Starting phenix.real_space_refine on Mon Aug 10 05:14:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e6s_27924/08_2026/8e6s_27924.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e6s_27924/08_2026/8e6s_27924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8e6s_27924/08_2026/8e6s_27924.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e6s_27924/08_2026/8e6s_27924.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e6s_27924/08_2026/8e6s_27924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e6s_27924/08_2026/8e6s_27924.map" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 16 5.49 5 S 200 5.16 5 C 27264 2.51 5 N 7356 2.21 5 O 7492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 42336 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1330, 10521 Classifications: {'peptide': 1330} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 65, 'TRANS': 1264} Chain breaks: 3 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 276 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 10, 'HIS:plan': 2, 'GLN:plan1': 6, 'TYR:plan': 1, 'ASP:plan': 8, 'ASN:plan1': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 142 Chain: "B" Number of atoms: 10521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1330, 10521 Classifications: {'peptide': 1330} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 65, 'TRANS': 1264} Chain breaks: 3 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 276 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 10, 'HIS:plan': 2, 'GLN:plan1': 6, 'TYR:plan': 1, 'ASP:plan': 8, 'ASN:plan1': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 142 Chain: "C" Number of atoms: 10521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1330, 10521 Classifications: {'peptide': 1330} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 65, 'TRANS': 1264} Chain breaks: 3 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 276 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 10, 'HIS:plan': 2, 'GLN:plan1': 6, 'TYR:plan': 1, 'ASP:plan': 8, 'ASN:plan1': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 142 Chain: "D" Number of atoms: 10521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1330, 10521 Classifications: {'peptide': 1330} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 65, 'TRANS': 1264} Chain breaks: 3 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 276 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 10, 'HIS:plan': 2, 'GLN:plan1': 6, 'TYR:plan': 1, 'ASP:plan': 8, 'ASN:plan1': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 142 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 63 Unusual residues: {' CA': 1, ' ZN': 1, 'APR': 1, 'DAT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 63 Unusual residues: {' CA': 1, ' ZN': 1, 'APR': 1, 'DAT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 63 Unusual residues: {' CA': 1, ' ZN': 1, 'APR': 1, 'DAT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 63 Unusual residues: {' CA': 1, ' ZN': 1, 'APR': 1, 'DAT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 225 SG CYS A 89 164.766 93.726 124.948 1.00812.00 S ATOM 240 SG CYS A 91 162.067 97.280 125.804 1.00790.05 S ATOM 10746 SG CYS B 89 93.356 14.596 124.706 1.00837.97 S ATOM 10761 SG CYS B 91 96.963 17.228 125.552 1.00805.73 S ATOM 21267 SG CYS C 89 14.457 85.607 124.496 1.00859.00 S ATOM 21282 SG CYS C 91 17.143 82.053 125.393 1.00829.90 S ATOM 31788 SG CYS D 89 85.855 164.701 124.911 1.00841.88 S ATOM 31803 SG CYS D 91 82.274 162.036 125.762 1.00818.53 S Time building chain proxies: 7.11, per 1000 atoms: 0.17 Number of scatterers: 42336 At special positions: 0 Unit cell: (180.36, 180.36, 172.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 200 16.00 P 16 15.00 O 7492 8.00 N 7356 7.00 C 27264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.20 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1603 " pdb="ZN ZN A1603 " - pdb=" NE2 HIS A 98 " pdb="ZN ZN A1603 " - pdb=" SG CYS A 91 " pdb="ZN ZN A1603 " - pdb=" SG CYS A 89 " pdb=" ZN B1603 " pdb="ZN ZN B1603 " - pdb=" NE2 HIS B 98 " pdb="ZN ZN B1603 " - pdb=" SG CYS B 91 " pdb="ZN ZN B1603 " - pdb=" SG CYS B 89 " pdb=" ZN C1603 " pdb="ZN ZN C1603 " - pdb=" NE2 HIS C 98 " pdb="ZN ZN C1603 " - pdb=" SG CYS C 91 " pdb="ZN ZN C1603 " - pdb=" SG CYS C 89 " pdb=" ZN D1603 " pdb="ZN ZN D1603 " - pdb=" NE2 HIS D 98 " pdb="ZN ZN D1603 " - pdb=" SG CYS D 91 " pdb="ZN ZN D1603 " - pdb=" SG CYS D 89 " 10576 Ramachandran restraints generated. 5288 Oldfield, 0 Emsley, 5288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10032 Finding SS restraints... Secondary structure from input PDB file: 236 helices and 20 sheets defined 51.6% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 114 through 118 removed outlier: 3.840A pdb=" N LYS A 117 " --> pdb=" O ASP A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 161 removed outlier: 3.664A pdb=" N ILE A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN A 160 " --> pdb=" O HIS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 200 removed outlier: 3.906A pdb=" N THR A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 227 removed outlier: 4.244A pdb=" N GLY A 219 " --> pdb=" O MET A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 247 No H-bonds generated for 'chain 'A' and resid 245 through 247' Processing helix chain 'A' and resid 298 through 312 removed outlier: 3.708A pdb=" N GLN A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 319 removed outlier: 4.151A pdb=" N VAL A 319 " --> pdb=" O ARG A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 347 Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 375 through 382 Processing helix chain 'A' and resid 395 through 400 removed outlier: 3.607A pdb=" N VAL A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 412 removed outlier: 4.482A pdb=" N LYS A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE A 406 " --> pdb=" O TRP A 402 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 451 through 462 removed outlier: 3.919A pdb=" N ALA A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 473 removed outlier: 3.669A pdb=" N ALA A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 472 " --> pdb=" O ALA A 468 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N PHE A 473 " --> pdb=" O ARG A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 483 removed outlier: 3.828A pdb=" N ASP A 483 " --> pdb=" O LYS A 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 480 through 483' Processing helix chain 'A' and resid 484 through 495 removed outlier: 3.505A pdb=" N ALA A 490 " --> pdb=" O PRO A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 507 removed outlier: 4.028A pdb=" N VAL A 500 " --> pdb=" O LYS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 525 removed outlier: 3.516A pdb=" N ASN A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 543 removed outlier: 3.905A pdb=" N SER A 534 " --> pdb=" O CYS A 530 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 567 removed outlier: 3.869A pdb=" N VAL A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 584 removed outlier: 3.508A pdb=" N ASP A 584 " --> pdb=" O ARG A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 620 through 631 removed outlier: 4.368A pdb=" N ASP A 624 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 627 " --> pdb=" O ARG A 623 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL A 631 " --> pdb=" O ILE A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 643 removed outlier: 4.100A pdb=" N GLY A 639 " --> pdb=" O ARG A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 666 removed outlier: 3.758A pdb=" N GLU A 666 " --> pdb=" O LEU A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 696 removed outlier: 3.846A pdb=" N LYS A 696 " --> pdb=" O GLU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 705 removed outlier: 4.048A pdb=" N LEU A 705 " --> pdb=" O ALA A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 717 Processing helix chain 'A' and resid 718 through 724 Processing helix chain 'A' and resid 728 through 732 removed outlier: 3.556A pdb=" N SER A 731 " --> pdb=" O LYS A 728 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N HIS A 732 " --> pdb=" O PHE A 729 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 728 through 732' Processing helix chain 'A' and resid 733 through 744 Processing helix chain 'A' and resid 752 through 762 removed outlier: 4.138A pdb=" N THR A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU A 758 " --> pdb=" O TRP A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 768 removed outlier: 3.781A pdb=" N LEU A 766 " --> pdb=" O PHE A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 778 Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'A' and resid 794 through 819 removed outlier: 3.949A pdb=" N VAL A 798 " --> pdb=" O ALA A 794 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A 799 " --> pdb=" O PRO A 795 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A 807 " --> pdb=" O ILE A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 850 removed outlier: 3.774A pdb=" N TRP A 835 " --> pdb=" O ALA A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 865 removed outlier: 3.919A pdb=" N ALA A 860 " --> pdb=" O LEU A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 888 removed outlier: 3.828A pdb=" N ILE A 876 " --> pdb=" O ASP A 872 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE A 879 " --> pdb=" O ALA A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 892 removed outlier: 3.729A pdb=" N LEU A 892 " --> pdb=" O PRO A 889 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 889 through 892' Processing helix chain 'A' and resid 893 through 913 removed outlier: 3.877A pdb=" N VAL A 897 " --> pdb=" O TYR A 893 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP A 902 " --> pdb=" O ILE A 898 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE A 903 " --> pdb=" O LEU A 899 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE A 904 " --> pdb=" O SER A 900 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU A 905 " --> pdb=" O LEU A 901 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE A 906 " --> pdb=" O ASP A 902 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET A 911 " --> pdb=" O CYS A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 934 removed outlier: 4.059A pdb=" N LYS A 923 " --> pdb=" O THR A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 953 removed outlier: 3.756A pdb=" N PHE A 939 " --> pdb=" O PHE A 935 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER A 947 " --> pdb=" O VAL A 943 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N PHE A 948 " --> pdb=" O TRP A 944 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY A 949 " --> pdb=" O VAL A 945 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A 950 " --> pdb=" O VAL A 946 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA A 951 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 956 No H-bonds generated for 'chain 'A' and resid 954 through 956' Processing helix chain 'A' and resid 964 through 969 removed outlier: 4.746A pdb=" N ARG A 968 " --> pdb=" O ASP A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 987 removed outlier: 4.313A pdb=" N ILE A 986 " --> pdb=" O PRO A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1040 removed outlier: 3.925A pdb=" N CYS A1030 " --> pdb=" O VAL A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1049 removed outlier: 3.747A pdb=" N LEU A1044 " --> pdb=" O LEU A1040 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A1045 " --> pdb=" O LEU A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1075 removed outlier: 4.876A pdb=" N ASP A1060 " --> pdb=" O GLN A1056 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLN A1061 " --> pdb=" O GLU A1057 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE A1062 " --> pdb=" O HIS A1058 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU A1073 " --> pdb=" O ASP A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1083 No H-bonds generated for 'chain 'A' and resid 1081 through 1083' Processing helix chain 'A' and resid 1084 through 1097 removed outlier: 4.458A pdb=" N SER A1088 " --> pdb=" O PHE A1084 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ILE A1094 " --> pdb=" O LEU A1090 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS A1095 " --> pdb=" O GLN A1091 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL A1097 " --> pdb=" O PHE A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1143 removed outlier: 3.540A pdb=" N TRP A1124 " --> pdb=" O ALA A1120 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN A1142 " --> pdb=" O PHE A1138 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG A1143 " --> pdb=" O GLN A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1163 removed outlier: 3.936A pdb=" N LYS A1147 " --> pdb=" O ARG A1143 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP A1156 " --> pdb=" O SER A1152 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP A1160 " --> pdb=" O ASP A1156 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LEU A1161 " --> pdb=" O ALA A1157 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU A1162 " --> pdb=" O MET A1158 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP A1163 " --> pdb=" O VAL A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1262 removed outlier: 3.615A pdb=" N VAL A1262 " --> pdb=" O ASN A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1419 removed outlier: 3.788A pdb=" N PHE A1414 " --> pdb=" O HIS A1410 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A1415 " --> pdb=" O TRP A1411 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN A1416 " --> pdb=" O PRO A1412 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A1417 " --> pdb=" O SER A1413 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS A1419 " --> pdb=" O GLU A1415 " (cutoff:3.500A) Processing helix chain 'A' and resid 1454 through 1464 removed outlier: 4.101A pdb=" N ASN A1458 " --> pdb=" O ASP A1454 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG A1459 " --> pdb=" O VAL A1455 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU A1460 " --> pdb=" O GLU A1456 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASN A1461 " --> pdb=" O LEU A1457 " (cutoff:3.500A) Processing helix chain 'A' and resid 1485 through 1496 removed outlier: 3.557A pdb=" N LYS A1489 " --> pdb=" O TYR A1485 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR A1490 " --> pdb=" O ALA A1486 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A1491 " --> pdb=" O ASN A1487 " (cutoff:3.500A) Processing helix chain 'A' and resid 1497 through 1499 No H-bonds generated for 'chain 'A' and resid 1497 through 1499' Processing helix chain 'B' and resid 114 through 118 removed outlier: 3.840A pdb=" N LYS B 117 " --> pdb=" O ASP B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 161 removed outlier: 3.665A pdb=" N ILE B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN B 160 " --> pdb=" O HIS B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 200 removed outlier: 3.905A pdb=" N THR B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 227 removed outlier: 4.244A pdb=" N GLY B 219 " --> pdb=" O MET B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 247 No H-bonds generated for 'chain 'B' and resid 245 through 247' Processing helix chain 'B' and resid 298 through 312 removed outlier: 3.708A pdb=" N GLN B 312 " --> pdb=" O PHE B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 319 removed outlier: 4.150A pdb=" N VAL B 319 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 347 Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 375 through 382 Processing helix chain 'B' and resid 395 through 400 removed outlier: 3.607A pdb=" N VAL B 400 " --> pdb=" O GLU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 412 removed outlier: 4.482A pdb=" N LYS B 404 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS B 405 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE B 406 " --> pdb=" O TRP B 402 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 442 Processing helix chain 'B' and resid 451 through 462 removed outlier: 3.918A pdb=" N ALA B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TRP B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 473 removed outlier: 3.669A pdb=" N ALA B 468 " --> pdb=" O ARG B 464 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 472 " --> pdb=" O ALA B 468 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N PHE B 473 " --> pdb=" O ARG B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 483 removed outlier: 3.828A pdb=" N ASP B 483 " --> pdb=" O LYS B 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 480 through 483' Processing helix chain 'B' and resid 484 through 495 removed outlier: 3.505A pdb=" N ALA B 490 " --> pdb=" O PRO B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 507 removed outlier: 4.028A pdb=" N VAL B 500 " --> pdb=" O LYS B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 525 removed outlier: 3.516A pdb=" N ASN B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 543 removed outlier: 3.905A pdb=" N SER B 534 " --> pdb=" O CYS B 530 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 567 removed outlier: 3.869A pdb=" N VAL B 561 " --> pdb=" O GLN B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 584 removed outlier: 3.509A pdb=" N ASP B 584 " --> pdb=" O ARG B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 598 Processing helix chain 'B' and resid 620 through 631 removed outlier: 4.367A pdb=" N ASP B 624 " --> pdb=" O ASP B 620 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 627 " --> pdb=" O ARG B 623 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL B 631 " --> pdb=" O ILE B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 643 removed outlier: 4.100A pdb=" N GLY B 639 " --> pdb=" O ARG B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 666 removed outlier: 3.758A pdb=" N GLU B 666 " --> pdb=" O LEU B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 696 removed outlier: 3.847A pdb=" N LYS B 696 " --> pdb=" O GLU B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 705 removed outlier: 4.049A pdb=" N LEU B 705 " --> pdb=" O ALA B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 717 Processing helix chain 'B' and resid 718 through 724 Processing helix chain 'B' and resid 728 through 732 removed outlier: 3.557A pdb=" N SER B 731 " --> pdb=" O LYS B 728 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N HIS B 732 " --> pdb=" O PHE B 729 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 728 through 732' Processing helix chain 'B' and resid 733 through 744 Processing helix chain 'B' and resid 752 through 762 removed outlier: 4.138A pdb=" N THR B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU B 758 " --> pdb=" O TRP B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 768 removed outlier: 3.781A pdb=" N LEU B 766 " --> pdb=" O PHE B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 778 Processing helix chain 'B' and resid 783 through 793 Processing helix chain 'B' and resid 794 through 819 removed outlier: 3.949A pdb=" N VAL B 798 " --> pdb=" O ALA B 794 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE B 799 " --> pdb=" O PRO B 795 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE B 807 " --> pdb=" O ILE B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 850 removed outlier: 3.774A pdb=" N TRP B 835 " --> pdb=" O ALA B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 865 removed outlier: 3.919A pdb=" N ALA B 860 " --> pdb=" O LEU B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 888 removed outlier: 3.828A pdb=" N ILE B 876 " --> pdb=" O ASP B 872 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE B 879 " --> pdb=" O ALA B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 892 removed outlier: 3.729A pdb=" N LEU B 892 " --> pdb=" O PRO B 889 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 889 through 892' Processing helix chain 'B' and resid 893 through 913 removed outlier: 3.877A pdb=" N VAL B 897 " --> pdb=" O TYR B 893 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP B 902 " --> pdb=" O ILE B 898 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE B 903 " --> pdb=" O LEU B 899 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE B 904 " --> pdb=" O SER B 900 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU B 905 " --> pdb=" O LEU B 901 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE B 906 " --> pdb=" O ASP B 902 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET B 911 " --> pdb=" O CYS B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 934 removed outlier: 4.060A pdb=" N LYS B 923 " --> pdb=" O THR B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 934 through 953 removed outlier: 3.755A pdb=" N PHE B 939 " --> pdb=" O PHE B 935 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 946 " --> pdb=" O ALA B 942 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SER B 947 " --> pdb=" O VAL B 943 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N PHE B 948 " --> pdb=" O TRP B 944 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY B 949 " --> pdb=" O VAL B 945 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL B 950 " --> pdb=" O VAL B 946 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA B 951 " --> pdb=" O SER B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 956 No H-bonds generated for 'chain 'B' and resid 954 through 956' Processing helix chain 'B' and resid 964 through 969 removed outlier: 4.745A pdb=" N ARG B 968 " --> pdb=" O ASP B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 987 removed outlier: 4.313A pdb=" N ILE B 986 " --> pdb=" O PRO B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1040 removed outlier: 3.924A pdb=" N CYS B1030 " --> pdb=" O VAL B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1049 removed outlier: 3.747A pdb=" N LEU B1044 " --> pdb=" O LEU B1040 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE B1045 " --> pdb=" O LEU B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1075 removed outlier: 4.875A pdb=" N ASP B1060 " --> pdb=" O GLN B1056 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLN B1061 " --> pdb=" O GLU B1057 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE B1062 " --> pdb=" O HIS B1058 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU B1073 " --> pdb=" O ASP B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1081 through 1083 No H-bonds generated for 'chain 'B' and resid 1081 through 1083' Processing helix chain 'B' and resid 1084 through 1097 removed outlier: 4.458A pdb=" N SER B1088 " --> pdb=" O PHE B1084 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ILE B1094 " --> pdb=" O LEU B1090 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS B1095 " --> pdb=" O GLN B1091 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL B1097 " --> pdb=" O PHE B1093 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1143 removed outlier: 3.540A pdb=" N TRP B1124 " --> pdb=" O ALA B1120 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN B1142 " --> pdb=" O PHE B1138 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG B1143 " --> pdb=" O GLN B1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1163 removed outlier: 3.937A pdb=" N LYS B1147 " --> pdb=" O ARG B1143 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP B1156 " --> pdb=" O SER B1152 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP B1160 " --> pdb=" O ASP B1156 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LEU B1161 " --> pdb=" O ALA B1157 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU B1162 " --> pdb=" O MET B1158 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP B1163 " --> pdb=" O VAL B1159 " (cutoff:3.500A) Processing helix chain 'B' and resid 1258 through 1262 removed outlier: 3.615A pdb=" N VAL B1262 " --> pdb=" O ASN B1259 " (cutoff:3.500A) Processing helix chain 'B' and resid 1410 through 1419 removed outlier: 3.788A pdb=" N PHE B1414 " --> pdb=" O HIS B1410 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU B1415 " --> pdb=" O TRP B1411 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN B1416 " --> pdb=" O PRO B1412 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU B1417 " --> pdb=" O SER B1413 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B1419 " --> pdb=" O GLU B1415 " (cutoff:3.500A) Processing helix chain 'B' and resid 1454 through 1464 removed outlier: 4.101A pdb=" N ASN B1458 " --> pdb=" O ASP B1454 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG B1459 " --> pdb=" O VAL B1455 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU B1460 " --> pdb=" O GLU B1456 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASN B1461 " --> pdb=" O LEU B1457 " (cutoff:3.500A) Processing helix chain 'B' and resid 1485 through 1496 removed outlier: 3.556A pdb=" N LYS B1489 " --> pdb=" O TYR B1485 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR B1490 " --> pdb=" O ALA B1486 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B1491 " --> pdb=" O ASN B1487 " (cutoff:3.500A) Processing helix chain 'B' and resid 1497 through 1499 No H-bonds generated for 'chain 'B' and resid 1497 through 1499' Processing helix chain 'C' and resid 114 through 118 removed outlier: 3.839A pdb=" N LYS C 117 " --> pdb=" O ASP C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 161 removed outlier: 3.665A pdb=" N ILE C 154 " --> pdb=" O PRO C 150 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN C 160 " --> pdb=" O HIS C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 200 removed outlier: 3.905A pdb=" N THR C 200 " --> pdb=" O LYS C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 227 removed outlier: 4.244A pdb=" N GLY C 219 " --> pdb=" O MET C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 247 No H-bonds generated for 'chain 'C' and resid 245 through 247' Processing helix chain 'C' and resid 298 through 312 removed outlier: 3.709A pdb=" N GLN C 312 " --> pdb=" O PHE C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 319 removed outlier: 4.151A pdb=" N VAL C 319 " --> pdb=" O ARG C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 347 Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 375 through 382 Processing helix chain 'C' and resid 395 through 400 removed outlier: 3.607A pdb=" N VAL C 400 " --> pdb=" O GLU C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 412 removed outlier: 4.483A pdb=" N LYS C 404 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS C 405 " --> pdb=" O GLU C 401 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE C 406 " --> pdb=" O TRP C 402 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 442 Processing helix chain 'C' and resid 451 through 462 removed outlier: 3.918A pdb=" N ALA C 461 " --> pdb=" O LYS C 457 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TRP C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 473 removed outlier: 3.670A pdb=" N ALA C 468 " --> pdb=" O ARG C 464 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C 472 " --> pdb=" O ALA C 468 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE C 473 " --> pdb=" O ARG C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 483 removed outlier: 3.828A pdb=" N ASP C 483 " --> pdb=" O LYS C 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 480 through 483' Processing helix chain 'C' and resid 484 through 495 removed outlier: 3.505A pdb=" N ALA C 490 " --> pdb=" O PRO C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 507 removed outlier: 4.028A pdb=" N VAL C 500 " --> pdb=" O LYS C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 525 removed outlier: 3.516A pdb=" N ASN C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 543 removed outlier: 3.905A pdb=" N SER C 534 " --> pdb=" O CYS C 530 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 567 removed outlier: 3.869A pdb=" N VAL C 561 " --> pdb=" O GLN C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 584 removed outlier: 3.508A pdb=" N ASP C 584 " --> pdb=" O ARG C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 598 Processing helix chain 'C' and resid 620 through 631 removed outlier: 4.367A pdb=" N ASP C 624 " --> pdb=" O ASP C 620 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE C 627 " --> pdb=" O ARG C 623 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL C 631 " --> pdb=" O ILE C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 643 removed outlier: 4.100A pdb=" N GLY C 639 " --> pdb=" O ARG C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 666 removed outlier: 3.758A pdb=" N GLU C 666 " --> pdb=" O LEU C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 696 removed outlier: 3.846A pdb=" N LYS C 696 " --> pdb=" O GLU C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 705 removed outlier: 4.048A pdb=" N LEU C 705 " --> pdb=" O ALA C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 717 Processing helix chain 'C' and resid 718 through 724 Processing helix chain 'C' and resid 728 through 732 removed outlier: 3.557A pdb=" N SER C 731 " --> pdb=" O LYS C 728 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N HIS C 732 " --> pdb=" O PHE C 729 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 728 through 732' Processing helix chain 'C' and resid 733 through 744 Processing helix chain 'C' and resid 752 through 762 removed outlier: 4.138A pdb=" N THR C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU C 758 " --> pdb=" O TRP C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 763 through 768 removed outlier: 3.781A pdb=" N LEU C 766 " --> pdb=" O PHE C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 778 Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'C' and resid 794 through 819 removed outlier: 3.949A pdb=" N VAL C 798 " --> pdb=" O ALA C 794 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE C 799 " --> pdb=" O PRO C 795 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE C 807 " --> pdb=" O ILE C 803 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 850 removed outlier: 3.773A pdb=" N TRP C 835 " --> pdb=" O ALA C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 865 removed outlier: 3.919A pdb=" N ALA C 860 " --> pdb=" O LEU C 856 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 888 removed outlier: 3.828A pdb=" N ILE C 876 " --> pdb=" O ASP C 872 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE C 879 " --> pdb=" O ALA C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 889 through 892 removed outlier: 3.729A pdb=" N LEU C 892 " --> pdb=" O PRO C 889 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 889 through 892' Processing helix chain 'C' and resid 893 through 913 removed outlier: 3.877A pdb=" N VAL C 897 " --> pdb=" O TYR C 893 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP C 902 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE C 903 " --> pdb=" O LEU C 899 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE C 904 " --> pdb=" O SER C 900 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU C 905 " --> pdb=" O LEU C 901 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE C 906 " --> pdb=" O ASP C 902 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET C 911 " --> pdb=" O CYS C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 934 removed outlier: 4.059A pdb=" N LYS C 923 " --> pdb=" O THR C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 934 through 953 removed outlier: 3.755A pdb=" N PHE C 939 " --> pdb=" O PHE C 935 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C 946 " --> pdb=" O ALA C 942 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER C 947 " --> pdb=" O VAL C 943 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N PHE C 948 " --> pdb=" O TRP C 944 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY C 949 " --> pdb=" O VAL C 945 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL C 950 " --> pdb=" O VAL C 946 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA C 951 " --> pdb=" O SER C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 956 No H-bonds generated for 'chain 'C' and resid 954 through 956' Processing helix chain 'C' and resid 964 through 969 removed outlier: 4.746A pdb=" N ARG C 968 " --> pdb=" O ASP C 964 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 987 removed outlier: 4.312A pdb=" N ILE C 986 " --> pdb=" O PRO C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1023 through 1040 removed outlier: 3.925A pdb=" N CYS C1030 " --> pdb=" O VAL C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1040 through 1049 removed outlier: 3.747A pdb=" N LEU C1044 " --> pdb=" O LEU C1040 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE C1045 " --> pdb=" O LEU C1041 " (cutoff:3.500A) Processing helix chain 'C' and resid 1054 through 1075 removed outlier: 4.876A pdb=" N ASP C1060 " --> pdb=" O GLN C1056 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLN C1061 " --> pdb=" O GLU C1057 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE C1062 " --> pdb=" O HIS C1058 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU C1073 " --> pdb=" O ASP C1069 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1083 No H-bonds generated for 'chain 'C' and resid 1081 through 1083' Processing helix chain 'C' and resid 1084 through 1097 removed outlier: 4.458A pdb=" N SER C1088 " --> pdb=" O PHE C1084 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ILE C1094 " --> pdb=" O LEU C1090 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LYS C1095 " --> pdb=" O GLN C1091 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL C1097 " --> pdb=" O PHE C1093 " (cutoff:3.500A) Processing helix chain 'C' and resid 1114 through 1143 removed outlier: 3.540A pdb=" N TRP C1124 " --> pdb=" O ALA C1120 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN C1142 " --> pdb=" O PHE C1138 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG C1143 " --> pdb=" O GLN C1139 " (cutoff:3.500A) Processing helix chain 'C' and resid 1143 through 1163 removed outlier: 3.935A pdb=" N LYS C1147 " --> pdb=" O ARG C1143 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP C1156 " --> pdb=" O SER C1152 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP C1160 " --> pdb=" O ASP C1156 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LEU C1161 " --> pdb=" O ALA C1157 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU C1162 " --> pdb=" O MET C1158 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP C1163 " --> pdb=" O VAL C1159 " (cutoff:3.500A) Processing helix chain 'C' and resid 1258 through 1262 removed outlier: 3.616A pdb=" N VAL C1262 " --> pdb=" O ASN C1259 " (cutoff:3.500A) Processing helix chain 'C' and resid 1410 through 1419 removed outlier: 3.787A pdb=" N PHE C1414 " --> pdb=" O HIS C1410 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU C1415 " --> pdb=" O TRP C1411 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN C1416 " --> pdb=" O PRO C1412 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU C1417 " --> pdb=" O SER C1413 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS C1419 " --> pdb=" O GLU C1415 " (cutoff:3.500A) Processing helix chain 'C' and resid 1454 through 1464 removed outlier: 4.102A pdb=" N ASN C1458 " --> pdb=" O ASP C1454 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG C1459 " --> pdb=" O VAL C1455 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU C1460 " --> pdb=" O GLU C1456 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASN C1461 " --> pdb=" O LEU C1457 " (cutoff:3.500A) Processing helix chain 'C' and resid 1485 through 1496 removed outlier: 3.556A pdb=" N LYS C1489 " --> pdb=" O TYR C1485 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR C1490 " --> pdb=" O ALA C1486 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU C1491 " --> pdb=" O ASN C1487 " (cutoff:3.500A) Processing helix chain 'C' and resid 1497 through 1499 No H-bonds generated for 'chain 'C' and resid 1497 through 1499' Processing helix chain 'D' and resid 114 through 118 removed outlier: 3.839A pdb=" N LYS D 117 " --> pdb=" O ASP D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 161 removed outlier: 3.665A pdb=" N ILE D 154 " --> pdb=" O PRO D 150 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN D 160 " --> pdb=" O HIS D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 200 removed outlier: 3.905A pdb=" N THR D 200 " --> pdb=" O LYS D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 227 removed outlier: 4.244A pdb=" N GLY D 219 " --> pdb=" O MET D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 247 No H-bonds generated for 'chain 'D' and resid 245 through 247' Processing helix chain 'D' and resid 298 through 312 removed outlier: 3.708A pdb=" N GLN D 312 " --> pdb=" O PHE D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 319 removed outlier: 4.151A pdb=" N VAL D 319 " --> pdb=" O ARG D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 347 Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 375 through 382 Processing helix chain 'D' and resid 395 through 400 removed outlier: 3.608A pdb=" N VAL D 400 " --> pdb=" O GLU D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 412 removed outlier: 4.482A pdb=" N LYS D 404 " --> pdb=" O VAL D 400 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS D 405 " --> pdb=" O GLU D 401 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE D 406 " --> pdb=" O TRP D 402 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG D 412 " --> pdb=" O ASP D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 442 Processing helix chain 'D' and resid 451 through 462 removed outlier: 3.919A pdb=" N ALA D 461 " --> pdb=" O LYS D 457 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 473 removed outlier: 3.670A pdb=" N ALA D 468 " --> pdb=" O ARG D 464 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE D 472 " --> pdb=" O ALA D 468 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N PHE D 473 " --> pdb=" O ARG D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 483 removed outlier: 3.828A pdb=" N ASP D 483 " --> pdb=" O LYS D 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 480 through 483' Processing helix chain 'D' and resid 484 through 495 removed outlier: 3.505A pdb=" N ALA D 490 " --> pdb=" O PRO D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 507 removed outlier: 4.029A pdb=" N VAL D 500 " --> pdb=" O LYS D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 525 removed outlier: 3.516A pdb=" N ASN D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 543 removed outlier: 3.905A pdb=" N SER D 534 " --> pdb=" O CYS D 530 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 567 removed outlier: 3.869A pdb=" N VAL D 561 " --> pdb=" O GLN D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 584 removed outlier: 3.509A pdb=" N ASP D 584 " --> pdb=" O ARG D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 598 Processing helix chain 'D' and resid 620 through 631 removed outlier: 4.367A pdb=" N ASP D 624 " --> pdb=" O ASP D 620 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE D 627 " --> pdb=" O ARG D 623 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL D 631 " --> pdb=" O ILE D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 643 removed outlier: 4.100A pdb=" N GLY D 639 " --> pdb=" O ARG D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 666 removed outlier: 3.758A pdb=" N GLU D 666 " --> pdb=" O LEU D 662 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 696 removed outlier: 3.847A pdb=" N LYS D 696 " --> pdb=" O GLU D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 705 removed outlier: 4.049A pdb=" N LEU D 705 " --> pdb=" O ALA D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 717 Processing helix chain 'D' and resid 718 through 724 Processing helix chain 'D' and resid 728 through 732 removed outlier: 3.557A pdb=" N SER D 731 " --> pdb=" O LYS D 728 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N HIS D 732 " --> pdb=" O PHE D 729 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 728 through 732' Processing helix chain 'D' and resid 733 through 744 Processing helix chain 'D' and resid 752 through 762 removed outlier: 4.138A pdb=" N THR D 757 " --> pdb=" O LEU D 753 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU D 758 " --> pdb=" O TRP D 754 " (cutoff:3.500A) Processing helix chain 'D' and resid 763 through 768 removed outlier: 3.781A pdb=" N LEU D 766 " --> pdb=" O PHE D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 773 through 778 Processing helix chain 'D' and resid 783 through 793 Processing helix chain 'D' and resid 794 through 819 removed outlier: 3.949A pdb=" N VAL D 798 " --> pdb=" O ALA D 794 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE D 799 " --> pdb=" O PRO D 795 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE D 807 " --> pdb=" O ILE D 803 " (cutoff:3.500A) Processing helix chain 'D' and resid 826 through 850 removed outlier: 3.775A pdb=" N TRP D 835 " --> pdb=" O ALA D 831 " (cutoff:3.500A) Processing helix chain 'D' and resid 856 through 865 removed outlier: 3.919A pdb=" N ALA D 860 " --> pdb=" O LEU D 856 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 888 removed outlier: 3.828A pdb=" N ILE D 876 " --> pdb=" O ASP D 872 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE D 879 " --> pdb=" O ALA D 875 " (cutoff:3.500A) Processing helix chain 'D' and resid 889 through 892 removed outlier: 3.730A pdb=" N LEU D 892 " --> pdb=" O PRO D 889 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 889 through 892' Processing helix chain 'D' and resid 893 through 913 removed outlier: 3.877A pdb=" N VAL D 897 " --> pdb=" O TYR D 893 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP D 902 " --> pdb=" O ILE D 898 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE D 903 " --> pdb=" O LEU D 899 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE D 904 " --> pdb=" O SER D 900 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU D 905 " --> pdb=" O LEU D 901 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE D 906 " --> pdb=" O ASP D 902 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET D 911 " --> pdb=" O CYS D 907 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 934 removed outlier: 4.059A pdb=" N LYS D 923 " --> pdb=" O THR D 919 " (cutoff:3.500A) Processing helix chain 'D' and resid 934 through 953 removed outlier: 3.754A pdb=" N PHE D 939 " --> pdb=" O PHE D 935 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL D 946 " --> pdb=" O ALA D 942 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SER D 947 " --> pdb=" O VAL D 943 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N PHE D 948 " --> pdb=" O TRP D 944 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY D 949 " --> pdb=" O VAL D 945 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL D 950 " --> pdb=" O VAL D 946 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA D 951 " --> pdb=" O SER D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 954 through 956 No H-bonds generated for 'chain 'D' and resid 954 through 956' Processing helix chain 'D' and resid 964 through 969 removed outlier: 4.746A pdb=" N ARG D 968 " --> pdb=" O ASP D 964 " (cutoff:3.500A) Processing helix chain 'D' and resid 983 through 987 removed outlier: 4.313A pdb=" N ILE D 986 " --> pdb=" O PRO D 983 " (cutoff:3.500A) Processing helix chain 'D' and resid 1023 through 1040 removed outlier: 3.924A pdb=" N CYS D1030 " --> pdb=" O VAL D1026 " (cutoff:3.500A) Processing helix chain 'D' and resid 1040 through 1049 removed outlier: 3.747A pdb=" N LEU D1044 " --> pdb=" O LEU D1040 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE D1045 " --> pdb=" O LEU D1041 " (cutoff:3.500A) Processing helix chain 'D' and resid 1054 through 1075 removed outlier: 4.875A pdb=" N ASP D1060 " --> pdb=" O GLN D1056 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLN D1061 " --> pdb=" O GLU D1057 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE D1062 " --> pdb=" O HIS D1058 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU D1073 " --> pdb=" O ASP D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1081 through 1083 No H-bonds generated for 'chain 'D' and resid 1081 through 1083' Processing helix chain 'D' and resid 1084 through 1097 removed outlier: 4.458A pdb=" N SER D1088 " --> pdb=" O PHE D1084 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ILE D1094 " --> pdb=" O LEU D1090 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LYS D1095 " --> pdb=" O GLN D1091 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL D1097 " --> pdb=" O PHE D1093 " (cutoff:3.500A) Processing helix chain 'D' and resid 1114 through 1143 removed outlier: 3.540A pdb=" N TRP D1124 " --> pdb=" O ALA D1120 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN D1142 " --> pdb=" O PHE D1138 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG D1143 " --> pdb=" O GLN D1139 " (cutoff:3.500A) Processing helix chain 'D' and resid 1143 through 1163 removed outlier: 3.936A pdb=" N LYS D1147 " --> pdb=" O ARG D1143 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP D1156 " --> pdb=" O SER D1152 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP D1160 " --> pdb=" O ASP D1156 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LEU D1161 " --> pdb=" O ALA D1157 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU D1162 " --> pdb=" O MET D1158 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP D1163 " --> pdb=" O VAL D1159 " (cutoff:3.500A) Processing helix chain 'D' and resid 1258 through 1262 removed outlier: 3.615A pdb=" N VAL D1262 " --> pdb=" O ASN D1259 " (cutoff:3.500A) Processing helix chain 'D' and resid 1410 through 1419 removed outlier: 3.787A pdb=" N PHE D1414 " --> pdb=" O HIS D1410 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU D1415 " --> pdb=" O TRP D1411 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASN D1416 " --> pdb=" O PRO D1412 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU D1417 " --> pdb=" O SER D1413 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS D1419 " --> pdb=" O GLU D1415 " (cutoff:3.500A) Processing helix chain 'D' and resid 1454 through 1464 removed outlier: 4.102A pdb=" N ASN D1458 " --> pdb=" O ASP D1454 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG D1459 " --> pdb=" O VAL D1455 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU D1460 " --> pdb=" O GLU D1456 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASN D1461 " --> pdb=" O LEU D1457 " (cutoff:3.500A) Processing helix chain 'D' and resid 1485 through 1496 removed outlier: 3.556A pdb=" N LYS D1489 " --> pdb=" O TYR D1485 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR D1490 " --> pdb=" O ALA D1486 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU D1491 " --> pdb=" O ASN D1487 " (cutoff:3.500A) Processing helix chain 'D' and resid 1497 through 1499 No H-bonds generated for 'chain 'D' and resid 1497 through 1499' Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 70 Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 130 removed outlier: 6.040A pdb=" N THR A 238 " --> pdb=" O HIS A 283 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE A 285 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLY A 240 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL A 287 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA A 242 " --> pdb=" O VAL A 287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 175 removed outlier: 6.364A pdb=" N SER A 172 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LEU A 330 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR A 174 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N CYS A 327 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL A 353 " --> pdb=" O CYS A 327 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL A 329 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N CYS A 350 " --> pdb=" O THR A 417 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE A 419 " --> pdb=" O CYS A 350 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL A 352 " --> pdb=" O PHE A 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 1319 through 1320 removed outlier: 3.535A pdb=" N GLN A1320 " --> pdb=" O LEU A1323 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1347 through 1349 removed outlier: 6.647A pdb=" N THR A1347 " --> pdb=" O VAL A1443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 68 through 70 Processing sheet with id=AA7, first strand: chain 'B' and resid 127 through 130 removed outlier: 6.040A pdb=" N THR B 238 " --> pdb=" O HIS B 283 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE B 285 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLY B 240 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL B 287 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA B 242 " --> pdb=" O VAL B 287 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 172 through 175 removed outlier: 6.364A pdb=" N SER B 172 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N LEU B 330 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR B 174 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N CYS B 327 " --> pdb=" O VAL B 351 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL B 353 " --> pdb=" O CYS B 327 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL B 329 " --> pdb=" O VAL B 353 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N CYS B 350 " --> pdb=" O THR B 417 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE B 419 " --> pdb=" O CYS B 350 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL B 352 " --> pdb=" O PHE B 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 1319 through 1320 removed outlier: 3.536A pdb=" N GLN B1320 " --> pdb=" O LEU B1323 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1347 through 1349 removed outlier: 6.646A pdb=" N THR B1347 " --> pdb=" O VAL B1443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 68 through 70 Processing sheet with id=AB3, first strand: chain 'C' and resid 127 through 130 removed outlier: 6.040A pdb=" N THR C 238 " --> pdb=" O HIS C 283 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE C 285 " --> pdb=" O THR C 238 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLY C 240 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL C 287 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA C 242 " --> pdb=" O VAL C 287 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 172 through 175 removed outlier: 6.364A pdb=" N SER C 172 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LEU C 330 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR C 174 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N CYS C 327 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL C 353 " --> pdb=" O CYS C 327 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL C 329 " --> pdb=" O VAL C 353 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N CYS C 350 " --> pdb=" O THR C 417 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N PHE C 419 " --> pdb=" O CYS C 350 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL C 352 " --> pdb=" O PHE C 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 1319 through 1320 removed outlier: 3.536A pdb=" N GLN C1320 " --> pdb=" O LEU C1323 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 1347 through 1349 removed outlier: 6.646A pdb=" N THR C1347 " --> pdb=" O VAL C1443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 68 through 70 Processing sheet with id=AB8, first strand: chain 'D' and resid 127 through 130 removed outlier: 6.040A pdb=" N THR D 238 " --> pdb=" O HIS D 283 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ILE D 285 " --> pdb=" O THR D 238 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLY D 240 " --> pdb=" O ILE D 285 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL D 287 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA D 242 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 172 through 175 removed outlier: 6.363A pdb=" N SER D 172 " --> pdb=" O VAL D 328 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N LEU D 330 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR D 174 " --> pdb=" O LEU D 330 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N CYS D 327 " --> pdb=" O VAL D 351 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL D 353 " --> pdb=" O CYS D 327 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N VAL D 329 " --> pdb=" O VAL D 353 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS D 350 " --> pdb=" O THR D 417 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE D 419 " --> pdb=" O CYS D 350 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL D 352 " --> pdb=" O PHE D 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 1319 through 1320 removed outlier: 3.536A pdb=" N GLN D1320 " --> pdb=" O LEU D1323 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 1347 through 1349 removed outlier: 6.646A pdb=" N THR D1347 " --> pdb=" O VAL D1443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 1540 hydrogen bonds defined for protein. 4476 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.99 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11247 1.33 - 1.45: 7842 1.45 - 1.57: 23979 1.57 - 1.69: 40 1.69 - 1.81: 304 Bond restraints: 43412 Sorted by residual: bond pdb=" O3A DAT D1602 " pdb=" PB DAT D1602 " ideal model delta sigma weight residual 1.750 1.603 0.147 2.00e-02 2.50e+03 5.38e+01 bond pdb=" O3A DAT B1602 " pdb=" PB DAT B1602 " ideal model delta sigma weight residual 1.750 1.604 0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" O3A DAT A1602 " pdb=" PB DAT A1602 " ideal model delta sigma weight residual 1.750 1.604 0.146 2.00e-02 2.50e+03 5.34e+01 bond pdb=" O3A DAT C1602 " pdb=" PB DAT C1602 " ideal model delta sigma weight residual 1.750 1.604 0.146 2.00e-02 2.50e+03 5.31e+01 bond pdb=" O3B DAT B1602 " pdb=" PB DAT B1602 " ideal model delta sigma weight residual 1.521 1.604 -0.083 2.00e-02 2.50e+03 1.73e+01 ... (remaining 43407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.83: 58394 3.83 - 7.66: 578 7.66 - 11.48: 52 11.48 - 15.31: 8 15.31 - 19.14: 4 Bond angle restraints: 59036 Sorted by residual: angle pdb=" N SER C 974 " pdb=" CA SER C 974 " pdb=" C SER C 974 " ideal model delta sigma weight residual 113.18 121.14 -7.96 1.33e+00 5.65e-01 3.58e+01 angle pdb=" N SER B 974 " pdb=" CA SER B 974 " pdb=" C SER B 974 " ideal model delta sigma weight residual 113.18 121.11 -7.93 1.33e+00 5.65e-01 3.56e+01 angle pdb=" N SER D 974 " pdb=" CA SER D 974 " pdb=" C SER D 974 " ideal model delta sigma weight residual 113.18 121.10 -7.92 1.33e+00 5.65e-01 3.55e+01 angle pdb=" N SER A 974 " pdb=" CA SER A 974 " pdb=" C SER A 974 " ideal model delta sigma weight residual 113.18 121.07 -7.89 1.33e+00 5.65e-01 3.52e+01 angle pdb=" CB LYS D 404 " pdb=" CG LYS D 404 " pdb=" CD LYS D 404 " ideal model delta sigma weight residual 111.30 124.69 -13.39 2.30e+00 1.89e-01 3.39e+01 ... (remaining 59031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 22867 17.44 - 34.87: 2369 34.87 - 52.31: 421 52.31 - 69.75: 175 69.75 - 87.19: 108 Dihedral angle restraints: 25940 sinusoidal: 10456 harmonic: 15484 Sorted by residual: dihedral pdb=" CA PRO D1021 " pdb=" C PRO D1021 " pdb=" N GLU D1022 " pdb=" CA GLU D1022 " ideal model delta harmonic sigma weight residual 180.00 109.74 70.26 0 5.00e+00 4.00e-02 1.97e+02 dihedral pdb=" CA PRO C1021 " pdb=" C PRO C1021 " pdb=" N GLU C1022 " pdb=" CA GLU C1022 " ideal model delta harmonic sigma weight residual 180.00 109.77 70.23 0 5.00e+00 4.00e-02 1.97e+02 dihedral pdb=" CA PRO B1021 " pdb=" C PRO B1021 " pdb=" N GLU B1022 " pdb=" CA GLU B1022 " ideal model delta harmonic sigma weight residual 180.00 109.81 70.19 0 5.00e+00 4.00e-02 1.97e+02 ... (remaining 25937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 5614 0.066 - 0.132: 872 0.132 - 0.198: 100 0.198 - 0.264: 18 0.264 - 0.330: 8 Chirality restraints: 6612 Sorted by residual: chirality pdb=" CA HIS C 973 " pdb=" N HIS C 973 " pdb=" C HIS C 973 " pdb=" CB HIS C 973 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA HIS A 973 " pdb=" N HIS A 973 " pdb=" C HIS A 973 " pdb=" CB HIS A 973 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA HIS B 973 " pdb=" N HIS B 973 " pdb=" C HIS B 973 " pdb=" CB HIS B 973 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 6609 not shown) Planarity restraints: 7460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 63 " -0.112 5.00e-02 4.00e+02 1.75e-01 4.91e+01 pdb=" N PRO B 64 " 0.303 5.00e-02 4.00e+02 pdb=" CA PRO B 64 " -0.105 5.00e-02 4.00e+02 pdb=" CD PRO B 64 " -0.086 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 63 " -0.112 5.00e-02 4.00e+02 1.75e-01 4.91e+01 pdb=" N PRO C 64 " 0.303 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " -0.105 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " -0.086 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 63 " 0.112 5.00e-02 4.00e+02 1.75e-01 4.91e+01 pdb=" N PRO D 64 " -0.303 5.00e-02 4.00e+02 pdb=" CA PRO D 64 " 0.105 5.00e-02 4.00e+02 pdb=" CD PRO D 64 " 0.086 5.00e-02 4.00e+02 ... (remaining 7457 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 431 2.57 - 3.15: 35462 3.15 - 3.73: 67008 3.73 - 4.32: 86361 4.32 - 4.90: 137343 Nonbonded interactions: 326605 Sorted by model distance: nonbonded pdb=" OG1 THR A1025 " pdb=" O HIS B 973 " model vdw 1.986 3.040 nonbonded pdb=" NE2 GLN B 981 " pdb=" OE1 GLN C 981 " model vdw 1.991 3.120 nonbonded pdb=" N PHE B1020 " pdb=" OD2 ASP C 964 " model vdw 2.073 3.120 nonbonded pdb=" OG1 THR C 159 " pdb=" OE1 GLN C 160 " model vdw 2.099 3.040 nonbonded pdb=" OG1 THR B 159 " pdb=" OE1 GLN B 160 " model vdw 2.099 3.040 ... (remaining 326600 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 35.770 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5497 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 : 0.004 0.147 43424 Z= 0.214 Angle : 0.942 19.138 59036 Z= 0.505 Chirality : 0.050 0.330 6612 Planarity : 0.007 0.175 7460 Dihedral : 16.116 87.186 15908 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.99 % Favored : 88.52 % Rotamer: Outliers : 2.52 % Allowed : 0.99 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.11), residues: 5288 helix: -0.38 (0.11), residues: 2140 sheet: -0.66 (0.28), residues: 272 loop : -2.36 (0.12), residues: 2876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 634 TYR 0.027 0.001 TYR C 577 PHE 0.046 0.002 PHE A 848 TRP 0.046 0.002 TRP C 452 HIS 0.008 0.001 HIS D 684 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.21 (43412) covalent geometry : angle 0.94206 / 0.50 (59036) hydrogen bonds : bond 0.15290 / 10.69 ( 1540) hydrogen bonds : angle 6.64530 / 4.67 ( 4476) metal coordination : bond 0.00937 / 0.60 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10576 Ramachandran restraints generated. 5288 Oldfield, 0 Emsley, 5288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10576 Ramachandran restraints generated. 5288 Oldfield, 0 Emsley, 5288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 PHE cc_start: 0.8218 (t80) cc_final: 0.7951 (t80) REVERT: A 485 HIS cc_start: 0.8797 (m90) cc_final: 0.8485 (m90) REVERT: A 488 MET cc_start: 0.7584 (ptm) cc_final: 0.7077 (tmm) REVERT: A 571 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7593 (p0) REVERT: A 678 LEU cc_start: 0.9168 (tp) cc_final: 0.8057 (tp) REVERT: A 682 TYR cc_start: 0.7495 (m-80) cc_final: 0.7094 (m-80) REVERT: A 699 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8347 (pp20) REVERT: A 1063 TRP cc_start: 0.8173 (t-100) cc_final: 0.7760 (t-100) outliers start: 28 outliers final: 6 residues processed: 135 average time/residue: 0.0867 time to fit residues: 17.3223 Evaluate side-chains 101 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 394 optimal weight: 10.0000 chunk 430 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 265 optimal weight: 6.9990 chunk 523 optimal weight: 7.9990 chunk 497 optimal weight: 8.9990 chunk 414 optimal weight: 7.9990 chunk 310 optimal weight: 4.9990 chunk 488 optimal weight: 4.9990 chunk 366 optimal weight: 7.9990 chunk 223 optimal weight: 0.0040 overall best weight: 4.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 ASN ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS A 495 ASN ** A 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.139181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.109831 restraints weight = 80676.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.112949 restraints weight = 57379.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.114775 restraints weight = 44847.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.116676 restraints weight = 37623.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.117601 restraints weight = 33029.579| |-----------------------------------------------------------------------------| r_work (final): 0.4298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5837 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 43424 Z= 0.212 Angle : 0.811 14.686 59036 Z= 0.420 Chirality : 0.048 0.353 6612 Planarity : 0.007 0.143 7460 Dihedral : 9.322 67.321 6036 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.45 % Allowed : 10.97 % Favored : 88.58 % Rotamer: Outliers : 0.27 % Allowed : 5.59 % Favored : 94.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.11), residues: 5288 helix: -0.33 (0.11), residues: 2148 sheet: -0.77 (0.30), residues: 288 loop : -2.35 (0.11), residues: 2852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 223 TYR 0.024 0.002 TYR B 577 PHE 0.031 0.002 PHE B 225 TRP 0.022 0.002 TRP B 642 HIS 0.009 0.002 HIS B 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.21 (43412) covalent geometry : angle 0.81058 / 0.42 (59036) hydrogen bonds : bond 0.05369 / 3.72 ( 1540) hydrogen bonds : angle 5.27465 / 3.74 ( 4476) metal coordination : bond 0.00511 / 0.33 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10576 Ramachandran restraints generated. 5288 Oldfield, 0 Emsley, 5288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10576 Ramachandran restraints generated. 5288 Oldfield, 0 Emsley, 5288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 122 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 PHE cc_start: 0.7556 (t80) cc_final: 0.7324 (t80) REVERT: A 321 ILE cc_start: 0.3199 (mt) cc_final: 0.2813 (mt) REVERT: A 452 TRP cc_start: 0.9102 (t60) cc_final: 0.8880 (t60) REVERT: A 488 MET cc_start: 0.8154 (ptm) cc_final: 0.7839 (tmm) REVERT: A 678 LEU cc_start: 0.9364 (tp) cc_final: 0.8253 (tp) REVERT: A 682 TYR cc_start: 0.8119 (m-80) cc_final: 0.7650 (m-80) REVERT: A 684 HIS cc_start: 0.9183 (m90) cc_final: 0.8976 (m90) REVERT: A 720 LEU cc_start: 0.9501 (tp) cc_final: 0.9288 (tp) REVERT: A 729 PHE cc_start: 0.8885 (t80) cc_final: 0.8418 (t80) REVERT: A 804 LEU cc_start: 0.9057 (tt) cc_final: 0.8812 (pp) REVERT: A 1063 TRP cc_start: 0.8348 (t-100) cc_final: 0.7849 (t-100) outliers start: 3 outliers final: 1 residues processed: 124 average time/residue: 0.0840 time to fit residues: 15.2109 Evaluate side-chains 95 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 311 optimal weight: 6.9990 chunk 145 optimal weight: 0.9990 chunk 219 optimal weight: 0.9980 chunk 265 optimal weight: 50.0000 chunk 470 optimal weight: 0.4980 chunk 300 optimal weight: 0.5980 chunk 287 optimal weight: 0.4980 chunk 150 optimal weight: 3.9990 chunk 261 optimal weight: 8.9990 chunk 231 optimal weight: 6.9990 chunk 426 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS A1061 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.141417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.112165 restraints weight = 82292.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.115507 restraints weight = 56495.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.116785 restraints weight = 43129.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.119359 restraints weight = 36738.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.120593 restraints weight = 31615.343| |-----------------------------------------------------------------------------| r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5720 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 43424 Z= 0.140 Angle : 0.747 15.185 59036 Z= 0.383 Chirality : 0.046 0.332 6612 Planarity : 0.006 0.151 7460 Dihedral : 7.825 64.431 6036 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.45 % Allowed : 10.36 % Favored : 89.18 % Rotamer: Outliers : 0.18 % Allowed : 3.61 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.11), residues: 5288 helix: 0.04 (0.11), residues: 2196 sheet: -0.76 (0.30), residues: 288 loop : -2.37 (0.12), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 192 TYR 0.022 0.001 TYR A 577 PHE 0.026 0.001 PHE C 225 TRP 0.014 0.001 TRP A 642 HIS 0.010 0.001 HIS C 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (43412) covalent geometry : angle 0.74735 / 0.38 (59036) hydrogen bonds : bond 0.04304 / 2.99 ( 1540) hydrogen bonds : angle 4.73328 / 3.37 ( 4476) metal coordination : bond 0.00743 / 0.48 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10576 Ramachandran restraints generated. 5288 Oldfield, 0 Emsley, 5288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10576 Ramachandran restraints generated. 5288 Oldfield, 0 Emsley, 5288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 PHE cc_start: 0.7422 (t80) cc_final: 0.7190 (t80) REVERT: A 308 PHE cc_start: 0.8647 (t80) cc_final: 0.8380 (t80) REVERT: A 321 ILE cc_start: 0.3152 (mt) cc_final: 0.2606 (mt) REVERT: A 458 LEU cc_start: 0.9133 (tt) cc_final: 0.8897 (pp) REVERT: A 488 MET cc_start: 0.7930 (ptm) cc_final: 0.7646 (tmm) REVERT: A 678 LEU cc_start: 0.9293 (tp) cc_final: 0.9091 (tp) REVERT: A 718 LEU cc_start: 0.9361 (mt) cc_final: 0.9151 (mt) REVERT: A 844 MET cc_start: 0.8803 (tpp) cc_final: 0.8482 (tmm) REVERT: A 1047 MET cc_start: 0.8236 (ppp) cc_final: 0.8021 (ppp) REVERT: A 1063 TRP cc_start: 0.8374 (t-100) cc_final: 0.7976 (t-100) outliers start: 2 outliers final: 1 residues processed: 123 average time/residue: 0.0874 time to fit residues: 15.9680 Evaluate side-chains 92 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 47 optimal weight: 2.9990 chunk 326 optimal weight: 0.9980 chunk 349 optimal weight: 4.9990 chunk 312 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 398 optimal weight: 0.0020 chunk 181 optimal weight: 0.0060 chunk 22 optimal weight: 5.9990 chunk 249 optimal weight: 0.8980 chunk 417 optimal weight: 0.0770 chunk 344 optimal weight: 10.0000 overall best weight: 0.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.141966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.113800 restraints weight = 84684.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.116977 restraints weight = 58999.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.119214 restraints weight = 45019.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.121003 restraints weight = 36941.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.121906 restraints weight = 32278.723| |-----------------------------------------------------------------------------| r_work (final): 0.4357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5694 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 43424 Z= 0.135 Angle : 0.734 15.108 59036 Z= 0.375 Chirality : 0.046 0.350 6612 Planarity : 0.006 0.136 7460 Dihedral : 7.386 60.958 6036 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.45 % Allowed : 10.14 % Favored : 89.41 % Rotamer: Outliers : 0.18 % Allowed : 4.51 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.11), residues: 5288 helix: 0.14 (0.11), residues: 2216 sheet: -0.70 (0.31), residues: 288 loop : -2.40 (0.12), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 185 TYR 0.021 0.001 TYR D 577 PHE 0.021 0.001 PHE B 848 TRP 0.017 0.001 TRP A 452 HIS 0.014 0.001 HIS C 958 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (43412) covalent geometry : angle 0.73404 / 0.38 (59036) hydrogen bonds : bond 0.04133 / 2.87 ( 1540) hydrogen bonds : angle 4.65364 / 3.31 ( 4476) metal coordination : bond 0.00703 / 0.45 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10576 Ramachandran restraints generated. 5288 Oldfield, 0 Emsley, 5288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10576 Ramachandran restraints generated. 5288 Oldfield, 0 Emsley, 5288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 121 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 PHE cc_start: 0.7410 (t80) cc_final: 0.7181 (t80) REVERT: A 308 PHE cc_start: 0.8652 (t80) cc_final: 0.8372 (t80) REVERT: A 321 ILE cc_start: 0.3124 (mt) cc_final: 0.2519 (mt) REVERT: A 458 LEU cc_start: 0.9107 (tt) cc_final: 0.8867 (pp) REVERT: A 684 HIS cc_start: 0.9141 (m90) cc_final: 0.8904 (m90) REVERT: A 718 LEU cc_start: 0.9259 (mt) cc_final: 0.9051 (mt) REVERT: A 903 PHE cc_start: 0.8817 (t80) cc_final: 0.8580 (t80) REVERT: A 1047 MET cc_start: 0.8212 (ppp) cc_final: 0.7985 (ppp) REVERT: A 1063 TRP cc_start: 0.8400 (t-100) cc_final: 0.7969 (t-100) outliers start: 2 outliers final: 1 residues processed: 122 average time/residue: 0.0927 time to fit residues: 16.5597 Evaluate side-chains 96 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 216 optimal weight: 9.9990 chunk 458 optimal weight: 0.5980 chunk 176 optimal weight: 0.0870 chunk 403 optimal weight: 0.2980 chunk 348 optimal weight: 8.9990 chunk 456 optimal weight: 3.9990 chunk 312 optimal weight: 4.9990 chunk 59 optimal weight: 0.0570 chunk 342 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 264 optimal weight: 5.9990 overall best weight: 1.0078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 ASN ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN ** A 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.140281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.118114 restraints weight = 84540.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.120733 restraints weight = 58353.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.122741 restraints weight = 43253.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.124113 restraints weight = 34458.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.125088 restraints weight = 28860.206| |-----------------------------------------------------------------------------| r_work (final): 0.4390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5507 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 43424 Z= 0.135 Angle : 0.735 15.463 59036 Z= 0.374 Chirality : 0.046 0.351 6612 Planarity : 0.006 0.155 7460 Dihedral : 7.141 60.172 6036 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.45 % Allowed : 10.14 % Favored : 89.41 % Rotamer: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.12), residues: 5288 helix: 0.27 (0.11), residues: 2212 sheet: -0.75 (0.30), residues: 288 loop : -2.38 (0.12), residues: 2788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 192 TYR 0.022 0.001 TYR C 577 PHE 0.015 0.001 PHE D1048 TRP 0.012 0.001 TRP A 965 HIS 0.008 0.001 HIS C 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (43412) covalent geometry : angle 0.73540 / 0.37 (59036) hydrogen bonds : bond 0.03994 / 2.78 ( 1540) hydrogen bonds : angle 4.68122 / 3.33 ( 4476) metal coordination : bond 0.00612 / 0.39 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10576 Ramachandran restraints generated. 5288 Oldfield, 0 Emsley, 5288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10576 Ramachandran restraints generated. 5288 Oldfield, 0 Emsley, 5288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 PHE cc_start: 0.8561 (t80) cc_final: 0.8318 (t80) REVERT: A 311 GLU cc_start: 0.9422 (mp0) cc_final: 0.9182 (mp0) REVERT: A 458 LEU cc_start: 0.9108 (tt) cc_final: 0.8847 (pp) REVERT: A 485 HIS cc_start: 0.9028 (m90) cc_final: 0.8585 (m170) REVERT: A 1042 ASN cc_start: 0.8842 (t0) cc_final: 0.8474 (m-40) REVERT: A 1047 MET cc_start: 0.7936 (ppp) cc_final: 0.7717 (ppp) REVERT: A 1063 TRP cc_start: 0.8334 (t-100) cc_final: 0.7856 (t-100) REVERT: A 1065 PHE cc_start: 0.7607 (t80) cc_final: 0.7159 (t80) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.0802 time to fit residues: 14.1833 Evaluate side-chains 95 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 417 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 324 optimal weight: 0.0010 chunk 270 optimal weight: 0.7980 chunk 434 optimal weight: 0.0000 chunk 245 optimal weight: 0.0070 chunk 260 optimal weight: 0.1980 chunk 17 optimal weight: 0.0020 chunk 388 optimal weight: 9.9990 chunk 450 optimal weight: 0.3980 chunk 363 optimal weight: 0.9990 overall best weight: 0.0416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN ** A 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.141565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.119016 restraints weight = 84175.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.121702 restraints weight = 57782.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.123837 restraints weight = 42799.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.125141 restraints weight = 34062.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.126298 restraints weight = 28562.595| |-----------------------------------------------------------------------------| r_work (final): 0.4415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5446 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 43424 Z= 0.132 Angle : 0.737 15.843 59036 Z= 0.374 Chirality : 0.047 0.350 6612 Planarity : 0.005 0.142 7460 Dihedral : 6.964 60.218 6036 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.83 % Favored : 89.71 % Rotamer: Outliers : 0.09 % Allowed : 1.98 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.12), residues: 5288 helix: 0.30 (0.11), residues: 2232 sheet: -0.73 (0.30), residues: 288 loop : -2.30 (0.12), residues: 2768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 185 TYR 0.023 0.001 TYR A 577 PHE 0.015 0.001 PHE C1048 TRP 0.014 0.001 TRP A 743 HIS 0.008 0.001 HIS B 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (43412) covalent geometry : angle 0.73701 / 0.37 (59036) hydrogen bonds : bond 0.03903 / 2.71 ( 1540) hydrogen bonds : angle 4.60948 / 3.28 ( 4476) metal coordination : bond 0.00719 / 0.46 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10576 Ramachandran restraints generated. 5288 Oldfield, 0 Emsley, 5288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10576 Ramachandran restraints generated. 5288 Oldfield, 0 Emsley, 5288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 MET cc_start: 0.5749 (mmt) cc_final: 0.5307 (mmt) REVERT: A 311 GLU cc_start: 0.9399 (mp0) cc_final: 0.9136 (mp0) REVERT: A 458 LEU cc_start: 0.9131 (tt) cc_final: 0.8868 (pp) REVERT: A 485 HIS cc_start: 0.9013 (m90) cc_final: 0.8585 (m170) REVERT: A 684 HIS cc_start: 0.9175 (t70) cc_final: 0.8845 (t70) REVERT: A 718 LEU cc_start: 0.9333 (mt) cc_final: 0.9103 (mt) REVERT: A 844 MET cc_start: 0.9203 (mmp) cc_final: 0.8942 (ttp) REVERT: A 1042 ASN cc_start: 0.8766 (t0) cc_final: 0.8406 (m-40) REVERT: A 1047 MET cc_start: 0.7733 (ppp) cc_final: 0.7340 (ppp) REVERT: A 1063 TRP cc_start: 0.8310 (t-100) cc_final: 0.7804 (t-100) REVERT: A 1328 MET cc_start: -0.3906 (tpt) cc_final: -0.4341 (mpp) outliers start: 1 outliers final: 1 residues processed: 115 average time/residue: 0.0785 time to fit residues: 13.3752 Evaluate side-chains 92 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 470 optimal weight: 0.7980 chunk 301 optimal weight: 1.9990 chunk 174 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 226 optimal weight: 4.9990 chunk 143 optimal weight: 0.0770 chunk 127 optimal weight: 0.2980 chunk 21 optimal weight: 0.0000 chunk 492 optimal weight: 4.9990 chunk 197 optimal weight: 0.0770 overall best weight: 0.2500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 ASN A 506 ASN ** A 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.142170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.113345 restraints weight = 84355.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.116781 restraints weight = 58610.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.118903 restraints weight = 45329.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.120734 restraints weight = 37613.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.121793 restraints weight = 32976.522| |-----------------------------------------------------------------------------| r_work (final): 0.4354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5697 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 43424 Z= 0.131 Angle : 0.731 15.652 59036 Z= 0.374 Chirality : 0.046 0.346 6612 Planarity : 0.005 0.135 7460 Dihedral : 6.842 59.282 6036 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.45 % Allowed : 10.44 % Favored : 89.11 % Rotamer: Outliers : 0.09 % Allowed : 2.43 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.12), residues: 5288 helix: 0.28 (0.11), residues: 2232 sheet: -0.68 (0.30), residues: 288 loop : -2.25 (0.12), residues: 2768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 700 TYR 0.022 0.001 TYR C 577 PHE 0.015 0.001 PHE C1048 TRP 0.012 0.001 TRP A 743 HIS 0.008 0.001 HIS A 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (43412) covalent geometry : angle 0.73136 / 0.37 (59036) hydrogen bonds : bond 0.03948 / 2.73 ( 1540) hydrogen bonds : angle 4.65218 / 3.32 ( 4476) metal coordination : bond 0.00710 / 0.46 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10576 Ramachandran restraints generated. 5288 Oldfield, 0 Emsley, 5288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10576 Ramachandran restraints generated. 5288 Oldfield, 0 Emsley, 5288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 PHE cc_start: 0.8387 (t80) cc_final: 0.8079 (t80) REVERT: A 485 HIS cc_start: 0.8929 (m90) cc_final: 0.8554 (m170) REVERT: A 684 HIS cc_start: 0.9156 (t70) cc_final: 0.8843 (t70) REVERT: A 718 LEU cc_start: 0.9291 (mt) cc_final: 0.9062 (mt) REVERT: A 844 MET cc_start: 0.9223 (mmp) cc_final: 0.8941 (ttp) REVERT: A 1042 ASN cc_start: 0.8832 (t0) cc_final: 0.8489 (m-40) REVERT: A 1047 MET cc_start: 0.7923 (ppp) cc_final: 0.7543 (ppp) REVERT: A 1065 PHE cc_start: 0.7754 (t80) cc_final: 0.7390 (t80) REVERT: A 1328 MET cc_start: -0.3977 (tpt) cc_final: -0.4383 (mpp) REVERT: A 1429 MET cc_start: 0.3056 (tpt) cc_final: 0.2605 (tpt) outliers start: 1 outliers final: 1 residues processed: 110 average time/residue: 0.0810 time to fit residues: 13.3426 Evaluate side-chains 93 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 122 optimal weight: 0.9980 chunk 366 optimal weight: 0.0030 chunk 204 optimal weight: 3.9990 chunk 297 optimal weight: 8.9990 chunk 227 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 440 optimal weight: 7.9990 chunk 38 optimal weight: 0.5980 chunk 481 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 381 optimal weight: 1.9990 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN ** A 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.140875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.111833 restraints weight = 83786.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.115175 restraints weight = 58759.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.117534 restraints weight = 45648.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.119213 restraints weight = 37923.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.120283 restraints weight = 33101.492| |-----------------------------------------------------------------------------| r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5767 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 43424 Z= 0.132 Angle : 0.741 16.056 59036 Z= 0.375 Chirality : 0.047 0.353 6612 Planarity : 0.006 0.164 7460 Dihedral : 6.775 59.328 6036 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.45 % Allowed : 10.06 % Favored : 89.49 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.12), residues: 5288 helix: 0.36 (0.11), residues: 2208 sheet: -0.69 (0.30), residues: 288 loop : -2.27 (0.12), residues: 2792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 358 TYR 0.022 0.001 TYR A 577 PHE 0.015 0.001 PHE D1048 TRP 0.011 0.001 TRP A 743 HIS 0.008 0.001 HIS B 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (43412) covalent geometry : angle 0.74134 / 0.38 (59036) hydrogen bonds : bond 0.03844 / 2.66 ( 1540) hydrogen bonds : angle 4.74463 / 3.39 ( 4476) metal coordination : bond 0.00656 / 0.42 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10576 Ramachandran restraints generated. 5288 Oldfield, 0 Emsley, 5288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10576 Ramachandran restraints generated. 5288 Oldfield, 0 Emsley, 5288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 MET cc_start: 0.7825 (mmt) cc_final: 0.7493 (mmt) REVERT: A 308 PHE cc_start: 0.8440 (t80) cc_final: 0.8113 (t80) REVERT: A 485 HIS cc_start: 0.8917 (m90) cc_final: 0.8595 (m170) REVERT: A 684 HIS cc_start: 0.9145 (t70) cc_final: 0.8787 (t70) REVERT: A 718 LEU cc_start: 0.9297 (mt) cc_final: 0.9065 (mt) REVERT: A 844 MET cc_start: 0.9248 (mmp) cc_final: 0.8896 (tmm) REVERT: A 1042 ASN cc_start: 0.8834 (t0) cc_final: 0.8499 (m-40) REVERT: A 1047 MET cc_start: 0.7818 (ppp) cc_final: 0.7435 (ppp) REVERT: A 1429 MET cc_start: 0.3388 (tpt) cc_final: 0.2757 (tpt) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.0940 time to fit residues: 14.6925 Evaluate side-chains 91 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 305 optimal weight: 0.8980 chunk 244 optimal weight: 0.0030 chunk 313 optimal weight: 0.0870 chunk 152 optimal weight: 0.0030 chunk 357 optimal weight: 7.9990 chunk 183 optimal weight: 8.9990 chunk 47 optimal weight: 0.0870 chunk 2 optimal weight: 0.0470 chunk 495 optimal weight: 7.9990 chunk 383 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.0454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 446 HIS A 495 ASN ** A 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.162610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.139869 restraints weight = 89849.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.142683 restraints weight = 62650.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.144529 restraints weight = 47608.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.146014 restraints weight = 38892.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.146745 restraints weight = 33420.050| |-----------------------------------------------------------------------------| r_work (final): 0.4452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5451 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 43424 Z= 0.130 Angle : 0.735 15.556 59036 Z= 0.371 Chirality : 0.047 0.350 6612 Planarity : 0.005 0.156 7460 Dihedral : 6.656 58.754 6036 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.61 % Favored : 89.94 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.12), residues: 5288 helix: 0.44 (0.11), residues: 2212 sheet: -0.70 (0.30), residues: 292 loop : -2.27 (0.12), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 223 TYR 0.024 0.001 TYR C 577 PHE 0.014 0.001 PHE D1048 TRP 0.015 0.001 TRP A 743 HIS 0.008 0.001 HIS A 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (43412) covalent geometry : angle 0.73546 / 0.37 (59036) hydrogen bonds : bond 0.03764 / 2.60 ( 1540) hydrogen bonds : angle 4.62283 / 3.31 ( 4476) metal coordination : bond 0.01919 / 1.25 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10576 Ramachandran restraints generated. 5288 Oldfield, 0 Emsley, 5288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10576 Ramachandran restraints generated. 5288 Oldfield, 0 Emsley, 5288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 MET cc_start: 0.6644 (mmt) cc_final: 0.6187 (mmt) REVERT: A 308 PHE cc_start: 0.8347 (t80) cc_final: 0.8027 (t80) REVERT: A 485 HIS cc_start: 0.8935 (m90) cc_final: 0.8602 (m170) REVERT: A 678 LEU cc_start: 0.9349 (tp) cc_final: 0.8349 (tp) REVERT: A 682 TYR cc_start: 0.7878 (m-80) cc_final: 0.7553 (m-80) REVERT: A 684 HIS cc_start: 0.9106 (t70) cc_final: 0.8747 (t70) REVERT: A 718 LEU cc_start: 0.9340 (mt) cc_final: 0.9113 (mt) REVERT: A 804 LEU cc_start: 0.8841 (tt) cc_final: 0.8638 (pp) REVERT: A 844 MET cc_start: 0.9256 (mmp) cc_final: 0.8902 (tmm) REVERT: A 1042 ASN cc_start: 0.8740 (t0) cc_final: 0.8429 (m-40) REVERT: A 1047 MET cc_start: 0.7506 (ppp) cc_final: 0.7105 (ppp) REVERT: A 1429 MET cc_start: 0.1917 (tpt) cc_final: 0.1034 (tpt) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.0843 time to fit residues: 13.7714 Evaluate side-chains 91 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 323 optimal weight: 0.9980 chunk 221 optimal weight: 2.9990 chunk 499 optimal weight: 5.9990 chunk 134 optimal weight: 0.0870 chunk 328 optimal weight: 6.9990 chunk 59 optimal weight: 0.5980 chunk 447 optimal weight: 4.9990 chunk 40 optimal weight: 0.3980 chunk 120 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN ** A 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.141461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.115709 restraints weight = 87314.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.118069 restraints weight = 62993.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.119941 restraints weight = 49879.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.121346 restraints weight = 41129.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.122255 restraints weight = 35454.132| |-----------------------------------------------------------------------------| r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5653 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 43424 Z= 0.127 Angle : 0.732 15.743 59036 Z= 0.371 Chirality : 0.047 0.350 6612 Planarity : 0.005 0.149 7460 Dihedral : 6.596 58.340 6036 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.76 % Favored : 89.71 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.12), residues: 5288 helix: 0.46 (0.11), residues: 2208 sheet: -0.65 (0.30), residues: 292 loop : -2.23 (0.12), residues: 2788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 700 TYR 0.023 0.001 TYR C 577 PHE 0.013 0.001 PHE B1048 TRP 0.012 0.001 TRP A 743 HIS 0.008 0.001 HIS C 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (43412) covalent geometry : angle 0.73161 / 0.37 (59036) hydrogen bonds : bond 0.03783 / 2.63 ( 1540) hydrogen bonds : angle 4.62651 / 3.30 ( 4476) metal coordination : bond 0.01119 / 0.72 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10576 Ramachandran restraints generated. 5288 Oldfield, 0 Emsley, 5288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10576 Ramachandran restraints generated. 5288 Oldfield, 0 Emsley, 5288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 MET cc_start: 0.7337 (mmt) cc_final: 0.6903 (mmt) REVERT: A 308 PHE cc_start: 0.8358 (t80) cc_final: 0.8022 (t80) REVERT: A 485 HIS cc_start: 0.8906 (m90) cc_final: 0.8645 (m170) REVERT: A 684 HIS cc_start: 0.9124 (t70) cc_final: 0.8738 (t70) REVERT: A 718 LEU cc_start: 0.9048 (mt) cc_final: 0.8789 (mt) REVERT: A 844 MET cc_start: 0.9258 (mmp) cc_final: 0.8885 (tmm) REVERT: A 1042 ASN cc_start: 0.8753 (t0) cc_final: 0.8441 (m-40) REVERT: A 1047 MET cc_start: 0.7466 (ppp) cc_final: 0.7071 (ppp) REVERT: A 1127 TYR cc_start: 0.8541 (t80) cc_final: 0.8158 (t80) REVERT: A 1429 MET cc_start: 0.3255 (tpt) cc_final: 0.2752 (tpt) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.0911 time to fit residues: 14.8706 Evaluate side-chains 91 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 504 optimal weight: 0.0980 chunk 230 optimal weight: 0.6980 chunk 345 optimal weight: 3.9990 chunk 113 optimal weight: 0.0020 chunk 502 optimal weight: 0.9990 chunk 121 optimal weight: 0.4980 chunk 250 optimal weight: 6.9990 chunk 403 optimal weight: 0.0070 chunk 192 optimal weight: 0.5980 chunk 72 optimal weight: 0.0020 chunk 0 optimal weight: 4.9990 overall best weight: 0.1214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.141644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.120248 restraints weight = 83973.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.122918 restraints weight = 57693.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.124918 restraints weight = 43078.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.126155 restraints weight = 34328.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.127221 restraints weight = 28679.719| |-----------------------------------------------------------------------------| r_work (final): 0.4436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5414 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 43424 Z= 0.131 Angle : 0.742 15.812 59036 Z= 0.375 Chirality : 0.047 0.348 6612 Planarity : 0.005 0.146 7460 Dihedral : 6.521 58.214 6036 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.68 % Favored : 89.79 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.12), residues: 5288 helix: 0.44 (0.11), residues: 2224 sheet: -0.63 (0.30), residues: 292 loop : -2.19 (0.12), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 634 TYR 0.024 0.001 TYR B 577 PHE 0.015 0.001 PHE B 903 TRP 0.015 0.001 TRP A 452 HIS 0.008 0.001 HIS C 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (43412) covalent geometry : angle 0.74168 / 0.38 (59036) hydrogen bonds : bond 0.03811 / 2.64 ( 1540) hydrogen bonds : angle 4.63364 / 3.31 ( 4476) metal coordination : bond 0.01060 / 0.68 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4048.62 seconds wall clock time: 71 minutes 48.49 seconds (4308.49 seconds total)