Starting phenix.real_space_refine (version: dev) on Sun Dec 18 16:10:56 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6drk_8901/12_2022/6drk_8901.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6drk_8901/12_2022/6drk_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6drk_8901/12_2022/6drk_8901.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6drk_8901/12_2022/6drk_8901.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6drk_8901/12_2022/6drk_8901.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6drk_8901/12_2022/6drk_8901.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 199": "NH1" <-> "NH2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A ARG 430": "NH1" <-> "NH2" Residue "A ARG 440": "NH1" <-> "NH2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A ARG 510": "NH1" <-> "NH2" Residue "A ARG 515": "NH1" <-> "NH2" Residue "A ARG 559": "NH1" <-> "NH2" Residue "A ARG 619": "NH1" <-> "NH2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A ARG 689": "NH1" <-> "NH2" Residue "A ARG 749": "NH1" <-> "NH2" Residue "A ARG 750": "NH1" <-> "NH2" Residue "A ARG 801": "NH1" <-> "NH2" Residue "A ARG 842": "NH1" <-> "NH2" Residue "A ARG 859": "NH1" <-> "NH2" Residue "A ARG 1092": "NH1" <-> "NH2" Residue "A ARG 1162": "NH1" <-> "NH2" Residue "A ARG 1404": "NH1" <-> "NH2" Residue "C ARG 199": "NH1" <-> "NH2" Residue "C ARG 226": "NH1" <-> "NH2" Residue "C ARG 430": "NH1" <-> "NH2" Residue "C ARG 440": "NH1" <-> "NH2" Residue "C ARG 487": "NH1" <-> "NH2" Residue "C ARG 510": "NH1" <-> "NH2" Residue "C ARG 515": "NH1" <-> "NH2" Residue "C ARG 559": "NH1" <-> "NH2" Residue "C ARG 619": "NH1" <-> "NH2" Residue "C ARG 675": "NH1" <-> "NH2" Residue "C ARG 689": "NH1" <-> "NH2" Residue "C ARG 749": "NH1" <-> "NH2" Residue "C ARG 750": "NH1" <-> "NH2" Residue "C ARG 801": "NH1" <-> "NH2" Residue "C ARG 842": "NH1" <-> "NH2" Residue "C ARG 859": "NH1" <-> "NH2" Residue "C ARG 1092": "NH1" <-> "NH2" Residue "C ARG 1162": "NH1" <-> "NH2" Residue "C ARG 1404": "NH1" <-> "NH2" Residue "B ARG 199": "NH1" <-> "NH2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B ARG 430": "NH1" <-> "NH2" Residue "B ARG 440": "NH1" <-> "NH2" Residue "B ARG 487": "NH1" <-> "NH2" Residue "B ARG 510": "NH1" <-> "NH2" Residue "B ARG 515": "NH1" <-> "NH2" Residue "B ARG 559": "NH1" <-> "NH2" Residue "B ARG 619": "NH1" <-> "NH2" Residue "B ARG 675": "NH1" <-> "NH2" Residue "B ARG 689": "NH1" <-> "NH2" Residue "B ARG 749": "NH1" <-> "NH2" Residue "B ARG 750": "NH1" <-> "NH2" Residue "B ARG 801": "NH1" <-> "NH2" Residue "B ARG 842": "NH1" <-> "NH2" Residue "B ARG 859": "NH1" <-> "NH2" Residue "B ARG 1092": "NH1" <-> "NH2" Residue "B ARG 1162": "NH1" <-> "NH2" Residue "B ARG 1404": "NH1" <-> "NH2" Residue "D ARG 199": "NH1" <-> "NH2" Residue "D ARG 226": "NH1" <-> "NH2" Residue "D ARG 430": "NH1" <-> "NH2" Residue "D ARG 440": "NH1" <-> "NH2" Residue "D ARG 487": "NH1" <-> "NH2" Residue "D ARG 510": "NH1" <-> "NH2" Residue "D ARG 515": "NH1" <-> "NH2" Residue "D ARG 559": "NH1" <-> "NH2" Residue "D ARG 619": "NH1" <-> "NH2" Residue "D ARG 675": "NH1" <-> "NH2" Residue "D ARG 689": "NH1" <-> "NH2" Residue "D ARG 749": "NH1" <-> "NH2" Residue "D ARG 750": "NH1" <-> "NH2" Residue "D ARG 801": "NH1" <-> "NH2" Residue "D ARG 842": "NH1" <-> "NH2" Residue "D ARG 859": "NH1" <-> "NH2" Residue "D ARG 1092": "NH1" <-> "NH2" Residue "D ARG 1162": "NH1" <-> "NH2" Residue "D ARG 1404": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 33120 Number of models: 1 Model: "" Number of chains: 4 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 Chain: "C" 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 Chain: "B" 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 Chain: "D" 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 Time building chain proxies: 18.83, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.42 Conformation dependent library (CDL) restraints added in 5.7 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: 2.30 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: 13.29 Time building geometry restraints manager: 14.65 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: 99.19 - 106.48: 1100 106.48 - 113.78: 19283 113.78 - 121.08: 16429 121.08 - 128.37: 9420 128.37 - 135.67: 404 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 2.520 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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. 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: 0.900 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: 9.010 Check model and map are aligned: 0.460 Convert atoms to be neutral: 0.270 Process input model: 85.010 Find NCS groups from input model: 2.160 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 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 33848 Z= 0.667 Angle : 1.176 10.672 46636 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 % 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 *********************** 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 fitting. rotamer outliers: 8 poor density : 716 time to evaluate : 4.498 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. outliers start: 8 outliers final: 4 residues processed: 720 average time/residue: 0.4140 time to fit residues: 484.7060 Evaluate side-chains 458 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 454 time to evaluate : 3.672 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2788 time to fit residues: 7.1422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 130 optimal weight: 20.0000 chunk 257 optimal weight: 9.9990 chunk 204 optimal weight: 1.9990 chunk 395 optimal weight: 9.9990 chunk 152 optimal weight: 0.0010 chunk 240 optimal weight: 20.0000 chunk 294 optimal weight: 0.9980 chunk 457 optimal weight: 9.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 HIS A 606 ASN A 716 GLN A 860 GLN A 997 ASN C 606 ASN C 860 GLN C 997 ASN C1164 HIS B 606 ASN B 816 ASN B 860 GLN B 997 ASN B1164 HIS D 606 ASN D 816 ASN D 860 GLN D1164 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 33848 Z= 0.157 Angle : 0.571 9.956 46636 Z= 0.298 Chirality : 0.039 0.140 5704 Planarity : 0.004 0.048 6036 Dihedral : 4.571 21.847 5260 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer Outliers : 3.42 % 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: -1.32 (0.11), residues: 5004 helix: 0.19 (0.10), residues: 2608 sheet: -2.00 (0.26), residues: 352 loop : -2.06 (0.12), residues: 2044 *********************** 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 646 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 569 time to evaluate : 4.267 Fit side-chains TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. outliers start: 77 outliers final: 46 residues processed: 609 average time/residue: 0.3788 time to fit residues: 398.4296 Evaluate side-chains 502 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 456 time to evaluate : 4.476 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.2921 time to fit residues: 31.0827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 254 optimal weight: 30.0000 chunk 142 optimal weight: 2.9990 chunk 380 optimal weight: 30.0000 chunk 311 optimal weight: 5.9990 chunk 126 optimal weight: 30.0000 chunk 458 optimal weight: 8.9990 chunk 495 optimal weight: 30.0000 chunk 408 optimal weight: 0.9980 chunk 454 optimal weight: 0.0470 chunk 156 optimal weight: 3.9990 chunk 367 optimal weight: 40.0000 overall best weight: 2.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 707 HIS A1164 HIS C 707 HIS B 707 HIS D 707 HIS D 997 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 33848 Z= 0.244 Angle : 0.576 7.759 46636 Z= 0.303 Chirality : 0.041 0.271 5704 Planarity : 0.004 0.037 6036 Dihedral : 4.280 21.709 5260 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer Outliers : 3.24 % 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: -0.52 (0.12), residues: 5004 helix: 1.03 (0.10), residues: 2588 sheet: -1.82 (0.26), residues: 352 loop : -1.91 (0.13), residues: 2064 *********************** 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 525 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 452 time to evaluate : 3.622 Fit side-chains TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. outliers start: 73 outliers final: 56 residues processed: 510 average time/residue: 0.3636 time to fit residues: 324.1286 Evaluate side-chains 472 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 416 time to evaluate : 3.787 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.2844 time to fit residues: 36.2622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 453 optimal weight: 2.9990 chunk 344 optimal weight: 8.9990 chunk 237 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 218 optimal weight: 20.0000 chunk 307 optimal weight: 2.9990 chunk 460 optimal weight: 9.9990 chunk 487 optimal weight: 7.9990 chunk 240 optimal weight: 2.9990 chunk 436 optimal weight: 3.9990 chunk 131 optimal weight: 20.0000 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN ** A1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 HIS C 606 ASN ** C1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN ** B1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 HIS D 606 ASN ** D1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 33848 Z= 0.199 Angle : 0.536 6.986 46636 Z= 0.280 Chirality : 0.039 0.343 5704 Planarity : 0.004 0.037 6036 Dihedral : 3.990 19.481 5260 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer Outliers : 1.91 % 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: 0.03 (0.12), residues: 5004 helix: 1.55 (0.10), residues: 2580 sheet: -1.32 (0.29), residues: 304 loop : -1.78 (0.13), residues: 2120 *********************** 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 509 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 466 time to evaluate : 3.718 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. revert: symmetry clash TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. outliers start: 43 outliers final: 22 residues processed: 488 average time/residue: 0.3876 time to fit residues: 332.7269 Evaluate side-chains 421 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 399 time to evaluate : 3.802 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2887 time to fit residues: 17.4428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 405 optimal weight: 9.9990 chunk 276 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 362 optimal weight: 50.0000 chunk 201 optimal weight: 0.9990 chunk 415 optimal weight: 5.9990 chunk 336 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 248 optimal weight: 0.0070 chunk 437 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN ** A1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN ** C1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 HIS B 606 ASN ** B1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 606 ASN ** D1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 33848 Z= 0.168 Angle : 0.523 10.461 46636 Z= 0.266 Chirality : 0.039 0.329 5704 Planarity : 0.003 0.037 6036 Dihedral : 3.757 17.072 5260 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer Outliers : 1.82 % 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: 0.35 (0.12), residues: 5004 helix: 1.81 (0.10), residues: 2596 sheet: -1.30 (0.29), residues: 300 loop : -1.63 (0.13), residues: 2108 *********************** 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 490 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 449 time to evaluate : 3.443 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. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. outliers start: 41 outliers final: 24 residues processed: 482 average time/residue: 0.3716 time to fit residues: 313.5439 Evaluate side-chains 424 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 400 time to evaluate : 3.718 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2854 time to fit residues: 17.9539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 163 optimal weight: 0.7980 chunk 438 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 286 optimal weight: 7.9990 chunk 120 optimal weight: 40.0000 chunk 487 optimal weight: 1.9990 chunk 404 optimal weight: 30.0000 chunk 225 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 161 optimal weight: 7.9990 chunk 256 optimal weight: 30.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS A 816 ASN ** A1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1325 ASN C 193 HIS C 816 ASN ** C1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1325 ASN ** B1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1325 ASN D 193 HIS ** D1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1325 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 33848 Z= 0.360 Angle : 0.658 8.598 46636 Z= 0.341 Chirality : 0.042 0.265 5704 Planarity : 0.004 0.040 6036 Dihedral : 4.350 16.213 5260 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer Outliers : 3.60 % 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: 0.05 (0.12), residues: 5004 helix: 1.50 (0.10), residues: 2572 sheet: -1.35 (0.29), residues: 292 loop : -1.66 (0.13), residues: 2140 *********************** 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 516 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 435 time to evaluate : 4.021 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. revert: symmetry clash TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. outliers start: 81 outliers final: 57 residues processed: 470 average time/residue: 0.3814 time to fit residues: 319.1120 Evaluate side-chains 452 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 395 time to evaluate : 3.890 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.3189 time to fit residues: 40.1287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 470 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 277 optimal weight: 8.9990 chunk 356 optimal weight: 30.0000 chunk 275 optimal weight: 2.9990 chunk 410 optimal weight: 8.9990 chunk 272 optimal weight: 10.0000 chunk 485 optimal weight: 0.0060 chunk 304 optimal weight: 6.9990 chunk 296 optimal weight: 4.9990 chunk 224 optimal weight: 4.9990 overall best weight: 2.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.5157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 33848 Z= 0.207 Angle : 0.555 12.840 46636 Z= 0.283 Chirality : 0.039 0.253 5704 Planarity : 0.004 0.038 6036 Dihedral : 3.943 16.916 5260 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer Outliers : 0.98 % 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: 0.41 (0.12), residues: 5004 helix: 1.85 (0.11), residues: 2572 sheet: -1.21 (0.28), residues: 312 loop : -1.56 (0.13), residues: 2120 *********************** 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 447 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 425 time to evaluate : 3.833 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. outliers start: 22 outliers final: 12 residues processed: 442 average time/residue: 0.3785 time to fit residues: 291.1257 Evaluate side-chains 406 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 394 time to evaluate : 3.729 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2908 time to fit residues: 12.0089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 300 optimal weight: 4.9990 chunk 193 optimal weight: 7.9990 chunk 290 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 308 optimal weight: 0.5980 chunk 330 optimal weight: 10.0000 chunk 240 optimal weight: 30.0000 chunk 45 optimal weight: 0.0030 chunk 381 optimal weight: 50.0000 overall best weight: 1.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.5404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 33848 Z= 0.174 Angle : 0.541 12.388 46636 Z= 0.272 Chirality : 0.038 0.239 5704 Planarity : 0.003 0.038 6036 Dihedral : 3.695 16.668 5260 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer Outliers : 1.47 % 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: 1.97 (0.11), residues: 2588 sheet: -1.02 (0.30), residues: 292 loop : -1.44 (0.14), residues: 2124 *********************** 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 448 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 415 time to evaluate : 3.475 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. revert: symmetry clash TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. outliers start: 33 outliers final: 19 residues processed: 430 average time/residue: 0.3532 time to fit residues: 268.5805 Evaluate side-chains 413 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 394 time to evaluate : 3.465 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2796 time to fit residues: 14.7317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 441 optimal weight: 5.9990 chunk 465 optimal weight: 30.0000 chunk 424 optimal weight: 7.9990 chunk 452 optimal weight: 6.9990 chunk 272 optimal weight: 0.6980 chunk 197 optimal weight: 7.9990 chunk 355 optimal weight: 5.9990 chunk 138 optimal weight: 20.0000 chunk 409 optimal weight: 10.0000 chunk 428 optimal weight: 2.9990 chunk 451 optimal weight: 10.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN ** C1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.5673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 33848 Z= 0.352 Angle : 0.658 12.036 46636 Z= 0.338 Chirality : 0.042 0.260 5704 Planarity : 0.004 0.041 6036 Dihedral : 4.269 17.115 5260 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer Outliers : 1.11 % 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: 0.26 (0.12), residues: 5004 helix: 1.59 (0.11), residues: 2588 sheet: -1.35 (0.27), residues: 320 loop : -1.44 (0.14), residues: 2096 *********************** 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 425 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 400 time to evaluate : 4.155 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. outliers start: 25 outliers final: 20 residues processed: 419 average time/residue: 0.3607 time to fit residues: 268.6057 Evaluate side-chains 396 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 376 time to evaluate : 3.670 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2876 time to fit residues: 16.1543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 297 optimal weight: 2.9990 chunk 478 optimal weight: 3.9990 chunk 292 optimal weight: 5.9990 chunk 227 optimal weight: 7.9990 chunk 332 optimal weight: 20.0000 chunk 502 optimal weight: 50.0000 chunk 462 optimal weight: 2.9990 chunk 399 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 308 optimal weight: 0.4980 chunk 245 optimal weight: 40.0000 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.5914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 33848 Z= 0.265 Angle : 0.595 11.758 46636 Z= 0.304 Chirality : 0.040 0.235 5704 Planarity : 0.004 0.039 6036 Dihedral : 4.046 17.387 5260 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer Outliers : 0.71 % 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: 0.38 (0.12), residues: 5004 helix: 1.74 (0.11), residues: 2584 sheet: -1.30 (0.27), residues: 320 loop : -1.44 (0.13), residues: 2100 ********************** 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 411 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 395 time to evaluate : 3.837 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. outliers start: 16 outliers final: 9 residues processed: 406 average time/residue: 0.3707 time to fit residues: 267.4044 Evaluate side-chains 381 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 372 time to evaluate : 3.871 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3109 time to fit residues: 10.6968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 317 optimal weight: 6.9990 chunk 425 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 368 optimal weight: 0.0470 chunk 59 optimal weight: 4.9990 chunk 111 optimal weight: 20.0000 chunk 400 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 411 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 40.0000 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3920 r_free = 0.3920 target = 0.137260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.093550 restraints weight = 84419.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.095604 restraints weight = 49552.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.096883 restraints weight = 35296.588| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.6131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 33848 Z= 0.226 Angle : 0.575 11.891 46636 Z= 0.291 Chirality : 0.040 0.232 5704 Planarity : 0.004 0.039 6036 Dihedral : 3.859 16.573 5260 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer Outliers : 0.40 % 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: 0.52 (0.12), residues: 5004 helix: 1.84 (0.11), residues: 2592 sheet: -1.07 (0.29), residues: 300 loop : -1.40 (0.14), residues: 2112 =============================================================================== Job complete usr+sys time: 6303.87 seconds wall clock time: 113 minutes 13.15 seconds (6793.15 seconds total)