-02 2.50e+03 1.36e-02 3.73e+00 pdb=" CG TYR B 797 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR B 797 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 797 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 797 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 797 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 797 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 797 " -0.001 2.00e-02 2.50e+03 ... (remaining 7011 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 514 2.64 - 3.20: 35195 3.20 - 3.77: 61515 3.77 - 4.33: 83529 4.33 - 4.90: 137491 Nonbonded interactions: 318244 Sorted by model distance: nonbonded pdb=" OD1 ASP A 484 " pdb="MG MG A1803 " model vdw 2.074 2.170 nonbonded pdb=" OD1 ASP A 482 " pdb="MG MG A1803 " model vdw 2.115 2.170 nonbonded pdb=" OH TYR A 916 " pdb=" O LEU A 983 " model vdw 2.143 3.040 nonbonded pdb=" OG1 THR B 264 " pdb=" OD1 ASP B 271 " model vdw 2.175 3.040 nonbonded pdb=" OD1 ASP A 486 " pdb="MG MG A1803 " model vdw 2.182 2.170 ... (remaining 318239 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.740 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 44.450 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 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 : 0.003 0.034 40159 Z= 0.121 Angle : 0.546 8.929 54234 Z= 0.280 Chirality : 0.043 0.203 5980 Planarity : 0.003 0.052 7014 Dihedral : 13.521 89.682 15313 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.49 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.02 % 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: 0.83 (0.12), residues: 4843 helix: 1.47 (0.13), residues: 1734 sheet: 0.35 (0.19), residues: 752 loop : 0.02 (0.13), residues: 2357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 231 TYR 0.034 0.001 TYR B 797 PHE 0.016 0.001 PHE R 860 TRP 0.034 0.001 TRP C 170 HIS 0.004 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00263 (40127) covalent geometry : angle 0.54222 (54189) hydrogen bonds : bond 0.14925 ( 1728) hydrogen bonds : angle 5.90405 ( 4866) metal coordination : bond 0.00450 ( 32) metal coordination : angle 2.34237 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 4357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8706 (t80) cc_final: 0.8185 (t80) REVERT: A 108 MET cc_start: 0.7424 (pmm) cc_final: 0.7184 (tmm) REVERT: A 212 PHE cc_start: 0.9349 (m-80) cc_final: 0.8964 (m-80) REVERT: A 850 MET cc_start: 0.8647 (ttp) cc_final: 0.8440 (ttt) REVERT: B 635 ASP cc_start: 0.8345 (p0) cc_final: 0.8077 (p0) REVERT: B 1156 ASP cc_start: 0.7464 (p0) cc_final: 0.7219 (p0) REVERT: B 1217 TYR cc_start: 0.8872 (m-80) cc_final: 0.7902 (m-80) REVERT: D 55 GLU cc_start: 0.7988 (pm20) cc_final: 0.7709 (pm20) REVERT: D 177 GLU cc_start: 0.7563 (pm20) cc_final: 0.7355 (pm20) REVERT: E 120 ASN cc_start: 0.9189 (m110) cc_final: 0.8960 (m110) REVERT: G 3 PHE cc_start: 0.6641 (m-80) cc_final: 0.6400 (m-80) REVERT: G 73 LYS cc_start: 0.8375 (tptp) cc_final: 0.8050 (tppt) REVERT: I 94 ASP cc_start: 0.8365 (p0) cc_final: 0.7583 (p0) REVERT: K 48 GLU cc_start: 0.7495 (tt0) cc_final: 0.7269 (tt0) REVERT: R 1 MET cc_start: -0.0510 (mpp) cc_final: -0.1893 (tmm) REVERT: R 256 PHE cc_start: 0.5314 (m-80) cc_final: 0.5073 (t80) REVERT: R 265 LEU cc_start: 0.5209 (mm) cc_final: 0.4832 (tp) REVERT: R 324 CYS cc_start: 0.5019 (m) cc_final: 0.4522 (m) REVERT: R 557 GLN cc_start: 0.6860 (tp40) cc_final: 0.6239 (tm-30) REVERT: R 566 MET cc_start: 0.2122 (mmt) cc_final: 0.1394 (mmt) REVERT: R 809 LEU cc_start: 0.6100 (mp) cc_final: 0.5865 (tp) REVERT: S 291 LEU cc_start: 0.8462 (mt) cc_final: 0.8197 (tp) REVERT: S 292 MET cc_start: 0.7775 (ttm) cc_final: 0.7235 (ptm) outliers start: 0 outliers final: 0 residues processed: 384 average time/residue: 0.2797 time to fit residues: 172.1993 Evaluate side-chains 275 residues out of total 4357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 50.0000 chunk 455 optimal weight: 40.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 50.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 470 optimal weight: 10.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN A 472 ASN A 518 ASN A 588 HIS A 649 ASN A 651 GLN A1208 GLN B 477 ASN I 11 ASN ** R 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 299 GLN R 402 ASN ** R 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 306 ASN ** S 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 376 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.100002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.057629 restraints weight = 143800.310| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 3.94 r_work: 0.2637 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 40159 Z= 0.348 Angle : 0.680 15.821 54234 Z= 0.345 Chirality : 0.046 0.176 5980 Planarity : 0.004 0.057 7014 Dihedral : 4.312 22.223 5360 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.17 % Favored : 95.75 % Rotamer: Outliers : 0.60 % Allowed : 6.54 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.02 % 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: 0.73 (0.12), residues: 4843 helix: 1.38 (0.13), residues: 1733 sheet: 0.28 (0.19), residues: 762 loop : -0.02 (0.13), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 6 TYR 0.044 0.002 TYR B 797 PHE 0.023 0.002 PHE G 2 TRP 0.028 0.002 TRP C 170 HIS 0.006 0.001 HIS A 660 Details of bonding type rmsd covalent geometry : bond 0.00795 (40127) covalent geometry : angle 0.66724 (54189) hydrogen bonds : bond 0.04886 ( 1728) hydrogen bonds : angle 5.15222 ( 4866) metal coordination : bond 0.01310 ( 32) metal coordination : angle 4.61328 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 4357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 277 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8637 (t80) cc_final: 0.8062 (t80) REVERT: A 84 MET cc_start: 0.8117 (mmm) cc_final: 0.7741 (mmm) REVERT: A 95 PHE cc_start: 0.9488 (m-80) cc_final: 0.9248 (m-80) REVERT: A 146 MET cc_start: 0.4795 (tpp) cc_final: 0.4594 (tpp) REVERT: A 212 PHE cc_start: 0.9542 (m-80) cc_final: 0.9227 (m-80) REVERT: A 839 GLN cc_start: 0.9390 (tm-30) cc_final: 0.9157 (tm-30) REVERT: A 850 MET cc_start: 0.9283 (ttp) cc_final: 0.8967 (ttt) REVERT: A 1211 MET cc_start: 0.8013 (tmm) cc_final: 0.7721 (tmm) REVERT: A 1432 MET cc_start: -0.0173 (ttm) cc_final: -0.0460 (ttm) REVERT: B 942 ARG cc_start: 0.7760 (mmm160) cc_final: 0.7551 (mmm160) REVERT: B 1198 TYR cc_start: 0.7950 (OUTLIER) cc_final: 0.7550 (p90) REVERT: B 1217 TYR cc_start: 0.8981 (m-80) cc_final: 0.8063 (m-80) REVERT: E 120 ASN cc_start: 0.9262 (m110) cc_final: 0.9055 (m110) REVERT: G 69 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8256 (tm-30) REVERT: I 91 ARG cc_start: 0.8209 (mmm160) cc_final: 0.7955 (mmm160) REVERT: I 94 ASP cc_start: 0.8742 (p0) cc_final: 0.8459 (p0) REVERT: K 48 GLU cc_start: 0.8853 (tt0) cc_final: 0.8345 (tt0) REVERT: R 1 MET cc_start: 0.1065 (mpp) cc_final: -0.1423 (tmm) REVERT: R 320 TRP cc_start: 0.8893 (t60) cc_final: 0.8493 (t60) REVERT: R 406 ARG cc_start: 0.5520 (tpm170) cc_final: 0.5309 (ppt170) REVERT: R 566 MET cc_start: 0.2114 (mmt) cc_final: 0.1457 (mmm) REVERT: S 105 MET cc_start: 0.8683 (mmm) cc_final: 0.8382 (mtm) REVERT: S 291 LEU cc_start: 0.8688 (mt) cc_final: 0.8445 (tp) REVERT: S 292 MET cc_start: 0.7645 (ttm) cc_final: 0.7282 (ptm) outliers start: 26 outliers final: 16 residues processed: 291 average time/residue: 0.2597 time to fit residues: 123.8634 Evaluate side-chains 280 residues out of total 4357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 263 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 863 ASP Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 1198 TYR Chi-restraints excluded: chain B residue 1207 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain S residue 203 ILE Chi-restraints excluded: chain S residue 288 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 243 optimal weight: 0.9990 chunk 159 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 394 optimal weight: 10.0000 chunk 189 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 365 optimal weight: 20.0000 chunk 349 optimal weight: 0.9990 chunk 245 optimal weight: 10.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 472 ASN A 651 GLN A 737 ASN A1212 ASN B 477 ASN I 51 ASN R 402 ASN R 565 ASN ** R 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 323 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 = 0.4038 r_free = 0.4038 target = 0.102073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.060349 restraints weight = 142943.278| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 4.01 r_work: 0.2692 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 40159 Z= 0.108 Angle : 0.524 10.250 54234 Z= 0.265 Chirality : 0.042 0.169 5980 Planarity : 0.003 0.037 7014 Dihedral : 4.018 20.160 5360 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.45 % Favored : 96.49 % Rotamer: Outliers : 0.69 % Allowed : 8.01 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.02 % 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: 0.88 (0.12), residues: 4843 helix: 1.54 (0.13), residues: 1741 sheet: 0.36 (0.19), residues: 760 loop : 0.02 (0.13), residues: 2342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 337 TYR 0.015 0.001 TYR B 797 PHE 0.015 0.001 PHE A1413 TRP 0.018 0.001 TRP R 588 HIS 0.004 0.001 HIS A 660 Details of bonding type rmsd covalent geometry : bond 0.00236 (40127) covalent geometry : angle 0.51491 (54189) hydrogen bonds : bond 0.03847 ( 1728) hydrogen bonds : angle 4.72963 ( 4866) metal coordination : bond 0.00552 ( 32) metal coordination : angle 3.39761 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 4357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 289 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8660 (t80) cc_final: 0.8114 (t80) REVERT: A 84 MET cc_start: 0.8125 (mmm) cc_final: 0.7702 (mmm) REVERT: A 212 PHE cc_start: 0.9499 (m-80) cc_final: 0.9292 (m-80) REVERT: A 480 ASN cc_start: 0.8430 (t0) cc_final: 0.7934 (p0) REVERT: A 488 MET cc_start: 0.8047 (mmm) cc_final: 0.7592 (mmt) REVERT: A 839 GLN cc_start: 0.9313 (tm-30) cc_final: 0.9015 (tm-30) REVERT: A 1076 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8613 (tm-30) REVERT: A 1211 MET cc_start: 0.8023 (tmm) cc_final: 0.7544 (tmm) REVERT: B 864 LYS cc_start: 0.9108 (ptpt) cc_final: 0.8882 (ptpp) REVERT: B 1098 MET cc_start: 0.7517 (pmm) cc_final: 0.7242 (pmm) REVERT: B 1156 ASP cc_start: 0.7637 (p0) cc_final: 0.7094 (p0) REVERT: B 1198 TYR cc_start: 0.7925 (OUTLIER) cc_final: 0.7426 (p90) REVERT: B 1217 TYR cc_start: 0.9048 (m-80) cc_final: 0.8099 (m-80) REVERT: E 120 ASN cc_start: 0.9252 (m110) cc_final: 0.9043 (m110) REVERT: G 71 GLU cc_start: 0.8321 (tp30) cc_final: 0.8121 (tp30) REVERT: I 91 ARG cc_start: 0.8240 (mmm160) cc_final: 0.7985 (mmm160) REVERT: K 88 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8613 (mp0) REVERT: R 1 MET cc_start: 0.0877 (mpp) cc_final: -0.1589 (tmm) REVERT: R 51 TYR cc_start: 0.7879 (m-80) cc_final: 0.7650 (m-80) REVERT: R 167 MET cc_start: 0.8427 (mmm) cc_final: 0.7990 (ppp) REVERT: R 320 TRP cc_start: 0.8777 (t60) cc_final: 0.8442 (t60) REVERT: R 406 ARG cc_start: 0.5655 (tpm170) cc_final: 0.5323 (tmm-80) REVERT: R 566 MET cc_start: 0.1754 (mmt) cc_final: 0.1218 (tpp) REVERT: S 105 MET cc_start: 0.8741 (mmm) cc_final: 0.8384 (mtm) REVERT: S 166 MET cc_start: 0.9047 (mmm) cc_final: 0.8690 (mmm) REVERT: S 245 MET cc_start: 0.7475 (mpp) cc_final: 0.7251 (mpp) REVERT: S 291 LEU cc_start: 0.8641 (mt) cc_final: 0.8366 (tp) REVERT: S 292 MET cc_start: 0.7743 (ttm) cc_final: 0.7421 (ptm) outliers start: 30 outliers final: 12 residues processed: 308 average time/residue: 0.2489 time to fit residues: 127.0789 Evaluate side-chains 274 residues out of total 4357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 260 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 863 ASP Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 1198 TYR Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain R residue 256 PHE Chi-restraints excluded: chain S residue 203 ILE Chi-restraints excluded: chain S residue 288 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 437 optimal weight: 50.0000 chunk 295 optimal weight: 5.9990 chunk 361 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 484 optimal weight: 6.9990 chunk 290 optimal weight: 10.0000 chunk 433 optimal weight: 10.0000 chunk 209 optimal weight: 9.9990 chunk 273 optimal weight: 0.2980 chunk 3 optimal weight: 30.0000 overall best weight: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 477 ASN I 51 ASN ** R 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 129 GLN ** S 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.100511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.058527 restraints weight = 143388.068| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.77 r_work: 0.2647 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 40159 Z= 0.226 Angle : 0.573 13.541 54234 Z= 0.287 Chirality : 0.043 0.178 5980 Planarity : 0.004 0.049 7014 Dihedral : 4.097 22.798 5360 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.88 % Favored : 96.06 % Rotamer: Outliers : 0.87 % Allowed : 9.27 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.02 % 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: 0.89 (0.12), residues: 4843 helix: 1.59 (0.13), residues: 1721 sheet: 0.25 (0.18), residues: 779 loop : 0.06 (0.13), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 6 TYR 0.015 0.001 TYR B 797 PHE 0.015 0.001 PHE A 943 TRP 0.030 0.002 TRP R 9 HIS 0.008 0.001 HIS K 103 Details of bonding type rmsd covalent geometry : bond 0.00518 (40127) covalent geometry : angle 0.56035 (54189) hydrogen bonds : bond 0.04106 ( 1728) hydrogen bonds : angle 4.76336 ( 4866) metal coordination : bond 0.01003 ( 32) metal coordination : angle 4.16873 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 4357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 275 time to evaluate : 2.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.6820 (tpt) cc_final: 0.6186 (tpp) REVERT: A 65 PHE cc_start: 0.8609 (t80) cc_final: 0.8090 (t80) REVERT: A 84 MET cc_start: 0.8115 (mmm) cc_final: 0.7701 (mmm) REVERT: A 212 PHE cc_start: 0.9522 (m-80) cc_final: 0.9283 (m-80) REVERT: A 480 ASN cc_start: 0.8439 (t0) cc_final: 0.7873 (p0) REVERT: A 770 MET cc_start: 0.9350 (mmt) cc_final: 0.8963 (mmm) REVERT: A 839 GLN cc_start: 0.9387 (tm-30) cc_final: 0.9047 (tm-30) REVERT: A 1211 MET cc_start: 0.8011 (tmm) cc_final: 0.7523 (tmm) REVERT: A 1227 PHE cc_start: 0.8541 (t80) cc_final: 0.8320 (t80) REVERT: B 245 MET cc_start: 0.8769 (tmm) cc_final: 0.8543 (tmm) REVERT: B 1156 ASP cc_start: 0.7691 (p0) cc_final: 0.7200 (p0) REVERT: B 1198 TYR cc_start: 0.7961 (OUTLIER) cc_final: 0.7479 (p90) REVERT: B 1217 TYR cc_start: 0.9029 (m-80) cc_final: 0.8053 (m-80) REVERT: E 3 ASP cc_start: 0.8837 (p0) cc_final: 0.7837 (p0) REVERT: E 6 ARG cc_start: 0.9078 (ttp80) cc_final: 0.8873 (ttp80) REVERT: G 28 GLU cc_start: 0.9267 (pp20) cc_final: 0.8853 (pt0) REVERT: G 119 LEU cc_start: 0.4186 (mm) cc_final: 0.3474 (tp) REVERT: I 34 TYR cc_start: 0.9227 (t80) cc_final: 0.8815 (t80) REVERT: I 91 ARG cc_start: 0.8292 (mmm160) cc_final: 0.7791 (mmp-170) REVERT: K 48 GLU cc_start: 0.8925 (tt0) cc_final: 0.8426 (tt0) REVERT: K 88 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8667 (mp0) REVERT: R 1 MET cc_start: 0.0546 (mpp) cc_final: -0.1685 (tmm) REVERT: R 9 TRP cc_start: 0.8003 (t-100) cc_final: 0.7761 (t60) REVERT: R 51 TYR cc_start: 0.7899 (m-80) cc_final: 0.7465 (m-80) REVERT: R 89 MET cc_start: 0.8410 (tpp) cc_final: 0.7894 (ppp) REVERT: R 241 LEU cc_start: 0.9063 (mt) cc_final: 0.8852 (mt) REVERT: R 320 TRP cc_start: 0.8838 (t60) cc_final: 0.8444 (t60) REVERT: R 359 MET cc_start: 0.5572 (mpp) cc_final: 0.5234 (mpp) REVERT: R 406 ARG cc_start: 0.5281 (tpm170) cc_final: 0.4982 (tmm-80) REVERT: R 566 MET cc_start: 0.1744 (mmt) cc_final: 0.0890 (mmm) REVERT: R 588 TRP cc_start: 0.7633 (OUTLIER) cc_final: 0.7407 (t60) REVERT: S 105 MET cc_start: 0.8632 (mmm) cc_final: 0.8281 (mtp) REVERT: S 291 LEU cc_start: 0.8729 (mt) cc_final: 0.8452 (tp) REVERT: S 292 MET cc_start: 0.7789 (ttm) cc_final: 0.7475 (ptm) outliers start: 38 outliers final: 17 residues processed: 300 average time/residue: 0.2583 time to fit residues: 129.0993 Evaluate side-chains 283 residues out of total 4357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 263 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 863 ASP Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 1198 TYR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain R residue 588 TRP Chi-restraints excluded: chain S residue 203 ILE Chi-restraints excluded: chain S residue 288 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 451 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 chunk 269 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 176 optimal weight: 0.9980 chunk 382 optimal weight: 0.0370 chunk 335 optimal weight: 3.9990 chunk 221 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 overall best weight: 2.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 477 ASN I 51 ASN I 64 GLN ** R 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 402 ASN ** R 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 323 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 = 0.4024 r_free = 0.4024 target = 0.101266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.059460 restraints weight = 142051.501| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.83 r_work: 0.2673 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 40159 Z= 0.135 Angle : 0.525 11.053 54234 Z= 0.263 Chirality : 0.042 0.184 5980 Planarity : 0.003 0.037 7014 Dihedral : 3.988 20.326 5360 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.63 % Favored : 96.30 % Rotamer: Outliers : 0.83 % Allowed : 9.94 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.02 % 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: 0.97 (0.12), residues: 4843 helix: 1.65 (0.13), residues: 1725 sheet: 0.33 (0.18), residues: 774 loop : 0.08 (0.13), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 57 TYR 0.014 0.001 TYR R 580 PHE 0.013 0.001 PHE K 35 TRP 0.026 0.001 TRP R 588 HIS 0.004 0.001 HIS A 660 Details of bonding type rmsd covalent geometry : bond 0.00306 (40127) covalent geometry : angle 0.51493 (54189) hydrogen bonds : bond 0.03690 ( 1728) hydrogen bonds : angle 4.60204 ( 4866) metal coordination : bond 0.00685 ( 32) metal coordination : angle 3.56368 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 4357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 272 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.6669 (tpt) cc_final: 0.6069 (tpp) REVERT: A 65 PHE cc_start: 0.8625 (t80) cc_final: 0.8124 (t80) REVERT: A 84 MET cc_start: 0.8261 (mmm) cc_final: 0.7894 (mmm) REVERT: A 480 ASN cc_start: 0.8440 (t0) cc_final: 0.7870 (p0) REVERT: A 488 MET cc_start: 0.8302 (mmm) cc_final: 0.7617 (mmt) REVERT: A 770 MET cc_start: 0.9324 (mmt) cc_final: 0.8938 (mmm) REVERT: A 839 GLN cc_start: 0.9359 (tm-30) cc_final: 0.9011 (tm-30) REVERT: A 1211 MET cc_start: 0.7994 (tmm) cc_final: 0.7509 (tmm) REVERT: B 245 MET cc_start: 0.8795 (tmm) cc_final: 0.8535 (tmm) REVERT: B 864 LYS cc_start: 0.9069 (ptpt) cc_final: 0.8862 (ptpp) REVERT: B 1098 MET cc_start: 0.7883 (pmm) cc_final: 0.7134 (pmm) REVERT: B 1156 ASP cc_start: 0.7682 (p0) cc_final: 0.7200 (p0) REVERT: B 1198 TYR cc_start: 0.7964 (OUTLIER) cc_final: 0.7394 (p90) REVERT: B 1217 TYR cc_start: 0.9033 (m-80) cc_final: 0.8043 (m-80) REVERT: E 3 ASP cc_start: 0.8903 (p0) cc_final: 0.7931 (p0) REVERT: E 6 ARG cc_start: 0.9083 (ttp80) cc_final: 0.8873 (ttp80) REVERT: E 120 ASN cc_start: 0.9261 (m110) cc_final: 0.9047 (m110) REVERT: G 28 GLU cc_start: 0.9254 (pp20) cc_final: 0.8861 (pt0) REVERT: G 119 LEU cc_start: 0.3765 (mm) cc_final: 0.3112 (tp) REVERT: H 104 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8548 (tp30) REVERT: I 64 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8807 (pm20) REVERT: I 87 GLN cc_start: 0.9169 (pt0) cc_final: 0.8956 (pt0) REVERT: I 91 ARG cc_start: 0.8340 (mmm160) cc_final: 0.8135 (mmm160) REVERT: K 48 GLU cc_start: 0.8850 (tt0) cc_final: 0.8638 (tt0) REVERT: K 88 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8621 (mp0) REVERT: R 1 MET cc_start: 0.0505 (mpp) cc_final: -0.1702 (tmm) REVERT: R 9 TRP cc_start: 0.7946 (t-100) cc_final: 0.7687 (t60) REVERT: R 51 TYR cc_start: 0.7924 (m-80) cc_final: 0.7480 (m-80) REVERT: R 89 MET cc_start: 0.8507 (tpp) cc_final: 0.8040 (ppp) REVERT: R 241 LEU cc_start: 0.9114 (mt) cc_final: 0.8900 (mt) REVERT: R 271 MET cc_start: -0.2178 (mmp) cc_final: -0.2393 (mmp) REVERT: R 320 TRP cc_start: 0.8896 (t60) cc_final: 0.8500 (t60) REVERT: R 402 ASN cc_start: 0.8745 (m110) cc_final: 0.8400 (p0) REVERT: R 406 ARG cc_start: 0.5210 (tpm170) cc_final: 0.4981 (tmm-80) REVERT: R 566 MET cc_start: 0.1602 (mmt) cc_final: 0.1183 (tpp) REVERT: R 588 TRP cc_start: 0.7729 (OUTLIER) cc_final: 0.7474 (t60) REVERT: R 783 MET cc_start: 0.5597 (tpp) cc_final: 0.5116 (tpp) REVERT: S 105 MET cc_start: 0.8650 (mmm) cc_final: 0.8255 (mtp) REVERT: S 166 MET cc_start: 0.8968 (mmm) cc_final: 0.8502 (mmm) REVERT: S 245 MET cc_start: 0.7276 (mpp) cc_final: 0.7036 (mpp) REVERT: S 291 LEU cc_start: 0.8723 (mt) cc_final: 0.8448 (tp) REVERT: S 292 MET cc_start: 0.7766 (ttm) cc_final: 0.7464 (ptm) outliers start: 36 outliers final: 21 residues processed: 298 average time/residue: 0.2488 time to fit residues: 122.9333 Evaluate side-chains 285 residues out of total 4357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 260 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 863 ASP Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1198 TYR Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain R residue 588 TRP Chi-restraints excluded: chain S residue 203 ILE Chi-restraints excluded: chain S residue 288 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 45 optimal weight: 7.9990 chunk 362 optimal weight: 6.9990 chunk 425 optimal weight: 20.0000 chunk 59 optimal weight: 7.9990 chunk 238 optimal weight: 2.9990 chunk 305 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 272 optimal weight: 0.3980 chunk 395 optimal weight: 20.0000 chunk 459 optimal weight: 20.0000 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 51 ASN ** R 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.100396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.058522 restraints weight = 143655.160| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.91 r_work: 0.2642 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 40159 Z= 0.210 Angle : 0.558 12.874 54234 Z= 0.279 Chirality : 0.043 0.185 5980 Planarity : 0.003 0.036 7014 Dihedral : 4.047 21.422 5360 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.76 % Favored : 96.18 % Rotamer: Outliers : 1.03 % Allowed : 10.40 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.02 % 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: 0.95 (0.12), residues: 4843 helix: 1.64 (0.13), residues: 1728 sheet: 0.27 (0.18), residues: 791 loop : 0.08 (0.13), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 57 TYR 0.013 0.001 TYR R 580 PHE 0.014 0.001 PHE A 943 TRP 0.025 0.001 TRP R 588 HIS 0.005 0.001 HIS A 660 Details of bonding type rmsd covalent geometry : bond 0.00482 (40127) covalent geometry : angle 0.54657 (54189) hydrogen bonds : bond 0.03887 ( 1728) hydrogen bonds : angle 4.65416 ( 4866) metal coordination : bond 0.00958 ( 32) metal coordination : angle 3.95279 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 4357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 271 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8616 (mp) REVERT: A 41 MET cc_start: 0.6710 (tpt) cc_final: 0.6161 (tpp) REVERT: A 65 PHE cc_start: 0.8613 (t80) cc_final: 0.8129 (t80) REVERT: A 84 MET cc_start: 0.8256 (mmm) cc_final: 0.7831 (mmm) REVERT: A 480 ASN cc_start: 0.8449 (t0) cc_final: 0.7821 (p0) REVERT: A 488 MET cc_start: 0.8385 (mmm) cc_final: 0.7629 (mmt) REVERT: A 709 MET cc_start: 0.8679 (ptm) cc_final: 0.8410 (ptm) REVERT: A 770 MET cc_start: 0.9371 (mmt) cc_final: 0.9013 (mmm) REVERT: A 839 GLN cc_start: 0.9382 (tm-30) cc_final: 0.9007 (tm-30) REVERT: A 1211 MET cc_start: 0.7931 (tmm) cc_final: 0.7485 (tmm) REVERT: A 1227 PHE cc_start: 0.8471 (t80) cc_final: 0.8177 (t80) REVERT: B 245 MET cc_start: 0.8805 (tmm) cc_final: 0.8490 (tmm) REVERT: B 1098 MET cc_start: 0.7948 (pmm) cc_final: 0.7302 (pmm) REVERT: B 1156 ASP cc_start: 0.7675 (p0) cc_final: 0.7152 (p0) REVERT: B 1198 TYR cc_start: 0.7942 (OUTLIER) cc_final: 0.7364 (p90) REVERT: B 1217 TYR cc_start: 0.9019 (m-80) cc_final: 0.8008 (m-80) REVERT: E 3 ASP cc_start: 0.8917 (p0) cc_final: 0.7954 (p0) REVERT: E 6 ARG cc_start: 0.9097 (ttp80) cc_final: 0.8892 (ttp80) REVERT: G 28 GLU cc_start: 0.9288 (pp20) cc_final: 0.8911 (pt0) REVERT: G 119 LEU cc_start: 0.3787 (mm) cc_final: 0.3173 (tp) REVERT: H 104 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8563 (tp30) REVERT: I 91 ARG cc_start: 0.8407 (mmm160) cc_final: 0.7980 (mmp-170) REVERT: K 48 GLU cc_start: 0.8928 (tt0) cc_final: 0.8440 (tt0) REVERT: K 88 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8653 (mp0) REVERT: R 1 MET cc_start: 0.0651 (mpp) cc_final: -0.1552 (tmm) REVERT: R 9 TRP cc_start: 0.7993 (t-100) cc_final: 0.7575 (t60) REVERT: R 89 MET cc_start: 0.8500 (tpp) cc_final: 0.8062 (ppp) REVERT: R 320 TRP cc_start: 0.8909 (t60) cc_final: 0.8589 (t60) REVERT: R 566 MET cc_start: 0.1580 (mmt) cc_final: 0.1248 (tpp) REVERT: R 588 TRP cc_start: 0.7717 (OUTLIER) cc_final: 0.7404 (t60) REVERT: R 687 LYS cc_start: 0.8332 (mmmt) cc_final: 0.8110 (pttt) REVERT: S 105 MET cc_start: 0.8668 (mmm) cc_final: 0.8334 (mtp) REVERT: S 166 MET cc_start: 0.9087 (mmm) cc_final: 0.8684 (mmm) REVERT: S 291 LEU cc_start: 0.8743 (mt) cc_final: 0.8442 (tp) REVERT: S 292 MET cc_start: 0.7839 (ttm) cc_final: 0.7522 (ptm) outliers start: 45 outliers final: 27 residues processed: 302 average time/residue: 0.2623 time to fit residues: 131.1408 Evaluate side-chains 293 residues out of total 4357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 262 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 863 ASP Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1147 LEU Chi-restraints excluded: chain B residue 1198 TYR Chi-restraints excluded: chain E residue 21 MET Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain R residue 258 GLN Chi-restraints excluded: chain R residue 588 TRP Chi-restraints excluded: chain S residue 203 ILE Chi-restraints excluded: chain S residue 288 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 444 optimal weight: 7.9990 chunk 181 optimal weight: 40.0000 chunk 225 optimal weight: 40.0000 chunk 461 optimal weight: 50.0000 chunk 306 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 449 optimal weight: 0.0870 chunk 359 optimal weight: 1.9990 chunk 302 optimal weight: 10.0000 chunk 189 optimal weight: 2.9990 chunk 198 optimal weight: 8.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 51 ASN ** R 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 402 ASN ** R 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.100764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.058943 restraints weight = 143123.455| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.79 r_work: 0.2661 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 40159 Z= 0.159 Angle : 0.545 11.790 54234 Z= 0.271 Chirality : 0.042 0.208 5980 Planarity : 0.003 0.036 7014 Dihedral : 4.008 22.856 5360 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.61 % Favored : 96.32 % Rotamer: Outliers : 0.92 % Allowed : 10.99 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.02 % 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: 0.97 (0.12), residues: 4843 helix: 1.65 (0.13), residues: 1729 sheet: 0.33 (0.18), residues: 778 loop : 0.08 (0.13), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 57 TYR 0.013 0.001 TYR R 580 PHE 0.013 0.001 PHE K 71 TRP 0.025 0.001 TRP R 588 HIS 0.004 0.001 HIS A 660 Details of bonding type rmsd covalent geometry : bond 0.00364 (40127) covalent geometry : angle 0.53485 (54189) hydrogen bonds : bond 0.03715 ( 1728) hydrogen bonds : angle 4.58949 ( 4866) metal coordination : bond 0.00773 ( 32) metal coordination : angle 3.73845 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 4357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 271 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8547 (mp) REVERT: A 41 MET cc_start: 0.6710 (tpt) cc_final: 0.6168 (tpp) REVERT: A 65 PHE cc_start: 0.8586 (t80) cc_final: 0.8123 (t80) REVERT: A 84 MET cc_start: 0.8272 (mmm) cc_final: 0.7904 (mmm) REVERT: A 480 ASN cc_start: 0.8428 (t0) cc_final: 0.8098 (t0) REVERT: A 488 MET cc_start: 0.8415 (mmm) cc_final: 0.7944 (mmt) REVERT: A 770 MET cc_start: 0.9356 (mmt) cc_final: 0.9000 (mmm) REVERT: A 839 GLN cc_start: 0.9374 (tm-30) cc_final: 0.8993 (tm-30) REVERT: A 1208 GLN cc_start: 0.9063 (mp10) cc_final: 0.8698 (mp10) REVERT: A 1211 MET cc_start: 0.7912 (tmm) cc_final: 0.7442 (tmm) REVERT: B 245 MET cc_start: 0.8790 (tmm) cc_final: 0.8477 (tmm) REVERT: B 1098 MET cc_start: 0.7931 (pmm) cc_final: 0.7363 (pmm) REVERT: B 1156 ASP cc_start: 0.7671 (p0) cc_final: 0.7160 (p0) REVERT: B 1198 TYR cc_start: 0.7973 (OUTLIER) cc_final: 0.7333 (p90) REVERT: B 1217 TYR cc_start: 0.9021 (m-80) cc_final: 0.8014 (m-80) REVERT: E 3 ASP cc_start: 0.8921 (p0) cc_final: 0.7969 (p0) REVERT: E 6 ARG cc_start: 0.9096 (ttp80) cc_final: 0.8889 (ttp80) REVERT: G 28 GLU cc_start: 0.9282 (pp20) cc_final: 0.8908 (pt0) REVERT: G 73 LYS cc_start: 0.8866 (mmmt) cc_final: 0.8447 (tppt) REVERT: G 119 LEU cc_start: 0.4021 (mm) cc_final: 0.3533 (tt) REVERT: H 104 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8600 (tp30) REVERT: I 91 ARG cc_start: 0.8418 (mmm160) cc_final: 0.8049 (mmp-170) REVERT: K 48 GLU cc_start: 0.8901 (tt0) cc_final: 0.8621 (tt0) REVERT: K 88 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8622 (mp0) REVERT: R 1 MET cc_start: 0.0696 (mpp) cc_final: -0.1505 (tmm) REVERT: R 9 TRP cc_start: 0.7968 (t-100) cc_final: 0.7701 (t60) REVERT: R 51 TYR cc_start: 0.8273 (m-80) cc_final: 0.7741 (m-80) REVERT: R 89 MET cc_start: 0.8539 (tpp) cc_final: 0.8088 (ppp) REVERT: R 167 MET cc_start: 0.8322 (mmm) cc_final: 0.7878 (ppp) REVERT: R 294 LEU cc_start: 0.8878 (mp) cc_final: 0.8660 (mt) REVERT: R 320 TRP cc_start: 0.8996 (t60) cc_final: 0.8587 (t60) REVERT: R 566 MET cc_start: 0.1660 (mmt) cc_final: 0.1332 (tpp) REVERT: R 664 MET cc_start: -0.0464 (pmm) cc_final: -0.0679 (pmm) REVERT: R 687 LYS cc_start: 0.8322 (mmmt) cc_final: 0.8112 (pttt) REVERT: S 105 MET cc_start: 0.8700 (mmm) cc_final: 0.8388 (mtp) REVERT: S 291 LEU cc_start: 0.8738 (mt) cc_final: 0.8426 (tp) REVERT: S 292 MET cc_start: 0.7892 (ttm) cc_final: 0.7577 (ptm) outliers start: 40 outliers final: 29 residues processed: 299 average time/residue: 0.2527 time to fit residues: 125.0172 Evaluate side-chains 291 residues out of total 4357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 259 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 863 ASP Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 1147 LEU Chi-restraints excluded: chain B residue 1198 TYR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain R residue 258 GLN Chi-restraints excluded: chain R residue 588 TRP Chi-restraints excluded: chain S residue 203 ILE Chi-restraints excluded: chain S residue 288 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 401 optimal weight: 30.0000 chunk 411 optimal weight: 6.9990 chunk 362 optimal weight: 6.9990 chunk 357 optimal weight: 10.0000 chunk 400 optimal weight: 7.9990 chunk 145 optimal weight: 8.9990 chunk 395 optimal weight: 50.0000 chunk 271 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 chunk 386 optimal weight: 50.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 HIS A 472 ASN A 651 GLN I 51 ASN ** R 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 403 GLN ** R 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 323 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 = 0.4004 r_free = 0.4004 target = 0.100198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.058416 restraints weight = 143651.042| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.78 r_work: 0.2648 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 40159 Z= 0.200 Angle : 0.576 13.309 54234 Z= 0.285 Chirality : 0.043 0.180 5980 Planarity : 0.003 0.036 7014 Dihedral : 4.078 24.309 5360 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.84 % Favored : 96.08 % Rotamer: Outliers : 0.96 % Allowed : 11.52 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.02 % 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: 0.92 (0.12), residues: 4843 helix: 1.61 (0.13), residues: 1738 sheet: 0.27 (0.18), residues: 782 loop : 0.06 (0.13), residues: 2323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 57 TYR 0.013 0.001 TYR R 580 PHE 0.043 0.001 PHE A1227 TRP 0.025 0.001 TRP R 588 HIS 0.005 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00458 (40127) covalent geometry : angle 0.56397 (54189) hydrogen bonds : bond 0.03874 ( 1728) hydrogen bonds : angle 4.62954 ( 4866) metal coordination : bond 0.00943 ( 32) metal coordination : angle 4.05452 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 4357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 270 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8652 (mp) REVERT: A 41 MET cc_start: 0.6837 (tpt) cc_final: 0.6349 (tpp) REVERT: A 65 PHE cc_start: 0.8562 (t80) cc_final: 0.8124 (t80) REVERT: A 84 MET cc_start: 0.8286 (mmm) cc_final: 0.7844 (mmm) REVERT: A 146 MET cc_start: 0.5264 (tpp) cc_final: 0.4185 (tmm) REVERT: A 480 ASN cc_start: 0.8338 (t0) cc_final: 0.8036 (t0) REVERT: A 488 MET cc_start: 0.8488 (mmm) cc_final: 0.7983 (mmt) REVERT: A 770 MET cc_start: 0.9325 (mmt) cc_final: 0.8953 (mmm) REVERT: A 839 GLN cc_start: 0.9392 (tm-30) cc_final: 0.9017 (tm-30) REVERT: A 850 MET cc_start: 0.9261 (ttp) cc_final: 0.9044 (ttt) REVERT: A 1211 MET cc_start: 0.7896 (tmm) cc_final: 0.7428 (tmm) REVERT: A 1227 PHE cc_start: 0.8414 (t80) cc_final: 0.8063 (t80) REVERT: A 1262 MET cc_start: 0.8764 (ppp) cc_final: 0.8334 (ppp) REVERT: A 1270 MET cc_start: 0.8770 (mmt) cc_final: 0.8552 (mmp) REVERT: B 1098 MET cc_start: 0.8057 (pmm) cc_final: 0.7624 (pmm) REVERT: B 1186 LYS cc_start: 0.8704 (mmmt) cc_final: 0.7633 (ttpp) REVERT: B 1198 TYR cc_start: 0.8086 (OUTLIER) cc_final: 0.7236 (p90) REVERT: B 1217 TYR cc_start: 0.8947 (m-80) cc_final: 0.7883 (m-80) REVERT: E 3 ASP cc_start: 0.8910 (p0) cc_final: 0.7905 (p0) REVERT: E 6 ARG cc_start: 0.9094 (ttp80) cc_final: 0.8865 (ttp80) REVERT: G 28 GLU cc_start: 0.9280 (pp20) cc_final: 0.8920 (pt0) REVERT: G 119 LEU cc_start: 0.4720 (mm) cc_final: 0.4153 (tt) REVERT: H 104 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8602 (tp30) REVERT: I 91 ARG cc_start: 0.8360 (mmm160) cc_final: 0.8069 (mmm160) REVERT: K 48 GLU cc_start: 0.8934 (tt0) cc_final: 0.8446 (tt0) REVERT: K 88 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8653 (mp0) REVERT: R 1 MET cc_start: 0.0400 (mpp) cc_final: -0.1574 (tmm) REVERT: R 9 TRP cc_start: 0.7927 (t-100) cc_final: 0.7618 (t60) REVERT: R 51 TYR cc_start: 0.8247 (m-80) cc_final: 0.7667 (m-80) REVERT: R 89 MET cc_start: 0.8559 (tpp) cc_final: 0.8093 (ppp) REVERT: R 167 MET cc_start: 0.8151 (mmm) cc_final: 0.7744 (ppp) REVERT: R 294 LEU cc_start: 0.8876 (mp) cc_final: 0.8635 (mt) REVERT: R 320 TRP cc_start: 0.8957 (t60) cc_final: 0.8545 (t60) REVERT: R 566 MET cc_start: 0.1657 (mmt) cc_final: 0.1272 (tpp) REVERT: R 687 LYS cc_start: 0.8352 (mmmt) cc_final: 0.8133 (pttt) REVERT: S 105 MET cc_start: 0.8725 (mmm) cc_final: 0.8442 (mtp) REVERT: S 166 MET cc_start: 0.9024 (mmm) cc_final: 0.8612 (mmm) REVERT: S 291 LEU cc_start: 0.8688 (mt) cc_final: 0.8360 (tp) REVERT: S 292 MET cc_start: 0.8039 (ttm) cc_final: 0.7726 (ptm) outliers start: 42 outliers final: 32 residues processed: 298 average time/residue: 0.2504 time to fit residues: 124.1234 Evaluate side-chains 298 residues out of total 4357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 263 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 863 ASP Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 1147 LEU Chi-restraints excluded: chain B residue 1198 TYR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain R residue 258 GLN Chi-restraints excluded: chain R residue 588 TRP Chi-restraints excluded: chain S residue 203 ILE Chi-restraints excluded: chain S residue 288 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 174 optimal weight: 4.9990 chunk 446 optimal weight: 0.1980 chunk 171 optimal weight: 7.9990 chunk 271 optimal weight: 0.0970 chunk 413 optimal weight: 30.0000 chunk 265 optimal weight: 0.9980 chunk 418 optimal weight: 10.0000 chunk 323 optimal weight: 20.0000 chunk 432 optimal weight: 0.0770 chunk 398 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN A 651 GLN I 51 ASN ** R 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 403 GLN ** R 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 323 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 = 0.4036 r_free = 0.4036 target = 0.101811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.060431 restraints weight = 143037.418| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.80 r_work: 0.2710 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 40159 Z= 0.094 Angle : 0.540 15.364 54234 Z= 0.267 Chirality : 0.042 0.187 5980 Planarity : 0.003 0.043 7014 Dihedral : 3.909 22.477 5360 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.41 % Favored : 96.53 % Rotamer: Outliers : 0.64 % Allowed : 12.07 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.02 % 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: 4843 helix: 1.69 (0.13), residues: 1730 sheet: 0.38 (0.19), residues: 762 loop : 0.08 (0.13), residues: 2351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 57 TYR 0.015 0.001 TYR I 34 PHE 0.027 0.001 PHE A1227 TRP 0.025 0.001 TRP R 588 HIS 0.003 0.001 HIS A 459 Details of bonding type rmsd covalent geometry : bond 0.00200 (40127) covalent geometry : angle 0.53329 (54189) hydrogen bonds : bond 0.03285 ( 1728) hydrogen bonds : angle 4.42419 ( 4866) metal coordination : bond 0.00442 ( 32) metal coordination : angle 3.02541 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 4357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 271 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8473 (mp) REVERT: A 41 MET cc_start: 0.6647 (tpt) cc_final: 0.6046 (tpp) REVERT: A 65 PHE cc_start: 0.8570 (t80) cc_final: 0.8135 (t80) REVERT: A 84 MET cc_start: 0.8291 (mmm) cc_final: 0.7880 (mmm) REVERT: A 454 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8224 (pmm) REVERT: A 480 ASN cc_start: 0.8318 (t0) cc_final: 0.8038 (t0) REVERT: A 488 MET cc_start: 0.8403 (mmm) cc_final: 0.7918 (mmt) REVERT: A 770 MET cc_start: 0.9331 (mmt) cc_final: 0.8951 (mmm) REVERT: A 839 GLN cc_start: 0.9366 (tm-30) cc_final: 0.8971 (tm-30) REVERT: A 850 MET cc_start: 0.9167 (ttp) cc_final: 0.8938 (ttt) REVERT: A 1211 MET cc_start: 0.7903 (tmm) cc_final: 0.7430 (tmm) REVERT: A 1227 PHE cc_start: 0.8389 (t80) cc_final: 0.8074 (t80) REVERT: A 1413 PHE cc_start: 0.7315 (t80) cc_final: 0.6757 (t80) REVERT: B 245 MET cc_start: 0.8707 (tmm) cc_final: 0.8504 (tmm) REVERT: B 702 MET cc_start: 0.9214 (tpp) cc_final: 0.8878 (tpp) REVERT: B 1098 MET cc_start: 0.7934 (pmm) cc_final: 0.7458 (pmm) REVERT: B 1156 ASP cc_start: 0.7638 (p0) cc_final: 0.7102 (p0) REVERT: B 1198 TYR cc_start: 0.7846 (OUTLIER) cc_final: 0.7252 (p90) REVERT: B 1217 TYR cc_start: 0.8977 (m-80) cc_final: 0.7973 (m-80) REVERT: E 3 ASP cc_start: 0.8956 (p0) cc_final: 0.8027 (p0) REVERT: E 6 ARG cc_start: 0.9093 (ttp80) cc_final: 0.8879 (ttp80) REVERT: E 120 ASN cc_start: 0.9293 (m110) cc_final: 0.9084 (m110) REVERT: G 73 LYS cc_start: 0.8904 (mmmt) cc_final: 0.8504 (tppt) REVERT: G 119 LEU cc_start: 0.3857 (mm) cc_final: 0.3452 (tt) REVERT: H 104 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8594 (tp30) REVERT: I 61 ASP cc_start: 0.8391 (m-30) cc_final: 0.7772 (t0) REVERT: K 88 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8593 (mp0) REVERT: R 1 MET cc_start: 0.0883 (mpp) cc_final: -0.1334 (tmm) REVERT: R 9 TRP cc_start: 0.8023 (t-100) cc_final: 0.7777 (t60) REVERT: R 51 TYR cc_start: 0.8156 (m-80) cc_final: 0.7585 (m-80) REVERT: R 167 MET cc_start: 0.8289 (mmm) cc_final: 0.7908 (ppp) REVERT: R 294 LEU cc_start: 0.8897 (mp) cc_final: 0.8687 (mt) REVERT: R 320 TRP cc_start: 0.9017 (t60) cc_final: 0.8591 (t60) REVERT: R 566 MET cc_start: 0.1792 (mmt) cc_final: 0.1458 (tpp) REVERT: R 783 MET cc_start: 0.5584 (tpt) cc_final: 0.5192 (tpt) REVERT: S 166 MET cc_start: 0.8994 (mmm) cc_final: 0.8561 (mmm) REVERT: S 291 LEU cc_start: 0.8653 (mt) cc_final: 0.8339 (tp) REVERT: S 292 MET cc_start: 0.7973 (ttm) cc_final: 0.7685 (ptm) outliers start: 28 outliers final: 22 residues processed: 290 average time/residue: 0.2502 time to fit residues: 120.8169 Evaluate side-chains 289 residues out of total 4357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 263 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 863 ASP Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 1147 LEU Chi-restraints excluded: chain B residue 1198 TYR Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain R residue 258 GLN Chi-restraints excluded: chain R residue 588 TRP Chi-restraints excluded: chain S residue 203 ILE Chi-restraints excluded: chain S residue 288 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 74 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 478 optimal weight: 30.0000 chunk 367 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 363 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 388 optimal weight: 50.0000 chunk 39 optimal weight: 6.9990 chunk 281 optimal weight: 30.0000 chunk 397 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN A 651 GLN ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 51 ASN ** R 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 63 HIS ** R 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 323 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 = 0.3994 r_free = 0.3994 target = 0.099645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.057953 restraints weight = 143057.305| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.80 r_work: 0.2631 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 40159 Z= 0.260 Angle : 0.617 14.290 54234 Z= 0.306 Chirality : 0.044 0.186 5980 Planarity : 0.004 0.041 7014 Dihedral : 4.092 22.741 5360 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.07 % Favored : 95.85 % Rotamer: Outliers : 0.78 % Allowed : 11.98 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.02 % 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: 0.92 (0.12), residues: 4843 helix: 1.61 (0.13), residues: 1740 sheet: 0.26 (0.18), residues: 783 loop : 0.06 (0.13), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG I 91 TYR 0.047 0.001 TYR G 25 PHE 0.038 0.002 PHE A 212 TRP 0.025 0.001 TRP R 588 HIS 0.006 0.001 HIS A 660 Details of bonding type rmsd covalent geometry : bond 0.00597 (40127) covalent geometry : angle 0.60565 (54189) hydrogen bonds : bond 0.03960 ( 1728) hydrogen bonds : angle 4.63256 ( 4866) metal coordination : bond 0.01082 ( 32) metal coordination : angle 4.17980 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9686 Ramachandran restraints generated. 4843 Oldfield, 0 Emsley, 4843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 4357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 264 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8576 (mp) REVERT: A 41 MET cc_start: 0.6841 (tpt) cc_final: 0.6410 (tpp) REVERT: A 65 PHE cc_start: 0.8574 (t80) cc_final: 0.8172 (t80) REVERT: A 84 MET cc_start: 0.8284 (mmm) cc_final: 0.7851 (mmm) REVERT: A 146 MET cc_start: 0.4903 (tpp) cc_final: 0.3695 (tmm) REVERT: A 454 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8215 (pmm) REVERT: A 480 ASN cc_start: 0.8379 (t0) cc_final: 0.8062 (t0) REVERT: A 488 MET cc_start: 0.8505 (mmm) cc_final: 0.7975 (mmt) REVERT: A 770 MET cc_start: 0.9342 (mmt) cc_final: 0.9052 (mmm) REVERT: A 839 GLN cc_start: 0.9418 (tm-30) cc_final: 0.9038 (tm-30) REVERT: A 850 MET cc_start: 0.9284 (ttp) cc_final: 0.9073 (ttt) REVERT: A 1211 MET cc_start: 0.7855 (tmm) cc_final: 0.7398 (tmm) REVERT: A 1227 PHE cc_start: 0.8504 (t80) cc_final: 0.8157 (t80) REVERT: A 1270 MET cc_start: 0.8775 (mmt) cc_final: 0.8569 (mmp) REVERT: B 245 MET cc_start: 0.8772 (tmm) cc_final: 0.8511 (tmm) REVERT: B 1098 MET cc_start: 0.8031 (pmm) cc_final: 0.7625 (pmm) REVERT: B 1198 TYR cc_start: 0.8086 (OUTLIER) cc_final: 0.7323 (p90) REVERT: B 1217 TYR cc_start: 0.8904 (m-80) cc_final: 0.7821 (m-80) REVERT: E 3 ASP cc_start: 0.8894 (p0) cc_final: 0.7947 (p0) REVERT: E 6 ARG cc_start: 0.9106 (ttp80) cc_final: 0.8882 (ttp80) REVERT: G 73 LYS cc_start: 0.8895 (mmmt) cc_final: 0.8480 (tppt) REVERT: G 119 LEU cc_start: 0.3895 (mm) cc_final: 0.3476 (tt) REVERT: H 104 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8612 (tp30) REVERT: I 61 ASP cc_start: 0.8607 (m-30) cc_final: 0.7959 (t0) REVERT: K 48 GLU cc_start: 0.8945 (tt0) cc_final: 0.8488 (tt0) REVERT: K 88 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8662 (mp0) REVERT: R 1 MET cc_start: 0.0907 (mpp) cc_final: -0.1351 (tmm) REVERT: R 9 TRP cc_start: 0.7950 (t-100) cc_final: 0.7672 (t60) REVERT: R 167 MET cc_start: 0.8181 (mmm) cc_final: 0.7793 (ppp) REVERT: R 294 LEU cc_start: 0.8916 (mp) cc_final: 0.8673 (mt) REVERT: R 320 TRP cc_start: 0.8996 (t60) cc_final: 0.8603 (t60) REVERT: R 566 MET cc_start: 0.1841 (mmt) cc_final: 0.1500 (tpp) REVERT: R 783 MET cc_start: 0.5806 (tpt) cc_final: 0.5192 (tpp) REVERT: S 166 MET cc_start: 0.9020 (mmm) cc_final: 0.8608 (mmm) REVERT: S 291 LEU cc_start: 0.8793 (mt) cc_final: 0.8472 (tp) REVERT: S 292 MET cc_start: 0.8068 (ttm) cc_final: 0.7751 (ptm) outliers start: 34 outliers final: 25 residues processed: 287 average time/residue: 0.2550 time to fit residues: 121.5830 Evaluate side-chains 288 residues out of total 4357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 259 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 863 ASP Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 1147 LEU Chi-restraints excluded: chain B residue 1198 TYR Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain R residue 258 GLN Chi-restraints excluded: chain R residue 588 TRP Chi-restraints excluded: chain S residue 203 ILE Chi-restraints excluded: chain S residue 288 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 459 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 397 optimal weight: 7.9990 chunk 425 optimal weight: 0.5980 chunk 329 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 47 optimal weight: 0.4980 chunk 372 optimal weight: 7.9990 chunk 284 optimal weight: 30.0000 chunk 171 optimal weight: 6.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN A 651 GLN ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 51 ASN ** R 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 403 GLN ** R 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 323 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 = 0.4005 r_free = 0.4005 target = 0.100241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.058709 restraints weight = 143537.430| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 3.90 r_work: 0.2653 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 40159 Z= 0.174 Angle : 0.577 12.055 54234 Z= 0.285 Chirality : 0.042 0.195 5980 Planarity : 0.003 0.043 7014 Dihedral : 4.054 23.876 5360 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.59 % Favored : 96.35 % Rotamer: Outliers : 0.85 % Allowed : 12.00 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.02 % 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: 0.93 (0.12), residues: 4843 helix: 1.63 (0.13), residues: 1736 sheet: 0.25 (0.19), residues: 772 loop : 0.06 (0.13), residues: 2335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 57 TYR 0.055 0.001 TYR G 25 PHE 0.031 0.001 PHE A 212 TRP 0.025 0.001 TRP R 588 HIS 0.004 0.001 HIS A 660 Details of bonding type rmsd covalent geometry : bond 0.00401 (40127) covalent geometry : angle 0.56658 (54189) hydrogen bonds : bond 0.03697 ( 1728) hydrogen bonds : angle 4.55181 ( 4866) metal coordination : bond 0.00810 ( 32) metal coordination : angle 3.75708 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13003.61 seconds wall clock time: 222 minutes 36.15 seconds (13356.15 seconds total)