Starting phenix.real_space_refine on Sat Jun 28 18:14:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6drk_8901/06_2025/6drk_8901.cif Found real_map, /net/cci-nas-00/data/ceres_data/6drk_8901/06_2025/6drk_8901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6drk_8901/06_2025/6drk_8901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6drk_8901/06_2025/6drk_8901.map" model { file = "/net/cci-nas-00/data/ceres_data/6drk_8901/06_2025/6drk_8901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6drk_8901/06_2025/6drk_8901.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.037 sd= 0.670 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: 4 Type Number sf(0) Gaussians S 116 5.16 5 C 21324 2.51 5 N 5996 2.21 5 O 5684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33120 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1265, 8280 Classifications: {'peptide': 1265} Incomplete info: {'truncation_to_alanine': 556} Link IDs: {'PTRANS': 50, 'TRANS': 1214} Chain breaks: 6 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2017 Unresolved non-hydrogen angles: 2540 Unresolved non-hydrogen dihedrals: 1636 Unresolved non-hydrogen chiralities: 149 Planarities with less than four sites: {'GLN:plan1': 32, 'HIS:plan': 20, 'TYR:plan': 15, 'ASN:plan1': 25, 'TRP:plan': 3, 'ASP:plan': 53, 'PHE:plan': 19, 'GLU:plan': 86, 'ARG:plan': 40} Unresolved non-hydrogen planarities: 1252 Restraints were copied for chains: C, B, D Time building chain proxies: 22.65, per 1000 atoms: 0.68 Number of scatterers: 33120 At special positions: 0 Unit cell: (172.914, 172.914, 172.914, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 116 16.00 O 5684 8.00 N 5996 7.00 C 21324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A1012 " - pdb=" SG CYS A1024 " distance=2.02 Simple disulfide: pdb=" SG CYS C1012 " - pdb=" SG CYS C1024 " distance=2.02 Simple disulfide: pdb=" SG CYS B1012 " - pdb=" SG CYS B1024 " distance=2.02 Simple disulfide: pdb=" SG CYS D1012 " - pdb=" SG CYS D1024 " distance=2.02 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: 8.83 Conformation dependent library (CDL) restraints added in 5.2 seconds 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9600 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 16 sheets defined 56.9% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.74 Creating SS restraints... Processing helix chain 'A' and resid 39 through 45 removed outlier: 4.134A pdb=" N TRP A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 136 Processing helix chain 'A' and resid 161 through 177 removed outlier: 3.878A pdb=" N LYS A 165 " --> pdb=" O HIS A 161 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 206 removed outlier: 3.737A pdb=" N LEU A 203 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER A 204 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 229 removed outlier: 3.812A pdb=" N THR A 228 " --> pdb=" O ASN A 225 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 229 " --> pdb=" O ARG A 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 225 through 229' Processing helix chain 'A' and resid 274 through 286 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 311 through 323 removed outlier: 3.615A pdb=" N THR A 315 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 343 Processing helix chain 'A' and resid 351 through 361 removed outlier: 4.175A pdb=" N ARG A 361 " --> pdb=" O ARG A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 386 Processing helix chain 'A' and resid 404 through 419 removed outlier: 4.302A pdb=" N ALA A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 438 removed outlier: 3.976A pdb=" N GLU A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 434 " --> pdb=" O ARG A 430 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A 435 " --> pdb=" O GLN A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 449 Processing helix chain 'A' and resid 460 through 470 Processing helix chain 'A' and resid 472 through 482 removed outlier: 3.578A pdb=" N VAL A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 490 Processing helix chain 'A' and resid 492 through 500 removed outlier: 4.036A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'A' and resid 506 through 516 Processing helix chain 'A' and resid 536 through 548 removed outlier: 3.769A pdb=" N GLU A 542 " --> pdb=" O HIS A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 604 removed outlier: 4.365A pdb=" N ASP A 597 " --> pdb=" O ASP A 593 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 598 " --> pdb=" O PRO A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 616 removed outlier: 3.868A pdb=" N ILE A 613 " --> pdb=" O GLU A 609 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU A 616 " --> pdb=" O GLU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 640 removed outlier: 3.545A pdb=" N SER A 639 " --> pdb=" O LEU A 635 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY A 640 " --> pdb=" O ALA A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 672 removed outlier: 4.366A pdb=" N MET A 650 " --> pdb=" O GLU A 646 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU A 651 " --> pdb=" O ALA A 647 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 670 " --> pdb=" O SER A 666 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TRP A 671 " --> pdb=" O GLU A 667 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP A 672 " --> pdb=" O CYS A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 682 removed outlier: 3.578A pdb=" N ALA A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS A 678 " --> pdb=" O GLN A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 699 Processing helix chain 'A' and resid 701 through 706 removed outlier: 3.668A pdb=" N ILE A 705 " --> pdb=" O ASP A 701 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A 706 " --> pdb=" O LYS A 702 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 701 through 706' Processing helix chain 'A' and resid 707 through 719 Processing helix chain 'A' and resid 727 through 737 Processing helix chain 'A' and resid 738 through 744 removed outlier: 4.279A pdb=" N TYR A 742 " --> pdb=" O PHE A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 770 Processing helix chain 'A' and resid 799 through 806 removed outlier: 4.294A pdb=" N MET A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 833 removed outlier: 3.734A pdb=" N TYR A 814 " --> pdb=" O GLN A 810 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 833 " --> pdb=" O VAL A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 863 removed outlier: 3.508A pdb=" N TYR A 862 " --> pdb=" O ILE A 858 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N HIS A 863 " --> pdb=" O ARG A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 878 Processing helix chain 'A' and resid 881 through 902 removed outlier: 4.246A pdb=" N LEU A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASP A 886 " --> pdb=" O TRP A 882 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 891 " --> pdb=" O VAL A 887 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 894 " --> pdb=" O ILE A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 925 removed outlier: 3.769A pdb=" N ILE A 910 " --> pdb=" O THR A 906 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE A 920 " --> pdb=" O CYS A 916 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE A 921 " --> pdb=" O ILE A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 930 removed outlier: 3.807A pdb=" N ILE A 929 " --> pdb=" O ARG A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 946 removed outlier: 3.930A pdb=" N ILE A 940 " --> pdb=" O LEU A 936 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE A 941 " --> pdb=" O GLY A 937 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A 942 " --> pdb=" O PRO A 938 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 943 " --> pdb=" O LYS A 939 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET A 946 " --> pdb=" O ILE A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 973 removed outlier: 4.191A pdb=" N PHE A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TRP A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 972 " --> pdb=" O LYS A 968 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE A 973 " --> pdb=" O GLN A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 987 Processing helix chain 'A' and resid 987 through 994 Processing helix chain 'A' and resid 997 through 1002 removed outlier: 3.646A pdb=" N ILE A1002 " --> pdb=" O PHE A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1071 removed outlier: 3.609A pdb=" N THR A1040 " --> pdb=" O PRO A1036 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A1053 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A1054 " --> pdb=" O PHE A1050 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A1055 " --> pdb=" O ALA A1051 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A1056 " --> pdb=" O ASN A1052 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN A1057 " --> pdb=" O ILE A1053 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU A1058 " --> pdb=" O LEU A1054 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE A1063 " --> pdb=" O LEU A1059 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR A1065 " --> pdb=" O ALA A1061 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN A1071 " --> pdb=" O PHE A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1090 removed outlier: 3.772A pdb=" N TRP A1078 " --> pdb=" O THR A1074 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS A1079 " --> pdb=" O ASP A1075 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS A1087 " --> pdb=" O TYR A1083 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU A1088 " --> pdb=" O GLU A1084 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TYR A1089 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS A1090 " --> pdb=" O ILE A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1112 Processing helix chain 'A' and resid 1129 through 1156 removed outlier: 4.002A pdb=" N ALA A1149 " --> pdb=" O ASP A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1158 through 1186 removed outlier: 4.440A pdb=" N HIS A1164 " --> pdb=" O GLU A1160 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A1168 " --> pdb=" O HIS A1164 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU A1175 " --> pdb=" O GLY A1171 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A1178 " --> pdb=" O SER A1174 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'A' and resid 1368 through 1378 Processing helix chain 'A' and resid 1382 through 1388 Processing helix chain 'A' and resid 1426 through 1433 removed outlier: 4.063A pdb=" N LEU A1430 " --> pdb=" O LEU A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1456 through 1471 removed outlier: 4.012A pdb=" N GLU A1461 " --> pdb=" O SER A1457 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A1462 " --> pdb=" O TYR A1458 " (cutoff:3.500A) Processing helix chain 'A' and resid 1472 through 1474 No H-bonds generated for 'chain 'A' and resid 1472 through 1474' Processing helix chain 'C' and resid 40 through 45 Processing helix chain 'C' and resid 126 through 136 Processing helix chain 'C' and resid 161 through 177 removed outlier: 3.878A pdb=" N LYS C 165 " --> pdb=" O HIS C 161 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA C 174 " --> pdb=" O LEU C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 206 removed outlier: 3.738A pdb=" N LEU C 203 " --> pdb=" O ARG C 199 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER C 204 " --> pdb=" O ASP C 200 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY C 206 " --> pdb=" O THR C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 229 removed outlier: 3.812A pdb=" N THR C 228 " --> pdb=" O ASN C 225 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 229 " --> pdb=" O ARG C 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 225 through 229' Processing helix chain 'C' and resid 274 through 286 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 311 through 323 removed outlier: 3.615A pdb=" N THR C 315 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 343 Processing helix chain 'C' and resid 351 through 361 removed outlier: 4.175A pdb=" N ARG C 361 " --> pdb=" O ARG C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 386 Processing helix chain 'C' and resid 404 through 419 removed outlier: 4.302A pdb=" N ALA C 408 " --> pdb=" O ASP C 404 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 438 removed outlier: 3.975A pdb=" N GLU C 433 " --> pdb=" O GLU C 429 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU C 434 " --> pdb=" O ARG C 430 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA C 435 " --> pdb=" O GLN C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 449 Processing helix chain 'C' and resid 460 through 470 Processing helix chain 'C' and resid 472 through 482 removed outlier: 3.577A pdb=" N VAL C 476 " --> pdb=" O LYS C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 490 Processing helix chain 'C' and resid 492 through 500 removed outlier: 4.036A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 503 No H-bonds generated for 'chain 'C' and resid 501 through 503' Processing helix chain 'C' and resid 506 through 516 Processing helix chain 'C' and resid 536 through 548 removed outlier: 3.770A pdb=" N GLU C 542 " --> pdb=" O HIS C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 604 removed outlier: 4.365A pdb=" N ASP C 597 " --> pdb=" O ASP C 593 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 598 " --> pdb=" O PRO C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 616 removed outlier: 3.868A pdb=" N ILE C 613 " --> pdb=" O GLU C 609 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU C 616 " --> pdb=" O GLU C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 640 removed outlier: 3.544A pdb=" N SER C 639 " --> pdb=" O LEU C 635 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY C 640 " --> pdb=" O ALA C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 642 through 672 removed outlier: 4.366A pdb=" N MET C 650 " --> pdb=" O GLU C 646 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LEU C 651 " --> pdb=" O ALA C 647 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER C 670 " --> pdb=" O SER C 666 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TRP C 671 " --> pdb=" O GLU C 667 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASP C 672 " --> pdb=" O CYS C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 682 removed outlier: 3.578A pdb=" N ALA C 676 " --> pdb=" O ASP C 672 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS C 678 " --> pdb=" O GLN C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 699 Processing helix chain 'C' and resid 701 through 706 removed outlier: 3.668A pdb=" N ILE C 705 " --> pdb=" O ASP C 701 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA C 706 " --> pdb=" O LYS C 702 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 701 through 706' Processing helix chain 'C' and resid 707 through 719 Processing helix chain 'C' and resid 727 through 737 Processing helix chain 'C' and resid 738 through 744 removed outlier: 4.279A pdb=" N TYR C 742 " --> pdb=" O PHE C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 770 Processing helix chain 'C' and resid 799 through 806 removed outlier: 4.294A pdb=" N MET C 803 " --> pdb=" O SER C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 808 through 833 removed outlier: 3.735A pdb=" N TYR C 814 " --> pdb=" O GLN C 810 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE C 833 " --> pdb=" O VAL C 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 863 removed outlier: 3.508A pdb=" N TYR C 862 " --> pdb=" O ILE C 858 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS C 863 " --> pdb=" O ARG C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 871 through 878 Processing helix chain 'C' and resid 881 through 902 removed outlier: 4.246A pdb=" N LEU C 885 " --> pdb=" O LEU C 881 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASP C 886 " --> pdb=" O TRP C 882 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL C 891 " --> pdb=" O VAL C 887 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE C 894 " --> pdb=" O ILE C 890 " (cutoff:3.500A) Processing helix chain 'C' and resid 906 through 925 removed outlier: 3.769A pdb=" N ILE C 910 " --> pdb=" O THR C 906 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE C 920 " --> pdb=" O CYS C 916 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE C 921 " --> pdb=" O ILE C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 930 removed outlier: 3.808A pdb=" N ILE C 929 " --> pdb=" O ARG C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 936 through 946 removed outlier: 3.930A pdb=" N ILE C 940 " --> pdb=" O LEU C 936 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE C 941 " --> pdb=" O GLY C 937 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE C 942 " --> pdb=" O PRO C 938 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 943 " --> pdb=" O LYS C 939 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET C 946 " --> pdb=" O ILE C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 948 through 973 removed outlier: 4.190A pdb=" N PHE C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TRP C 960 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU C 972 " --> pdb=" O LYS C 968 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE C 973 " --> pdb=" O GLN C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 987 Processing helix chain 'C' and resid 987 through 994 Processing helix chain 'C' and resid 997 through 1002 removed outlier: 3.646A pdb=" N ILE C1002 " --> pdb=" O PHE C 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1071 removed outlier: 3.609A pdb=" N THR C1040 " --> pdb=" O PRO C1036 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C1053 " --> pdb=" O LEU C1049 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU C1054 " --> pdb=" O PHE C1050 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU C1055 " --> pdb=" O ALA C1051 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C1056 " --> pdb=" O ASN C1052 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASN C1057 " --> pdb=" O ILE C1053 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU C1058 " --> pdb=" O LEU C1054 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE C1063 " --> pdb=" O LEU C1059 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR C1065 " --> pdb=" O ALA C1061 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN C1071 " --> pdb=" O PHE C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1074 through 1090 removed outlier: 3.772A pdb=" N TRP C1078 " --> pdb=" O THR C1074 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS C1079 " --> pdb=" O ASP C1075 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS C1087 " --> pdb=" O TYR C1083 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLU C1088 " --> pdb=" O GLU C1084 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TYR C1089 " --> pdb=" O LEU C1085 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS C1090 " --> pdb=" O ILE C1086 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1112 Processing helix chain 'C' and resid 1129 through 1156 removed outlier: 4.002A pdb=" N ALA C1149 " --> pdb=" O ASP C1145 " (cutoff:3.500A) Processing helix chain 'C' and resid 1158 through 1186 removed outlier: 4.440A pdb=" N HIS C1164 " --> pdb=" O GLU C1160 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU C1168 " --> pdb=" O HIS C1164 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU C1175 " --> pdb=" O GLY C1171 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU C1178 " --> pdb=" O SER C1174 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'C' and resid 1368 through 1378 Processing helix chain 'C' and resid 1382 through 1388 Processing helix chain 'C' and resid 1426 through 1433 removed outlier: 4.063A pdb=" N LEU C1430 " --> pdb=" O LEU C1426 " (cutoff:3.500A) Processing helix chain 'C' and resid 1456 through 1471 removed outlier: 4.012A pdb=" N GLU C1461 " --> pdb=" O SER C1457 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA C1462 " --> pdb=" O TYR C1458 " (cutoff:3.500A) Processing helix chain 'C' and resid 1472 through 1474 No H-bonds generated for 'chain 'C' and resid 1472 through 1474' Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 126 through 136 Processing helix chain 'B' and resid 161 through 177 removed outlier: 3.878A pdb=" N LYS B 165 " --> pdb=" O HIS B 161 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 206 removed outlier: 3.737A pdb=" N LEU B 203 " --> pdb=" O ARG B 199 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER B 204 " --> pdb=" O ASP B 200 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 removed outlier: 3.812A pdb=" N THR B 228 " --> pdb=" O ASN B 225 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 229 " --> pdb=" O ARG B 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 225 through 229' Processing helix chain 'B' and resid 274 through 286 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 311 through 323 removed outlier: 3.614A pdb=" N THR B 315 " --> pdb=" O GLY B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 343 Processing helix chain 'B' and resid 351 through 361 removed outlier: 4.176A pdb=" N ARG B 361 " --> pdb=" O ARG B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 386 Processing helix chain 'B' and resid 404 through 419 removed outlier: 4.302A pdb=" N ALA B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER B 419 " --> pdb=" O LYS B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 438 removed outlier: 3.975A pdb=" N GLU B 433 " --> pdb=" O GLU B 429 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 434 " --> pdb=" O ARG B 430 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA B 435 " --> pdb=" O GLN B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 449 Processing helix chain 'B' and resid 460 through 470 Processing helix chain 'B' and resid 472 through 482 removed outlier: 3.577A pdb=" N VAL B 476 " --> pdb=" O LYS B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 490 Processing helix chain 'B' and resid 492 through 500 removed outlier: 4.035A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 503 No H-bonds generated for 'chain 'B' and resid 501 through 503' Processing helix chain 'B' and resid 506 through 516 Processing helix chain 'B' and resid 536 through 548 removed outlier: 3.769A pdb=" N GLU B 542 " --> pdb=" O HIS B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 604 removed outlier: 4.365A pdb=" N ASP B 597 " --> pdb=" O ASP B 593 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 598 " --> pdb=" O PRO B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 616 removed outlier: 3.868A pdb=" N ILE B 613 " --> pdb=" O GLU B 609 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU B 616 " --> pdb=" O GLU B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 640 removed outlier: 3.545A pdb=" N SER B 639 " --> pdb=" O LEU B 635 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY B 640 " --> pdb=" O ALA B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 672 removed outlier: 4.366A pdb=" N MET B 650 " --> pdb=" O GLU B 646 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LEU B 651 " --> pdb=" O ALA B 647 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER B 670 " --> pdb=" O SER B 666 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TRP B 671 " --> pdb=" O GLU B 667 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP B 672 " --> pdb=" O CYS B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 682 removed outlier: 3.579A pdb=" N ALA B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS B 678 " --> pdb=" O GLN B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 699 Processing helix chain 'B' and resid 701 through 706 removed outlier: 3.668A pdb=" N ILE B 705 " --> pdb=" O ASP B 701 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA B 706 " --> pdb=" O LYS B 702 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 701 through 706' Processing helix chain 'B' and resid 707 through 719 Processing helix chain 'B' and resid 727 through 737 Processing helix chain 'B' and resid 738 through 744 removed outlier: 4.279A pdb=" N TYR B 742 " --> pdb=" O PHE B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 770 Processing helix chain 'B' and resid 799 through 806 removed outlier: 4.295A pdb=" N MET B 803 " --> pdb=" O SER B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 833 removed outlier: 3.735A pdb=" N TYR B 814 " --> pdb=" O GLN B 810 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 833 " --> pdb=" O VAL B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 863 removed outlier: 3.508A pdb=" N TYR B 862 " --> pdb=" O ILE B 858 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N HIS B 863 " --> pdb=" O ARG B 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 878 Processing helix chain 'B' and resid 881 through 902 removed outlier: 4.246A pdb=" N LEU B 885 " --> pdb=" O LEU B 881 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASP B 886 " --> pdb=" O TRP B 882 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL B 891 " --> pdb=" O VAL B 887 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 894 " --> pdb=" O ILE B 890 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 925 removed outlier: 3.769A pdb=" N ILE B 910 " --> pdb=" O THR B 906 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE B 920 " --> pdb=" O CYS B 916 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B 921 " --> pdb=" O ILE B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 930 removed outlier: 3.807A pdb=" N ILE B 929 " --> pdb=" O ARG B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 946 removed outlier: 3.930A pdb=" N ILE B 940 " --> pdb=" O LEU B 936 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE B 941 " --> pdb=" O GLY B 937 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE B 942 " --> pdb=" O PRO B 938 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 943 " --> pdb=" O LYS B 939 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET B 946 " --> pdb=" O ILE B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 973 removed outlier: 4.191A pdb=" N PHE B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TRP B 960 " --> pdb=" O LEU B 956 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU B 972 " --> pdb=" O LYS B 968 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE B 973 " --> pdb=" O GLN B 969 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 987 Processing helix chain 'B' and resid 987 through 994 Processing helix chain 'B' and resid 997 through 1002 removed outlier: 3.646A pdb=" N ILE B1002 " --> pdb=" O PHE B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1071 removed outlier: 3.608A pdb=" N THR B1040 " --> pdb=" O PRO B1036 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B1053 " --> pdb=" O LEU B1049 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU B1054 " --> pdb=" O PHE B1050 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU B1055 " --> pdb=" O ALA B1051 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B1056 " --> pdb=" O ASN B1052 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN B1057 " --> pdb=" O ILE B1053 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU B1058 " --> pdb=" O LEU B1054 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE B1063 " --> pdb=" O LEU B1059 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR B1065 " --> pdb=" O ALA B1061 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN B1071 " --> pdb=" O PHE B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1074 through 1090 removed outlier: 3.771A pdb=" N TRP B1078 " --> pdb=" O THR B1074 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS B1079 " --> pdb=" O ASP B1075 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS B1087 " --> pdb=" O TYR B1083 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLU B1088 " --> pdb=" O GLU B1084 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TYR B1089 " --> pdb=" O LEU B1085 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS B1090 " --> pdb=" O ILE B1086 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1112 Processing helix chain 'B' and resid 1129 through 1156 removed outlier: 4.002A pdb=" N ALA B1149 " --> pdb=" O ASP B1145 " (cutoff:3.500A) Processing helix chain 'B' and resid 1158 through 1186 removed outlier: 4.440A pdb=" N HIS B1164 " --> pdb=" O GLU B1160 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B1168 " --> pdb=" O HIS B1164 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B1175 " --> pdb=" O GLY B1171 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU B1178 " --> pdb=" O SER B1174 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'B' and resid 1368 through 1378 Processing helix chain 'B' and resid 1382 through 1388 Processing helix chain 'B' and resid 1426 through 1433 removed outlier: 4.063A pdb=" N LEU B1430 " --> pdb=" O LEU B1426 " (cutoff:3.500A) Processing helix chain 'B' and resid 1456 through 1471 removed outlier: 4.011A pdb=" N GLU B1461 " --> pdb=" O SER B1457 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B1462 " --> pdb=" O TYR B1458 " (cutoff:3.500A) Processing helix chain 'B' and resid 1472 through 1474 No H-bonds generated for 'chain 'B' and resid 1472 through 1474' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 126 through 136 Processing helix chain 'D' and resid 161 through 177 removed outlier: 3.878A pdb=" N LYS D 165 " --> pdb=" O HIS D 161 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA D 174 " --> pdb=" O LEU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 206 removed outlier: 3.737A pdb=" N LEU D 203 " --> pdb=" O ARG D 199 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER D 204 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY D 206 " --> pdb=" O THR D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 229 removed outlier: 3.812A pdb=" N THR D 228 " --> pdb=" O ASN D 225 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 229 " --> pdb=" O ARG D 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 225 through 229' Processing helix chain 'D' and resid 274 through 286 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 311 through 323 removed outlier: 3.616A pdb=" N THR D 315 " --> pdb=" O GLY D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 343 Processing helix chain 'D' and resid 351 through 361 removed outlier: 4.175A pdb=" N ARG D 361 " --> pdb=" O ARG D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 386 Processing helix chain 'D' and resid 404 through 419 removed outlier: 4.302A pdb=" N ALA D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER D 419 " --> pdb=" O LYS D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 438 removed outlier: 3.976A pdb=" N GLU D 433 " --> pdb=" O GLU D 429 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU D 434 " --> pdb=" O ARG D 430 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA D 435 " --> pdb=" O GLN D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 449 Processing helix chain 'D' and resid 460 through 470 Processing helix chain 'D' and resid 472 through 482 removed outlier: 3.577A pdb=" N VAL D 476 " --> pdb=" O LYS D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 490 Processing helix chain 'D' and resid 492 through 500 removed outlier: 4.036A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 503 No H-bonds generated for 'chain 'D' and resid 501 through 503' Processing helix chain 'D' and resid 506 through 516 Processing helix chain 'D' and resid 536 through 548 removed outlier: 3.769A pdb=" N GLU D 542 " --> pdb=" O HIS D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 604 removed outlier: 4.365A pdb=" N ASP D 597 " --> pdb=" O ASP D 593 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU D 598 " --> pdb=" O PRO D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 616 removed outlier: 3.868A pdb=" N ILE D 613 " --> pdb=" O GLU D 609 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU D 616 " --> pdb=" O GLU D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 640 removed outlier: 3.544A pdb=" N SER D 639 " --> pdb=" O LEU D 635 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY D 640 " --> pdb=" O ALA D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 642 through 672 removed outlier: 4.365A pdb=" N MET D 650 " --> pdb=" O GLU D 646 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU D 651 " --> pdb=" O ALA D 647 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER D 670 " --> pdb=" O SER D 666 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TRP D 671 " --> pdb=" O GLU D 667 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP D 672 " --> pdb=" O CYS D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 682 removed outlier: 3.578A pdb=" N ALA D 676 " --> pdb=" O ASP D 672 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS D 678 " --> pdb=" O GLN D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 699 Processing helix chain 'D' and resid 701 through 706 removed outlier: 3.669A pdb=" N ILE D 705 " --> pdb=" O ASP D 701 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA D 706 " --> pdb=" O LYS D 702 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 701 through 706' Processing helix chain 'D' and resid 707 through 719 Processing helix chain 'D' and resid 727 through 737 Processing helix chain 'D' and resid 738 through 744 removed outlier: 4.279A pdb=" N TYR D 742 " --> pdb=" O PHE D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 770 Processing helix chain 'D' and resid 799 through 806 removed outlier: 4.294A pdb=" N MET D 803 " --> pdb=" O SER D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 808 through 833 removed outlier: 3.734A pdb=" N TYR D 814 " --> pdb=" O GLN D 810 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE D 833 " --> pdb=" O VAL D 829 " (cutoff:3.500A) Processing helix chain 'D' and resid 840 through 863 removed outlier: 3.508A pdb=" N TYR D 862 " --> pdb=" O ILE D 858 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N HIS D 863 " --> pdb=" O ARG D 859 " (cutoff:3.500A) Processing helix chain 'D' and resid 871 through 878 Processing helix chain 'D' and resid 881 through 902 removed outlier: 4.245A pdb=" N LEU D 885 " --> pdb=" O LEU D 881 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASP D 886 " --> pdb=" O TRP D 882 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL D 891 " --> pdb=" O VAL D 887 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE D 894 " --> pdb=" O ILE D 890 " (cutoff:3.500A) Processing helix chain 'D' and resid 906 through 925 removed outlier: 3.769A pdb=" N ILE D 910 " --> pdb=" O THR D 906 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE D 920 " --> pdb=" O CYS D 916 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE D 921 " --> pdb=" O ILE D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 930 removed outlier: 3.808A pdb=" N ILE D 929 " --> pdb=" O ARG D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 936 through 946 removed outlier: 3.930A pdb=" N ILE D 940 " --> pdb=" O LEU D 936 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE D 941 " --> pdb=" O GLY D 937 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE D 942 " --> pdb=" O PRO D 938 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL D 943 " --> pdb=" O LYS D 939 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET D 946 " --> pdb=" O ILE D 942 " (cutoff:3.500A) Processing helix chain 'D' and resid 948 through 973 removed outlier: 4.191A pdb=" N PHE D 952 " --> pdb=" O LEU D 948 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TRP D 960 " --> pdb=" O LEU D 956 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU D 972 " --> pdb=" O LYS D 968 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE D 973 " --> pdb=" O GLN D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 978 through 987 Processing helix chain 'D' and resid 987 through 994 Processing helix chain 'D' and resid 997 through 1002 removed outlier: 3.647A pdb=" N ILE D1002 " --> pdb=" O PHE D 998 " (cutoff:3.500A) Processing helix chain 'D' and resid 1036 through 1071 removed outlier: 3.609A pdb=" N THR D1040 " --> pdb=" O PRO D1036 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE D1053 " --> pdb=" O LEU D1049 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU D1054 " --> pdb=" O PHE D1050 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU D1055 " --> pdb=" O ALA D1051 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU D1056 " --> pdb=" O ASN D1052 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN D1057 " --> pdb=" O ILE D1053 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU D1058 " --> pdb=" O LEU D1054 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE D1063 " --> pdb=" O LEU D1059 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR D1065 " --> pdb=" O ALA D1061 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN D1071 " --> pdb=" O PHE D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1074 through 1090 removed outlier: 3.771A pdb=" N TRP D1078 " --> pdb=" O THR D1074 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS D1079 " --> pdb=" O ASP D1075 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS D1087 " --> pdb=" O TYR D1083 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU D1088 " --> pdb=" O GLU D1084 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR D1089 " --> pdb=" O LEU D1085 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS D1090 " --> pdb=" O ILE D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 1099 through 1112 Processing helix chain 'D' and resid 1129 through 1156 removed outlier: 4.002A pdb=" N ALA D1149 " --> pdb=" O ASP D1145 " (cutoff:3.500A) Processing helix chain 'D' and resid 1158 through 1186 removed outlier: 4.439A pdb=" N HIS D1164 " --> pdb=" O GLU D1160 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU D1168 " --> pdb=" O HIS D1164 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU D1175 " --> pdb=" O GLY D1171 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU D1178 " --> pdb=" O SER D1174 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'D' and resid 1368 through 1378 Processing helix chain 'D' and resid 1382 through 1388 Processing helix chain 'D' and resid 1426 through 1433 removed outlier: 4.063A pdb=" N LEU D1430 " --> pdb=" O LEU D1426 " (cutoff:3.500A) Processing helix chain 'D' and resid 1456 through 1471 removed outlier: 4.012A pdb=" N GLU D1461 " --> pdb=" O SER D1457 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA D1462 " --> pdb=" O TYR D1458 " (cutoff:3.500A) Processing helix chain 'D' and resid 1472 through 1474 No H-bonds generated for 'chain 'D' and resid 1472 through 1474' Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 52 removed outlier: 3.784A pdb=" N ARG A 96 " --> pdb=" O GLU A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 237 through 240 removed outlier: 3.644A pdb=" N ALA A 238 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 119 " --> pdb=" O PHE A 260 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL A 214 " --> pdb=" O HIS A 259 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LEU A 261 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLY A 216 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL A 263 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA A 218 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE A 181 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N VAL A 217 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR A 183 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLY A 184 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU A 146 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL A 304 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N SER A 148 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS A 326 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 305 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR A 393 " --> pdb=" O VAL A 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1356 through 1357 removed outlier: 5.600A pdb=" N PHE A1332 " --> pdb=" O LEU A1346 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N VAL A1348 " --> pdb=" O PRO A1330 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLY A1323 " --> pdb=" O TRP A1410 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU A1412 " --> pdb=" O GLY A1323 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ASN A1325 " --> pdb=" O GLU A1412 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N SER A1414 " --> pdb=" O ASN A1325 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE A1327 " --> pdb=" O SER A1414 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE A1416 " --> pdb=" O ILE A1327 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N HIS A1329 " --> pdb=" O ILE A1416 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU A1418 " --> pdb=" O HIS A1329 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE A1331 " --> pdb=" O LEU A1418 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1356 through 1357 removed outlier: 3.678A pdb=" N GLN A1445 " --> pdb=" O ALA A1347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 49 through 52 removed outlier: 3.784A pdb=" N ARG C 96 " --> pdb=" O GLU C 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 237 through 240 removed outlier: 3.644A pdb=" N ALA C 238 " --> pdb=" O ASP C 105 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL C 119 " --> pdb=" O PHE C 260 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL C 214 " --> pdb=" O HIS C 259 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LEU C 261 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLY C 216 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL C 263 " --> pdb=" O GLY C 216 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA C 218 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE C 181 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N VAL C 217 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR C 183 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLY C 184 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU C 146 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL C 304 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N SER C 148 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS C 326 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL C 305 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR C 393 " --> pdb=" O VAL C 327 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 1356 through 1357 removed outlier: 5.601A pdb=" N PHE C1332 " --> pdb=" O LEU C1346 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N VAL C1348 " --> pdb=" O PRO C1330 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLY C1323 " --> pdb=" O TRP C1410 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU C1412 " --> pdb=" O GLY C1323 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ASN C1325 " --> pdb=" O GLU C1412 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N SER C1414 " --> pdb=" O ASN C1325 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE C1327 " --> pdb=" O SER C1414 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE C1416 " --> pdb=" O ILE C1327 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N HIS C1329 " --> pdb=" O ILE C1416 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU C1418 " --> pdb=" O HIS C1329 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE C1331 " --> pdb=" O LEU C1418 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 1356 through 1357 removed outlier: 3.678A pdb=" N GLN C1445 " --> pdb=" O ALA C1347 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 49 through 52 removed outlier: 3.784A pdb=" N ARG B 96 " --> pdb=" O GLU B 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 237 through 240 removed outlier: 3.644A pdb=" N ALA B 238 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B 119 " --> pdb=" O PHE B 260 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL B 214 " --> pdb=" O HIS B 259 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LEU B 261 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLY B 216 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL B 263 " --> pdb=" O GLY B 216 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA B 218 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE B 181 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N VAL B 217 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR B 183 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLY B 184 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU B 146 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL B 304 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N SER B 148 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS B 326 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL B 305 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR B 393 " --> pdb=" O VAL B 327 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1356 through 1357 removed outlier: 5.600A pdb=" N PHE B1332 " --> pdb=" O LEU B1346 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N VAL B1348 " --> pdb=" O PRO B1330 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLY B1323 " --> pdb=" O TRP B1410 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU B1412 " --> pdb=" O GLY B1323 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ASN B1325 " --> pdb=" O GLU B1412 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N SER B1414 " --> pdb=" O ASN B1325 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE B1327 " --> pdb=" O SER B1414 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE B1416 " --> pdb=" O ILE B1327 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N HIS B1329 " --> pdb=" O ILE B1416 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU B1418 " --> pdb=" O HIS B1329 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE B1331 " --> pdb=" O LEU B1418 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1356 through 1357 removed outlier: 3.678A pdb=" N GLN B1445 " --> pdb=" O ALA B1347 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 49 through 52 removed outlier: 3.784A pdb=" N ARG D 96 " --> pdb=" O GLU D 52 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 237 through 240 removed outlier: 3.644A pdb=" N ALA D 238 " --> pdb=" O ASP D 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL D 119 " --> pdb=" O PHE D 260 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL D 214 " --> pdb=" O HIS D 259 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LEU D 261 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLY D 216 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL D 263 " --> pdb=" O GLY D 216 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA D 218 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE D 181 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N VAL D 217 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR D 183 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLY D 184 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU D 146 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL D 304 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N SER D 148 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS D 326 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL D 305 " --> pdb=" O VAL D 328 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR D 393 " --> pdb=" O VAL D 327 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 1356 through 1357 removed outlier: 5.600A pdb=" N PHE D1332 " --> pdb=" O LEU D1346 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N VAL D1348 " --> pdb=" O PRO D1330 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLY D1323 " --> pdb=" O TRP D1410 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU D1412 " --> pdb=" O GLY D1323 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ASN D1325 " --> pdb=" O GLU D1412 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N SER D1414 " --> pdb=" O ASN D1325 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE D1327 " --> pdb=" O SER D1414 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ILE D1416 " --> pdb=" O ILE D1327 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N HIS D1329 " --> pdb=" O ILE D1416 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU D1418 " --> pdb=" O HIS D1329 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE D1331 " --> pdb=" O LEU D1418 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 1356 through 1357 removed outlier: 3.678A pdb=" N GLN D1445 " --> pdb=" O ALA D1347 " (cutoff:3.500A) 1840 hydrogen bonds defined for protein. 5484 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: 15.24 Time building geometry restraints manager: 10.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5354 1.30 - 1.42: 8862 1.42 - 1.55: 19464 1.55 - 1.68: 4 1.68 - 1.81: 164 Bond restraints: 33848 Sorted by residual: bond pdb=" C SER A1281 " pdb=" N PRO A1282 " ideal model delta sigma weight residual 1.331 1.386 -0.054 7.90e-03 1.60e+04 4.71e+01 bond pdb=" C SER D1281 " pdb=" N PRO D1282 " ideal model delta sigma weight residual 1.331 1.385 -0.054 7.90e-03 1.60e+04 4.59e+01 bond pdb=" C SER C1281 " pdb=" N PRO C1282 " ideal model delta sigma weight residual 1.331 1.385 -0.054 7.90e-03 1.60e+04 4.59e+01 bond pdb=" C SER B1281 " pdb=" N PRO B1282 " ideal model delta sigma weight residual 1.331 1.385 -0.053 7.90e-03 1.60e+04 4.54e+01 bond pdb=" CA THR C 177 " pdb=" C THR C 177 " ideal model delta sigma weight residual 1.525 1.447 0.079 1.27e-02 6.20e+03 3.83e+01 ... (remaining 33843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 43586 2.13 - 4.27: 2430 4.27 - 6.40: 424 6.40 - 8.54: 148 8.54 - 10.67: 48 Bond angle restraints: 46636 Sorted by residual: angle pdb=" N ASP C1072 " pdb=" CA ASP C1072 " pdb=" C ASP C1072 " ideal model delta sigma weight residual 111.28 121.70 -10.42 1.09e+00 8.42e-01 9.15e+01 angle pdb=" N ASP A1072 " pdb=" CA ASP A1072 " pdb=" C ASP A1072 " ideal model delta sigma weight residual 111.28 121.67 -10.39 1.09e+00 8.42e-01 9.09e+01 angle pdb=" N ASP B1072 " pdb=" CA ASP B1072 " pdb=" C ASP B1072 " ideal model delta sigma weight residual 111.28 121.67 -10.39 1.09e+00 8.42e-01 9.09e+01 angle pdb=" N ASP D1072 " pdb=" CA ASP D1072 " pdb=" C ASP D1072 " ideal model delta sigma weight residual 111.28 121.65 -10.37 1.09e+00 8.42e-01 9.05e+01 angle pdb=" N THR D1074 " pdb=" CA THR D1074 " pdb=" C THR D1074 " ideal model delta sigma weight residual 111.28 120.86 -9.58 1.09e+00 8.42e-01 7.72e+01 ... (remaining 46631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 19014 17.92 - 35.85: 502 35.85 - 53.77: 96 53.77 - 71.70: 4 71.70 - 89.62: 8 Dihedral angle restraints: 19624 sinusoidal: 4904 harmonic: 14720 Sorted by residual: dihedral pdb=" CA MET B 364 " pdb=" C MET B 364 " pdb=" N GLN B 365 " pdb=" CA GLN B 365 " ideal model delta harmonic sigma weight residual 180.00 150.28 29.72 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA MET A 364 " pdb=" C MET A 364 " pdb=" N GLN A 365 " pdb=" CA GLN A 365 " ideal model delta harmonic sigma weight residual 180.00 150.32 29.68 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA MET C 364 " pdb=" C MET C 364 " pdb=" N GLN C 365 " pdb=" CA GLN C 365 " ideal model delta harmonic sigma weight residual 180.00 150.34 29.66 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 19621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 4654 0.078 - 0.155: 877 0.155 - 0.233: 116 0.233 - 0.310: 44 0.310 - 0.388: 13 Chirality restraints: 5704 Sorted by residual: chirality pdb=" CA ASP B 725 " pdb=" N ASP B 725 " pdb=" C ASP B 725 " pdb=" CB ASP B 725 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CA ASP D 725 " pdb=" N ASP D 725 " pdb=" C ASP D 725 " pdb=" CB ASP D 725 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CA ASP A 725 " pdb=" N ASP A 725 " pdb=" C ASP A 725 " pdb=" CB ASP A 725 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.39 2.00e-01 2.50e+01 3.71e+00 ... (remaining 5701 not shown) Planarity restraints: 6036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 170 " -0.026 2.00e-02 2.50e+03 5.35e-02 2.87e+01 pdb=" C LEU C 170 " 0.093 2.00e-02 2.50e+03 pdb=" O LEU C 170 " -0.034 2.00e-02 2.50e+03 pdb=" N ILE C 171 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 170 " 0.026 2.00e-02 2.50e+03 5.34e-02 2.85e+01 pdb=" C LEU B 170 " -0.092 2.00e-02 2.50e+03 pdb=" O LEU B 170 " 0.034 2.00e-02 2.50e+03 pdb=" N ILE B 171 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 170 " -0.026 2.00e-02 2.50e+03 5.33e-02 2.85e+01 pdb=" C LEU D 170 " 0.092 2.00e-02 2.50e+03 pdb=" O LEU D 170 " -0.034 2.00e-02 2.50e+03 pdb=" N ILE D 171 " -0.032 2.00e-02 2.50e+03 ... (remaining 6033 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1107 2.70 - 3.25: 32435 3.25 - 3.80: 50067 3.80 - 4.35: 53297 4.35 - 4.90: 91645 Nonbonded interactions: 228551 Sorted by model distance: nonbonded pdb=" O ALA D1016 " pdb=" C SER D1017 " model vdw 2.150 3.270 nonbonded pdb=" O ALA C1016 " pdb=" C SER C1017 " model vdw 2.150 3.270 nonbonded pdb=" O ALA B1016 " pdb=" C SER B1017 " model vdw 2.150 3.270 nonbonded pdb=" O ALA A1016 " pdb=" C SER A1017 " model vdw 2.150 3.270 nonbonded pdb=" O LEU A 432 " pdb=" N ALA A 435 " model vdw 2.188 3.120 ... (remaining 228546 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: 0.30 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 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: 1.280 Check model and map are aligned: 0.250 Set scattering table: 0.300 Process input model: 83.650 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 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 : 0.010 0.093 33852 Z= 0.535 Angle : 1.176 10.672 46644 Z= 0.722 Chirality : 0.067 0.388 5704 Planarity : 0.008 0.062 6036 Dihedral : 9.745 89.624 10012 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.36 % Allowed : 5.15 % Favored : 94.49 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.10), residues: 5004 helix: -1.66 (0.08), residues: 2544 sheet: -2.12 (0.25), residues: 312 loop : -2.39 (0.11), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.004 TRP B 849 HIS 0.011 0.003 HIS A 545 PHE 0.023 0.003 PHE D1035 TYR 0.018 0.003 TYR C 500 ARG 0.018 0.002 ARG C1092 Details of bonding type rmsd hydrogen bonds : bond 0.17725 ( 1832) hydrogen bonds : angle 6.49439 ( 5484) SS BOND : bond 0.00868 ( 4) SS BOND : angle 1.17844 ( 8) covalent geometry : bond 0.00980 (33848) covalent geometry : angle 1.17591 (46636) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 716 time to evaluate : 3.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. REVERT: A 187 HIS cc_start: 0.8592 (t70) cc_final: 0.8127 (t70) REVERT: A 307 ASP cc_start: 0.7554 (t0) cc_final: 0.7238 (p0) REVERT: A 603 VAL cc_start: 0.9339 (t) cc_final: 0.9084 (p) REVERT: A 604 VAL cc_start: 0.9634 (m) cc_final: 0.9428 (p) REVERT: A 658 GLU cc_start: 0.8506 (tp30) cc_final: 0.7620 (tp30) REVERT: A 667 GLU cc_start: 0.9309 (tp30) cc_final: 0.9071 (tp30) REVERT: A 701 ASP cc_start: 0.8270 (m-30) cc_final: 0.7702 (m-30) REVERT: A 806 LEU cc_start: 0.9221 (mm) cc_final: 0.9007 (tt) REVERT: A 859 ARG cc_start: 0.6361 (mmt180) cc_final: 0.5593 (ttp80) REVERT: A 923 CYS cc_start: 0.8787 (m) cc_final: 0.8284 (m) REVERT: A 1140 GLU cc_start: 0.8665 (pp20) cc_final: 0.8423 (pp20) REVERT: A 1252 MET cc_start: 0.6938 (mtm) cc_final: 0.6622 (mtt) REVERT: A 1253 PHE cc_start: 0.8487 (m-10) cc_final: 0.8235 (t80) REVERT: C 604 VAL cc_start: 0.9593 (m) cc_final: 0.9384 (p) REVERT: C 658 GLU cc_start: 0.8405 (tp30) cc_final: 0.7450 (tp30) REVERT: C 667 GLU cc_start: 0.9236 (tp30) cc_final: 0.8848 (tp30) REVERT: C 686 SER cc_start: 0.9466 (m) cc_final: 0.9253 (p) REVERT: C 701 ASP cc_start: 0.8311 (m-30) cc_final: 0.7784 (m-30) REVERT: C 859 ARG cc_start: 0.6501 (mmt180) cc_final: 0.5742 (ttp80) REVERT: C 923 CYS cc_start: 0.8932 (m) cc_final: 0.8444 (m) REVERT: C 1140 GLU cc_start: 0.8594 (pp20) cc_final: 0.8297 (pp20) REVERT: C 1252 MET cc_start: 0.7037 (mtm) cc_final: 0.6759 (mtt) REVERT: C 1253 PHE cc_start: 0.8565 (m-10) cc_final: 0.8256 (t80) REVERT: B 604 VAL cc_start: 0.9587 (m) cc_final: 0.9381 (p) REVERT: B 658 GLU cc_start: 0.8469 (tp30) cc_final: 0.7460 (tp30) REVERT: B 686 SER cc_start: 0.9453 (m) cc_final: 0.9244 (p) REVERT: B 701 ASP cc_start: 0.8293 (m-30) cc_final: 0.7774 (m-30) REVERT: B 859 ARG cc_start: 0.6576 (mmt180) cc_final: 0.5725 (ttp80) REVERT: B 893 PHE cc_start: 0.8584 (t80) cc_final: 0.8383 (t80) REVERT: B 923 CYS cc_start: 0.8896 (m) cc_final: 0.8417 (m) REVERT: B 1140 GLU cc_start: 0.8591 (pp20) cc_final: 0.8308 (pp20) REVERT: B 1143 MET cc_start: 0.9163 (mmm) cc_final: 0.8956 (tpp) REVERT: B 1252 MET cc_start: 0.7065 (mtm) cc_final: 0.6794 (mtt) REVERT: B 1253 PHE cc_start: 0.8522 (m-10) cc_final: 0.8217 (t80) REVERT: D 658 GLU cc_start: 0.8454 (tp30) cc_final: 0.7452 (tp30) REVERT: D 686 SER cc_start: 0.9462 (m) cc_final: 0.9260 (p) REVERT: D 701 ASP cc_start: 0.8307 (m-30) cc_final: 0.7796 (m-30) REVERT: D 859 ARG cc_start: 0.6600 (mmt180) cc_final: 0.5740 (ttp80) REVERT: D 893 PHE cc_start: 0.8624 (t80) cc_final: 0.8422 (t80) REVERT: D 923 CYS cc_start: 0.8915 (m) cc_final: 0.8440 (m) REVERT: D 998 PHE cc_start: 0.8741 (t80) cc_final: 0.8505 (t80) REVERT: D 1140 GLU cc_start: 0.8615 (pp20) cc_final: 0.8306 (pp20) REVERT: D 1143 MET cc_start: 0.9162 (mmm) cc_final: 0.8947 (tpp) REVERT: D 1173 MET cc_start: 0.8362 (mtp) cc_final: 0.7671 (ttm) REVERT: D 1252 MET cc_start: 0.6925 (mtm) cc_final: 0.6603 (mtt) REVERT: D 1253 PHE cc_start: 0.8522 (m-10) cc_final: 0.8233 (t80) outliers start: 8 outliers final: 4 residues processed: 720 average time/residue: 0.4733 time to fit residues: 558.6718 Evaluate side-chains 477 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 473 time to evaluate : 3.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain D residue 697 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 425 optimal weight: 0.7980 chunk 382 optimal weight: 20.0000 chunk 211 optimal weight: 0.9990 chunk 130 optimal weight: 20.0000 chunk 257 optimal weight: 10.0000 chunk 204 optimal weight: 5.9990 chunk 395 optimal weight: 10.0000 chunk 152 optimal weight: 0.0870 chunk 240 optimal weight: 30.0000 chunk 294 optimal weight: 0.9980 chunk 457 optimal weight: 5.9990 overall best weight: 1.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN A 716 GLN A 997 ASN A1164 HIS C 606 ASN C 997 ASN C1164 HIS B 606 ASN B 816 ASN B 997 ASN B1164 HIS D 606 ASN D 816 ASN D 997 ASN D1164 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.144907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.107863 restraints weight = 85506.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.104364 restraints weight = 54392.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.105107 restraints weight = 52800.674| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33852 Z= 0.138 Angle : 0.579 8.521 46644 Z= 0.307 Chirality : 0.039 0.147 5704 Planarity : 0.005 0.049 6036 Dihedral : 4.724 24.913 5268 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.86 % Allowed : 13.32 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.11), residues: 5004 helix: 0.15 (0.10), residues: 2612 sheet: -1.97 (0.26), residues: 352 loop : -2.05 (0.12), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 849 HIS 0.007 0.001 HIS A1251 PHE 0.027 0.002 PHE B 995 TYR 0.020 0.002 TYR B 201 ARG 0.005 0.000 ARG D1152 Details of bonding type rmsd hydrogen bonds : bond 0.04530 ( 1832) hydrogen bonds : angle 4.12488 ( 5484) SS BOND : bond 0.00249 ( 4) SS BOND : angle 0.71559 ( 8) covalent geometry : bond 0.00289 (33848) covalent geometry : angle 0.57849 (46636) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 547 time to evaluate : 3.554 Fit side-chains TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. REVERT: A 307 ASP cc_start: 0.7379 (t0) cc_final: 0.7019 (p0) REVERT: A 314 ASN cc_start: 0.8049 (m-40) cc_final: 0.7771 (m110) REVERT: A 667 GLU cc_start: 0.9160 (tp30) cc_final: 0.8748 (tp30) REVERT: A 859 ARG cc_start: 0.5940 (mmt180) cc_final: 0.5354 (ttp80) REVERT: A 893 PHE cc_start: 0.8544 (t80) cc_final: 0.8187 (t80) REVERT: A 901 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7736 (tt) REVERT: A 1040 THR cc_start: 0.9385 (p) cc_final: 0.9146 (t) REVERT: A 1140 GLU cc_start: 0.8244 (pp20) cc_final: 0.7947 (pp20) REVERT: C 314 ASN cc_start: 0.7896 (m-40) cc_final: 0.7584 (m110) REVERT: C 392 LEU cc_start: 0.9339 (tt) cc_final: 0.9133 (mm) REVERT: C 667 GLU cc_start: 0.9067 (tp30) cc_final: 0.8665 (tp30) REVERT: C 680 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9367 (tt) REVERT: C 893 PHE cc_start: 0.8459 (t80) cc_final: 0.8035 (t80) REVERT: C 923 CYS cc_start: 0.8931 (m) cc_final: 0.8555 (m) REVERT: C 1040 THR cc_start: 0.9375 (p) cc_final: 0.9129 (t) REVERT: C 1140 GLU cc_start: 0.8151 (pp20) cc_final: 0.7860 (pp20) REVERT: C 1142 TYR cc_start: 0.8438 (t80) cc_final: 0.8098 (t80) REVERT: B 314 ASN cc_start: 0.7819 (m-40) cc_final: 0.7484 (m110) REVERT: B 392 LEU cc_start: 0.9327 (tt) cc_final: 0.9112 (mm) REVERT: B 667 GLU cc_start: 0.9098 (tp30) cc_final: 0.8761 (tp30) REVERT: B 680 LEU cc_start: 0.9599 (OUTLIER) cc_final: 0.9389 (tt) REVERT: B 859 ARG cc_start: 0.6069 (mmt180) cc_final: 0.5376 (ttp80) REVERT: B 893 PHE cc_start: 0.8604 (t80) cc_final: 0.8243 (t80) REVERT: B 923 CYS cc_start: 0.8894 (m) cc_final: 0.8518 (m) REVERT: B 1040 THR cc_start: 0.9354 (p) cc_final: 0.9123 (t) REVERT: B 1140 GLU cc_start: 0.8209 (pp20) cc_final: 0.7924 (pp20) REVERT: B 1142 TYR cc_start: 0.8527 (t80) cc_final: 0.8128 (t80) REVERT: D 314 ASN cc_start: 0.7853 (m-40) cc_final: 0.7562 (m110) REVERT: D 667 GLU cc_start: 0.9096 (tp30) cc_final: 0.8764 (tp30) REVERT: D 680 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9379 (tt) REVERT: D 859 ARG cc_start: 0.6118 (mmt180) cc_final: 0.5418 (ttp80) REVERT: D 893 PHE cc_start: 0.8638 (t80) cc_final: 0.8316 (t80) REVERT: D 923 CYS cc_start: 0.8906 (m) cc_final: 0.8425 (m) REVERT: D 1040 THR cc_start: 0.9364 (p) cc_final: 0.9117 (t) REVERT: D 1140 GLU cc_start: 0.8172 (pp20) cc_final: 0.7873 (pp20) REVERT: D 1142 TYR cc_start: 0.8482 (t80) cc_final: 0.8078 (t80) outliers start: 87 outliers final: 56 residues processed: 599 average time/residue: 0.3758 time to fit residues: 382.8444 Evaluate side-chains 498 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 438 time to evaluate : 3.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 997 ASN Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1045 CYS Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 618 CYS Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 914 ILE Chi-restraints excluded: chain C residue 958 SER Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 997 ASN Chi-restraints excluded: chain C residue 1041 ILE Chi-restraints excluded: chain C residue 1045 CYS Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1151 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 618 CYS Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 958 SER Chi-restraints excluded: chain B residue 961 VAL Chi-restraints excluded: chain B residue 997 ASN Chi-restraints excluded: chain B residue 1041 ILE Chi-restraints excluded: chain B residue 1045 CYS Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1404 ARG Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 618 CYS Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 802 LEU Chi-restraints excluded: chain D residue 914 ILE Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain D residue 961 VAL Chi-restraints excluded: chain D residue 997 ASN Chi-restraints excluded: chain D residue 1041 ILE Chi-restraints excluded: chain D residue 1045 CYS Chi-restraints excluded: chain D residue 1058 LEU Chi-restraints excluded: chain D residue 1151 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 449 optimal weight: 1.9990 chunk 144 optimal weight: 0.0570 chunk 431 optimal weight: 3.9990 chunk 202 optimal weight: 9.9990 chunk 346 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 280 optimal weight: 50.0000 chunk 28 optimal weight: 40.0000 chunk 441 optimal weight: 10.0000 chunk 320 optimal weight: 7.9990 chunk 87 optimal weight: 30.0000 overall best weight: 4.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS A 707 HIS A 816 ASN ** A1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1325 ASN C 193 HIS C 707 HIS C 816 ASN B 193 HIS B 707 HIS D 193 HIS D 707 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.139529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.093405 restraints weight = 86103.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.095604 restraints weight = 49964.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.096992 restraints weight = 35272.803| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 33852 Z= 0.222 Angle : 0.645 8.356 46644 Z= 0.341 Chirality : 0.043 0.272 5704 Planarity : 0.004 0.040 6036 Dihedral : 4.642 28.107 5268 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 5.82 % Allowed : 17.50 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.12), residues: 5004 helix: 0.79 (0.10), residues: 2620 sheet: -1.73 (0.27), residues: 340 loop : -1.94 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 825 HIS 0.008 0.001 HIS D1251 PHE 0.035 0.002 PHE C 995 TYR 0.021 0.002 TYR D1083 ARG 0.005 0.001 ARG D1152 Details of bonding type rmsd hydrogen bonds : bond 0.05126 ( 1832) hydrogen bonds : angle 4.37671 ( 5484) SS BOND : bond 0.00439 ( 4) SS BOND : angle 0.83209 ( 8) covalent geometry : bond 0.00483 (33848) covalent geometry : angle 0.64535 (46636) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 460 time to evaluate : 3.619 Fit side-chains TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. REVERT: A 314 ASN cc_start: 0.8014 (m-40) cc_final: 0.7796 (m110) REVERT: A 667 GLU cc_start: 0.9095 (tp30) cc_final: 0.8607 (tp30) REVERT: A 845 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7839 (tt) REVERT: A 859 ARG cc_start: 0.6768 (mmt180) cc_final: 0.5857 (ttp80) REVERT: A 1026 MET cc_start: 0.6538 (mpp) cc_final: 0.6240 (mpp) REVERT: A 1173 MET cc_start: 0.8206 (ttp) cc_final: 0.7851 (ttm) REVERT: A 1253 PHE cc_start: 0.8688 (t80) cc_final: 0.8460 (t80) REVERT: A 1276 TRP cc_start: 0.3680 (m100) cc_final: 0.3288 (m100) REVERT: C 149 VAL cc_start: 0.8958 (t) cc_final: 0.8678 (p) REVERT: C 314 ASN cc_start: 0.8007 (m-40) cc_final: 0.7685 (m110) REVERT: C 667 GLU cc_start: 0.9037 (tp30) cc_final: 0.8587 (tp30) REVERT: C 803 MET cc_start: 0.8635 (tpt) cc_final: 0.8344 (tpp) REVERT: C 852 SER cc_start: 0.8849 (m) cc_final: 0.8615 (t) REVERT: C 997 ASN cc_start: 0.8788 (OUTLIER) cc_final: 0.8546 (p0) REVERT: C 1253 PHE cc_start: 0.8536 (t80) cc_final: 0.8154 (t80) REVERT: B 314 ASN cc_start: 0.7991 (m-40) cc_final: 0.7694 (m110) REVERT: B 667 GLU cc_start: 0.9109 (tp30) cc_final: 0.8744 (tp30) REVERT: B 803 MET cc_start: 0.8597 (tpt) cc_final: 0.8300 (tpp) REVERT: B 852 SER cc_start: 0.8925 (m) cc_final: 0.8680 (t) REVERT: B 859 ARG cc_start: 0.6808 (mmt180) cc_final: 0.5874 (ttp80) REVERT: D 314 ASN cc_start: 0.8016 (m-40) cc_final: 0.7692 (m110) REVERT: D 667 GLU cc_start: 0.9125 (tp30) cc_final: 0.8674 (tp30) REVERT: D 803 MET cc_start: 0.8640 (tpt) cc_final: 0.8352 (tpp) REVERT: D 852 SER cc_start: 0.8932 (m) cc_final: 0.8695 (t) REVERT: D 859 ARG cc_start: 0.6808 (mmt180) cc_final: 0.5886 (ttp80) REVERT: D 1142 TYR cc_start: 0.8591 (t80) cc_final: 0.8273 (t80) REVERT: D 1253 PHE cc_start: 0.8564 (t80) cc_final: 0.8164 (t80) REVERT: D 1276 TRP cc_start: 0.3806 (m100) cc_final: 0.3561 (m100) outliers start: 131 outliers final: 98 residues processed: 545 average time/residue: 0.3681 time to fit residues: 351.2341 Evaluate side-chains 531 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 431 time to evaluate : 3.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 692 CYS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 855 CYS Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1045 CYS Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain A residue 1263 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 618 CYS Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain C residue 854 VAL Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 914 ILE Chi-restraints excluded: chain C residue 915 LEU Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 958 SER Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 966 VAL Chi-restraints excluded: chain C residue 994 ILE Chi-restraints excluded: chain C residue 997 ASN Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1041 ILE Chi-restraints excluded: chain C residue 1045 CYS Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1151 THR Chi-restraints excluded: chain C residue 1263 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 618 CYS Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 819 SER Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 855 CYS Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 958 SER Chi-restraints excluded: chain B residue 961 VAL Chi-restraints excluded: chain B residue 994 ILE Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1041 ILE Chi-restraints excluded: chain B residue 1045 CYS Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1263 THR Chi-restraints excluded: chain B residue 1404 ARG Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 618 CYS Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 802 LEU Chi-restraints excluded: chain D residue 819 SER Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 855 CYS Chi-restraints excluded: chain D residue 914 ILE Chi-restraints excluded: chain D residue 929 ILE Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain D residue 961 VAL Chi-restraints excluded: chain D residue 994 ILE Chi-restraints excluded: chain D residue 1039 LEU Chi-restraints excluded: chain D residue 1041 ILE Chi-restraints excluded: chain D residue 1045 CYS Chi-restraints excluded: chain D residue 1058 LEU Chi-restraints excluded: chain D residue 1151 THR Chi-restraints excluded: chain D residue 1263 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 138 optimal weight: 4.9990 chunk 433 optimal weight: 3.9990 chunk 262 optimal weight: 9.9990 chunk 221 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 152 optimal weight: 0.6980 chunk 106 optimal weight: 10.0000 chunk 117 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 410 optimal weight: 0.5980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN C 606 ASN C 997 ASN B 606 ASN D 606 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.140980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.095085 restraints weight = 85946.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.097318 restraints weight = 49734.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.098757 restraints weight = 35049.746| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33852 Z= 0.141 Angle : 0.547 6.997 46644 Z= 0.285 Chirality : 0.040 0.284 5704 Planarity : 0.004 0.039 6036 Dihedral : 4.213 25.919 5268 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.71 % Allowed : 19.40 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.12), residues: 5004 helix: 1.35 (0.10), residues: 2592 sheet: -1.63 (0.27), residues: 340 loop : -1.79 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 729 HIS 0.007 0.001 HIS A1251 PHE 0.012 0.001 PHE D 893 TYR 0.018 0.001 TYR C1083 ARG 0.005 0.000 ARG D1152 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 1832) hydrogen bonds : angle 3.86258 ( 5484) SS BOND : bond 0.00245 ( 4) SS BOND : angle 0.41547 ( 8) covalent geometry : bond 0.00312 (33848) covalent geometry : angle 0.54733 (46636) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 469 time to evaluate : 3.642 Fit side-chains TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. REVERT: A 314 ASN cc_start: 0.7987 (m-40) cc_final: 0.7770 (m110) REVERT: A 667 GLU cc_start: 0.9090 (tp30) cc_final: 0.8625 (tp30) REVERT: A 806 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8998 (tt) REVERT: A 845 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7686 (tt) REVERT: A 847 TYR cc_start: 0.7708 (m-80) cc_final: 0.7478 (m-80) REVERT: A 859 ARG cc_start: 0.6654 (mmt180) cc_final: 0.5671 (ttp80) REVERT: A 897 LEU cc_start: 0.8144 (mt) cc_final: 0.7761 (tt) REVERT: A 1026 MET cc_start: 0.6840 (mpp) cc_final: 0.6583 (mpp) REVERT: A 1253 PHE cc_start: 0.8688 (t80) cc_final: 0.8199 (t80) REVERT: A 1276 TRP cc_start: 0.3808 (m100) cc_final: 0.3468 (m100) REVERT: C 314 ASN cc_start: 0.7983 (m-40) cc_final: 0.7660 (m110) REVERT: C 667 GLU cc_start: 0.9070 (tp30) cc_final: 0.8610 (tp30) REVERT: C 803 MET cc_start: 0.8609 (tpt) cc_final: 0.8272 (tpp) REVERT: C 1068 GLN cc_start: 0.9006 (tp40) cc_final: 0.8005 (pt0) REVERT: C 1142 TYR cc_start: 0.8563 (t80) cc_final: 0.8207 (t80) REVERT: C 1253 PHE cc_start: 0.8648 (t80) cc_final: 0.8144 (t80) REVERT: C 1276 TRP cc_start: 0.3899 (m100) cc_final: 0.3549 (m100) REVERT: B 214 VAL cc_start: 0.9242 (t) cc_final: 0.8951 (m) REVERT: B 314 ASN cc_start: 0.7979 (m-40) cc_final: 0.7659 (m110) REVERT: B 667 GLU cc_start: 0.9075 (tp30) cc_final: 0.8609 (tp30) REVERT: B 803 MET cc_start: 0.8597 (tpt) cc_final: 0.8259 (tpp) REVERT: B 859 ARG cc_start: 0.6658 (mmt180) cc_final: 0.5697 (ttp80) REVERT: B 1068 GLN cc_start: 0.9018 (tp40) cc_final: 0.8057 (pt0) REVERT: B 1142 TYR cc_start: 0.8531 (t80) cc_final: 0.8195 (t80) REVERT: B 1253 PHE cc_start: 0.8593 (t80) cc_final: 0.7899 (t80) REVERT: B 1276 TRP cc_start: 0.3887 (m100) cc_final: 0.3545 (m100) REVERT: D 214 VAL cc_start: 0.9146 (t) cc_final: 0.8900 (m) REVERT: D 314 ASN cc_start: 0.7972 (m-40) cc_final: 0.7671 (m110) REVERT: D 667 GLU cc_start: 0.9072 (tp30) cc_final: 0.8598 (tp30) REVERT: D 803 MET cc_start: 0.8644 (tpt) cc_final: 0.8316 (tpp) REVERT: D 806 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9021 (tt) REVERT: D 852 SER cc_start: 0.8878 (m) cc_final: 0.8665 (t) REVERT: D 859 ARG cc_start: 0.6686 (mmt180) cc_final: 0.5736 (ttp80) REVERT: D 1068 GLN cc_start: 0.9021 (tp40) cc_final: 0.8049 (pt0) REVERT: D 1142 TYR cc_start: 0.8540 (t80) cc_final: 0.8206 (t80) REVERT: D 1253 PHE cc_start: 0.8698 (t80) cc_final: 0.8194 (t80) REVERT: D 1276 TRP cc_start: 0.3775 (m100) cc_final: 0.3166 (m100) outliers start: 106 outliers final: 72 residues processed: 531 average time/residue: 0.3828 time to fit residues: 357.7340 Evaluate side-chains 502 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 427 time to evaluate : 3.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 855 CYS Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 923 CYS Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1045 CYS Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 618 CYS Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 854 VAL Chi-restraints excluded: chain C residue 855 CYS Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 914 ILE Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 958 SER Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1045 CYS Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1151 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 CYS Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 855 CYS Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 958 SER Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1045 CYS Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1165 ASP Chi-restraints excluded: chain B residue 1404 ARG Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 618 CYS Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 855 CYS Chi-restraints excluded: chain D residue 914 ILE Chi-restraints excluded: chain D residue 915 LEU Chi-restraints excluded: chain D residue 929 ILE Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain D residue 961 VAL Chi-restraints excluded: chain D residue 1039 LEU Chi-restraints excluded: chain D residue 1045 CYS Chi-restraints excluded: chain D residue 1058 LEU Chi-restraints excluded: chain D residue 1151 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 434 optimal weight: 0.0970 chunk 496 optimal weight: 40.0000 chunk 21 optimal weight: 40.0000 chunk 418 optimal weight: 6.9990 chunk 305 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 186 optimal weight: 9.9990 chunk 488 optimal weight: 50.0000 chunk 116 optimal weight: 8.9990 chunk 499 optimal weight: 0.0770 chunk 331 optimal weight: 0.5980 overall best weight: 1.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 997 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.141793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.096396 restraints weight = 86122.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.098651 restraints weight = 49917.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.100066 restraints weight = 35192.642| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33852 Z= 0.115 Angle : 0.515 9.071 46644 Z= 0.266 Chirality : 0.039 0.254 5704 Planarity : 0.003 0.038 6036 Dihedral : 3.887 26.083 5268 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 5.24 % Allowed : 19.40 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.12), residues: 5004 helix: 1.63 (0.10), residues: 2612 sheet: -1.09 (0.30), residues: 300 loop : -1.61 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP D 729 HIS 0.003 0.001 HIS D1251 PHE 0.010 0.001 PHE C 813 TYR 0.018 0.001 TYR D1083 ARG 0.004 0.000 ARG D1152 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 1832) hydrogen bonds : angle 3.60878 ( 5484) SS BOND : bond 0.00156 ( 4) SS BOND : angle 0.36286 ( 8) covalent geometry : bond 0.00254 (33848) covalent geometry : angle 0.51523 (46636) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 469 time to evaluate : 3.424 Fit side-chains TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. REVERT: A 667 GLU cc_start: 0.9066 (tp30) cc_final: 0.8578 (tp30) REVERT: A 806 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9021 (tt) REVERT: A 845 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7652 (tt) REVERT: A 847 TYR cc_start: 0.7723 (m-80) cc_final: 0.7444 (m-80) REVERT: A 859 ARG cc_start: 0.6633 (mmt180) cc_final: 0.5636 (ttp80) REVERT: A 897 LEU cc_start: 0.8178 (mt) cc_final: 0.7866 (tt) REVERT: A 1026 MET cc_start: 0.6992 (mpp) cc_final: 0.6749 (mpp) REVERT: A 1038 TRP cc_start: 0.8476 (p-90) cc_final: 0.8088 (p-90) REVERT: A 1068 GLN cc_start: 0.8969 (tp40) cc_final: 0.7916 (pt0) REVERT: A 1140 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7743 (pp20) REVERT: A 1253 PHE cc_start: 0.8834 (t80) cc_final: 0.8294 (t80) REVERT: A 1276 TRP cc_start: 0.4067 (m100) cc_final: 0.3453 (m100) REVERT: C 314 ASN cc_start: 0.7900 (m-40) cc_final: 0.7669 (m110) REVERT: C 667 GLU cc_start: 0.9066 (tp30) cc_final: 0.8561 (tp30) REVERT: C 847 TYR cc_start: 0.7778 (m-80) cc_final: 0.7568 (m-80) REVERT: C 894 ILE cc_start: 0.9167 (tt) cc_final: 0.8917 (tp) REVERT: C 925 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8579 (tpp80) REVERT: C 1038 TRP cc_start: 0.8490 (p-90) cc_final: 0.8013 (p-90) REVERT: C 1068 GLN cc_start: 0.8949 (tp40) cc_final: 0.7952 (pt0) REVERT: C 1140 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7660 (pp20) REVERT: C 1142 TYR cc_start: 0.8494 (t80) cc_final: 0.8139 (t80) REVERT: C 1253 PHE cc_start: 0.8732 (t80) cc_final: 0.8335 (t80) REVERT: C 1276 TRP cc_start: 0.4000 (m100) cc_final: 0.3323 (m100) REVERT: B 314 ASN cc_start: 0.7905 (m-40) cc_final: 0.7671 (m110) REVERT: B 667 GLU cc_start: 0.9057 (tp30) cc_final: 0.8571 (tp30) REVERT: B 859 ARG cc_start: 0.6616 (mmt180) cc_final: 0.5611 (ttp80) REVERT: B 894 ILE cc_start: 0.9205 (tt) cc_final: 0.8961 (tp) REVERT: B 925 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8596 (tpp80) REVERT: B 1038 TRP cc_start: 0.8485 (p-90) cc_final: 0.8016 (p-90) REVERT: B 1068 GLN cc_start: 0.9049 (tp40) cc_final: 0.8038 (pt0) REVERT: B 1140 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7753 (pp20) REVERT: B 1142 TYR cc_start: 0.8503 (t80) cc_final: 0.8150 (t80) REVERT: B 1253 PHE cc_start: 0.8534 (t80) cc_final: 0.7962 (t80) REVERT: B 1276 TRP cc_start: 0.3830 (m100) cc_final: 0.3193 (m100) REVERT: D 149 VAL cc_start: 0.8866 (t) cc_final: 0.8584 (p) REVERT: D 214 VAL cc_start: 0.9064 (t) cc_final: 0.8777 (m) REVERT: D 314 ASN cc_start: 0.7913 (m-40) cc_final: 0.7651 (m110) REVERT: D 667 GLU cc_start: 0.9065 (tp30) cc_final: 0.8559 (tp30) REVERT: D 806 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8971 (tt) REVERT: D 859 ARG cc_start: 0.6650 (mmt180) cc_final: 0.5654 (ttp80) REVERT: D 894 ILE cc_start: 0.9191 (tt) cc_final: 0.8935 (tp) REVERT: D 925 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8557 (tpp80) REVERT: D 1038 TRP cc_start: 0.8463 (p-90) cc_final: 0.7995 (p-90) REVERT: D 1068 GLN cc_start: 0.8974 (tp40) cc_final: 0.7970 (pt0) REVERT: D 1140 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7720 (pp20) REVERT: D 1142 TYR cc_start: 0.8511 (t80) cc_final: 0.8157 (t80) REVERT: D 1253 PHE cc_start: 0.8756 (t80) cc_final: 0.8242 (t80) REVERT: D 1276 TRP cc_start: 0.3849 (m100) cc_final: 0.3278 (m100) outliers start: 118 outliers final: 72 residues processed: 546 average time/residue: 0.3746 time to fit residues: 354.4566 Evaluate side-chains 530 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 448 time to evaluate : 3.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 855 CYS Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 923 CYS Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 930 PHE Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1140 GLU Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 618 CYS Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 855 CYS Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 914 ILE Chi-restraints excluded: chain C residue 915 LEU Chi-restraints excluded: chain C residue 925 ARG Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 930 PHE Chi-restraints excluded: chain C residue 958 SER Chi-restraints excluded: chain C residue 994 ILE Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1045 CYS Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1140 GLU Chi-restraints excluded: chain C residue 1151 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 618 CYS Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 855 CYS Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 925 ARG Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 930 PHE Chi-restraints excluded: chain B residue 958 SER Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1140 GLU Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1404 ARG Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 618 CYS Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain D residue 855 CYS Chi-restraints excluded: chain D residue 914 ILE Chi-restraints excluded: chain D residue 915 LEU Chi-restraints excluded: chain D residue 925 ARG Chi-restraints excluded: chain D residue 929 ILE Chi-restraints excluded: chain D residue 930 PHE Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain D residue 1039 LEU Chi-restraints excluded: chain D residue 1045 CYS Chi-restraints excluded: chain D residue 1058 LEU Chi-restraints excluded: chain D residue 1140 GLU Chi-restraints excluded: chain D residue 1151 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 398 optimal weight: 3.9990 chunk 120 optimal weight: 50.0000 chunk 485 optimal weight: 30.0000 chunk 20 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 405 optimal weight: 5.9990 chunk 326 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 12 optimal weight: 20.0000 chunk 124 optimal weight: 50.0000 chunk 391 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN C 606 ASN C1325 ASN B 606 ASN B1325 ASN D 606 ASN D1325 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.139166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.093659 restraints weight = 85668.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.095868 restraints weight = 49719.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.097264 restraints weight = 35072.745| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33852 Z= 0.152 Angle : 0.552 8.303 46644 Z= 0.286 Chirality : 0.040 0.208 5704 Planarity : 0.004 0.040 6036 Dihedral : 3.939 26.043 5266 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 5.46 % Allowed : 19.63 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.12), residues: 5004 helix: 1.71 (0.10), residues: 2592 sheet: -0.91 (0.30), residues: 300 loop : -1.50 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 729 HIS 0.004 0.001 HIS D1251 PHE 0.015 0.001 PHE B 995 TYR 0.018 0.001 TYR D1083 ARG 0.003 0.000 ARG D1092 Details of bonding type rmsd hydrogen bonds : bond 0.04022 ( 1832) hydrogen bonds : angle 3.80510 ( 5484) SS BOND : bond 0.00182 ( 4) SS BOND : angle 0.54856 ( 8) covalent geometry : bond 0.00338 (33848) covalent geometry : angle 0.55173 (46636) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 451 time to evaluate : 3.524 Fit side-chains TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. REVERT: A 667 GLU cc_start: 0.9095 (tp30) cc_final: 0.8587 (tp30) REVERT: A 806 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9047 (tt) REVERT: A 845 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7663 (tt) REVERT: A 859 ARG cc_start: 0.6813 (mmt180) cc_final: 0.5886 (ttp80) REVERT: A 1026 MET cc_start: 0.7083 (mpp) cc_final: 0.6842 (mpp) REVERT: A 1038 TRP cc_start: 0.8537 (p-90) cc_final: 0.8120 (p-90) REVERT: A 1047 TYR cc_start: 0.9070 (t80) cc_final: 0.8825 (t80) REVERT: A 1068 GLN cc_start: 0.9011 (tp40) cc_final: 0.8015 (pt0) REVERT: A 1140 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7879 (pp20) REVERT: A 1173 MET cc_start: 0.7875 (ttm) cc_final: 0.7494 (ttp) REVERT: A 1253 PHE cc_start: 0.8904 (t80) cc_final: 0.8324 (t80) REVERT: A 1276 TRP cc_start: 0.3668 (m100) cc_final: 0.2979 (m100) REVERT: C 314 ASN cc_start: 0.7941 (m-40) cc_final: 0.7708 (m110) REVERT: C 480 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9277 (tt) REVERT: C 667 GLU cc_start: 0.9104 (tp30) cc_final: 0.8599 (tp30) REVERT: C 852 SER cc_start: 0.8894 (m) cc_final: 0.8633 (t) REVERT: C 894 ILE cc_start: 0.9230 (tt) cc_final: 0.8989 (tp) REVERT: C 925 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8602 (tpp80) REVERT: C 995 PHE cc_start: 0.7903 (m-80) cc_final: 0.7566 (m-10) REVERT: C 1026 MET cc_start: 0.7403 (mtp) cc_final: 0.7128 (mpp) REVERT: C 1038 TRP cc_start: 0.8589 (p-90) cc_final: 0.8018 (p-90) REVERT: C 1068 GLN cc_start: 0.9008 (tp40) cc_final: 0.8045 (pt0) REVERT: C 1140 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7891 (pp20) REVERT: C 1253 PHE cc_start: 0.8752 (t80) cc_final: 0.8097 (t80) REVERT: C 1276 TRP cc_start: 0.3728 (m100) cc_final: 0.2923 (m100) REVERT: B 314 ASN cc_start: 0.7965 (m-40) cc_final: 0.7740 (m110) REVERT: B 667 GLU cc_start: 0.9066 (tp30) cc_final: 0.8535 (tp30) REVERT: B 859 ARG cc_start: 0.6845 (mmt180) cc_final: 0.5855 (ttp80) REVERT: B 894 ILE cc_start: 0.9306 (tt) cc_final: 0.9064 (tp) REVERT: B 925 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8597 (tpp80) REVERT: B 1026 MET cc_start: 0.7448 (mtp) cc_final: 0.7189 (mpp) REVERT: B 1038 TRP cc_start: 0.8576 (p-90) cc_final: 0.8009 (p-90) REVERT: B 1068 GLN cc_start: 0.8978 (tp40) cc_final: 0.8020 (pt0) REVERT: B 1140 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7914 (pp20) REVERT: B 1276 TRP cc_start: 0.3814 (m100) cc_final: 0.2990 (m100) REVERT: D 149 VAL cc_start: 0.8870 (t) cc_final: 0.8660 (p) REVERT: D 314 ASN cc_start: 0.7938 (m-40) cc_final: 0.7698 (m110) REVERT: D 667 GLU cc_start: 0.9068 (tp30) cc_final: 0.8557 (tp30) REVERT: D 806 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9013 (tt) REVERT: D 852 SER cc_start: 0.8949 (m) cc_final: 0.8694 (t) REVERT: D 859 ARG cc_start: 0.6850 (mmt180) cc_final: 0.5915 (ttp80) REVERT: D 925 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8587 (tpp80) REVERT: D 1026 MET cc_start: 0.7364 (mtp) cc_final: 0.7100 (mpp) REVERT: D 1038 TRP cc_start: 0.8581 (p-90) cc_final: 0.8175 (p-90) REVERT: D 1068 GLN cc_start: 0.8988 (tp40) cc_final: 0.8027 (pt0) REVERT: D 1140 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7922 (pp20) REVERT: D 1253 PHE cc_start: 0.8837 (t80) cc_final: 0.8131 (t80) REVERT: D 1276 TRP cc_start: 0.3772 (m100) cc_final: 0.3020 (m100) outliers start: 123 outliers final: 94 residues processed: 533 average time/residue: 0.3849 time to fit residues: 358.9562 Evaluate side-chains 538 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 433 time to evaluate : 3.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 855 CYS Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 923 CYS Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1140 GLU Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 618 CYS Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 854 VAL Chi-restraints excluded: chain C residue 855 CYS Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 914 ILE Chi-restraints excluded: chain C residue 915 LEU Chi-restraints excluded: chain C residue 923 CYS Chi-restraints excluded: chain C residue 925 ARG Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 930 PHE Chi-restraints excluded: chain C residue 958 SER Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 994 ILE Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1140 GLU Chi-restraints excluded: chain C residue 1151 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 CYS Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 855 CYS Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 923 CYS Chi-restraints excluded: chain B residue 925 ARG Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 930 PHE Chi-restraints excluded: chain B residue 958 SER Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1045 CYS Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1140 GLU Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1404 ARG Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 618 CYS Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 855 CYS Chi-restraints excluded: chain D residue 914 ILE Chi-restraints excluded: chain D residue 915 LEU Chi-restraints excluded: chain D residue 923 CYS Chi-restraints excluded: chain D residue 925 ARG Chi-restraints excluded: chain D residue 929 ILE Chi-restraints excluded: chain D residue 930 PHE Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain D residue 1039 LEU Chi-restraints excluded: chain D residue 1058 LEU Chi-restraints excluded: chain D residue 1140 GLU Chi-restraints excluded: chain D residue 1151 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 437 optimal weight: 1.9990 chunk 198 optimal weight: 50.0000 chunk 115 optimal weight: 0.0470 chunk 158 optimal weight: 5.9990 chunk 277 optimal weight: 7.9990 chunk 373 optimal weight: 50.0000 chunk 220 optimal weight: 3.9990 chunk 330 optimal weight: 10.0000 chunk 114 optimal weight: 40.0000 chunk 433 optimal weight: 4.9990 chunk 378 optimal weight: 30.0000 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.137583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.092325 restraints weight = 85735.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.094483 restraints weight = 50020.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.095841 restraints weight = 35406.117| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33852 Z= 0.177 Angle : 0.579 10.104 46644 Z= 0.300 Chirality : 0.040 0.196 5704 Planarity : 0.004 0.040 6036 Dihedral : 4.053 27.409 5266 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 5.37 % Allowed : 20.52 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.12), residues: 5004 helix: 1.66 (0.10), residues: 2600 sheet: -0.87 (0.30), residues: 300 loop : -1.44 (0.14), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 729 HIS 0.005 0.001 HIS B1251 PHE 0.024 0.001 PHE C 998 TYR 0.018 0.001 TYR B1083 ARG 0.004 0.000 ARG D1092 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 1832) hydrogen bonds : angle 3.93663 ( 5484) SS BOND : bond 0.00168 ( 4) SS BOND : angle 0.60336 ( 8) covalent geometry : bond 0.00396 (33848) covalent geometry : angle 0.57923 (46636) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 441 time to evaluate : 3.606 Fit side-chains TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 667 GLU cc_start: 0.9093 (tp30) cc_final: 0.8604 (tp30) REVERT: A 729 TRP cc_start: 0.8695 (p-90) cc_final: 0.8295 (p-90) REVERT: A 806 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9031 (tt) REVERT: A 845 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7750 (tt) REVERT: A 859 ARG cc_start: 0.6905 (mmt180) cc_final: 0.5949 (ttp80) REVERT: A 1026 MET cc_start: 0.7334 (mpp) cc_final: 0.6907 (mpp) REVERT: A 1038 TRP cc_start: 0.8524 (p-90) cc_final: 0.8081 (p-90) REVERT: A 1068 GLN cc_start: 0.9017 (tp40) cc_final: 0.7998 (pt0) REVERT: A 1140 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7951 (pp20) REVERT: A 1253 PHE cc_start: 0.8979 (t80) cc_final: 0.8322 (t80) REVERT: A 1276 TRP cc_start: 0.3981 (m100) cc_final: 0.3148 (m100) REVERT: C 667 GLU cc_start: 0.9103 (tp30) cc_final: 0.8591 (tp30) REVERT: C 852 SER cc_start: 0.8882 (m) cc_final: 0.8612 (t) REVERT: C 925 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8619 (tpp80) REVERT: C 995 PHE cc_start: 0.8004 (m-80) cc_final: 0.7722 (m-10) REVERT: C 1038 TRP cc_start: 0.8565 (p-90) cc_final: 0.8163 (p-90) REVERT: C 1068 GLN cc_start: 0.8996 (tp40) cc_final: 0.7965 (pt0) REVERT: C 1140 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7985 (pp20) REVERT: C 1253 PHE cc_start: 0.8872 (t80) cc_final: 0.8145 (t80) REVERT: C 1276 TRP cc_start: 0.3825 (m100) cc_final: 0.2839 (m100) REVERT: B 213 VAL cc_start: 0.9396 (t) cc_final: 0.9195 (p) REVERT: B 314 ASN cc_start: 0.7927 (m-40) cc_final: 0.7721 (m110) REVERT: B 480 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9252 (tt) REVERT: B 667 GLU cc_start: 0.9099 (tp30) cc_final: 0.8593 (tp30) REVERT: B 729 TRP cc_start: 0.8711 (p-90) cc_final: 0.8406 (p-90) REVERT: B 852 SER cc_start: 0.8922 (m) cc_final: 0.8656 (t) REVERT: B 859 ARG cc_start: 0.6932 (mmt180) cc_final: 0.5979 (ttp80) REVERT: B 894 ILE cc_start: 0.9376 (tt) cc_final: 0.9174 (tp) REVERT: B 925 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8612 (tpp80) REVERT: B 1038 TRP cc_start: 0.8502 (p-90) cc_final: 0.8116 (p-90) REVERT: B 1068 GLN cc_start: 0.9008 (tp40) cc_final: 0.8065 (pt0) REVERT: B 1140 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7988 (pp20) REVERT: B 1253 PHE cc_start: 0.8582 (t80) cc_final: 0.7855 (t80) REVERT: B 1276 TRP cc_start: 0.3948 (m100) cc_final: 0.2949 (m100) REVERT: D 314 ASN cc_start: 0.7920 (m-40) cc_final: 0.7713 (m110) REVERT: D 667 GLU cc_start: 0.9081 (tp30) cc_final: 0.8584 (tp30) REVERT: D 806 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9028 (tt) REVERT: D 852 SER cc_start: 0.8954 (m) cc_final: 0.8703 (t) REVERT: D 859 ARG cc_start: 0.6920 (mmt180) cc_final: 0.5927 (ttp80) REVERT: D 925 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8618 (tpp80) REVERT: D 1038 TRP cc_start: 0.8490 (p-90) cc_final: 0.8136 (p-90) REVERT: D 1068 GLN cc_start: 0.9022 (tp40) cc_final: 0.8066 (pt0) REVERT: D 1140 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7988 (pp20) REVERT: D 1276 TRP cc_start: 0.3942 (m100) cc_final: 0.3012 (m100) outliers start: 121 outliers final: 103 residues processed: 521 average time/residue: 0.4000 time to fit residues: 362.7794 Evaluate side-chains 535 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 421 time to evaluate : 3.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 701 ASP Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 855 CYS Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 923 CYS Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 930 PHE Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1140 GLU Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 618 CYS Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 701 ASP Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain C residue 854 VAL Chi-restraints excluded: chain C residue 855 CYS Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 914 ILE Chi-restraints excluded: chain C residue 915 LEU Chi-restraints excluded: chain C residue 925 ARG Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 930 PHE Chi-restraints excluded: chain C residue 958 SER Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 994 ILE Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1140 GLU Chi-restraints excluded: chain C residue 1151 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 CYS Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 855 CYS Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 925 ARG Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 930 PHE Chi-restraints excluded: chain B residue 994 ILE Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1045 CYS Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1140 GLU Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1404 ARG Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 855 CYS Chi-restraints excluded: chain D residue 914 ILE Chi-restraints excluded: chain D residue 915 LEU Chi-restraints excluded: chain D residue 925 ARG Chi-restraints excluded: chain D residue 929 ILE Chi-restraints excluded: chain D residue 930 PHE Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain D residue 994 ILE Chi-restraints excluded: chain D residue 1039 LEU Chi-restraints excluded: chain D residue 1058 LEU Chi-restraints excluded: chain D residue 1140 GLU Chi-restraints excluded: chain D residue 1151 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 428 optimal weight: 3.9990 chunk 109 optimal weight: 40.0000 chunk 36 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 238 optimal weight: 40.0000 chunk 449 optimal weight: 3.9990 chunk 361 optimal weight: 30.0000 chunk 81 optimal weight: 0.6980 chunk 202 optimal weight: 8.9990 chunk 348 optimal weight: 7.9990 chunk 263 optimal weight: 6.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.137747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.092723 restraints weight = 85254.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.094818 restraints weight = 49739.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.096229 restraints weight = 35462.487| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.5509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33852 Z= 0.155 Angle : 0.555 10.996 46644 Z= 0.286 Chirality : 0.040 0.193 5704 Planarity : 0.004 0.040 6036 Dihedral : 3.929 27.365 5266 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 5.20 % Allowed : 20.60 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.12), residues: 5004 helix: 1.76 (0.10), residues: 2604 sheet: -0.85 (0.30), residues: 300 loop : -1.45 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 729 HIS 0.004 0.001 HIS D1251 PHE 0.019 0.001 PHE D 995 TYR 0.017 0.001 TYR D1083 ARG 0.005 0.000 ARG D1092 Details of bonding type rmsd hydrogen bonds : bond 0.03800 ( 1832) hydrogen bonds : angle 3.81252 ( 5484) SS BOND : bond 0.00147 ( 4) SS BOND : angle 0.60899 ( 8) covalent geometry : bond 0.00345 (33848) covalent geometry : angle 0.55532 (46636) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 428 time to evaluate : 3.722 Fit side-chains TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 667 GLU cc_start: 0.9119 (tp30) cc_final: 0.8635 (tp30) REVERT: A 806 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9032 (tt) REVERT: A 859 ARG cc_start: 0.6787 (mmt180) cc_final: 0.5934 (tmm160) REVERT: A 1026 MET cc_start: 0.7509 (mpp) cc_final: 0.7074 (mpp) REVERT: A 1038 TRP cc_start: 0.8464 (p-90) cc_final: 0.8128 (p-90) REVERT: A 1068 GLN cc_start: 0.9003 (tp40) cc_final: 0.8023 (pt0) REVERT: A 1140 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7956 (pp20) REVERT: A 1253 PHE cc_start: 0.8995 (t80) cc_final: 0.8303 (t80) REVERT: A 1276 TRP cc_start: 0.3583 (m100) cc_final: 0.3373 (m100) REVERT: C 667 GLU cc_start: 0.9122 (tp30) cc_final: 0.8638 (tp30) REVERT: C 729 TRP cc_start: 0.8075 (OUTLIER) cc_final: 0.6867 (p90) REVERT: C 847 TYR cc_start: 0.7909 (m-80) cc_final: 0.7598 (m-80) REVERT: C 852 SER cc_start: 0.8890 (m) cc_final: 0.8640 (t) REVERT: C 925 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8645 (tpp80) REVERT: C 995 PHE cc_start: 0.7961 (m-80) cc_final: 0.7680 (m-10) REVERT: C 1026 MET cc_start: 0.7549 (mtp) cc_final: 0.7240 (mpp) REVERT: C 1038 TRP cc_start: 0.8489 (p-90) cc_final: 0.8136 (p-90) REVERT: C 1068 GLN cc_start: 0.9023 (tp40) cc_final: 0.8005 (pt0) REVERT: C 1140 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7953 (pp20) REVERT: C 1253 PHE cc_start: 0.8919 (t80) cc_final: 0.8134 (t80) REVERT: C 1276 TRP cc_start: 0.3791 (m100) cc_final: 0.3581 (m100) REVERT: B 171 ILE cc_start: 0.9163 (tp) cc_final: 0.8947 (tp) REVERT: B 480 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9224 (tt) REVERT: B 667 GLU cc_start: 0.9095 (tp30) cc_final: 0.8605 (tp30) REVERT: B 852 SER cc_start: 0.8906 (m) cc_final: 0.8655 (t) REVERT: B 859 ARG cc_start: 0.6819 (mmt180) cc_final: 0.5978 (tmm160) REVERT: B 925 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8626 (tpp80) REVERT: B 939 LYS cc_start: 0.8933 (mmtt) cc_final: 0.8608 (mmtp) REVERT: B 1026 MET cc_start: 0.7510 (mtp) cc_final: 0.7230 (mpp) REVERT: B 1038 TRP cc_start: 0.8449 (p-90) cc_final: 0.8080 (p-90) REVERT: B 1068 GLN cc_start: 0.9009 (tp40) cc_final: 0.7997 (pt0) REVERT: B 1140 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7990 (pp20) REVERT: B 1253 PHE cc_start: 0.8598 (t80) cc_final: 0.7855 (t80) REVERT: B 1276 TRP cc_start: 0.3922 (m100) cc_final: 0.3692 (m100) REVERT: D 480 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9235 (tt) REVERT: D 667 GLU cc_start: 0.9077 (tp30) cc_final: 0.8561 (tp30) REVERT: D 806 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9034 (tt) REVERT: D 852 SER cc_start: 0.8977 (m) cc_final: 0.8711 (t) REVERT: D 859 ARG cc_start: 0.6880 (mmt180) cc_final: 0.6021 (tmm160) REVERT: D 925 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8620 (tpp80) REVERT: D 1026 MET cc_start: 0.7524 (mtp) cc_final: 0.7219 (mpp) REVERT: D 1038 TRP cc_start: 0.8405 (p-90) cc_final: 0.8056 (p-90) REVERT: D 1068 GLN cc_start: 0.9017 (tp40) cc_final: 0.7990 (pt0) REVERT: D 1140 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7988 (pp20) REVERT: D 1276 TRP cc_start: 0.3659 (m100) cc_final: 0.3372 (m100) outliers start: 117 outliers final: 98 residues processed: 499 average time/residue: 0.3806 time to fit residues: 331.6122 Evaluate side-chains 526 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 416 time to evaluate : 3.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 855 CYS Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 923 CYS Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1140 GLU Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 701 ASP Chi-restraints excluded: chain C residue 729 TRP Chi-restraints excluded: chain C residue 817 ILE Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain C residue 854 VAL Chi-restraints excluded: chain C residue 855 CYS Chi-restraints excluded: chain C residue 914 ILE Chi-restraints excluded: chain C residue 915 LEU Chi-restraints excluded: chain C residue 923 CYS Chi-restraints excluded: chain C residue 925 ARG Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 958 SER Chi-restraints excluded: chain C residue 994 ILE Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1045 CYS Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1140 GLU Chi-restraints excluded: chain C residue 1151 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 817 ILE Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 855 CYS Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 923 CYS Chi-restraints excluded: chain B residue 925 ARG Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 994 ILE Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1045 CYS Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1140 GLU Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1404 ARG Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 817 ILE Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 855 CYS Chi-restraints excluded: chain D residue 914 ILE Chi-restraints excluded: chain D residue 915 LEU Chi-restraints excluded: chain D residue 925 ARG Chi-restraints excluded: chain D residue 929 ILE Chi-restraints excluded: chain D residue 930 PHE Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain D residue 1039 LEU Chi-restraints excluded: chain D residue 1058 LEU Chi-restraints excluded: chain D residue 1140 GLU Chi-restraints excluded: chain D residue 1151 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 279 optimal weight: 8.9990 chunk 334 optimal weight: 9.9990 chunk 441 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 354 optimal weight: 1.9990 chunk 489 optimal weight: 20.0000 chunk 494 optimal weight: 1.9990 chunk 414 optimal weight: 6.9990 chunk 501 optimal weight: 50.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.136325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.091490 restraints weight = 85385.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.093597 restraints weight = 49989.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.094977 restraints weight = 35515.578| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.5765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33852 Z= 0.179 Angle : 0.584 9.098 46644 Z= 0.302 Chirality : 0.040 0.183 5704 Planarity : 0.004 0.041 6036 Dihedral : 4.078 28.504 5266 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 5.42 % Allowed : 21.05 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.12), residues: 5004 helix: 1.68 (0.10), residues: 2604 sheet: -0.92 (0.29), residues: 304 loop : -1.42 (0.14), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 729 HIS 0.005 0.001 HIS B1251 PHE 0.013 0.001 PHE C 998 TYR 0.019 0.001 TYR D1083 ARG 0.006 0.000 ARG B1092 Details of bonding type rmsd hydrogen bonds : bond 0.04262 ( 1832) hydrogen bonds : angle 3.98918 ( 5484) SS BOND : bond 0.00139 ( 4) SS BOND : angle 0.59771 ( 8) covalent geometry : bond 0.00399 (33848) covalent geometry : angle 0.58379 (46636) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 425 time to evaluate : 3.440 Fit side-chains TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. REVERT: A 667 GLU cc_start: 0.9143 (tp30) cc_final: 0.8679 (tp30) REVERT: A 806 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9011 (tt) REVERT: A 859 ARG cc_start: 0.6857 (mmt180) cc_final: 0.5955 (ttp80) REVERT: A 1026 MET cc_start: 0.7567 (mpp) cc_final: 0.7132 (mpp) REVERT: A 1038 TRP cc_start: 0.8469 (p-90) cc_final: 0.8039 (p-90) REVERT: A 1068 GLN cc_start: 0.8996 (tp40) cc_final: 0.8002 (pt0) REVERT: A 1140 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7965 (pp20) REVERT: A 1253 PHE cc_start: 0.9014 (t80) cc_final: 0.8281 (t80) REVERT: C 667 GLU cc_start: 0.9131 (tp30) cc_final: 0.8638 (tp30) REVERT: C 729 TRP cc_start: 0.8115 (OUTLIER) cc_final: 0.6832 (p90) REVERT: C 852 SER cc_start: 0.8952 (m) cc_final: 0.8706 (t) REVERT: C 899 CYS cc_start: 0.8858 (m) cc_final: 0.8644 (m) REVERT: C 925 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8661 (tpp80) REVERT: C 995 PHE cc_start: 0.7954 (m-80) cc_final: 0.7729 (m-10) REVERT: C 1026 MET cc_start: 0.7646 (mtp) cc_final: 0.7317 (mpp) REVERT: C 1038 TRP cc_start: 0.8447 (p-90) cc_final: 0.8101 (p-90) REVERT: C 1068 GLN cc_start: 0.9025 (tp40) cc_final: 0.8025 (pt0) REVERT: C 1140 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7988 (pp20) REVERT: C 1253 PHE cc_start: 0.8983 (t80) cc_final: 0.8367 (t80) REVERT: B 480 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9245 (tt) REVERT: B 667 GLU cc_start: 0.9107 (tp30) cc_final: 0.8609 (tp30) REVERT: B 852 SER cc_start: 0.9034 (m) cc_final: 0.8807 (t) REVERT: B 859 ARG cc_start: 0.6947 (mmt180) cc_final: 0.6047 (tmm160) REVERT: B 925 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8684 (tpp80) REVERT: B 1026 MET cc_start: 0.7622 (mtp) cc_final: 0.7312 (mpp) REVERT: B 1038 TRP cc_start: 0.8419 (p-90) cc_final: 0.8112 (p-90) REVERT: B 1068 GLN cc_start: 0.9026 (tp40) cc_final: 0.8043 (pt0) REVERT: B 1140 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8001 (pp20) REVERT: D 480 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9245 (tt) REVERT: D 667 GLU cc_start: 0.9099 (tp30) cc_final: 0.8607 (tp30) REVERT: D 806 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9001 (tt) REVERT: D 852 SER cc_start: 0.9033 (m) cc_final: 0.8792 (t) REVERT: D 859 ARG cc_start: 0.7033 (mmt180) cc_final: 0.6025 (tmm160) REVERT: D 925 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8656 (tpp80) REVERT: D 1026 MET cc_start: 0.7605 (mtp) cc_final: 0.7284 (mpp) REVERT: D 1038 TRP cc_start: 0.8432 (p-90) cc_final: 0.8125 (p-90) REVERT: D 1068 GLN cc_start: 0.9038 (tp40) cc_final: 0.8044 (pt0) REVERT: D 1140 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7995 (pp20) REVERT: D 1253 PHE cc_start: 0.8941 (t80) cc_final: 0.8323 (t80) outliers start: 122 outliers final: 105 residues processed: 506 average time/residue: 0.3742 time to fit residues: 327.6118 Evaluate side-chains 528 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 411 time to evaluate : 3.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 855 CYS Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 923 CYS Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1140 GLU Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 701 ASP Chi-restraints excluded: chain C residue 729 TRP Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 848 VAL Chi-restraints excluded: chain C residue 854 VAL Chi-restraints excluded: chain C residue 855 CYS Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 914 ILE Chi-restraints excluded: chain C residue 915 LEU Chi-restraints excluded: chain C residue 923 CYS Chi-restraints excluded: chain C residue 925 ARG Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 994 ILE Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1045 CYS Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1140 GLU Chi-restraints excluded: chain C residue 1151 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 855 CYS Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 923 CYS Chi-restraints excluded: chain B residue 925 ARG Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 994 ILE Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1045 CYS Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1140 GLU Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1404 ARG Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 817 ILE Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain D residue 830 VAL Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 855 CYS Chi-restraints excluded: chain D residue 914 ILE Chi-restraints excluded: chain D residue 915 LEU Chi-restraints excluded: chain D residue 923 CYS Chi-restraints excluded: chain D residue 925 ARG Chi-restraints excluded: chain D residue 929 ILE Chi-restraints excluded: chain D residue 930 PHE Chi-restraints excluded: chain D residue 994 ILE Chi-restraints excluded: chain D residue 1039 LEU Chi-restraints excluded: chain D residue 1045 CYS Chi-restraints excluded: chain D residue 1058 LEU Chi-restraints excluded: chain D residue 1140 GLU Chi-restraints excluded: chain D residue 1151 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 30 optimal weight: 8.9990 chunk 380 optimal weight: 0.8980 chunk 502 optimal weight: 50.0000 chunk 356 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 222 optimal weight: 7.9990 chunk 230 optimal weight: 0.9980 chunk 283 optimal weight: 0.7980 chunk 177 optimal weight: 3.9990 chunk 240 optimal weight: 30.0000 chunk 102 optimal weight: 2.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.137989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.093394 restraints weight = 85192.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.095574 restraints weight = 49364.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.096942 restraints weight = 34781.581| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.5936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33852 Z= 0.121 Angle : 0.536 10.399 46644 Z= 0.274 Chirality : 0.039 0.171 5704 Planarity : 0.003 0.039 6036 Dihedral : 3.816 26.687 5266 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.31 % Allowed : 22.69 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.12), residues: 5004 helix: 1.90 (0.11), residues: 2608 sheet: -1.08 (0.29), residues: 320 loop : -1.36 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 729 HIS 0.003 0.001 HIS B1251 PHE 0.013 0.001 PHE B1050 TYR 0.020 0.001 TYR B1283 ARG 0.004 0.000 ARG D1152 Details of bonding type rmsd hydrogen bonds : bond 0.03475 ( 1832) hydrogen bonds : angle 3.64673 ( 5484) SS BOND : bond 0.00120 ( 4) SS BOND : angle 0.51660 ( 8) covalent geometry : bond 0.00270 (33848) covalent geometry : angle 0.53594 (46636) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10008 Ramachandran restraints generated. 5004 Oldfield, 0 Emsley, 5004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 443 time to evaluate : 3.406 Fit side-chains TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 260 PHE cc_start: 0.8736 (m-80) cc_final: 0.7999 (m-10) REVERT: A 667 GLU cc_start: 0.9106 (tp30) cc_final: 0.8643 (tp30) REVERT: A 806 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9029 (tt) REVERT: A 859 ARG cc_start: 0.6849 (mmt180) cc_final: 0.5942 (tmm160) REVERT: A 1026 MET cc_start: 0.7535 (mpp) cc_final: 0.7160 (mpp) REVERT: A 1038 TRP cc_start: 0.8420 (p-90) cc_final: 0.8082 (p-90) REVERT: A 1068 GLN cc_start: 0.8972 (tp40) cc_final: 0.7967 (pt0) REVERT: A 1140 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7884 (pp20) REVERT: A 1253 PHE cc_start: 0.9039 (t80) cc_final: 0.8304 (t80) REVERT: A 1276 TRP cc_start: 0.3923 (m100) cc_final: 0.3097 (m100) REVERT: C 667 GLU cc_start: 0.9103 (tp30) cc_final: 0.8647 (tp30) REVERT: C 852 SER cc_start: 0.9013 (m) cc_final: 0.8783 (t) REVERT: C 899 CYS cc_start: 0.8850 (m) cc_final: 0.8600 (m) REVERT: C 925 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8634 (tpp80) REVERT: C 954 MET cc_start: 0.8725 (ppp) cc_final: 0.8486 (ppp) REVERT: C 995 PHE cc_start: 0.7877 (m-80) cc_final: 0.7629 (m-10) REVERT: C 1038 TRP cc_start: 0.8448 (p-90) cc_final: 0.8110 (p-90) REVERT: C 1068 GLN cc_start: 0.8997 (tp40) cc_final: 0.7973 (pt0) REVERT: C 1140 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7881 (pp20) REVERT: C 1253 PHE cc_start: 0.8957 (t80) cc_final: 0.8138 (t80) REVERT: C 1276 TRP cc_start: 0.4095 (m100) cc_final: 0.3769 (m100) REVERT: B 171 ILE cc_start: 0.9122 (tp) cc_final: 0.8910 (tp) REVERT: B 667 GLU cc_start: 0.9096 (tp30) cc_final: 0.8601 (tp30) REVERT: B 852 SER cc_start: 0.9029 (m) cc_final: 0.8809 (t) REVERT: B 859 ARG cc_start: 0.6872 (mmt180) cc_final: 0.5941 (tmm160) REVERT: B 899 CYS cc_start: 0.8848 (m) cc_final: 0.8644 (m) REVERT: B 925 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8639 (tpp80) REVERT: B 1026 MET cc_start: 0.7547 (mtp) cc_final: 0.7277 (mpp) REVERT: B 1038 TRP cc_start: 0.8456 (p-90) cc_final: 0.8110 (p-90) REVERT: B 1068 GLN cc_start: 0.8969 (tp40) cc_final: 0.7969 (pt0) REVERT: B 1140 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7919 (pp20) REVERT: B 1276 TRP cc_start: 0.4759 (m100) cc_final: 0.4376 (m100) REVERT: D 171 ILE cc_start: 0.9132 (tp) cc_final: 0.8899 (tp) REVERT: D 480 LEU cc_start: 0.9484 (tt) cc_final: 0.9255 (tt) REVERT: D 667 GLU cc_start: 0.9084 (tp30) cc_final: 0.8573 (tp30) REVERT: D 806 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9021 (tt) REVERT: D 852 SER cc_start: 0.9047 (m) cc_final: 0.8818 (t) REVERT: D 859 ARG cc_start: 0.6905 (mmt180) cc_final: 0.5969 (tmm160) REVERT: D 899 CYS cc_start: 0.8848 (m) cc_final: 0.8633 (m) REVERT: D 925 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8623 (tpp80) REVERT: D 939 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8694 (tptm) REVERT: D 954 MET cc_start: 0.8783 (ppp) cc_final: 0.8546 (ppp) REVERT: D 1038 TRP cc_start: 0.8466 (p-90) cc_final: 0.8145 (p-90) REVERT: D 1068 GLN cc_start: 0.9000 (tp40) cc_final: 0.7990 (pt0) REVERT: D 1140 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7905 (pp20) REVERT: D 1276 TRP cc_start: 0.4271 (m100) cc_final: 0.3501 (m100) outliers start: 97 outliers final: 79 residues processed: 495 average time/residue: 0.3898 time to fit residues: 336.8682 Evaluate side-chains 515 residues out of total 4484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 427 time to evaluate : 3.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 855 CYS Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 923 CYS Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1045 CYS Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1140 GLU Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 817 ILE Chi-restraints excluded: chain C residue 855 CYS Chi-restraints excluded: chain C residue 914 ILE Chi-restraints excluded: chain C residue 915 LEU Chi-restraints excluded: chain C residue 923 CYS Chi-restraints excluded: chain C residue 925 ARG Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 994 ILE Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1045 CYS Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1140 GLU Chi-restraints excluded: chain C residue 1151 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 855 CYS Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 923 CYS Chi-restraints excluded: chain B residue 925 ARG Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 994 ILE Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1045 CYS Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1140 GLU Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1404 ARG Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 618 CYS Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 817 ILE Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 855 CYS Chi-restraints excluded: chain D residue 914 ILE Chi-restraints excluded: chain D residue 915 LEU Chi-restraints excluded: chain D residue 923 CYS Chi-restraints excluded: chain D residue 925 ARG Chi-restraints excluded: chain D residue 929 ILE Chi-restraints excluded: chain D residue 994 ILE Chi-restraints excluded: chain D residue 1039 LEU Chi-restraints excluded: chain D residue 1058 LEU Chi-restraints excluded: chain D residue 1140 GLU Chi-restraints excluded: chain D residue 1151 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 105 optimal weight: 5.9990 chunk 360 optimal weight: 0.4980 chunk 145 optimal weight: 40.0000 chunk 44 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 113 optimal weight: 50.0000 chunk 376 optimal weight: 50.0000 chunk 349 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 277 optimal weight: 5.9990 chunk 80 optimal weight: 30.0000 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 606 ASN ** D1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.133971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.089257 restraints weight = 86098.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.091305 restraints weight = 50915.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.092607 restraints weight = 36405.794| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.6122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 33852 Z= 0.255 Angle : 0.657 9.630 46644 Z= 0.342 Chirality : 0.042 0.186 5704 Planarity : 0.004 0.042 6036 Dihedral : 4.356 29.456 5266 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 4.66 % Allowed : 22.60 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.12), residues: 5004 helix: 1.51 (0.10), residues: 2612 sheet: -1.03 (0.29), residues: 284 loop : -1.47 (0.14), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 729 HIS 0.007 0.002 HIS B1251 PHE 0.017 0.002 PHE B 998 TYR 0.026 0.002 TYR A1047 ARG 0.007 0.001 ARG B1092 Details of bonding type rmsd hydrogen bonds : bond 0.04908 ( 1832) hydrogen bonds : angle 4.36530 ( 5484) SS BOND : bond 0.00149 ( 4) SS BOND : angle 0.92507 ( 8) covalent geometry : bond 0.00569 (33848) covalent geometry : angle 0.65649 (46636) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12414.14 seconds wall clock time: 212 minutes 57.39 seconds (12777.39 seconds total)