Starting phenix.real_space_refine on Tue Sep 15 20:58:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6baa_7073/09_2026/6baa_7073.cif Found real_map, /net/cci-nas-00/data/ceres_data/6baa_7073/09_2026/6baa_7073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6baa_7073/09_2026/6baa_7073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6baa_7073/09_2026/6baa_7073.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6baa_7073/09_2026/6baa_7073.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6baa_7073/09_2026/6baa_7073.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6baa_7073/09_2026/6baa_7073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6baa_7073/09_2026/6baa_7073.map" } resolution = 3.63 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= 0.167 sd= 1.369 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 188 5.16 5 Cl 4 4.86 5 C 28728 2.51 5 N 7884 2.21 5 O 8036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.21s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 44852 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2507 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 306} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 8642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1317, 8642 Classifications: {'peptide': 1317} Incomplete info: {'truncation_to_alanine': 531} Link IDs: {'PTRANS': 41, 'TRANS': 1275} Chain breaks: 9 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1814 Unresolved non-hydrogen angles: 2312 Unresolved non-hydrogen dihedrals: 1455 Unresolved non-hydrogen chiralities: 225 Planarities with less than four sites: {'GLU:plan': 30, 'ASN:plan1': 19, 'HIS:plan': 13, 'TYR:plan': 6, 'ARG:plan': 33, 'ASP:plan': 33, 'GLN:plan1': 31, 'TRP:plan': 6, 'PHE:plan': 26} Unresolved non-hydrogen planarities: 882 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'GBM': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, F, G, H Time building chain proxies: 13.15, per 1000 atoms: 0.29 Number of scatterers: 44852 At special positions: 0 Unit cell: (233.415, 233.415, 141.075, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 4 17.00 S 188 16.00 P 12 15.00 O 8036 8.00 N 7884 7.00 C 28728 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.02 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 142 " distance=2.02 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.02 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.05 Conformation dependent library (CDL) restraints added in 2.2 seconds 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12384 Finding SS restraints... Secondary structure from input PDB file: 260 helices and 40 sheets defined 66.1% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 58 through 66 Processing helix chain 'A' and resid 67 through 98 removed outlier: 3.635A pdb=" N VAL A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 129 Processing helix chain 'A' and resid 142 through 171 Processing helix chain 'A' and resid 174 through 179 removed outlier: 3.505A pdb=" N ALA A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 removed outlier: 4.280A pdb=" N HIS A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'B' and resid 53 through 58 Processing helix chain 'B' and resid 58 through 66 Processing helix chain 'B' and resid 67 through 98 removed outlier: 3.635A pdb=" N VAL B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 129 Processing helix chain 'B' and resid 142 through 171 Processing helix chain 'B' and resid 174 through 179 removed outlier: 3.505A pdb=" N ALA B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 removed outlier: 4.280A pdb=" N HIS B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 345 through 352 Processing helix chain 'C' and resid 53 through 58 Processing helix chain 'C' and resid 58 through 66 Processing helix chain 'C' and resid 67 through 98 removed outlier: 3.635A pdb=" N VAL C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 129 Processing helix chain 'C' and resid 142 through 171 Processing helix chain 'C' and resid 174 through 179 removed outlier: 3.505A pdb=" N ALA C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 278 removed outlier: 4.280A pdb=" N HIS C 277 " --> pdb=" O SER C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 333 No H-bonds generated for 'chain 'C' and resid 331 through 333' Processing helix chain 'C' and resid 345 through 352 Processing helix chain 'D' and resid 53 through 58 Processing helix chain 'D' and resid 58 through 66 Processing helix chain 'D' and resid 67 through 98 removed outlier: 3.635A pdb=" N VAL D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 129 Processing helix chain 'D' and resid 142 through 171 Processing helix chain 'D' and resid 174 through 179 removed outlier: 3.504A pdb=" N ALA D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 278 removed outlier: 4.280A pdb=" N HIS D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 333 No H-bonds generated for 'chain 'D' and resid 331 through 333' Processing helix chain 'D' and resid 345 through 352 Processing helix chain 'E' and resid 13 through 18 removed outlier: 3.504A pdb=" N ASP E 18 " --> pdb=" O ALA E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 57 removed outlier: 3.506A pdb=" N VAL E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) Proline residue: E 35 - end of helix Proline residue: E 45 - end of helix Processing helix chain 'E' and resid 60 through 64 removed outlier: 3.942A pdb=" N THR E 64 " --> pdb=" O HIS E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 97 Processing helix chain 'E' and resid 103 through 106 Processing helix chain 'E' and resid 107 through 130 removed outlier: 3.915A pdb=" N TYR E 124 " --> pdb=" O SER E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 160 Processing helix chain 'E' and resid 166 through 194 removed outlier: 3.601A pdb=" N GLU E 186 " --> pdb=" O LEU E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 211 Processing helix chain 'E' and resid 212 through 214 No H-bonds generated for 'chain 'E' and resid 212 through 214' Processing helix chain 'E' and resid 223 through 230 Processing helix chain 'E' and resid 230 through 243 removed outlier: 3.684A pdb=" N ASN E 234 " --> pdb=" O TYR E 230 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA E 235 " --> pdb=" O TRP E 231 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE E 236 " --> pdb=" O TRP E 232 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS E 238 " --> pdb=" O ASN E 234 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR E 239 " --> pdb=" O ALA E 235 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA E 240 " --> pdb=" O PHE E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 272 Processing helix chain 'E' and resid 286 through 327 removed outlier: 5.775A pdb=" N ARG E 297 " --> pdb=" O HIS E 293 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ARG E 298 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU E 301 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER E 302 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY E 316 " --> pdb=" O LEU E 312 " (cutoff:3.500A) Proline residue: E 317 - end of helix Processing helix chain 'E' and resid 355 through 401 Processing helix chain 'E' and resid 415 through 434 removed outlier: 3.657A pdb=" N THR E 425 " --> pdb=" O VAL E 421 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASN E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 457 removed outlier: 3.510A pdb=" N THR E 440 " --> pdb=" O PRO E 436 " (cutoff:3.500A) Proline residue: E 442 - end of helix Processing helix chain 'E' and resid 459 through 505 removed outlier: 3.867A pdb=" N GLY E 463 " --> pdb=" O SER E 459 " (cutoff:3.500A) Proline residue: E 472 - end of helix Processing helix chain 'E' and resid 505 through 513 Processing helix chain 'E' and resid 514 through 566 removed outlier: 3.950A pdb=" N PHE E 518 " --> pdb=" O TRP E 514 " (cutoff:3.500A) Proline residue: E 551 - end of helix removed outlier: 3.574A pdb=" N VAL E 555 " --> pdb=" O PRO E 551 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE E 566 " --> pdb=" O HIS E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 586 removed outlier: 3.805A pdb=" N ALA E 578 " --> pdb=" O SER E 574 " (cutoff:3.500A) Processing helix chain 'E' and resid 587 through 615 removed outlier: 4.299A pdb=" N SER E 595 " --> pdb=" O PHE E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 718 through 727 Processing helix chain 'E' and resid 784 through 790 Processing helix chain 'E' and resid 795 through 806 Processing helix chain 'E' and resid 808 through 814 Processing helix chain 'E' and resid 817 through 820 Processing helix chain 'E' and resid 831 through 847 removed outlier: 3.684A pdb=" N GLN E 847 " --> pdb=" O ALA E 843 " (cutoff:3.500A) Processing helix chain 'E' and resid 861 through 874 Processing helix chain 'E' and resid 893 through 897 removed outlier: 3.680A pdb=" N ALA E 897 " --> pdb=" O LEU E 894 " (cutoff:3.500A) Processing helix chain 'E' and resid 913 through 920 Processing helix chain 'E' and resid 922 through 928 Processing helix chain 'E' and resid 1001 through 1009 removed outlier: 3.756A pdb=" N LEU E1005 " --> pdb=" O CYS E1001 " (cutoff:3.500A) Processing helix chain 'E' and resid 1009 through 1039 removed outlier: 3.632A pdb=" N LEU E1013 " --> pdb=" O GLY E1009 " (cutoff:3.500A) Processing helix chain 'E' and resid 1065 through 1078 removed outlier: 3.971A pdb=" N VAL E1077 " --> pdb=" O SER E1073 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU E1078 " --> pdb=" O LEU E1074 " (cutoff:3.500A) Processing helix chain 'E' and resid 1080 through 1108 Processing helix chain 'E' and resid 1109 through 1116 removed outlier: 3.835A pdb=" N PHE E1113 " --> pdb=" O PRO E1109 " (cutoff:3.500A) Processing helix chain 'E' and resid 1118 through 1135 removed outlier: 3.970A pdb=" N ARG E1124 " --> pdb=" O SER E1120 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS E1129 " --> pdb=" O PHE E1125 " (cutoff:3.500A) Processing helix chain 'E' and resid 1135 through 1161 Processing helix chain 'E' and resid 1163 through 1210 removed outlier: 4.412A pdb=" N ALA E1167 " --> pdb=" O VAL E1163 " (cutoff:3.500A) Proline residue: E1170 - end of helix removed outlier: 4.013A pdb=" N LEU E1198 " --> pdb=" O ASP E1194 " (cutoff:3.500A) Proline residue: E1199 - end of helix Processing helix chain 'E' and resid 1210 through 1218 Processing helix chain 'E' and resid 1219 through 1272 Processing helix chain 'E' and resid 1278 through 1317 removed outlier: 4.408A pdb=" N SER E1292 " --> pdb=" O ALA E1288 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASN E1293 " --> pdb=" O LEU E1289 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN E1296 " --> pdb=" O SER E1292 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY E1310 " --> pdb=" O GLU E1306 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA E1311 " --> pdb=" O ILE E1307 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL E1312 " --> pdb=" O GLN E1308 " (cutoff:3.500A) Processing helix chain 'E' and resid 1384 through 1393 Processing helix chain 'E' and resid 1411 through 1413 No H-bonds generated for 'chain 'E' and resid 1411 through 1413' Processing helix chain 'E' and resid 1414 through 1421 removed outlier: 3.678A pdb=" N SER E1420 " --> pdb=" O HIS E1416 " (cutoff:3.500A) Processing helix chain 'E' and resid 1435 through 1440 Processing helix chain 'E' and resid 1447 through 1458 Processing helix chain 'E' and resid 1460 through 1466 Processing helix chain 'E' and resid 1469 through 1473 Processing helix chain 'E' and resid 1475 through 1479 removed outlier: 3.584A pdb=" N GLY E1479 " --> pdb=" O THR E1476 " (cutoff:3.500A) Processing helix chain 'E' and resid 1483 through 1499 Processing helix chain 'E' and resid 1513 through 1529 Processing helix chain 'E' and resid 1542 through 1546 removed outlier: 3.783A pdb=" N SER E1545 " --> pdb=" O THR E1542 " (cutoff:3.500A) Processing helix chain 'E' and resid 1565 through 1570 Processing helix chain 'E' and resid 1571 through 1577 Processing helix chain 'F' and resid 13 through 18 removed outlier: 3.504A pdb=" N ASP F 18 " --> pdb=" O ALA F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 57 removed outlier: 3.506A pdb=" N VAL F 34 " --> pdb=" O ALA F 30 " (cutoff:3.500A) Proline residue: F 35 - end of helix Proline residue: F 45 - end of helix Processing helix chain 'F' and resid 60 through 64 removed outlier: 3.942A pdb=" N THR F 64 " --> pdb=" O HIS F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 97 Processing helix chain 'F' and resid 103 through 106 Processing helix chain 'F' and resid 107 through 130 removed outlier: 3.915A pdb=" N TYR F 124 " --> pdb=" O SER F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 160 Processing helix chain 'F' and resid 166 through 194 removed outlier: 3.601A pdb=" N GLU F 186 " --> pdb=" O LEU F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 211 Processing helix chain 'F' and resid 212 through 214 No H-bonds generated for 'chain 'F' and resid 212 through 214' Processing helix chain 'F' and resid 223 through 230 Processing helix chain 'F' and resid 230 through 243 removed outlier: 3.685A pdb=" N ASN F 234 " --> pdb=" O TYR F 230 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA F 235 " --> pdb=" O TRP F 231 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE F 236 " --> pdb=" O TRP F 232 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS F 238 " --> pdb=" O ASN F 234 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR F 239 " --> pdb=" O ALA F 235 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA F 240 " --> pdb=" O PHE F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 272 Processing helix chain 'F' and resid 286 through 327 removed outlier: 5.775A pdb=" N ARG F 297 " --> pdb=" O HIS F 293 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ARG F 298 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU F 301 " --> pdb=" O ARG F 297 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER F 302 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY F 316 " --> pdb=" O LEU F 312 " (cutoff:3.500A) Proline residue: F 317 - end of helix Processing helix chain 'F' and resid 355 through 401 Processing helix chain 'F' and resid 415 through 434 removed outlier: 3.657A pdb=" N THR F 425 " --> pdb=" O VAL F 421 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASN F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 457 removed outlier: 3.510A pdb=" N THR F 440 " --> pdb=" O PRO F 436 " (cutoff:3.500A) Proline residue: F 442 - end of helix Processing helix chain 'F' and resid 459 through 505 removed outlier: 3.867A pdb=" N GLY F 463 " --> pdb=" O SER F 459 " (cutoff:3.500A) Proline residue: F 472 - end of helix Processing helix chain 'F' and resid 505 through 513 Processing helix chain 'F' and resid 514 through 566 removed outlier: 3.950A pdb=" N PHE F 518 " --> pdb=" O TRP F 514 " (cutoff:3.500A) Proline residue: F 551 - end of helix removed outlier: 3.574A pdb=" N VAL F 555 " --> pdb=" O PRO F 551 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE F 566 " --> pdb=" O HIS F 562 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 586 removed outlier: 3.805A pdb=" N ALA F 578 " --> pdb=" O SER F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 587 through 615 removed outlier: 4.299A pdb=" N SER F 595 " --> pdb=" O PHE F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 718 through 727 Processing helix chain 'F' and resid 784 through 790 Processing helix chain 'F' and resid 795 through 806 Processing helix chain 'F' and resid 808 through 814 Processing helix chain 'F' and resid 817 through 820 Processing helix chain 'F' and resid 831 through 847 removed outlier: 3.684A pdb=" N GLN F 847 " --> pdb=" O ALA F 843 " (cutoff:3.500A) Processing helix chain 'F' and resid 861 through 874 Processing helix chain 'F' and resid 893 through 897 removed outlier: 3.680A pdb=" N ALA F 897 " --> pdb=" O LEU F 894 " (cutoff:3.500A) Processing helix chain 'F' and resid 913 through 920 Processing helix chain 'F' and resid 922 through 928 Processing helix chain 'F' and resid 1001 through 1009 removed outlier: 3.756A pdb=" N LEU F1005 " --> pdb=" O CYS F1001 " (cutoff:3.500A) Processing helix chain 'F' and resid 1009 through 1039 removed outlier: 3.632A pdb=" N LEU F1013 " --> pdb=" O GLY F1009 " (cutoff:3.500A) Processing helix chain 'F' and resid 1065 through 1078 removed outlier: 3.971A pdb=" N VAL F1077 " --> pdb=" O SER F1073 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU F1078 " --> pdb=" O LEU F1074 " (cutoff:3.500A) Processing helix chain 'F' and resid 1080 through 1108 Processing helix chain 'F' and resid 1109 through 1116 removed outlier: 3.835A pdb=" N PHE F1113 " --> pdb=" O PRO F1109 " (cutoff:3.500A) Processing helix chain 'F' and resid 1118 through 1135 removed outlier: 3.970A pdb=" N ARG F1124 " --> pdb=" O SER F1120 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS F1129 " --> pdb=" O PHE F1125 " (cutoff:3.500A) Processing helix chain 'F' and resid 1135 through 1161 Processing helix chain 'F' and resid 1163 through 1210 removed outlier: 4.412A pdb=" N ALA F1167 " --> pdb=" O VAL F1163 " (cutoff:3.500A) Proline residue: F1170 - end of helix removed outlier: 4.012A pdb=" N LEU F1198 " --> pdb=" O ASP F1194 " (cutoff:3.500A) Proline residue: F1199 - end of helix Processing helix chain 'F' and resid 1210 through 1218 Processing helix chain 'F' and resid 1219 through 1272 Processing helix chain 'F' and resid 1278 through 1317 removed outlier: 4.408A pdb=" N SER F1292 " --> pdb=" O ALA F1288 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASN F1293 " --> pdb=" O LEU F1289 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN F1296 " --> pdb=" O SER F1292 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY F1310 " --> pdb=" O GLU F1306 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA F1311 " --> pdb=" O ILE F1307 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL F1312 " --> pdb=" O GLN F1308 " (cutoff:3.500A) Processing helix chain 'F' and resid 1384 through 1393 Processing helix chain 'F' and resid 1411 through 1413 No H-bonds generated for 'chain 'F' and resid 1411 through 1413' Processing helix chain 'F' and resid 1414 through 1421 removed outlier: 3.678A pdb=" N SER F1420 " --> pdb=" O HIS F1416 " (cutoff:3.500A) Processing helix chain 'F' and resid 1435 through 1440 Processing helix chain 'F' and resid 1447 through 1458 Processing helix chain 'F' and resid 1460 through 1466 Processing helix chain 'F' and resid 1469 through 1473 Processing helix chain 'F' and resid 1475 through 1479 removed outlier: 3.584A pdb=" N GLY F1479 " --> pdb=" O THR F1476 " (cutoff:3.500A) Processing helix chain 'F' and resid 1483 through 1499 Processing helix chain 'F' and resid 1513 through 1529 Processing helix chain 'F' and resid 1542 through 1546 removed outlier: 3.782A pdb=" N SER F1545 " --> pdb=" O THR F1542 " (cutoff:3.500A) Processing helix chain 'F' and resid 1565 through 1570 Processing helix chain 'F' and resid 1571 through 1577 Processing helix chain 'G' and resid 13 through 18 removed outlier: 3.504A pdb=" N ASP G 18 " --> pdb=" O ALA G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 57 removed outlier: 3.506A pdb=" N VAL G 34 " --> pdb=" O ALA G 30 " (cutoff:3.500A) Proline residue: G 35 - end of helix Proline residue: G 45 - end of helix Processing helix chain 'G' and resid 60 through 64 removed outlier: 3.942A pdb=" N THR G 64 " --> pdb=" O HIS G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 97 Processing helix chain 'G' and resid 103 through 106 Processing helix chain 'G' and resid 107 through 130 removed outlier: 3.915A pdb=" N TYR G 124 " --> pdb=" O SER G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 160 Processing helix chain 'G' and resid 166 through 194 removed outlier: 3.601A pdb=" N GLU G 186 " --> pdb=" O LEU G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 211 Processing helix chain 'G' and resid 212 through 214 No H-bonds generated for 'chain 'G' and resid 212 through 214' Processing helix chain 'G' and resid 223 through 230 Processing helix chain 'G' and resid 230 through 243 removed outlier: 3.684A pdb=" N ASN G 234 " --> pdb=" O TYR G 230 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA G 235 " --> pdb=" O TRP G 231 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE G 236 " --> pdb=" O TRP G 232 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS G 238 " --> pdb=" O ASN G 234 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR G 239 " --> pdb=" O ALA G 235 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA G 240 " --> pdb=" O PHE G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 272 Processing helix chain 'G' and resid 286 through 327 removed outlier: 5.775A pdb=" N ARG G 297 " --> pdb=" O HIS G 293 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ARG G 298 " --> pdb=" O ALA G 294 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU G 301 " --> pdb=" O ARG G 297 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER G 302 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY G 316 " --> pdb=" O LEU G 312 " (cutoff:3.500A) Proline residue: G 317 - end of helix Processing helix chain 'G' and resid 355 through 401 Processing helix chain 'G' and resid 415 through 434 removed outlier: 3.657A pdb=" N THR G 425 " --> pdb=" O VAL G 421 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASN G 426 " --> pdb=" O ALA G 422 " (cutoff:3.500A) Processing helix chain 'G' and resid 436 through 457 removed outlier: 3.510A pdb=" N THR G 440 " --> pdb=" O PRO G 436 " (cutoff:3.500A) Proline residue: G 442 - end of helix Processing helix chain 'G' and resid 459 through 505 removed outlier: 3.867A pdb=" N GLY G 463 " --> pdb=" O SER G 459 " (cutoff:3.500A) Proline residue: G 472 - end of helix Processing helix chain 'G' and resid 505 through 513 Processing helix chain 'G' and resid 514 through 566 removed outlier: 3.950A pdb=" N PHE G 518 " --> pdb=" O TRP G 514 " (cutoff:3.500A) Proline residue: G 551 - end of helix removed outlier: 3.574A pdb=" N VAL G 555 " --> pdb=" O PRO G 551 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE G 566 " --> pdb=" O HIS G 562 " (cutoff:3.500A) Processing helix chain 'G' and resid 572 through 586 removed outlier: 3.806A pdb=" N ALA G 578 " --> pdb=" O SER G 574 " (cutoff:3.500A) Processing helix chain 'G' and resid 587 through 615 removed outlier: 4.299A pdb=" N SER G 595 " --> pdb=" O PHE G 591 " (cutoff:3.500A) Processing helix chain 'G' and resid 718 through 727 Processing helix chain 'G' and resid 784 through 790 Processing helix chain 'G' and resid 795 through 806 Processing helix chain 'G' and resid 808 through 814 Processing helix chain 'G' and resid 817 through 820 Processing helix chain 'G' and resid 831 through 847 removed outlier: 3.684A pdb=" N GLN G 847 " --> pdb=" O ALA G 843 " (cutoff:3.500A) Processing helix chain 'G' and resid 861 through 874 Processing helix chain 'G' and resid 893 through 897 removed outlier: 3.680A pdb=" N ALA G 897 " --> pdb=" O LEU G 894 " (cutoff:3.500A) Processing helix chain 'G' and resid 913 through 920 Processing helix chain 'G' and resid 922 through 928 Processing helix chain 'G' and resid 1001 through 1009 removed outlier: 3.756A pdb=" N LEU G1005 " --> pdb=" O CYS G1001 " (cutoff:3.500A) Processing helix chain 'G' and resid 1009 through 1039 removed outlier: 3.632A pdb=" N LEU G1013 " --> pdb=" O GLY G1009 " (cutoff:3.500A) Processing helix chain 'G' and resid 1065 through 1078 removed outlier: 3.971A pdb=" N VAL G1077 " --> pdb=" O SER G1073 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU G1078 " --> pdb=" O LEU G1074 " (cutoff:3.500A) Processing helix chain 'G' and resid 1080 through 1108 Processing helix chain 'G' and resid 1109 through 1116 removed outlier: 3.835A pdb=" N PHE G1113 " --> pdb=" O PRO G1109 " (cutoff:3.500A) Processing helix chain 'G' and resid 1118 through 1135 removed outlier: 3.970A pdb=" N ARG G1124 " --> pdb=" O SER G1120 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS G1129 " --> pdb=" O PHE G1125 " (cutoff:3.500A) Processing helix chain 'G' and resid 1135 through 1161 Processing helix chain 'G' and resid 1163 through 1210 removed outlier: 4.412A pdb=" N ALA G1167 " --> pdb=" O VAL G1163 " (cutoff:3.500A) Proline residue: G1170 - end of helix removed outlier: 4.013A pdb=" N LEU G1198 " --> pdb=" O ASP G1194 " (cutoff:3.500A) Proline residue: G1199 - end of helix Processing helix chain 'G' and resid 1210 through 1218 Processing helix chain 'G' and resid 1219 through 1272 Processing helix chain 'G' and resid 1278 through 1317 removed outlier: 4.408A pdb=" N SER G1292 " --> pdb=" O ALA G1288 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASN G1293 " --> pdb=" O LEU G1289 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN G1296 " --> pdb=" O SER G1292 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY G1310 " --> pdb=" O GLU G1306 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA G1311 " --> pdb=" O ILE G1307 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL G1312 " --> pdb=" O GLN G1308 " (cutoff:3.500A) Processing helix chain 'G' and resid 1384 through 1393 Processing helix chain 'G' and resid 1411 through 1413 No H-bonds generated for 'chain 'G' and resid 1411 through 1413' Processing helix chain 'G' and resid 1414 through 1421 removed outlier: 3.678A pdb=" N SER G1420 " --> pdb=" O HIS G1416 " (cutoff:3.500A) Processing helix chain 'G' and resid 1435 through 1440 Processing helix chain 'G' and resid 1447 through 1458 Processing helix chain 'G' and resid 1460 through 1466 Processing helix chain 'G' and resid 1469 through 1473 Processing helix chain 'G' and resid 1475 through 1479 removed outlier: 3.584A pdb=" N GLY G1479 " --> pdb=" O THR G1476 " (cutoff:3.500A) Processing helix chain 'G' and resid 1483 through 1499 Processing helix chain 'G' and resid 1513 through 1529 Processing helix chain 'G' and resid 1542 through 1546 removed outlier: 3.782A pdb=" N SER G1545 " --> pdb=" O THR G1542 " (cutoff:3.500A) Processing helix chain 'G' and resid 1565 through 1570 Processing helix chain 'G' and resid 1571 through 1577 Processing helix chain 'H' and resid 13 through 18 removed outlier: 3.505A pdb=" N ASP H 18 " --> pdb=" O ALA H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 57 removed outlier: 3.505A pdb=" N VAL H 34 " --> pdb=" O ALA H 30 " (cutoff:3.500A) Proline residue: H 35 - end of helix Proline residue: H 45 - end of helix Processing helix chain 'H' and resid 60 through 64 removed outlier: 3.942A pdb=" N THR H 64 " --> pdb=" O HIS H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 97 Processing helix chain 'H' and resid 103 through 106 Processing helix chain 'H' and resid 107 through 130 removed outlier: 3.915A pdb=" N TYR H 124 " --> pdb=" O SER H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 160 Processing helix chain 'H' and resid 166 through 194 removed outlier: 3.602A pdb=" N GLU H 186 " --> pdb=" O LEU H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 211 Processing helix chain 'H' and resid 212 through 214 No H-bonds generated for 'chain 'H' and resid 212 through 214' Processing helix chain 'H' and resid 223 through 230 Processing helix chain 'H' and resid 230 through 243 removed outlier: 3.684A pdb=" N ASN H 234 " --> pdb=" O TYR H 230 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA H 235 " --> pdb=" O TRP H 231 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE H 236 " --> pdb=" O TRP H 232 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS H 238 " --> pdb=" O ASN H 234 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR H 239 " --> pdb=" O ALA H 235 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA H 240 " --> pdb=" O PHE H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 272 Processing helix chain 'H' and resid 286 through 327 removed outlier: 5.775A pdb=" N ARG H 297 " --> pdb=" O HIS H 293 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ARG H 298 " --> pdb=" O ALA H 294 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU H 301 " --> pdb=" O ARG H 297 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER H 302 " --> pdb=" O ARG H 298 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY H 316 " --> pdb=" O LEU H 312 " (cutoff:3.500A) Proline residue: H 317 - end of helix Processing helix chain 'H' and resid 355 through 401 Processing helix chain 'H' and resid 415 through 434 removed outlier: 3.658A pdb=" N THR H 425 " --> pdb=" O VAL H 421 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASN H 426 " --> pdb=" O ALA H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 436 through 457 removed outlier: 3.510A pdb=" N THR H 440 " --> pdb=" O PRO H 436 " (cutoff:3.500A) Proline residue: H 442 - end of helix Processing helix chain 'H' and resid 459 through 505 removed outlier: 3.868A pdb=" N GLY H 463 " --> pdb=" O SER H 459 " (cutoff:3.500A) Proline residue: H 472 - end of helix Processing helix chain 'H' and resid 505 through 513 Processing helix chain 'H' and resid 514 through 566 removed outlier: 3.950A pdb=" N PHE H 518 " --> pdb=" O TRP H 514 " (cutoff:3.500A) Proline residue: H 551 - end of helix removed outlier: 3.574A pdb=" N VAL H 555 " --> pdb=" O PRO H 551 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE H 566 " --> pdb=" O HIS H 562 " (cutoff:3.500A) Processing helix chain 'H' and resid 572 through 586 removed outlier: 3.805A pdb=" N ALA H 578 " --> pdb=" O SER H 574 " (cutoff:3.500A) Processing helix chain 'H' and resid 587 through 615 removed outlier: 4.298A pdb=" N SER H 595 " --> pdb=" O PHE H 591 " (cutoff:3.500A) Processing helix chain 'H' and resid 718 through 727 Processing helix chain 'H' and resid 784 through 790 Processing helix chain 'H' and resid 795 through 806 Processing helix chain 'H' and resid 808 through 814 Processing helix chain 'H' and resid 817 through 820 Processing helix chain 'H' and resid 831 through 847 removed outlier: 3.684A pdb=" N GLN H 847 " --> pdb=" O ALA H 843 " (cutoff:3.500A) Processing helix chain 'H' and resid 861 through 874 Processing helix chain 'H' and resid 893 through 897 removed outlier: 3.681A pdb=" N ALA H 897 " --> pdb=" O LEU H 894 " (cutoff:3.500A) Processing helix chain 'H' and resid 913 through 920 Processing helix chain 'H' and resid 922 through 928 Processing helix chain 'H' and resid 1001 through 1009 removed outlier: 3.756A pdb=" N LEU H1005 " --> pdb=" O CYS H1001 " (cutoff:3.500A) Processing helix chain 'H' and resid 1009 through 1039 removed outlier: 3.632A pdb=" N LEU H1013 " --> pdb=" O GLY H1009 " (cutoff:3.500A) Processing helix chain 'H' and resid 1065 through 1078 removed outlier: 3.971A pdb=" N VAL H1077 " --> pdb=" O SER H1073 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU H1078 " --> pdb=" O LEU H1074 " (cutoff:3.500A) Processing helix chain 'H' and resid 1080 through 1108 Processing helix chain 'H' and resid 1109 through 1116 removed outlier: 3.835A pdb=" N PHE H1113 " --> pdb=" O PRO H1109 " (cutoff:3.500A) Processing helix chain 'H' and resid 1118 through 1135 removed outlier: 3.970A pdb=" N ARG H1124 " --> pdb=" O SER H1120 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS H1129 " --> pdb=" O PHE H1125 " (cutoff:3.500A) Processing helix chain 'H' and resid 1135 through 1161 Processing helix chain 'H' and resid 1163 through 1210 removed outlier: 4.413A pdb=" N ALA H1167 " --> pdb=" O VAL H1163 " (cutoff:3.500A) Proline residue: H1170 - end of helix removed outlier: 4.013A pdb=" N LEU H1198 " --> pdb=" O ASP H1194 " (cutoff:3.500A) Proline residue: H1199 - end of helix Processing helix chain 'H' and resid 1210 through 1218 Processing helix chain 'H' and resid 1219 through 1272 Processing helix chain 'H' and resid 1278 through 1317 removed outlier: 4.407A pdb=" N SER H1292 " --> pdb=" O ALA H1288 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASN H1293 " --> pdb=" O LEU H1289 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN H1296 " --> pdb=" O SER H1292 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY H1310 " --> pdb=" O GLU H1306 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA H1311 " --> pdb=" O ILE H1307 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL H1312 " --> pdb=" O GLN H1308 " (cutoff:3.500A) Processing helix chain 'H' and resid 1384 through 1393 Processing helix chain 'H' and resid 1411 through 1413 No H-bonds generated for 'chain 'H' and resid 1411 through 1413' Processing helix chain 'H' and resid 1414 through 1421 removed outlier: 3.678A pdb=" N SER H1420 " --> pdb=" O HIS H1416 " (cutoff:3.500A) Processing helix chain 'H' and resid 1435 through 1440 Processing helix chain 'H' and resid 1447 through 1458 Processing helix chain 'H' and resid 1460 through 1466 Processing helix chain 'H' and resid 1469 through 1473 Processing helix chain 'H' and resid 1475 through 1479 removed outlier: 3.584A pdb=" N GLY H1479 " --> pdb=" O THR H1476 " (cutoff:3.500A) Processing helix chain 'H' and resid 1483 through 1499 Processing helix chain 'H' and resid 1513 through 1529 Processing helix chain 'H' and resid 1542 through 1546 removed outlier: 3.782A pdb=" N SER H1545 " --> pdb=" O THR H1542 " (cutoff:3.500A) Processing helix chain 'H' and resid 1565 through 1570 Processing helix chain 'H' and resid 1571 through 1577 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 47 Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA3, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA4, first strand: chain 'A' and resid 230 through 238 removed outlier: 4.783A pdb=" N LEU A 233 " --> pdb=" O ARG A 221 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ARG A 221 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLN A 235 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N VAL A 219 " --> pdb=" O GLN A 235 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP A 237 " --> pdb=" O MET A 217 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N MET A 217 " --> pdb=" O ASP A 237 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N SER A 212 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N VAL A 290 " --> pdb=" O SER A 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 313 through 315 Processing sheet with id=AA6, first strand: chain 'A' and resid 319 through 321 removed outlier: 6.457A pdb=" N TYR A 326 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LYS D 47 " --> pdb=" O TYR A 326 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL A 328 " --> pdb=" O LYS D 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 44 through 47 Processing sheet with id=AA8, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AA9, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AB1, first strand: chain 'B' and resid 230 through 238 removed outlier: 4.783A pdb=" N LEU B 233 " --> pdb=" O ARG B 221 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ARG B 221 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLN B 235 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL B 219 " --> pdb=" O GLN B 235 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP B 237 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N MET B 217 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N SER B 212 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N VAL B 290 " --> pdb=" O SER B 212 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 313 through 315 Processing sheet with id=AB3, first strand: chain 'C' and resid 44 through 47 Processing sheet with id=AB4, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AB5, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AB6, first strand: chain 'C' and resid 230 through 238 removed outlier: 4.783A pdb=" N LEU C 233 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ARG C 221 " --> pdb=" O LEU C 233 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLN C 235 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N VAL C 219 " --> pdb=" O GLN C 235 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP C 237 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N MET C 217 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N SER C 212 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N VAL C 290 " --> pdb=" O SER C 212 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 313 through 315 Processing sheet with id=AB8, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AB9, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AC1, first strand: chain 'D' and resid 230 through 238 removed outlier: 4.783A pdb=" N LEU D 233 " --> pdb=" O ARG D 221 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ARG D 221 " --> pdb=" O LEU D 233 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLN D 235 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N VAL D 219 " --> pdb=" O GLN D 235 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP D 237 " --> pdb=" O MET D 217 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N MET D 217 " --> pdb=" O ASP D 237 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N SER D 212 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N VAL D 290 " --> pdb=" O SER D 212 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 313 through 315 Processing sheet with id=AC3, first strand: chain 'E' and resid 696 through 703 removed outlier: 5.165A pdb=" N SER E 697 " --> pdb=" O PHE E 686 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N PHE E 686 " --> pdb=" O SER E 697 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ILE E 701 " --> pdb=" O ILE E 682 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ILE E 682 " --> pdb=" O ILE E 701 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE E 703 " --> pdb=" O GLN E 680 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLN E 680 " --> pdb=" O ILE E 703 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 771 through 773 removed outlier: 5.772A pdb=" N VAL E 851 " --> pdb=" O VAL E 885 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL E 887 " --> pdb=" O VAL E 851 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LEU E 853 " --> pdb=" O VAL E 887 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N THR E 709 " --> pdb=" O LEU E 886 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE E 900 " --> pdb=" O GLU E 911 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU E 911 " --> pdb=" O ILE E 900 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ALA E 902 " --> pdb=" O GLN E 909 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 782 through 783 Processing sheet with id=AC6, first strand: chain 'E' and resid 1362 through 1369 removed outlier: 6.882A pdb=" N LYS E1363 " --> pdb=" O SER E1351 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N SER E1351 " --> pdb=" O LYS E1363 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL E1365 " --> pdb=" O ASN E1349 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE E1347 " --> pdb=" O ILE E1404 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE E1404 " --> pdb=" O ILE E1347 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ASN E1349 " --> pdb=" O ARG E1402 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ARG E1402 " --> pdb=" O ASN E1349 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 1502 through 1506 removed outlier: 6.331A pdb=" N PHE E1503 " --> pdb=" O VAL E1534 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ILE E1536 " --> pdb=" O PHE E1503 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N MET E1505 " --> pdb=" O ILE E1536 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE E1375 " --> pdb=" O THR E1535 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LYS E1374 " --> pdb=" O LEU E1548 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N MET E1550 " --> pdb=" O LYS E1374 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLY E1376 " --> pdb=" O MET E1550 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU E1552 " --> pdb=" O GLY E1376 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N CYS E1378 " --> pdb=" O LEU E1552 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL E1549 " --> pdb=" O PHE E1560 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE E1560 " --> pdb=" O VAL E1549 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL E1551 " --> pdb=" O LEU E1558 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 696 through 703 removed outlier: 5.165A pdb=" N SER F 697 " --> pdb=" O PHE F 686 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE F 686 " --> pdb=" O SER F 697 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ILE F 701 " --> pdb=" O ILE F 682 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ILE F 682 " --> pdb=" O ILE F 701 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE F 703 " --> pdb=" O GLN F 680 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLN F 680 " --> pdb=" O ILE F 703 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 771 through 773 removed outlier: 5.772A pdb=" N VAL F 851 " --> pdb=" O VAL F 885 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL F 887 " --> pdb=" O VAL F 851 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LEU F 853 " --> pdb=" O VAL F 887 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N THR F 709 " --> pdb=" O LEU F 886 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE F 900 " --> pdb=" O GLU F 911 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU F 911 " --> pdb=" O ILE F 900 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ALA F 902 " --> pdb=" O GLN F 909 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 782 through 783 Processing sheet with id=AD2, first strand: chain 'F' and resid 1362 through 1369 removed outlier: 6.882A pdb=" N LYS F1363 " --> pdb=" O SER F1351 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N SER F1351 " --> pdb=" O LYS F1363 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL F1365 " --> pdb=" O ASN F1349 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE F1347 " --> pdb=" O ILE F1404 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE F1404 " --> pdb=" O ILE F1347 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ASN F1349 " --> pdb=" O ARG F1402 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ARG F1402 " --> pdb=" O ASN F1349 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 1502 through 1506 removed outlier: 6.331A pdb=" N PHE F1503 " --> pdb=" O VAL F1534 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ILE F1536 " --> pdb=" O PHE F1503 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N MET F1505 " --> pdb=" O ILE F1536 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE F1375 " --> pdb=" O THR F1535 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LYS F1374 " --> pdb=" O LEU F1548 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N MET F1550 " --> pdb=" O LYS F1374 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLY F1376 " --> pdb=" O MET F1550 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU F1552 " --> pdb=" O GLY F1376 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N CYS F1378 " --> pdb=" O LEU F1552 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL F1549 " --> pdb=" O PHE F1560 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE F1560 " --> pdb=" O VAL F1549 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL F1551 " --> pdb=" O LEU F1558 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 696 through 703 removed outlier: 5.165A pdb=" N SER G 697 " --> pdb=" O PHE G 686 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE G 686 " --> pdb=" O SER G 697 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ILE G 701 " --> pdb=" O ILE G 682 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ILE G 682 " --> pdb=" O ILE G 701 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ILE G 703 " --> pdb=" O GLN G 680 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLN G 680 " --> pdb=" O ILE G 703 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 771 through 773 removed outlier: 5.772A pdb=" N VAL G 851 " --> pdb=" O VAL G 885 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL G 887 " --> pdb=" O VAL G 851 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LEU G 853 " --> pdb=" O VAL G 887 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N THR G 709 " --> pdb=" O LEU G 886 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE G 900 " --> pdb=" O GLU G 911 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU G 911 " --> pdb=" O ILE G 900 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ALA G 902 " --> pdb=" O GLN G 909 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 782 through 783 Processing sheet with id=AD7, first strand: chain 'G' and resid 1362 through 1369 removed outlier: 6.881A pdb=" N LYS G1363 " --> pdb=" O SER G1351 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N SER G1351 " --> pdb=" O LYS G1363 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL G1365 " --> pdb=" O ASN G1349 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE G1347 " --> pdb=" O ILE G1404 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE G1404 " --> pdb=" O ILE G1347 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ASN G1349 " --> pdb=" O ARG G1402 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ARG G1402 " --> pdb=" O ASN G1349 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 1502 through 1506 removed outlier: 6.331A pdb=" N PHE G1503 " --> pdb=" O VAL G1534 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ILE G1536 " --> pdb=" O PHE G1503 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N MET G1505 " --> pdb=" O ILE G1536 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE G1375 " --> pdb=" O THR G1535 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LYS G1374 " --> pdb=" O LEU G1548 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N MET G1550 " --> pdb=" O LYS G1374 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLY G1376 " --> pdb=" O MET G1550 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU G1552 " --> pdb=" O GLY G1376 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N CYS G1378 " --> pdb=" O LEU G1552 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL G1549 " --> pdb=" O PHE G1560 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE G1560 " --> pdb=" O VAL G1549 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL G1551 " --> pdb=" O LEU G1558 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 696 through 703 removed outlier: 5.165A pdb=" N SER H 697 " --> pdb=" O PHE H 686 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE H 686 " --> pdb=" O SER H 697 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ILE H 701 " --> pdb=" O ILE H 682 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ILE H 682 " --> pdb=" O ILE H 701 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ILE H 703 " --> pdb=" O GLN H 680 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLN H 680 " --> pdb=" O ILE H 703 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 771 through 773 removed outlier: 5.772A pdb=" N VAL H 851 " --> pdb=" O VAL H 885 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL H 887 " --> pdb=" O VAL H 851 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU H 853 " --> pdb=" O VAL H 887 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N THR H 709 " --> pdb=" O LEU H 886 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE H 900 " --> pdb=" O GLU H 911 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU H 911 " --> pdb=" O ILE H 900 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ALA H 902 " --> pdb=" O GLN H 909 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 782 through 783 Processing sheet with id=AE3, first strand: chain 'H' and resid 1362 through 1369 removed outlier: 6.882A pdb=" N LYS H1363 " --> pdb=" O SER H1351 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER H1351 " --> pdb=" O LYS H1363 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL H1365 " --> pdb=" O ASN H1349 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE H1347 " --> pdb=" O ILE H1404 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILE H1404 " --> pdb=" O ILE H1347 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ASN H1349 " --> pdb=" O ARG H1402 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ARG H1402 " --> pdb=" O ASN H1349 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 1502 through 1506 removed outlier: 6.331A pdb=" N PHE H1503 " --> pdb=" O VAL H1534 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ILE H1536 " --> pdb=" O PHE H1503 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N MET H1505 " --> pdb=" O ILE H1536 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE H1375 " --> pdb=" O THR H1535 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LYS H1374 " --> pdb=" O LEU H1548 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N MET H1550 " --> pdb=" O LYS H1374 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLY H1376 " --> pdb=" O MET H1550 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU H1552 " --> pdb=" O GLY H1376 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N CYS H1378 " --> pdb=" O LEU H1552 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL H1549 " --> pdb=" O PHE H1560 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE H1560 " --> pdb=" O VAL H1549 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL H1551 " --> pdb=" O LEU H1558 " (cutoff:3.500A) 3341 hydrogen bonds defined for protein. 9783 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: 12.30 Time building geometry restraints manager: 5.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 7328 1.31 - 1.44: 12027 1.44 - 1.57: 26061 1.57 - 1.69: 28 1.69 - 1.82: 292 Bond restraints: 45736 Sorted by residual: bond pdb=" O5 GBM E2001 " pdb=" S2 GBM E2001 " ideal model delta sigma weight residual 1.448 1.650 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" O5 GBM F2001 " pdb=" S2 GBM F2001 " ideal model delta sigma weight residual 1.448 1.650 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" O5 GBM G2001 " pdb=" S2 GBM G2001 " ideal model delta sigma weight residual 1.448 1.650 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" O5 GBM H2001 " pdb=" S2 GBM H2001 " ideal model delta sigma weight residual 1.448 1.650 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" O4 GBM E2001 " pdb=" S2 GBM E2001 " ideal model delta sigma weight residual 1.453 1.650 -0.197 2.00e-02 2.50e+03 9.70e+01 ... (remaining 45731 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.96: 62141 4.96 - 9.92: 531 9.92 - 14.88: 36 14.88 - 19.84: 8 19.84 - 24.80: 8 Bond angle restraints: 62724 Sorted by residual: angle pdb=" PB ATP A 401 " pdb=" O3B ATP A 401 " pdb=" PG ATP A 401 " ideal model delta sigma weight residual 139.87 115.07 24.80 1.00e+00 1.00e+00 6.15e+02 angle pdb=" PB ATP C 401 " pdb=" O3B ATP C 401 " pdb=" PG ATP C 401 " ideal model delta sigma weight residual 139.87 115.07 24.80 1.00e+00 1.00e+00 6.15e+02 angle pdb=" PB ATP D 401 " pdb=" O3B ATP D 401 " pdb=" PG ATP D 401 " ideal model delta sigma weight residual 139.87 115.08 24.79 1.00e+00 1.00e+00 6.14e+02 angle pdb=" PB ATP B 401 " pdb=" O3B ATP B 401 " pdb=" PG ATP B 401 " ideal model delta sigma weight residual 139.87 115.08 24.79 1.00e+00 1.00e+00 6.14e+02 angle pdb=" PA ATP B 401 " pdb=" O3A ATP B 401 " pdb=" PB ATP B 401 " ideal model delta sigma weight residual 136.83 114.29 22.54 1.00e+00 1.00e+00 5.08e+02 ... (remaining 62719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 25304 16.56 - 33.12: 972 33.12 - 49.68: 272 49.68 - 66.24: 68 66.24 - 82.80: 16 Dihedral angle restraints: 26632 sinusoidal: 7604 harmonic: 19028 Sorted by residual: dihedral pdb=" CA PHE H 197 " pdb=" C PHE H 197 " pdb=" N PHE H 198 " pdb=" CA PHE H 198 " ideal model delta harmonic sigma weight residual 180.00 151.30 28.70 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA PHE F 197 " pdb=" C PHE F 197 " pdb=" N PHE F 198 " pdb=" CA PHE F 198 " ideal model delta harmonic sigma weight residual 180.00 151.30 28.70 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA PHE G 197 " pdb=" C PHE G 197 " pdb=" N PHE G 198 " pdb=" CA PHE G 198 " ideal model delta harmonic sigma weight residual 180.00 151.30 28.70 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 26629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 6486 0.094 - 0.187: 1017 0.187 - 0.281: 124 0.281 - 0.374: 25 0.374 - 0.468: 20 Chirality restraints: 7672 Sorted by residual: chirality pdb=" CA LEU D 100 " pdb=" N LEU D 100 " pdb=" C LEU D 100 " pdb=" CB LEU D 100 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.47e+00 chirality pdb=" CA LEU C 100 " pdb=" N LEU C 100 " pdb=" C LEU C 100 " pdb=" CB LEU C 100 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.42e+00 chirality pdb=" CA LEU A 100 " pdb=" N LEU A 100 " pdb=" C LEU A 100 " pdb=" CB LEU A 100 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.42e+00 ... (remaining 7669 not shown) Planarity restraints: 8064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL H 33 " 0.025 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C VAL H 33 " -0.089 2.00e-02 2.50e+03 pdb=" O VAL H 33 " 0.034 2.00e-02 2.50e+03 pdb=" N VAL H 34 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 33 " 0.025 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C VAL E 33 " -0.089 2.00e-02 2.50e+03 pdb=" O VAL E 33 " 0.034 2.00e-02 2.50e+03 pdb=" N VAL E 34 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 33 " -0.025 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C VAL G 33 " 0.089 2.00e-02 2.50e+03 pdb=" O VAL G 33 " -0.034 2.00e-02 2.50e+03 pdb=" N VAL G 34 " -0.030 2.00e-02 2.50e+03 ... (remaining 8061 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 466 2.62 - 3.19: 41505 3.19 - 3.76: 73641 3.76 - 4.33: 91653 4.33 - 4.90: 147297 Nonbonded interactions: 354562 Sorted by model distance: nonbonded pdb=" SG CYS E 6 " pdb=" SG CYS E 26 " model vdw 2.044 3.760 nonbonded pdb=" SG CYS G 6 " pdb=" SG CYS G 26 " model vdw 2.044 3.760 nonbonded pdb=" SG CYS F 6 " pdb=" SG CYS F 26 " model vdw 2.044 3.760 nonbonded pdb=" SG CYS H 6 " pdb=" SG CYS H 26 " model vdw 2.044 3.760 nonbonded pdb=" O LEU F1192 " pdb=" OG1 THR F1196 " model vdw 2.235 3.040 ... (remaining 354557 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 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: 0.840 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 47.770 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 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 : 0.008 0.202 45740 Z= 0.449 Angle : 1.289 24.805 62732 Z= 0.847 Chirality : 0.073 0.468 7672 Planarity : 0.009 0.105 8064 Dihedral : 11.078 82.803 14236 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.01 % Allowed : 4.60 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.10), residues: 6464 helix: -0.32 (0.07), residues: 3904 sheet: -1.04 (0.20), residues: 552 loop : -1.24 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 258 TYR 0.033 0.004 TYR H 179 PHE 0.032 0.003 PHE D 75 TRP 0.052 0.004 TRP H 688 HIS 0.011 0.002 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00774 / 0.45 (45736) covalent geometry : angle 1.28855 / 0.85 (62724) SS BOND : bond 0.00877 / 0.44 ( 4) SS BOND : angle 0.80501 / 0.52 ( 8) hydrogen bonds : bond 0.16067 / 10.82 ( 3333) hydrogen bonds : angle 6.71645 / 4.91 ( 9783) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1656 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 1620 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ASP cc_start: 0.5842 (p0) cc_final: 0.5626 (p0) REVERT: B 262 ASP cc_start: 0.5863 (p0) cc_final: 0.5592 (p0) REVERT: C 262 ASP cc_start: 0.5821 (p0) cc_final: 0.5544 (p0) REVERT: D 262 ASP cc_start: 0.5868 (p0) cc_final: 0.5615 (p0) REVERT: E 42 ILE cc_start: 0.8296 (tt) cc_final: 0.7957 (tt) REVERT: E 91 GLU cc_start: 0.8238 (tt0) cc_final: 0.7932 (tt0) REVERT: E 166 GLN cc_start: 0.5803 (tt0) cc_final: 0.4916 (tt0) REVERT: E 232 TRP cc_start: 0.9029 (p-90) cc_final: 0.8804 (p-90) REVERT: E 247 LEU cc_start: 0.8654 (tt) cc_final: 0.8262 (mm) REVERT: E 297 ARG cc_start: 0.7861 (mmt180) cc_final: 0.7650 (ttm110) REVERT: E 298 ARG cc_start: 0.8310 (tpt170) cc_final: 0.7770 (mmm-85) REVERT: E 400 MET cc_start: 0.8101 (mmp) cc_final: 0.7816 (mmp) REVERT: E 483 GLN cc_start: 0.8370 (tp40) cc_final: 0.8132 (mt0) REVERT: E 574 SER cc_start: 0.8281 (p) cc_final: 0.7968 (p) REVERT: E 598 ARG cc_start: 0.8829 (ttp-170) cc_final: 0.8612 (mmm-85) REVERT: E 772 TYR cc_start: 0.6923 (t80) cc_final: 0.6403 (t80) REVERT: E 1120 SER cc_start: 0.8800 (t) cc_final: 0.8369 (p) REVERT: E 1125 PHE cc_start: 0.7545 (t80) cc_final: 0.7059 (t80) REVERT: E 1176 TYR cc_start: 0.8462 (t80) cc_final: 0.7955 (t80) REVERT: E 1196 THR cc_start: 0.8123 (m) cc_final: 0.7587 (m) REVERT: E 1197 GLN cc_start: 0.8377 (pp30) cc_final: 0.8161 (tm-30) REVERT: E 1222 ARG cc_start: 0.8468 (mtt-85) cc_final: 0.8232 (ttm-80) REVERT: E 1229 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8447 (mt-10) REVERT: E 1230 TYR cc_start: 0.9069 (m-10) cc_final: 0.8672 (m-80) REVERT: E 1304 ASP cc_start: 0.8978 (t70) cc_final: 0.8665 (t70) REVERT: E 1496 PHE cc_start: 0.6030 (t80) cc_final: 0.5598 (t80) REVERT: F 42 ILE cc_start: 0.8263 (tt) cc_final: 0.7922 (tt) REVERT: F 91 GLU cc_start: 0.8250 (tt0) cc_final: 0.7932 (tt0) REVERT: F 166 GLN cc_start: 0.5808 (tt0) cc_final: 0.4918 (tt0) REVERT: F 232 TRP cc_start: 0.9035 (p-90) cc_final: 0.8817 (p-90) REVERT: F 247 LEU cc_start: 0.8660 (tt) cc_final: 0.8274 (mm) REVERT: F 297 ARG cc_start: 0.7833 (mmt180) cc_final: 0.7632 (ttm110) REVERT: F 298 ARG cc_start: 0.8319 (tpt170) cc_final: 0.7776 (mmm-85) REVERT: F 400 MET cc_start: 0.8081 (mmp) cc_final: 0.7786 (mmp) REVERT: F 483 GLN cc_start: 0.8351 (tp40) cc_final: 0.8120 (mt0) REVERT: F 574 SER cc_start: 0.8278 (p) cc_final: 0.7958 (p) REVERT: F 598 ARG cc_start: 0.8827 (ttp-170) cc_final: 0.8618 (mmm-85) REVERT: F 772 TYR cc_start: 0.6926 (t80) cc_final: 0.6404 (t80) REVERT: F 1120 SER cc_start: 0.8817 (t) cc_final: 0.8374 (p) REVERT: F 1125 PHE cc_start: 0.7542 (t80) cc_final: 0.7052 (t80) REVERT: F 1176 TYR cc_start: 0.8454 (t80) cc_final: 0.7946 (t80) REVERT: F 1196 THR cc_start: 0.8113 (m) cc_final: 0.7576 (m) REVERT: F 1197 GLN cc_start: 0.8388 (pp30) cc_final: 0.8164 (tm-30) REVERT: F 1206 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8440 (mt-10) REVERT: F 1222 ARG cc_start: 0.8468 (mtt-85) cc_final: 0.8250 (ttm-80) REVERT: F 1229 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8451 (mt-10) REVERT: F 1230 TYR cc_start: 0.9068 (m-10) cc_final: 0.8677 (m-80) REVERT: F 1304 ASP cc_start: 0.8954 (t70) cc_final: 0.8646 (t70) REVERT: F 1496 PHE cc_start: 0.6038 (t80) cc_final: 0.5609 (t80) REVERT: G 42 ILE cc_start: 0.8282 (tt) cc_final: 0.7944 (tt) REVERT: G 91 GLU cc_start: 0.8254 (tt0) cc_final: 0.7926 (tt0) REVERT: G 145 LEU cc_start: 0.8394 (tt) cc_final: 0.8153 (tp) REVERT: G 166 GLN cc_start: 0.5821 (tt0) cc_final: 0.4891 (tt0) REVERT: G 232 TRP cc_start: 0.9046 (p-90) cc_final: 0.8786 (p-90) REVERT: G 247 LEU cc_start: 0.8676 (tt) cc_final: 0.8299 (mm) REVERT: G 297 ARG cc_start: 0.7821 (mmt180) cc_final: 0.7616 (ttm110) REVERT: G 298 ARG cc_start: 0.8327 (tpt170) cc_final: 0.7784 (mmm-85) REVERT: G 370 ARG cc_start: 0.8389 (mmt-90) cc_final: 0.7968 (mpt-90) REVERT: G 400 MET cc_start: 0.8043 (mmp) cc_final: 0.7739 (mmp) REVERT: G 574 SER cc_start: 0.8300 (p) cc_final: 0.7981 (p) REVERT: G 598 ARG cc_start: 0.8820 (ttp-170) cc_final: 0.8611 (mmm-85) REVERT: G 772 TYR cc_start: 0.6936 (t80) cc_final: 0.6417 (t80) REVERT: G 1120 SER cc_start: 0.8815 (t) cc_final: 0.8368 (p) REVERT: G 1125 PHE cc_start: 0.7465 (t80) cc_final: 0.6971 (t80) REVERT: G 1176 TYR cc_start: 0.8464 (t80) cc_final: 0.7977 (t80) REVERT: G 1193 ASP cc_start: 0.8161 (t70) cc_final: 0.7922 (t70) REVERT: G 1222 ARG cc_start: 0.8457 (mtt-85) cc_final: 0.8240 (ttm-80) REVERT: G 1229 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8449 (mt-10) REVERT: G 1230 TYR cc_start: 0.9072 (m-10) cc_final: 0.8678 (m-80) REVERT: G 1304 ASP cc_start: 0.8954 (t70) cc_final: 0.8648 (t70) REVERT: G 1496 PHE cc_start: 0.6004 (t80) cc_final: 0.5579 (t80) REVERT: H 42 ILE cc_start: 0.8283 (tt) cc_final: 0.7950 (tt) REVERT: H 91 GLU cc_start: 0.8241 (tt0) cc_final: 0.7927 (tt0) REVERT: H 166 GLN cc_start: 0.5807 (tt0) cc_final: 0.4901 (tt0) REVERT: H 232 TRP cc_start: 0.9038 (p-90) cc_final: 0.8771 (p-90) REVERT: H 247 LEU cc_start: 0.8675 (tt) cc_final: 0.8287 (mm) REVERT: H 298 ARG cc_start: 0.8335 (tpt170) cc_final: 0.7808 (mmm-85) REVERT: H 400 MET cc_start: 0.8079 (mmp) cc_final: 0.7776 (mmp) REVERT: H 483 GLN cc_start: 0.8372 (tp40) cc_final: 0.8136 (mt0) REVERT: H 574 SER cc_start: 0.8280 (p) cc_final: 0.7956 (p) REVERT: H 598 ARG cc_start: 0.8836 (ttp-170) cc_final: 0.8618 (mmm-85) REVERT: H 772 TYR cc_start: 0.6945 (t80) cc_final: 0.6417 (t80) REVERT: H 1120 SER cc_start: 0.8806 (t) cc_final: 0.8369 (p) REVERT: H 1125 PHE cc_start: 0.7485 (t80) cc_final: 0.6981 (t80) REVERT: H 1176 TYR cc_start: 0.8460 (t80) cc_final: 0.7975 (t80) REVERT: H 1196 THR cc_start: 0.8115 (m) cc_final: 0.7599 (m) REVERT: H 1197 GLN cc_start: 0.8372 (pp30) cc_final: 0.8159 (tm-30) REVERT: H 1222 ARG cc_start: 0.8479 (mtt-85) cc_final: 0.8239 (ttm-80) REVERT: H 1229 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8452 (mt-10) REVERT: H 1230 TYR cc_start: 0.9055 (m-10) cc_final: 0.8675 (m-80) REVERT: H 1304 ASP cc_start: 0.8977 (t70) cc_final: 0.8659 (t70) REVERT: H 1496 PHE cc_start: 0.5990 (t80) cc_final: 0.5562 (t80) outliers start: 36 outliers final: 20 residues processed: 1644 average time/residue: 0.2561 time to fit residues: 707.9927 Evaluate side-chains 1094 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 1074 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 1248 LEU Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 604 LEU Chi-restraints excluded: chain F residue 1248 LEU Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 604 LEU Chi-restraints excluded: chain G residue 1248 LEU Chi-restraints excluded: chain H residue 44 PHE Chi-restraints excluded: chain H residue 604 LEU Chi-restraints excluded: chain H residue 1248 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 394 optimal weight: 8.9990 chunk 430 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 265 optimal weight: 2.9990 chunk 523 optimal weight: 7.9990 chunk 497 optimal weight: 8.9990 chunk 414 optimal weight: 0.9990 chunk 310 optimal weight: 30.0000 chunk 488 optimal weight: 4.9990 chunk 366 optimal weight: 10.0000 chunk 597 optimal weight: 50.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 HIS A 216 HIS A 235 GLN B 70 HIS B 216 HIS B 235 GLN C 70 HIS C 216 HIS C 235 GLN D 43 ASN D 70 HIS D 216 HIS D 235 GLN E 71 HIS E 131 ASN E1179 GLN E1224 GLN E1245 ASN F 71 HIS F 131 ASN F1179 GLN F1224 GLN F1245 ASN G 71 HIS G 131 ASN G1179 GLN G1224 GLN G1245 ASN H 71 HIS H 131 ASN H1179 GLN H1224 GLN H1245 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.139510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.111599 restraints weight = 123215.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.114398 restraints weight = 61325.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.116243 restraints weight = 37706.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.117435 restraints weight = 26622.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.118285 restraints weight = 20922.224| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 45740 Z= 0.204 Angle : 0.709 12.644 62732 Z= 0.365 Chirality : 0.046 0.149 7672 Planarity : 0.005 0.058 8064 Dihedral : 6.235 84.635 6928 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.41 % Allowed : 14.73 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.10), residues: 6464 helix: 1.13 (0.08), residues: 4004 sheet: -0.58 (0.22), residues: 476 loop : -0.63 (0.14), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 370 TYR 0.031 0.002 TYR H 179 PHE 0.023 0.002 PHE F 433 TRP 0.024 0.002 TRP E 688 HIS 0.008 0.001 HIS G 867 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (45736) covalent geometry : angle 0.70716 / 0.36 (62724) SS BOND : bond 0.02897 / 1.45 ( 4) SS BOND : angle 4.29416 / 2.51 ( 8) hydrogen bonds : bond 0.05172 / 3.51 ( 3333) hydrogen bonds : angle 4.54645 / 3.31 ( 9783) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1375 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 1218 time to evaluate : 1.786 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 47 LYS cc_start: 0.9079 (mmtm) cc_final: 0.8829 (mmtp) REVERT: A 75 PHE cc_start: 0.8674 (m-80) cc_final: 0.8471 (m-80) REVERT: B 47 LYS cc_start: 0.9083 (mmtm) cc_final: 0.8852 (mmtp) REVERT: B 75 PHE cc_start: 0.8676 (m-80) cc_final: 0.8448 (m-80) REVERT: C 47 LYS cc_start: 0.9088 (mmtm) cc_final: 0.8858 (mmtp) REVERT: C 75 PHE cc_start: 0.8673 (m-80) cc_final: 0.8445 (m-80) REVERT: D 47 LYS cc_start: 0.9044 (mmtm) cc_final: 0.8822 (mmtm) REVERT: D 75 PHE cc_start: 0.8670 (m-80) cc_final: 0.8464 (m-80) REVERT: E 145 LEU cc_start: 0.8918 (tt) cc_final: 0.8701 (tp) REVERT: E 232 TRP cc_start: 0.8977 (p-90) cc_final: 0.8526 (p-90) REVERT: E 264 GLN cc_start: 0.8598 (tp-100) cc_final: 0.8175 (tm-30) REVERT: E 267 CYS cc_start: 0.8861 (m) cc_final: 0.8504 (t) REVERT: E 319 CYS cc_start: 0.8818 (m) cc_final: 0.8417 (m) REVERT: E 378 TYR cc_start: 0.8358 (t80) cc_final: 0.8079 (t80) REVERT: E 574 SER cc_start: 0.8228 (p) cc_final: 0.7897 (p) REVERT: E 602 LYS cc_start: 0.9110 (mttt) cc_final: 0.8894 (mmtt) REVERT: E 1125 PHE cc_start: 0.7840 (t80) cc_final: 0.7579 (t80) REVERT: E 1149 LEU cc_start: 0.8876 (mt) cc_final: 0.8507 (mp) REVERT: E 1152 SER cc_start: 0.8881 (m) cc_final: 0.8620 (p) REVERT: E 1191 GLN cc_start: 0.8443 (pp30) cc_final: 0.8225 (pp30) REVERT: E 1224 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8499 (tp40) REVERT: E 1225 GLN cc_start: 0.9089 (mm-40) cc_final: 0.8669 (mm-40) REVERT: E 1230 TYR cc_start: 0.8980 (m-10) cc_final: 0.8727 (m-80) REVERT: E 1304 ASP cc_start: 0.9008 (t70) cc_final: 0.8772 (t70) REVERT: F 145 LEU cc_start: 0.8933 (tt) cc_final: 0.8716 (tp) REVERT: F 232 TRP cc_start: 0.8990 (p-90) cc_final: 0.8546 (p-90) REVERT: F 264 GLN cc_start: 0.8590 (tp-100) cc_final: 0.8161 (tm-30) REVERT: F 267 CYS cc_start: 0.8864 (m) cc_final: 0.8499 (t) REVERT: F 319 CYS cc_start: 0.8819 (m) cc_final: 0.8434 (m) REVERT: F 432 PHE cc_start: 0.8714 (m-80) cc_final: 0.8465 (t80) REVERT: F 574 SER cc_start: 0.8253 (p) cc_final: 0.7923 (p) REVERT: F 1125 PHE cc_start: 0.7802 (t80) cc_final: 0.7545 (t80) REVERT: F 1149 LEU cc_start: 0.8876 (mt) cc_final: 0.8511 (mp) REVERT: F 1152 SER cc_start: 0.8922 (m) cc_final: 0.8668 (p) REVERT: F 1191 GLN cc_start: 0.8431 (pp30) cc_final: 0.8215 (pp30) REVERT: F 1224 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8512 (tp40) REVERT: F 1230 TYR cc_start: 0.8982 (m-10) cc_final: 0.8739 (m-80) REVERT: F 1304 ASP cc_start: 0.9009 (t70) cc_final: 0.8774 (t70) REVERT: G 232 TRP cc_start: 0.8988 (p-90) cc_final: 0.8524 (p-90) REVERT: G 264 GLN cc_start: 0.8591 (tp-100) cc_final: 0.8152 (tm-30) REVERT: G 267 CYS cc_start: 0.8875 (m) cc_final: 0.8506 (t) REVERT: G 319 CYS cc_start: 0.8820 (m) cc_final: 0.8507 (m) REVERT: G 370 ARG cc_start: 0.8348 (mmt-90) cc_final: 0.7778 (mpt-90) REVERT: G 378 TYR cc_start: 0.8367 (t80) cc_final: 0.8071 (t80) REVERT: G 432 PHE cc_start: 0.8715 (m-80) cc_final: 0.8458 (t80) REVERT: G 574 SER cc_start: 0.8221 (p) cc_final: 0.7890 (p) REVERT: G 1125 PHE cc_start: 0.7794 (t80) cc_final: 0.7511 (t80) REVERT: G 1149 LEU cc_start: 0.8888 (mt) cc_final: 0.8582 (mm) REVERT: G 1152 SER cc_start: 0.8942 (m) cc_final: 0.8678 (p) REVERT: G 1191 GLN cc_start: 0.8414 (pp30) cc_final: 0.8170 (pp30) REVERT: G 1224 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8501 (tp40) REVERT: G 1225 GLN cc_start: 0.9087 (mm-40) cc_final: 0.8670 (mm-40) REVERT: G 1230 TYR cc_start: 0.8978 (m-10) cc_final: 0.8730 (m-80) REVERT: G 1253 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7175 (mm-30) REVERT: G 1294 TYR cc_start: 0.8849 (m-10) cc_final: 0.8646 (m-10) REVERT: H 232 TRP cc_start: 0.8992 (p-90) cc_final: 0.8538 (p-90) REVERT: H 264 GLN cc_start: 0.8600 (tp-100) cc_final: 0.8165 (tm-30) REVERT: H 267 CYS cc_start: 0.8867 (m) cc_final: 0.8503 (t) REVERT: H 319 CYS cc_start: 0.8825 (m) cc_final: 0.8491 (m) REVERT: H 378 TYR cc_start: 0.8366 (t80) cc_final: 0.8089 (t80) REVERT: H 574 SER cc_start: 0.8232 (p) cc_final: 0.7904 (p) REVERT: H 602 LYS cc_start: 0.9108 (mttt) cc_final: 0.8891 (mmtt) REVERT: H 1125 PHE cc_start: 0.7792 (t80) cc_final: 0.7513 (t80) REVERT: H 1149 LEU cc_start: 0.8901 (mt) cc_final: 0.8677 (mm) REVERT: H 1152 SER cc_start: 0.8918 (m) cc_final: 0.8662 (p) REVERT: H 1191 GLN cc_start: 0.8433 (pp30) cc_final: 0.8220 (pp30) REVERT: H 1224 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8490 (tp40) REVERT: H 1225 GLN cc_start: 0.9087 (mm-40) cc_final: 0.8673 (mm-40) REVERT: H 1230 TYR cc_start: 0.8982 (m-10) cc_final: 0.8729 (m-80) outliers start: 157 outliers final: 104 residues processed: 1314 average time/residue: 0.2491 time to fit residues: 558.8187 Evaluate side-chains 1097 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 989 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 97 HIS Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 198 PHE Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 1140 LEU Chi-restraints excluded: chain E residue 1224 GLN Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1248 LEU Chi-restraints excluded: chain E residue 1250 VAL Chi-restraints excluded: chain E residue 1285 LEU Chi-restraints excluded: chain E residue 1307 ILE Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 71 HIS Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 198 PHE Chi-restraints excluded: chain F residue 221 PHE Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 1140 LEU Chi-restraints excluded: chain F residue 1224 GLN Chi-restraints excluded: chain F residue 1227 LEU Chi-restraints excluded: chain F residue 1248 LEU Chi-restraints excluded: chain F residue 1250 VAL Chi-restraints excluded: chain F residue 1285 LEU Chi-restraints excluded: chain F residue 1307 ILE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 65 TRP Chi-restraints excluded: chain G residue 71 HIS Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 198 PHE Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 449 VAL Chi-restraints excluded: chain G residue 1140 LEU Chi-restraints excluded: chain G residue 1224 GLN Chi-restraints excluded: chain G residue 1227 LEU Chi-restraints excluded: chain G residue 1248 LEU Chi-restraints excluded: chain G residue 1250 VAL Chi-restraints excluded: chain G residue 1285 LEU Chi-restraints excluded: chain G residue 1307 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 44 PHE Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 71 HIS Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 198 PHE Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 449 VAL Chi-restraints excluded: chain H residue 1140 LEU Chi-restraints excluded: chain H residue 1224 GLN Chi-restraints excluded: chain H residue 1227 LEU Chi-restraints excluded: chain H residue 1248 LEU Chi-restraints excluded: chain H residue 1250 VAL Chi-restraints excluded: chain H residue 1285 LEU Chi-restraints excluded: chain H residue 1307 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 244 optimal weight: 0.4980 chunk 8 optimal weight: 6.9990 chunk 199 optimal weight: 20.0000 chunk 19 optimal weight: 3.9990 chunk 588 optimal weight: 0.0970 chunk 465 optimal weight: 0.3980 chunk 606 optimal weight: 30.0000 chunk 6 optimal weight: 4.9990 chunk 392 optimal weight: 2.9990 chunk 318 optimal weight: 30.0000 chunk 272 optimal weight: 0.8980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 GLN A 173 GLN A 235 GLN B 173 GLN C 57 GLN C 173 GLN D 173 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.140348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.112439 restraints weight = 121246.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.115403 restraints weight = 59074.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.117294 restraints weight = 35572.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.118591 restraints weight = 24832.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.119425 restraints weight = 19202.193| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 45740 Z= 0.131 Angle : 0.631 10.453 62732 Z= 0.314 Chirality : 0.043 0.166 7672 Planarity : 0.004 0.048 8064 Dihedral : 5.639 82.973 6912 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.32 % Allowed : 19.70 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.24 (0.11), residues: 6464 helix: 1.71 (0.08), residues: 4040 sheet: -0.55 (0.21), residues: 556 loop : -0.64 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 370 TYR 0.028 0.001 TYR E 123 PHE 0.030 0.002 PHE G 363 TRP 0.013 0.001 TRP F 75 HIS 0.015 0.001 HIS G 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (45736) covalent geometry : angle 0.63083 / 0.31 (62724) SS BOND : bond 0.00407 / 0.20 ( 4) SS BOND : angle 2.53464 / 1.47 ( 8) hydrogen bonds : bond 0.04519 / 3.07 ( 3333) hydrogen bonds : angle 4.15602 / 3.03 ( 9783) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1259 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 1105 time to evaluate : 1.578 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 47 LYS cc_start: 0.9026 (mmtm) cc_final: 0.8801 (mmtm) REVERT: B 47 LYS cc_start: 0.9042 (mmtm) cc_final: 0.8805 (mmtm) REVERT: C 47 LYS cc_start: 0.9029 (mmtm) cc_final: 0.8788 (mmtm) REVERT: D 42 CYS cc_start: 0.7744 (p) cc_final: 0.7525 (p) REVERT: D 47 LYS cc_start: 0.8933 (mmtm) cc_final: 0.8733 (mmtp) REVERT: E 183 LEU cc_start: 0.9061 (tp) cc_final: 0.8680 (tp) REVERT: E 226 SER cc_start: 0.8935 (m) cc_final: 0.8572 (p) REVERT: E 248 ARG cc_start: 0.8074 (ptt180) cc_final: 0.7860 (ptt-90) REVERT: E 264 GLN cc_start: 0.8535 (tp-100) cc_final: 0.8287 (tm-30) REVERT: E 319 CYS cc_start: 0.8815 (m) cc_final: 0.8498 (m) REVERT: E 432 PHE cc_start: 0.8663 (m-80) cc_final: 0.8425 (t80) REVERT: E 483 GLN cc_start: 0.7804 (mt0) cc_final: 0.7571 (mt0) REVERT: E 574 SER cc_start: 0.7976 (p) cc_final: 0.7626 (p) REVERT: E 1125 PHE cc_start: 0.7816 (t80) cc_final: 0.7539 (t80) REVERT: E 1145 ARG cc_start: 0.8124 (ttp80) cc_final: 0.7578 (tmm160) REVERT: E 1225 GLN cc_start: 0.8951 (mm-40) cc_final: 0.8702 (mm-40) REVERT: E 1226 LYS cc_start: 0.8942 (mttt) cc_final: 0.8619 (mttp) REVERT: E 1230 TYR cc_start: 0.8999 (m-10) cc_final: 0.8733 (m-80) REVERT: F 168 ARG cc_start: 0.7942 (ttm110) cc_final: 0.7694 (mtm-85) REVERT: F 183 LEU cc_start: 0.9054 (tp) cc_final: 0.8674 (tp) REVERT: F 226 SER cc_start: 0.8942 (m) cc_final: 0.8572 (p) REVERT: F 248 ARG cc_start: 0.8075 (ptt180) cc_final: 0.7868 (ptt-90) REVERT: F 264 GLN cc_start: 0.8533 (tp-100) cc_final: 0.8286 (tm-30) REVERT: F 319 CYS cc_start: 0.8818 (m) cc_final: 0.8499 (m) REVERT: F 432 PHE cc_start: 0.8689 (m-80) cc_final: 0.8431 (t80) REVERT: F 483 GLN cc_start: 0.7821 (mt0) cc_final: 0.7595 (mt0) REVERT: F 574 SER cc_start: 0.8002 (p) cc_final: 0.7661 (p) REVERT: F 1125 PHE cc_start: 0.7815 (t80) cc_final: 0.7547 (t80) REVERT: F 1145 ARG cc_start: 0.8123 (ttp80) cc_final: 0.7572 (tmm160) REVERT: F 1206 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7875 (mt-10) REVERT: F 1225 GLN cc_start: 0.8834 (mm-40) cc_final: 0.7814 (mm-40) REVERT: F 1226 LYS cc_start: 0.9038 (mttt) cc_final: 0.8244 (mttp) REVERT: F 1230 TYR cc_start: 0.8993 (m-10) cc_final: 0.8713 (m-80) REVERT: F 1304 ASP cc_start: 0.9017 (t70) cc_final: 0.8736 (t0) REVERT: G 71 HIS cc_start: 0.8517 (OUTLIER) cc_final: 0.8033 (p-80) REVERT: G 76 ILE cc_start: 0.9390 (pp) cc_final: 0.8991 (tp) REVERT: G 96 ASP cc_start: 0.8181 (t70) cc_final: 0.7873 (t0) REVERT: G 183 LEU cc_start: 0.9072 (tp) cc_final: 0.8655 (tp) REVERT: G 226 SER cc_start: 0.8934 (m) cc_final: 0.8445 (p) REVERT: G 264 GLN cc_start: 0.8537 (tp-100) cc_final: 0.8274 (tm-30) REVERT: G 319 CYS cc_start: 0.8737 (m) cc_final: 0.8438 (m) REVERT: G 370 ARG cc_start: 0.8434 (mmt-90) cc_final: 0.7713 (mpt-90) REVERT: G 432 PHE cc_start: 0.8689 (m-80) cc_final: 0.8430 (t80) REVERT: G 574 SER cc_start: 0.7983 (p) cc_final: 0.7629 (p) REVERT: G 1125 PHE cc_start: 0.7821 (t80) cc_final: 0.7469 (t80) REVERT: G 1198 LEU cc_start: 0.9339 (tp) cc_final: 0.9023 (mt) REVERT: G 1225 GLN cc_start: 0.8951 (mm-40) cc_final: 0.8703 (mm-40) REVERT: G 1230 TYR cc_start: 0.8996 (m-10) cc_final: 0.8737 (m-80) REVERT: G 1304 ASP cc_start: 0.9038 (t70) cc_final: 0.8755 (t0) REVERT: H 76 ILE cc_start: 0.9379 (pp) cc_final: 0.8981 (tp) REVERT: H 183 LEU cc_start: 0.9050 (tp) cc_final: 0.8675 (tp) REVERT: H 226 SER cc_start: 0.8927 (m) cc_final: 0.8572 (p) REVERT: H 264 GLN cc_start: 0.8545 (tp-100) cc_final: 0.8292 (tm-30) REVERT: H 319 CYS cc_start: 0.8756 (m) cc_final: 0.8444 (m) REVERT: H 432 PHE cc_start: 0.8667 (m-80) cc_final: 0.8426 (t80) REVERT: H 483 GLN cc_start: 0.7817 (mt0) cc_final: 0.7595 (mt0) REVERT: H 574 SER cc_start: 0.8011 (p) cc_final: 0.7661 (p) REVERT: H 1125 PHE cc_start: 0.7800 (t80) cc_final: 0.7473 (t80) REVERT: H 1225 GLN cc_start: 0.8953 (mm-40) cc_final: 0.8710 (mm-40) REVERT: H 1230 TYR cc_start: 0.8996 (m-10) cc_final: 0.8736 (m-80) REVERT: H 1253 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7589 (mm-30) outliers start: 154 outliers final: 110 residues processed: 1187 average time/residue: 0.2323 time to fit residues: 479.7547 Evaluate side-chains 1079 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 968 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 97 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 1129 CYS Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1140 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1255 ILE Chi-restraints excluded: chain E residue 1307 ILE Chi-restraints excluded: chain E residue 1315 ILE Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 221 PHE Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 1129 CYS Chi-restraints excluded: chain F residue 1136 ILE Chi-restraints excluded: chain F residue 1140 LEU Chi-restraints excluded: chain F residue 1175 CYS Chi-restraints excluded: chain F residue 1227 LEU Chi-restraints excluded: chain F residue 1255 ILE Chi-restraints excluded: chain F residue 1307 ILE Chi-restraints excluded: chain F residue 1315 ILE Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 65 TRP Chi-restraints excluded: chain G residue 71 HIS Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 418 CYS Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 440 THR Chi-restraints excluded: chain G residue 1129 CYS Chi-restraints excluded: chain G residue 1136 ILE Chi-restraints excluded: chain G residue 1140 LEU Chi-restraints excluded: chain G residue 1146 SER Chi-restraints excluded: chain G residue 1175 CYS Chi-restraints excluded: chain G residue 1227 LEU Chi-restraints excluded: chain G residue 1307 ILE Chi-restraints excluded: chain G residue 1315 ILE Chi-restraints excluded: chain H residue 44 PHE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain H residue 418 CYS Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 1129 CYS Chi-restraints excluded: chain H residue 1136 ILE Chi-restraints excluded: chain H residue 1140 LEU Chi-restraints excluded: chain H residue 1146 SER Chi-restraints excluded: chain H residue 1175 CYS Chi-restraints excluded: chain H residue 1227 LEU Chi-restraints excluded: chain H residue 1307 ILE Chi-restraints excluded: chain H residue 1315 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 145 optimal weight: 9.9990 chunk 508 optimal weight: 30.0000 chunk 112 optimal weight: 10.0000 chunk 251 optimal weight: 9.9990 chunk 539 optimal weight: 0.8980 chunk 239 optimal weight: 0.0070 chunk 445 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 358 optimal weight: 9.9990 chunk 213 optimal weight: 30.0000 chunk 267 optimal weight: 0.9990 overall best weight: 4.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN B 57 GLN D 57 GLN E 125 HIS E 386 ASN E 474 GLN F 125 HIS F 386 ASN F 474 GLN G 125 HIS G 223 ASN G 386 ASN G 483 GLN H 125 HIS ** H 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 386 ASN H 474 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.136119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.108180 restraints weight = 122078.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.110984 restraints weight = 59654.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.112860 restraints weight = 36269.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.114071 restraints weight = 25460.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.114868 restraints weight = 19845.392| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 45740 Z= 0.193 Angle : 0.659 9.484 62732 Z= 0.335 Chirality : 0.045 0.238 7672 Planarity : 0.004 0.040 8064 Dihedral : 5.364 74.609 6904 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 7.86 % Allowed : 18.32 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.49 (0.11), residues: 6464 helix: 1.89 (0.08), residues: 4028 sheet: -0.50 (0.23), residues: 516 loop : -0.49 (0.15), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 201 TYR 0.019 0.002 TYR H 123 PHE 0.025 0.002 PHE H 363 TRP 0.022 0.002 TRP H 688 HIS 0.006 0.001 HIS H 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (45736) covalent geometry : angle 0.65850 / 0.33 (62724) SS BOND : bond 0.00041 / 0.02 ( 4) SS BOND : angle 2.69698 / 1.61 ( 8) hydrogen bonds : bond 0.04607 / 3.12 ( 3333) hydrogen bonds : angle 4.15155 / 3.02 ( 9783) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1284 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 280 poor density : 1004 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.9173 (mmtm) cc_final: 0.8906 (mmtm) REVERT: B 47 LYS cc_start: 0.9182 (mmtm) cc_final: 0.8945 (mmtp) REVERT: C 47 LYS cc_start: 0.9177 (mmtm) cc_final: 0.8958 (mmtp) REVERT: D 282 GLU cc_start: 0.7180 (mp0) cc_final: 0.6853 (mp0) REVERT: E 41 PHE cc_start: 0.8426 (m-10) cc_final: 0.8176 (m-80) REVERT: E 76 ILE cc_start: 0.9528 (pp) cc_final: 0.9174 (tp) REVERT: E 96 ASP cc_start: 0.8215 (t70) cc_final: 0.7763 (t0) REVERT: E 226 SER cc_start: 0.8767 (m) cc_final: 0.8455 (p) REVERT: E 248 ARG cc_start: 0.8064 (ptt180) cc_final: 0.7852 (ptt-90) REVERT: E 264 GLN cc_start: 0.8584 (tp-100) cc_final: 0.8207 (tm-30) REVERT: E 319 CYS cc_start: 0.8822 (m) cc_final: 0.8493 (m) REVERT: E 402 MET cc_start: 0.5652 (tmm) cc_final: 0.5297 (tmm) REVERT: E 432 PHE cc_start: 0.8743 (m-80) cc_final: 0.8402 (t80) REVERT: E 483 GLN cc_start: 0.7948 (mt0) cc_final: 0.7609 (mt0) REVERT: E 574 SER cc_start: 0.8164 (p) cc_final: 0.7931 (m) REVERT: E 1125 PHE cc_start: 0.7819 (t80) cc_final: 0.7459 (t80) REVERT: E 1226 LYS cc_start: 0.8985 (mttt) cc_final: 0.8742 (mttp) REVERT: E 1230 TYR cc_start: 0.8979 (m-10) cc_final: 0.8657 (m-80) REVERT: E 1283 LEU cc_start: 0.8808 (mt) cc_final: 0.8598 (tp) REVERT: E 1304 ASP cc_start: 0.8985 (t70) cc_final: 0.8757 (t70) REVERT: F 41 PHE cc_start: 0.8377 (m-10) cc_final: 0.8122 (m-80) REVERT: F 76 ILE cc_start: 0.9529 (pp) cc_final: 0.9178 (tp) REVERT: F 96 ASP cc_start: 0.8412 (t0) cc_final: 0.7986 (t0) REVERT: F 226 SER cc_start: 0.8764 (m) cc_final: 0.8453 (p) REVERT: F 248 ARG cc_start: 0.8049 (ptt180) cc_final: 0.7841 (ptt-90) REVERT: F 264 GLN cc_start: 0.8582 (tp-100) cc_final: 0.8205 (tm-30) REVERT: F 319 CYS cc_start: 0.8822 (m) cc_final: 0.8481 (m) REVERT: F 402 MET cc_start: 0.5647 (tmm) cc_final: 0.5280 (tmm) REVERT: F 432 PHE cc_start: 0.8745 (m-80) cc_final: 0.8433 (t80) REVERT: F 483 GLN cc_start: 0.7942 (mt0) cc_final: 0.7592 (mt0) REVERT: F 574 SER cc_start: 0.8164 (p) cc_final: 0.7925 (m) REVERT: F 1125 PHE cc_start: 0.7828 (t80) cc_final: 0.7477 (t80) REVERT: F 1304 ASP cc_start: 0.8979 (t70) cc_final: 0.8687 (t70) REVERT: G 41 PHE cc_start: 0.8371 (m-10) cc_final: 0.8116 (m-80) REVERT: G 66 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8483 (tp) REVERT: G 76 ILE cc_start: 0.9534 (pp) cc_final: 0.9186 (tp) REVERT: G 96 ASP cc_start: 0.8282 (t70) cc_final: 0.7961 (t0) REVERT: G 145 LEU cc_start: 0.8942 (tt) cc_final: 0.8696 (tp) REVERT: G 168 ARG cc_start: 0.5101 (mtt90) cc_final: 0.4525 (mtm-85) REVERT: G 226 SER cc_start: 0.8922 (m) cc_final: 0.8466 (p) REVERT: G 264 GLN cc_start: 0.8589 (tp-100) cc_final: 0.8205 (tm-30) REVERT: G 319 CYS cc_start: 0.8814 (m) cc_final: 0.8490 (m) REVERT: G 370 ARG cc_start: 0.8520 (mmt-90) cc_final: 0.8064 (mpt-90) REVERT: G 402 MET cc_start: 0.5647 (tmm) cc_final: 0.5293 (tmm) REVERT: G 432 PHE cc_start: 0.8749 (m-80) cc_final: 0.8426 (t80) REVERT: G 574 SER cc_start: 0.8171 (p) cc_final: 0.7931 (m) REVERT: G 1125 PHE cc_start: 0.7827 (t80) cc_final: 0.7460 (t80) REVERT: G 1145 ARG cc_start: 0.8636 (ttp80) cc_final: 0.7918 (tmm160) REVERT: G 1226 LYS cc_start: 0.8985 (mttt) cc_final: 0.8726 (mttp) REVERT: G 1230 TYR cc_start: 0.9005 (m-10) cc_final: 0.8672 (m-80) REVERT: G 1253 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7602 (mm-30) REVERT: G 1304 ASP cc_start: 0.8983 (t70) cc_final: 0.8752 (t70) REVERT: H 41 PHE cc_start: 0.8370 (m-10) cc_final: 0.8126 (m-80) REVERT: H 76 ILE cc_start: 0.9526 (pp) cc_final: 0.9176 (tp) REVERT: H 96 ASP cc_start: 0.8188 (t70) cc_final: 0.7718 (t0) REVERT: H 168 ARG cc_start: 0.5183 (mtt90) cc_final: 0.4579 (mtm-85) REVERT: H 226 SER cc_start: 0.8750 (m) cc_final: 0.8469 (p) REVERT: H 264 GLN cc_start: 0.8586 (tp-100) cc_final: 0.8204 (tm-30) REVERT: H 319 CYS cc_start: 0.8825 (m) cc_final: 0.8496 (m) REVERT: H 402 MET cc_start: 0.5668 (tmm) cc_final: 0.5244 (tmm) REVERT: H 432 PHE cc_start: 0.8744 (m-80) cc_final: 0.8396 (t80) REVERT: H 483 GLN cc_start: 0.7945 (mt0) cc_final: 0.7608 (mt0) REVERT: H 574 SER cc_start: 0.8171 (p) cc_final: 0.7933 (m) REVERT: H 1125 PHE cc_start: 0.7730 (t80) cc_final: 0.7377 (t80) REVERT: H 1145 ARG cc_start: 0.8399 (ttp80) cc_final: 0.7834 (tmm160) REVERT: H 1226 LYS cc_start: 0.8998 (mttt) cc_final: 0.8739 (mttp) REVERT: H 1230 TYR cc_start: 0.8997 (m-10) cc_final: 0.8661 (m-80) REVERT: H 1253 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7677 (mm-30) outliers start: 280 outliers final: 208 residues processed: 1195 average time/residue: 0.2244 time to fit residues: 468.0152 Evaluate side-chains 1114 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 905 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 97 HIS Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 198 PHE Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 739 TRP Chi-restraints excluded: chain E residue 1129 CYS Chi-restraints excluded: chain E residue 1140 LEU Chi-restraints excluded: chain E residue 1146 SER Chi-restraints excluded: chain E residue 1173 VAL Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1250 VAL Chi-restraints excluded: chain E residue 1285 LEU Chi-restraints excluded: chain E residue 1307 ILE Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 198 PHE Chi-restraints excluded: chain F residue 221 PHE Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 440 THR Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 739 TRP Chi-restraints excluded: chain F residue 1129 CYS Chi-restraints excluded: chain F residue 1140 LEU Chi-restraints excluded: chain F residue 1146 SER Chi-restraints excluded: chain F residue 1173 VAL Chi-restraints excluded: chain F residue 1175 CYS Chi-restraints excluded: chain F residue 1227 LEU Chi-restraints excluded: chain F residue 1250 VAL Chi-restraints excluded: chain F residue 1272 LEU Chi-restraints excluded: chain F residue 1283 LEU Chi-restraints excluded: chain F residue 1285 LEU Chi-restraints excluded: chain F residue 1307 ILE Chi-restraints excluded: chain F residue 1316 HIS Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 65 TRP Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 71 HIS Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 198 PHE Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 320 ILE Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 366 LEU Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 418 CYS Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 440 THR Chi-restraints excluded: chain G residue 449 VAL Chi-restraints excluded: chain G residue 473 VAL Chi-restraints excluded: chain G residue 739 TRP Chi-restraints excluded: chain G residue 1129 CYS Chi-restraints excluded: chain G residue 1140 LEU Chi-restraints excluded: chain G residue 1146 SER Chi-restraints excluded: chain G residue 1169 LEU Chi-restraints excluded: chain G residue 1175 CYS Chi-restraints excluded: chain G residue 1227 LEU Chi-restraints excluded: chain G residue 1250 VAL Chi-restraints excluded: chain G residue 1258 CYS Chi-restraints excluded: chain G residue 1272 LEU Chi-restraints excluded: chain G residue 1285 LEU Chi-restraints excluded: chain G residue 1307 ILE Chi-restraints excluded: chain G residue 1316 HIS Chi-restraints excluded: chain H residue 44 PHE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 71 HIS Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 198 PHE Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 320 ILE Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain H residue 373 LEU Chi-restraints excluded: chain H residue 418 CYS Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain H residue 440 THR Chi-restraints excluded: chain H residue 449 VAL Chi-restraints excluded: chain H residue 473 VAL Chi-restraints excluded: chain H residue 739 TRP Chi-restraints excluded: chain H residue 1129 CYS Chi-restraints excluded: chain H residue 1140 LEU Chi-restraints excluded: chain H residue 1175 CYS Chi-restraints excluded: chain H residue 1227 LEU Chi-restraints excluded: chain H residue 1250 VAL Chi-restraints excluded: chain H residue 1272 LEU Chi-restraints excluded: chain H residue 1283 LEU Chi-restraints excluded: chain H residue 1285 LEU Chi-restraints excluded: chain H residue 1307 ILE Chi-restraints excluded: chain H residue 1316 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 105 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 338 optimal weight: 30.0000 chunk 465 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 chunk 443 optimal weight: 7.9990 chunk 181 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 640 optimal weight: 40.0000 chunk 565 optimal weight: 10.0000 chunk 299 optimal weight: 8.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 166 GLN E 262 ASN E 326 HIS E 474 GLN E1270 ASN F 262 ASN F 326 HIS ** F 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 474 GLN F1270 ASN G 223 ASN G 262 ASN G 326 HIS G 474 GLN G 483 GLN G1270 ASN H 166 GLN H 262 ASN H 326 HIS ** H 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 474 GLN H1270 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.133990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.106248 restraints weight = 121066.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.108945 restraints weight = 58921.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.110754 restraints weight = 35978.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.111941 restraints weight = 25386.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.112723 restraints weight = 19856.379| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 45740 Z= 0.214 Angle : 0.674 10.247 62732 Z= 0.341 Chirality : 0.046 0.209 7672 Planarity : 0.004 0.037 8064 Dihedral : 5.281 68.967 6904 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 7.07 % Allowed : 18.41 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.11), residues: 6464 helix: 1.97 (0.08), residues: 4036 sheet: -0.69 (0.22), residues: 552 loop : -0.38 (0.15), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H1124 TYR 0.021 0.002 TYR H 123 PHE 0.028 0.002 PHE C 168 TRP 0.029 0.002 TRP E 688 HIS 0.007 0.001 HIS H 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 (45736) covalent geometry : angle 0.67317 / 0.34 (62724) SS BOND : bond 0.01683 / 0.84 ( 4) SS BOND : angle 2.35848 / 1.49 ( 8) hydrogen bonds : bond 0.04553 / 3.09 ( 3333) hydrogen bonds : angle 4.15725 / 3.03 ( 9783) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1234 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 252 poor density : 982 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.9192 (mmtm) cc_final: 0.8917 (mmtm) REVERT: A 58 ASP cc_start: 0.7751 (t0) cc_final: 0.7187 (t0) REVERT: B 41 ASN cc_start: 0.8780 (t0) cc_final: 0.8518 (t0) REVERT: B 47 LYS cc_start: 0.9206 (mmtm) cc_final: 0.8931 (mmtm) REVERT: B 58 ASP cc_start: 0.7739 (t0) cc_final: 0.7177 (t0) REVERT: C 47 LYS cc_start: 0.9180 (mmtm) cc_final: 0.8909 (mmtm) REVERT: C 58 ASP cc_start: 0.7773 (t0) cc_final: 0.7201 (t0) REVERT: D 47 LYS cc_start: 0.9205 (mmtp) cc_final: 0.8973 (mmtm) REVERT: D 282 GLU cc_start: 0.7208 (mp0) cc_final: 0.6859 (mp0) REVERT: E 264 GLN cc_start: 0.8584 (tp-100) cc_final: 0.8141 (tm-30) REVERT: E 402 MET cc_start: 0.5476 (tmm) cc_final: 0.3705 (tmm) REVERT: E 432 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8418 (t80) REVERT: E 480 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7355 (tmtt) REVERT: E 483 GLN cc_start: 0.7834 (mt0) cc_final: 0.7508 (mt0) REVERT: E 739 TRP cc_start: 0.6415 (OUTLIER) cc_final: 0.5626 (t60) REVERT: E 1125 PHE cc_start: 0.7785 (t80) cc_final: 0.7431 (t80) REVERT: E 1226 LYS cc_start: 0.9045 (mttt) cc_final: 0.8652 (mttp) REVERT: E 1230 TYR cc_start: 0.8991 (m-10) cc_final: 0.8633 (m-80) REVERT: E 1283 LEU cc_start: 0.8865 (mt) cc_final: 0.8651 (tp) REVERT: E 1306 GLU cc_start: 0.8486 (tm-30) cc_final: 0.7785 (tp30) REVERT: F 168 ARG cc_start: 0.5016 (mtt90) cc_final: 0.4401 (mtm-85) REVERT: F 264 GLN cc_start: 0.8594 (tp-100) cc_final: 0.8145 (tm-30) REVERT: F 432 PHE cc_start: 0.8818 (m-80) cc_final: 0.8420 (t80) REVERT: F 480 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7357 (tmtt) REVERT: F 483 GLN cc_start: 0.7845 (mt0) cc_final: 0.7513 (mt0) REVERT: F 739 TRP cc_start: 0.6421 (OUTLIER) cc_final: 0.5624 (t60) REVERT: F 1125 PHE cc_start: 0.7851 (t80) cc_final: 0.7496 (t80) REVERT: F 1306 GLU cc_start: 0.8483 (tm-30) cc_final: 0.7787 (tp30) REVERT: G 96 ASP cc_start: 0.8305 (t70) cc_final: 0.7658 (t0) REVERT: G 168 ARG cc_start: 0.5284 (mtt90) cc_final: 0.4778 (mtm-85) REVERT: G 264 GLN cc_start: 0.8586 (tp-100) cc_final: 0.8147 (tm-30) REVERT: G 370 ARG cc_start: 0.8526 (mmt-90) cc_final: 0.7808 (mpt-90) REVERT: G 432 PHE cc_start: 0.8809 (m-80) cc_final: 0.8420 (t80) REVERT: G 441 MET cc_start: 0.8807 (mmp) cc_final: 0.8605 (mmt) REVERT: G 739 TRP cc_start: 0.6416 (OUTLIER) cc_final: 0.5655 (t60) REVERT: G 1125 PHE cc_start: 0.7837 (t80) cc_final: 0.7513 (t80) REVERT: G 1145 ARG cc_start: 0.8779 (ttp80) cc_final: 0.8516 (ttp80) REVERT: G 1198 LEU cc_start: 0.9313 (tp) cc_final: 0.9001 (mt) REVERT: G 1226 LYS cc_start: 0.9040 (mttt) cc_final: 0.8653 (mttp) REVERT: G 1230 TYR cc_start: 0.9002 (m-10) cc_final: 0.8638 (m-80) REVERT: G 1253 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7543 (mm-30) REVERT: G 1304 ASP cc_start: 0.9038 (t70) cc_final: 0.8818 (t70) REVERT: G 1306 GLU cc_start: 0.8515 (tm-30) cc_final: 0.7813 (tp30) REVERT: H 168 ARG cc_start: 0.5316 (mtt90) cc_final: 0.4823 (mtm-85) REVERT: H 226 SER cc_start: 0.8834 (m) cc_final: 0.8467 (p) REVERT: H 264 GLN cc_start: 0.8588 (tp-100) cc_final: 0.8182 (tm-30) REVERT: H 432 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.8407 (t80) REVERT: H 480 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7372 (tmtt) REVERT: H 483 GLN cc_start: 0.7835 (mt0) cc_final: 0.7508 (mt0) REVERT: H 739 TRP cc_start: 0.6386 (OUTLIER) cc_final: 0.5621 (t60) REVERT: H 1125 PHE cc_start: 0.7745 (t80) cc_final: 0.7420 (t80) REVERT: H 1226 LYS cc_start: 0.9044 (mttt) cc_final: 0.8658 (mttp) REVERT: H 1230 TYR cc_start: 0.9005 (m-10) cc_final: 0.8647 (m-80) REVERT: H 1253 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7780 (mm-30) REVERT: H 1306 GLU cc_start: 0.8520 (tm-30) cc_final: 0.7808 (tp30) outliers start: 252 outliers final: 187 residues processed: 1131 average time/residue: 0.2366 time to fit residues: 466.3526 Evaluate side-chains 1085 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 889 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 223 ASN Chi-restraints excluded: chain E residue 292 CYS Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 432 PHE Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 480 LYS Chi-restraints excluded: chain E residue 739 TRP Chi-restraints excluded: chain E residue 1140 LEU Chi-restraints excluded: chain E residue 1146 SER Chi-restraints excluded: chain E residue 1169 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1250 VAL Chi-restraints excluded: chain E residue 1258 CYS Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 221 PHE Chi-restraints excluded: chain F residue 223 ASN Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 480 LYS Chi-restraints excluded: chain F residue 543 SER Chi-restraints excluded: chain F residue 739 TRP Chi-restraints excluded: chain F residue 1140 LEU Chi-restraints excluded: chain F residue 1157 ILE Chi-restraints excluded: chain F residue 1169 LEU Chi-restraints excluded: chain F residue 1175 CYS Chi-restraints excluded: chain F residue 1204 PHE Chi-restraints excluded: chain F residue 1227 LEU Chi-restraints excluded: chain F residue 1258 CYS Chi-restraints excluded: chain F residue 1272 LEU Chi-restraints excluded: chain F residue 1283 LEU Chi-restraints excluded: chain F residue 1316 HIS Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 65 TRP Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 320 ILE Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 373 LEU Chi-restraints excluded: chain G residue 418 CYS Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 428 LEU Chi-restraints excluded: chain G residue 449 VAL Chi-restraints excluded: chain G residue 473 VAL Chi-restraints excluded: chain G residue 474 GLN Chi-restraints excluded: chain G residue 739 TRP Chi-restraints excluded: chain G residue 1140 LEU Chi-restraints excluded: chain G residue 1157 ILE Chi-restraints excluded: chain G residue 1169 LEU Chi-restraints excluded: chain G residue 1175 CYS Chi-restraints excluded: chain G residue 1202 SER Chi-restraints excluded: chain G residue 1227 LEU Chi-restraints excluded: chain G residue 1250 VAL Chi-restraints excluded: chain G residue 1272 LEU Chi-restraints excluded: chain G residue 1307 ILE Chi-restraints excluded: chain G residue 1316 HIS Chi-restraints excluded: chain H residue 44 PHE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 292 CYS Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 320 ILE Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain H residue 361 LEU Chi-restraints excluded: chain H residue 373 LEU Chi-restraints excluded: chain H residue 418 CYS Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 432 PHE Chi-restraints excluded: chain H residue 449 VAL Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain H residue 473 VAL Chi-restraints excluded: chain H residue 480 LYS Chi-restraints excluded: chain H residue 739 TRP Chi-restraints excluded: chain H residue 1129 CYS Chi-restraints excluded: chain H residue 1140 LEU Chi-restraints excluded: chain H residue 1175 CYS Chi-restraints excluded: chain H residue 1227 LEU Chi-restraints excluded: chain H residue 1250 VAL Chi-restraints excluded: chain H residue 1258 CYS Chi-restraints excluded: chain H residue 1272 LEU Chi-restraints excluded: chain H residue 1283 LEU Chi-restraints excluded: chain H residue 1285 LEU Chi-restraints excluded: chain H residue 1316 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 168 optimal weight: 20.0000 chunk 261 optimal weight: 3.9990 chunk 513 optimal weight: 6.9990 chunk 399 optimal weight: 10.0000 chunk 567 optimal weight: 40.0000 chunk 190 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 150 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 GLN C 313 GLN D 313 GLN E 474 GLN ** F 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 474 GLN G 483 GLN H 474 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.134193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.106523 restraints weight = 121966.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.110213 restraints weight = 60284.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.111950 restraints weight = 31440.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.112248 restraints weight = 23067.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.112571 restraints weight = 20652.299| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 45740 Z= 0.187 Angle : 0.650 9.329 62732 Z= 0.330 Chirality : 0.045 0.223 7672 Planarity : 0.004 0.088 8064 Dihedral : 5.139 71.866 6904 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 6.87 % Allowed : 19.78 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.11), residues: 6464 helix: 2.02 (0.08), residues: 4040 sheet: -0.62 (0.23), residues: 512 loop : -0.41 (0.15), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H1145 TYR 0.015 0.001 TYR E 123 PHE 0.029 0.002 PHE F 169 TRP 0.025 0.001 TRP H 688 HIS 0.007 0.001 HIS F 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 (45736) covalent geometry : angle 0.64923 / 0.33 (62724) SS BOND : bond 0.00379 / 0.19 ( 4) SS BOND : angle 2.29475 / 1.40 ( 8) hydrogen bonds : bond 0.04481 / 3.03 ( 3333) hydrogen bonds : angle 4.10720 / 3.00 ( 9783) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1229 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 245 poor density : 984 time to evaluate : 1.719 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 58 ASP cc_start: 0.7741 (t0) cc_final: 0.7179 (t0) REVERT: A 185 LYS cc_start: 0.8867 (ttmt) cc_final: 0.8525 (ttmm) REVERT: B 41 ASN cc_start: 0.8830 (t0) cc_final: 0.8596 (t0) REVERT: B 47 LYS cc_start: 0.9220 (mmtm) cc_final: 0.9013 (mmtm) REVERT: B 58 ASP cc_start: 0.7724 (t0) cc_final: 0.7160 (t0) REVERT: B 185 LYS cc_start: 0.8845 (ttmt) cc_final: 0.8506 (ttmm) REVERT: B 328 VAL cc_start: 0.9447 (t) cc_final: 0.9168 (p) REVERT: C 41 ASN cc_start: 0.8774 (t0) cc_final: 0.8484 (t0) REVERT: C 47 LYS cc_start: 0.9206 (mmtm) cc_final: 0.8922 (mmtm) REVERT: C 58 ASP cc_start: 0.7749 (t0) cc_final: 0.7173 (t0) REVERT: C 185 LYS cc_start: 0.8841 (ttmt) cc_final: 0.8500 (ttmm) REVERT: C 328 VAL cc_start: 0.9440 (t) cc_final: 0.9160 (p) REVERT: D 58 ASP cc_start: 0.7724 (t0) cc_final: 0.7158 (t0) REVERT: D 185 LYS cc_start: 0.8836 (ttmt) cc_final: 0.8522 (ttmm) REVERT: D 282 GLU cc_start: 0.7171 (mp0) cc_final: 0.6869 (mp0) REVERT: D 328 VAL cc_start: 0.9435 (t) cc_final: 0.9162 (p) REVERT: E 264 GLN cc_start: 0.8579 (tp-100) cc_final: 0.8150 (tm-30) REVERT: E 432 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8393 (t80) REVERT: E 480 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7298 (tttm) REVERT: E 483 GLN cc_start: 0.7831 (mt0) cc_final: 0.7483 (mt0) REVERT: E 739 TRP cc_start: 0.6586 (OUTLIER) cc_final: 0.5730 (t60) REVERT: E 1125 PHE cc_start: 0.7760 (t80) cc_final: 0.7433 (t80) REVERT: E 1198 LEU cc_start: 0.9276 (tp) cc_final: 0.8963 (mt) REVERT: E 1283 LEU cc_start: 0.8841 (mt) cc_final: 0.8638 (tp) REVERT: E 1306 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7703 (tp30) REVERT: F 96 ASP cc_start: 0.8372 (t0) cc_final: 0.7920 (t0) REVERT: F 168 ARG cc_start: 0.5118 (mtt90) cc_final: 0.4628 (mtm-85) REVERT: F 230 TYR cc_start: 0.9153 (m-80) cc_final: 0.8891 (m-80) REVERT: F 264 GLN cc_start: 0.8584 (tp-100) cc_final: 0.8148 (tm-30) REVERT: F 402 MET cc_start: 0.6030 (tmm) cc_final: 0.4136 (tmm) REVERT: F 432 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8393 (t80) REVERT: F 483 GLN cc_start: 0.7822 (mt0) cc_final: 0.7488 (mt0) REVERT: F 739 TRP cc_start: 0.6574 (OUTLIER) cc_final: 0.5709 (t60) REVERT: F 1125 PHE cc_start: 0.7674 (t80) cc_final: 0.7318 (t80) REVERT: F 1198 LEU cc_start: 0.9281 (tp) cc_final: 0.8961 (mt) REVERT: F 1292 SER cc_start: 0.8816 (m) cc_final: 0.8529 (p) REVERT: F 1306 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7697 (tp30) REVERT: G 145 LEU cc_start: 0.8924 (tt) cc_final: 0.8650 (tp) REVERT: G 168 ARG cc_start: 0.5284 (mtt90) cc_final: 0.4814 (mtm-85) REVERT: G 226 SER cc_start: 0.8888 (m) cc_final: 0.8639 (p) REVERT: G 230 TYR cc_start: 0.9143 (m-80) cc_final: 0.8888 (m-80) REVERT: G 264 GLN cc_start: 0.8584 (tp-100) cc_final: 0.8161 (tm-30) REVERT: G 402 MET cc_start: 0.6029 (tmm) cc_final: 0.4144 (tmm) REVERT: G 432 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8402 (t80) REVERT: G 483 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7857 (mm-40) REVERT: G 739 TRP cc_start: 0.6585 (OUTLIER) cc_final: 0.5726 (t60) REVERT: G 1125 PHE cc_start: 0.7676 (t80) cc_final: 0.7216 (t80) REVERT: G 1143 LEU cc_start: 0.9049 (tt) cc_final: 0.8737 (tt) REVERT: G 1145 ARG cc_start: 0.8776 (ttp80) cc_final: 0.8532 (ttp80) REVERT: G 1198 LEU cc_start: 0.9305 (tp) cc_final: 0.9057 (mt) REVERT: G 1225 GLN cc_start: 0.8924 (mm-40) cc_final: 0.7893 (mm-40) REVERT: G 1226 LYS cc_start: 0.9036 (mttt) cc_final: 0.8498 (mttp) REVERT: G 1304 ASP cc_start: 0.9016 (t70) cc_final: 0.8795 (t70) REVERT: G 1306 GLU cc_start: 0.8425 (tm-30) cc_final: 0.7669 (tp30) REVERT: H 145 LEU cc_start: 0.8915 (tt) cc_final: 0.8638 (tp) REVERT: H 168 ARG cc_start: 0.5307 (mtt90) cc_final: 0.4846 (mtm-85) REVERT: H 226 SER cc_start: 0.8652 (m) cc_final: 0.8389 (p) REVERT: H 264 GLN cc_start: 0.8588 (tp-100) cc_final: 0.8160 (tm-30) REVERT: H 402 MET cc_start: 0.6030 (tmm) cc_final: 0.4104 (tmm) REVERT: H 432 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.8391 (t80) REVERT: H 483 GLN cc_start: 0.7800 (mt0) cc_final: 0.7455 (mt0) REVERT: H 739 TRP cc_start: 0.6570 (OUTLIER) cc_final: 0.5756 (t60) REVERT: H 1145 ARG cc_start: 0.8470 (ttp80) cc_final: 0.7744 (tmm160) REVERT: H 1198 LEU cc_start: 0.9282 (tp) cc_final: 0.8968 (mt) REVERT: H 1225 GLN cc_start: 0.8928 (mm-40) cc_final: 0.7907 (mm-40) REVERT: H 1226 LYS cc_start: 0.9038 (mttt) cc_final: 0.8505 (mttp) REVERT: H 1253 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7738 (mm-30) REVERT: H 1306 GLU cc_start: 0.8415 (tm-30) cc_final: 0.7725 (tp30) outliers start: 245 outliers final: 191 residues processed: 1125 average time/residue: 0.2365 time to fit residues: 461.2801 Evaluate side-chains 1119 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 918 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 97 HIS Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 223 ASN Chi-restraints excluded: chain E residue 292 CYS Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 432 PHE Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 474 GLN Chi-restraints excluded: chain E residue 480 LYS Chi-restraints excluded: chain E residue 739 TRP Chi-restraints excluded: chain E residue 1140 LEU Chi-restraints excluded: chain E residue 1169 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1202 SER Chi-restraints excluded: chain E residue 1204 PHE Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1250 VAL Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1285 LEU Chi-restraints excluded: chain E residue 1307 ILE Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 223 ASN Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 432 PHE Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 739 TRP Chi-restraints excluded: chain F residue 1129 CYS Chi-restraints excluded: chain F residue 1140 LEU Chi-restraints excluded: chain F residue 1146 SER Chi-restraints excluded: chain F residue 1169 LEU Chi-restraints excluded: chain F residue 1175 CYS Chi-restraints excluded: chain F residue 1202 SER Chi-restraints excluded: chain F residue 1227 LEU Chi-restraints excluded: chain F residue 1250 VAL Chi-restraints excluded: chain F residue 1261 LEU Chi-restraints excluded: chain F residue 1272 LEU Chi-restraints excluded: chain F residue 1283 LEU Chi-restraints excluded: chain F residue 1285 LEU Chi-restraints excluded: chain F residue 1316 HIS Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 65 TRP Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 320 ILE Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 366 LEU Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 373 LEU Chi-restraints excluded: chain G residue 418 CYS Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 432 PHE Chi-restraints excluded: chain G residue 449 VAL Chi-restraints excluded: chain G residue 483 GLN Chi-restraints excluded: chain G residue 739 TRP Chi-restraints excluded: chain G residue 1129 CYS Chi-restraints excluded: chain G residue 1140 LEU Chi-restraints excluded: chain G residue 1175 CYS Chi-restraints excluded: chain G residue 1202 SER Chi-restraints excluded: chain G residue 1227 LEU Chi-restraints excluded: chain G residue 1250 VAL Chi-restraints excluded: chain G residue 1261 LEU Chi-restraints excluded: chain G residue 1272 LEU Chi-restraints excluded: chain G residue 1316 HIS Chi-restraints excluded: chain H residue 44 PHE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 292 CYS Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 320 ILE Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain H residue 361 LEU Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 418 CYS Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 432 PHE Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 449 VAL Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain H residue 473 VAL Chi-restraints excluded: chain H residue 474 GLN Chi-restraints excluded: chain H residue 739 TRP Chi-restraints excluded: chain H residue 1140 LEU Chi-restraints excluded: chain H residue 1157 ILE Chi-restraints excluded: chain H residue 1169 LEU Chi-restraints excluded: chain H residue 1175 CYS Chi-restraints excluded: chain H residue 1202 SER Chi-restraints excluded: chain H residue 1227 LEU Chi-restraints excluded: chain H residue 1250 VAL Chi-restraints excluded: chain H residue 1261 LEU Chi-restraints excluded: chain H residue 1272 LEU Chi-restraints excluded: chain H residue 1283 LEU Chi-restraints excluded: chain H residue 1285 LEU Chi-restraints excluded: chain H residue 1316 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 354 optimal weight: 8.9990 chunk 119 optimal weight: 0.4980 chunk 450 optimal weight: 30.0000 chunk 418 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 199 optimal weight: 40.0000 chunk 5 optimal weight: 2.9990 chunk 441 optimal weight: 9.9990 chunk 120 optimal weight: 7.9990 chunk 485 optimal weight: 20.0000 chunk 218 optimal weight: 7.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 173 GLN E 474 GLN ** F 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 474 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.133791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.106275 restraints weight = 119967.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.108904 restraints weight = 59161.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.110625 restraints weight = 36468.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.111785 restraints weight = 26014.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.112537 restraints weight = 20509.031| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 45740 Z= 0.197 Angle : 0.667 12.796 62732 Z= 0.338 Chirality : 0.045 0.251 7672 Planarity : 0.004 0.105 8064 Dihedral : 5.110 73.317 6904 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 7.10 % Allowed : 20.06 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.11), residues: 6464 helix: 1.99 (0.08), residues: 4036 sheet: -0.57 (0.23), residues: 512 loop : -0.49 (0.15), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 314 TYR 0.021 0.001 TYR F1230 PHE 0.034 0.002 PHE H1164 TRP 0.027 0.001 TRP H 688 HIS 0.006 0.001 HIS E 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 (45736) covalent geometry : angle 0.66634 / 0.34 (62724) SS BOND : bond 0.00765 / 0.38 ( 4) SS BOND : angle 2.32677 / 1.46 ( 8) hydrogen bonds : bond 0.04532 / 3.06 ( 3333) hydrogen bonds : angle 4.12549 / 3.01 ( 9783) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1205 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 253 poor density : 952 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.9246 (mmtm) cc_final: 0.9008 (mmtm) REVERT: A 58 ASP cc_start: 0.7731 (t0) cc_final: 0.7217 (t0) REVERT: A 185 LYS cc_start: 0.8879 (ttmt) cc_final: 0.8599 (ttmm) REVERT: A 211 ILE cc_start: 0.9431 (mp) cc_final: 0.9210 (mp) REVERT: B 41 ASN cc_start: 0.8848 (t0) cc_final: 0.8629 (t0) REVERT: B 58 ASP cc_start: 0.7726 (t0) cc_final: 0.7195 (t0) REVERT: B 185 LYS cc_start: 0.8880 (ttmt) cc_final: 0.8607 (ttmm) REVERT: B 211 ILE cc_start: 0.9433 (mp) cc_final: 0.9209 (mp) REVERT: B 328 VAL cc_start: 0.9508 (t) cc_final: 0.9273 (p) REVERT: C 41 ASN cc_start: 0.8813 (t0) cc_final: 0.8517 (t0) REVERT: C 47 LYS cc_start: 0.9215 (mmtm) cc_final: 0.9004 (mmtm) REVERT: C 58 ASP cc_start: 0.7734 (t0) cc_final: 0.7191 (t0) REVERT: C 185 LYS cc_start: 0.8885 (ttmt) cc_final: 0.8604 (ttmm) REVERT: C 328 VAL cc_start: 0.9476 (t) cc_final: 0.9226 (p) REVERT: D 58 ASP cc_start: 0.7718 (t0) cc_final: 0.7207 (t0) REVERT: D 185 LYS cc_start: 0.8875 (ttmt) cc_final: 0.8574 (ttmm) REVERT: D 221 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8664 (ttp-170) REVERT: D 328 VAL cc_start: 0.9477 (t) cc_final: 0.9229 (p) REVERT: E 264 GLN cc_start: 0.8573 (tp-100) cc_final: 0.8155 (tm-30) REVERT: E 402 MET cc_start: 0.6067 (tmm) cc_final: 0.4428 (tmm) REVERT: E 432 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8398 (t80) REVERT: E 483 GLN cc_start: 0.7866 (mt0) cc_final: 0.7540 (mt0) REVERT: E 739 TRP cc_start: 0.6520 (OUTLIER) cc_final: 0.5687 (t60) REVERT: E 1125 PHE cc_start: 0.7747 (t80) cc_final: 0.7464 (t80) REVERT: E 1145 ARG cc_start: 0.8542 (ttp80) cc_final: 0.7794 (tmm160) REVERT: E 1191 GLN cc_start: 0.8286 (pp30) cc_final: 0.8034 (pp30) REVERT: E 1198 LEU cc_start: 0.9294 (tp) cc_final: 0.8942 (mt) REVERT: E 1225 GLN cc_start: 0.8972 (mm-40) cc_final: 0.7924 (mm-40) REVERT: E 1304 ASP cc_start: 0.9055 (t70) cc_final: 0.8795 (t70) REVERT: E 1306 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7654 (tp30) REVERT: F 96 ASP cc_start: 0.8318 (t0) cc_final: 0.7923 (t0) REVERT: F 168 ARG cc_start: 0.5269 (mtt90) cc_final: 0.4718 (mtm-85) REVERT: F 230 TYR cc_start: 0.9167 (m-80) cc_final: 0.8883 (m-80) REVERT: F 264 GLN cc_start: 0.8572 (tp-100) cc_final: 0.8154 (tm-30) REVERT: F 402 MET cc_start: 0.6083 (tmm) cc_final: 0.4266 (tmm) REVERT: F 432 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8386 (t80) REVERT: F 483 GLN cc_start: 0.7876 (mt0) cc_final: 0.7529 (mt0) REVERT: F 739 TRP cc_start: 0.6500 (OUTLIER) cc_final: 0.5655 (t60) REVERT: F 1125 PHE cc_start: 0.7543 (t80) cc_final: 0.7243 (t80) REVERT: F 1145 ARG cc_start: 0.8557 (ttp80) cc_final: 0.7813 (tmm160) REVERT: F 1191 GLN cc_start: 0.8218 (pp30) cc_final: 0.7973 (pp30) REVERT: F 1198 LEU cc_start: 0.9300 (tp) cc_final: 0.8957 (mt) REVERT: F 1292 SER cc_start: 0.8788 (m) cc_final: 0.8425 (p) REVERT: F 1306 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7629 (tp30) REVERT: G 145 LEU cc_start: 0.8905 (tt) cc_final: 0.8627 (tp) REVERT: G 168 ARG cc_start: 0.5415 (mtt90) cc_final: 0.4688 (mtm-85) REVERT: G 226 SER cc_start: 0.9018 (m) cc_final: 0.8720 (p) REVERT: G 230 TYR cc_start: 0.9161 (m-80) cc_final: 0.8880 (m-80) REVERT: G 264 GLN cc_start: 0.8593 (tp-100) cc_final: 0.8165 (tm-30) REVERT: G 402 MET cc_start: 0.6073 (tmm) cc_final: 0.4262 (tmm) REVERT: G 432 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8416 (t80) REVERT: G 483 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.7930 (mm110) REVERT: G 739 TRP cc_start: 0.6520 (OUTLIER) cc_final: 0.5672 (t60) REVERT: G 1125 PHE cc_start: 0.7509 (t80) cc_final: 0.7256 (t80) REVERT: G 1145 ARG cc_start: 0.8803 (ttp80) cc_final: 0.8560 (ttp80) REVERT: G 1191 GLN cc_start: 0.8247 (pp30) cc_final: 0.7999 (pp30) REVERT: G 1198 LEU cc_start: 0.9308 (tp) cc_final: 0.9058 (mt) REVERT: G 1226 LYS cc_start: 0.9068 (mttt) cc_final: 0.8626 (mttp) REVERT: G 1229 GLU cc_start: 0.8140 (mp0) cc_final: 0.7925 (pm20) REVERT: G 1253 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7773 (mm-30) REVERT: H 168 ARG cc_start: 0.5463 (mtt90) cc_final: 0.4736 (mtm-85) REVERT: H 226 SER cc_start: 0.8677 (m) cc_final: 0.8442 (p) REVERT: H 264 GLN cc_start: 0.8590 (tp-100) cc_final: 0.8162 (tm-30) REVERT: H 402 MET cc_start: 0.6067 (tmm) cc_final: 0.4216 (tmm) REVERT: H 432 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.8415 (t80) REVERT: H 483 GLN cc_start: 0.7886 (mt0) cc_final: 0.7533 (mt0) REVERT: H 739 TRP cc_start: 0.6503 (OUTLIER) cc_final: 0.5718 (t60) REVERT: H 1191 GLN cc_start: 0.8218 (pp30) cc_final: 0.7979 (pp30) REVERT: H 1198 LEU cc_start: 0.9294 (tp) cc_final: 0.8944 (mt) REVERT: H 1226 LYS cc_start: 0.9067 (mttt) cc_final: 0.8625 (mttp) REVERT: H 1229 GLU cc_start: 0.8141 (mp0) cc_final: 0.7930 (pm20) REVERT: H 1253 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7731 (mm-30) outliers start: 253 outliers final: 203 residues processed: 1089 average time/residue: 0.2362 time to fit residues: 447.2056 Evaluate side-chains 1130 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 917 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 221 ARG Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 223 ASN Chi-restraints excluded: chain E residue 292 CYS Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 432 PHE Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 739 TRP Chi-restraints excluded: chain E residue 1140 LEU Chi-restraints excluded: chain E residue 1146 SER Chi-restraints excluded: chain E residue 1157 ILE Chi-restraints excluded: chain E residue 1169 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1202 SER Chi-restraints excluded: chain E residue 1204 PHE Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1250 VAL Chi-restraints excluded: chain E residue 1253 GLU Chi-restraints excluded: chain E residue 1258 CYS Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1285 LEU Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 221 PHE Chi-restraints excluded: chain F residue 223 ASN Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 432 PHE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 739 TRP Chi-restraints excluded: chain F residue 1129 CYS Chi-restraints excluded: chain F residue 1140 LEU Chi-restraints excluded: chain F residue 1169 LEU Chi-restraints excluded: chain F residue 1175 CYS Chi-restraints excluded: chain F residue 1202 SER Chi-restraints excluded: chain F residue 1204 PHE Chi-restraints excluded: chain F residue 1227 LEU Chi-restraints excluded: chain F residue 1250 VAL Chi-restraints excluded: chain F residue 1261 LEU Chi-restraints excluded: chain F residue 1272 LEU Chi-restraints excluded: chain F residue 1283 LEU Chi-restraints excluded: chain F residue 1285 LEU Chi-restraints excluded: chain F residue 1316 HIS Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 65 TRP Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 320 ILE Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 373 LEU Chi-restraints excluded: chain G residue 418 CYS Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 432 PHE Chi-restraints excluded: chain G residue 449 VAL Chi-restraints excluded: chain G residue 473 VAL Chi-restraints excluded: chain G residue 483 GLN Chi-restraints excluded: chain G residue 548 THR Chi-restraints excluded: chain G residue 739 TRP Chi-restraints excluded: chain G residue 1129 CYS Chi-restraints excluded: chain G residue 1140 LEU Chi-restraints excluded: chain G residue 1175 CYS Chi-restraints excluded: chain G residue 1202 SER Chi-restraints excluded: chain G residue 1227 LEU Chi-restraints excluded: chain G residue 1250 VAL Chi-restraints excluded: chain G residue 1272 LEU Chi-restraints excluded: chain G residue 1285 LEU Chi-restraints excluded: chain G residue 1307 ILE Chi-restraints excluded: chain G residue 1316 HIS Chi-restraints excluded: chain H residue 44 PHE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 292 CYS Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 320 ILE Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain H residue 361 LEU Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 391 ILE Chi-restraints excluded: chain H residue 418 CYS Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 432 PHE Chi-restraints excluded: chain H residue 449 VAL Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain H residue 473 VAL Chi-restraints excluded: chain H residue 548 THR Chi-restraints excluded: chain H residue 739 TRP Chi-restraints excluded: chain H residue 1140 LEU Chi-restraints excluded: chain H residue 1157 ILE Chi-restraints excluded: chain H residue 1175 CYS Chi-restraints excluded: chain H residue 1202 SER Chi-restraints excluded: chain H residue 1227 LEU Chi-restraints excluded: chain H residue 1250 VAL Chi-restraints excluded: chain H residue 1258 CYS Chi-restraints excluded: chain H residue 1272 LEU Chi-restraints excluded: chain H residue 1283 LEU Chi-restraints excluded: chain H residue 1285 LEU Chi-restraints excluded: chain H residue 1316 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 473 optimal weight: 30.0000 chunk 481 optimal weight: 20.0000 chunk 262 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 329 optimal weight: 7.9990 chunk 570 optimal weight: 6.9990 chunk 579 optimal weight: 30.0000 chunk 253 optimal weight: 9.9990 chunk 186 optimal weight: 30.0000 chunk 518 optimal weight: 50.0000 chunk 346 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 ASN F 103 HIS F 166 GLN F 262 ASN ** F 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 262 ASN G 483 GLN H 262 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.130409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.102554 restraints weight = 121609.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.105194 restraints weight = 59167.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.106956 restraints weight = 36153.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.108134 restraints weight = 25650.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.108893 restraints weight = 20117.598| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.6230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 45740 Z= 0.288 Angle : 0.754 11.205 62732 Z= 0.388 Chirality : 0.048 0.228 7672 Planarity : 0.004 0.094 8064 Dihedral : 5.263 80.848 6900 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 7.49 % Allowed : 20.57 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.11), residues: 6464 helix: 1.66 (0.08), residues: 4052 sheet: -0.79 (0.23), residues: 504 loop : -0.78 (0.15), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 314 TYR 0.019 0.002 TYR F1230 PHE 0.032 0.002 PHE F 169 TRP 0.041 0.002 TRP H 688 HIS 0.008 0.001 HIS G 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.29 (45736) covalent geometry : angle 0.75290 / 0.39 (62724) SS BOND : bond 0.01036 / 0.52 ( 4) SS BOND : angle 2.83772 / 1.72 ( 8) hydrogen bonds : bond 0.05000 / 3.37 ( 3333) hydrogen bonds : angle 4.48827 / 3.28 ( 9783) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1180 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 267 poor density : 913 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.7845 (t0) cc_final: 0.7395 (t0) REVERT: B 41 ASN cc_start: 0.8969 (t0) cc_final: 0.8743 (t0) REVERT: B 47 LYS cc_start: 0.9285 (mmtm) cc_final: 0.9029 (mmtp) REVERT: B 58 ASP cc_start: 0.7812 (t0) cc_final: 0.7368 (t0) REVERT: B 328 VAL cc_start: 0.9456 (t) cc_final: 0.9192 (p) REVERT: C 41 ASN cc_start: 0.8942 (t0) cc_final: 0.8707 (t0) REVERT: C 58 ASP cc_start: 0.7839 (t0) cc_final: 0.7377 (t0) REVERT: C 328 VAL cc_start: 0.9431 (t) cc_final: 0.9161 (p) REVERT: D 47 LYS cc_start: 0.9281 (mmtm) cc_final: 0.9024 (mmtp) REVERT: D 58 ASP cc_start: 0.7829 (t0) cc_final: 0.7377 (t0) REVERT: D 221 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8617 (ttp-170) REVERT: D 328 VAL cc_start: 0.9440 (t) cc_final: 0.9182 (p) REVERT: E 264 GLN cc_start: 0.8680 (tp-100) cc_final: 0.8335 (tm-30) REVERT: E 402 MET cc_start: 0.5997 (tmm) cc_final: 0.4874 (tmm) REVERT: E 432 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.8460 (t80) REVERT: E 483 GLN cc_start: 0.8019 (mt0) cc_final: 0.7698 (mt0) REVERT: E 739 TRP cc_start: 0.6781 (OUTLIER) cc_final: 0.5637 (t60) REVERT: E 1191 GLN cc_start: 0.8355 (pp30) cc_final: 0.8090 (pp30) REVERT: E 1229 GLU cc_start: 0.8260 (mp0) cc_final: 0.8007 (pm20) REVERT: E 1304 ASP cc_start: 0.9076 (t70) cc_final: 0.8796 (p0) REVERT: F 96 ASP cc_start: 0.8422 (t0) cc_final: 0.8068 (t0) REVERT: F 264 GLN cc_start: 0.8673 (tp-100) cc_final: 0.8332 (tm-30) REVERT: F 306 ARG cc_start: 0.8582 (tpp80) cc_final: 0.8351 (tpt-90) REVERT: F 402 MET cc_start: 0.5930 (tmm) cc_final: 0.4909 (tmm) REVERT: F 432 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8427 (t80) REVERT: F 739 TRP cc_start: 0.6766 (OUTLIER) cc_final: 0.5622 (t60) REVERT: F 1191 GLN cc_start: 0.8360 (pp30) cc_final: 0.8095 (pp30) REVERT: G 145 LEU cc_start: 0.9115 (tt) cc_final: 0.8881 (tp) REVERT: G 168 ARG cc_start: 0.5747 (mtt90) cc_final: 0.5311 (mtm-85) REVERT: G 264 GLN cc_start: 0.8686 (tp-100) cc_final: 0.8361 (tm-30) REVERT: G 402 MET cc_start: 0.5900 (tmm) cc_final: 0.4870 (tmm) REVERT: G 432 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8467 (t80) REVERT: G 739 TRP cc_start: 0.6775 (OUTLIER) cc_final: 0.5634 (t60) REVERT: G 1145 ARG cc_start: 0.8776 (ttp80) cc_final: 0.8543 (ttp80) REVERT: G 1198 LEU cc_start: 0.9319 (tp) cc_final: 0.9047 (mt) REVERT: G 1253 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7782 (mm-30) REVERT: H 139 LEU cc_start: 0.9386 (mt) cc_final: 0.9098 (mt) REVERT: H 168 ARG cc_start: 0.5778 (mtt90) cc_final: 0.5346 (mtm-85) REVERT: H 264 GLN cc_start: 0.8689 (tp-100) cc_final: 0.8340 (tm-30) REVERT: H 402 MET cc_start: 0.5907 (tmm) cc_final: 0.4868 (tmm) REVERT: H 432 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.8432 (t80) REVERT: H 441 MET cc_start: 0.8919 (mmm) cc_final: 0.8679 (mmt) REVERT: H 483 GLN cc_start: 0.7997 (mt0) cc_final: 0.7667 (mt0) REVERT: H 739 TRP cc_start: 0.6776 (OUTLIER) cc_final: 0.5695 (t60) REVERT: H 1145 ARG cc_start: 0.8549 (ttp80) cc_final: 0.7765 (tmm160) REVERT: H 1191 GLN cc_start: 0.8366 (pp30) cc_final: 0.8100 (pp30) REVERT: H 1253 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7742 (mm-30) outliers start: 267 outliers final: 209 residues processed: 1057 average time/residue: 0.2243 time to fit residues: 412.3791 Evaluate side-chains 1066 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 848 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 221 ARG Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 198 PHE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 223 ASN Chi-restraints excluded: chain E residue 292 CYS Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 432 PHE Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 739 TRP Chi-restraints excluded: chain E residue 1140 LEU Chi-restraints excluded: chain E residue 1157 ILE Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1202 SER Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1253 GLU Chi-restraints excluded: chain E residue 1258 CYS Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1285 LEU Chi-restraints excluded: chain E residue 1307 ILE Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 198 PHE Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 221 PHE Chi-restraints excluded: chain F residue 223 ASN Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 432 PHE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 739 TRP Chi-restraints excluded: chain F residue 1129 CYS Chi-restraints excluded: chain F residue 1140 LEU Chi-restraints excluded: chain F residue 1157 ILE Chi-restraints excluded: chain F residue 1175 CYS Chi-restraints excluded: chain F residue 1202 SER Chi-restraints excluded: chain F residue 1227 LEU Chi-restraints excluded: chain F residue 1261 LEU Chi-restraints excluded: chain F residue 1272 LEU Chi-restraints excluded: chain F residue 1285 LEU Chi-restraints excluded: chain F residue 1307 ILE Chi-restraints excluded: chain F residue 1316 HIS Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 65 TRP Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 198 PHE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 320 ILE Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 373 LEU Chi-restraints excluded: chain G residue 391 ILE Chi-restraints excluded: chain G residue 418 CYS Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 432 PHE Chi-restraints excluded: chain G residue 449 VAL Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 473 VAL Chi-restraints excluded: chain G residue 548 THR Chi-restraints excluded: chain G residue 739 TRP Chi-restraints excluded: chain G residue 1140 LEU Chi-restraints excluded: chain G residue 1157 ILE Chi-restraints excluded: chain G residue 1175 CYS Chi-restraints excluded: chain G residue 1202 SER Chi-restraints excluded: chain G residue 1227 LEU Chi-restraints excluded: chain G residue 1258 CYS Chi-restraints excluded: chain G residue 1272 LEU Chi-restraints excluded: chain G residue 1285 LEU Chi-restraints excluded: chain G residue 1307 ILE Chi-restraints excluded: chain G residue 1316 HIS Chi-restraints excluded: chain H residue 44 PHE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 198 PHE Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 257 MET Chi-restraints excluded: chain H residue 292 CYS Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 320 ILE Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain H residue 361 LEU Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 391 ILE Chi-restraints excluded: chain H residue 418 CYS Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 432 PHE Chi-restraints excluded: chain H residue 449 VAL Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain H residue 473 VAL Chi-restraints excluded: chain H residue 548 THR Chi-restraints excluded: chain H residue 739 TRP Chi-restraints excluded: chain H residue 1157 ILE Chi-restraints excluded: chain H residue 1175 CYS Chi-restraints excluded: chain H residue 1202 SER Chi-restraints excluded: chain H residue 1227 LEU Chi-restraints excluded: chain H residue 1258 CYS Chi-restraints excluded: chain H residue 1272 LEU Chi-restraints excluded: chain H residue 1285 LEU Chi-restraints excluded: chain H residue 1307 ILE Chi-restraints excluded: chain H residue 1316 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 193 optimal weight: 9.9990 chunk 151 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 448 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 chunk 631 optimal weight: 0.5980 chunk 490 optimal weight: 2.9990 chunk 526 optimal weight: 0.2980 chunk 551 optimal weight: 5.9990 chunk 341 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN B 277 HIS D 277 HIS E 262 ASN F 72 ASN F 262 ASN F 427 GLN G 72 ASN G 262 ASN H 262 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.134928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.106638 restraints weight = 121358.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.109497 restraints weight = 57904.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.111345 restraints weight = 34785.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.112587 restraints weight = 24444.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.113393 restraints weight = 19069.220| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.6263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 45740 Z= 0.137 Angle : 0.653 11.638 62732 Z= 0.326 Chirality : 0.044 0.278 7672 Planarity : 0.004 0.073 8064 Dihedral : 4.818 73.857 6896 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.88 % Allowed : 24.13 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.11), residues: 6464 helix: 2.09 (0.08), residues: 4052 sheet: -0.61 (0.23), residues: 512 loop : -0.59 (0.15), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F1145 TYR 0.023 0.001 TYR F1230 PHE 0.037 0.002 PHE B 168 TRP 0.021 0.001 TRP H 688 HIS 0.007 0.001 HIS F 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (45736) covalent geometry : angle 0.65263 / 0.33 (62724) SS BOND : bond 0.00110 / 0.06 ( 4) SS BOND : angle 1.31627 / 0.80 ( 8) hydrogen bonds : bond 0.04346 / 2.94 ( 3333) hydrogen bonds : angle 4.04591 / 2.95 ( 9783) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1143 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 969 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.7649 (t0) cc_final: 0.7130 (t0) REVERT: B 41 ASN cc_start: 0.8920 (t0) cc_final: 0.8671 (t0) REVERT: B 47 LYS cc_start: 0.9158 (mmtm) cc_final: 0.8929 (mmtp) REVERT: B 58 ASP cc_start: 0.7606 (t0) cc_final: 0.7103 (t0) REVERT: B 160 ASN cc_start: 0.8759 (m-40) cc_final: 0.8472 (t0) REVERT: B 169 MET cc_start: 0.8820 (mtt) cc_final: 0.8531 (mtp) REVERT: B 328 VAL cc_start: 0.9316 (t) cc_final: 0.9081 (p) REVERT: C 41 ASN cc_start: 0.8871 (t0) cc_final: 0.8541 (t0) REVERT: C 58 ASP cc_start: 0.7652 (t0) cc_final: 0.7118 (t0) REVERT: C 160 ASN cc_start: 0.8761 (m-40) cc_final: 0.8445 (t0) REVERT: C 328 VAL cc_start: 0.9300 (t) cc_final: 0.9063 (p) REVERT: D 47 LYS cc_start: 0.9182 (mmtm) cc_final: 0.8967 (mmtp) REVERT: D 58 ASP cc_start: 0.7628 (t0) cc_final: 0.7123 (t0) REVERT: D 328 VAL cc_start: 0.9345 (t) cc_final: 0.9120 (p) REVERT: E 248 ARG cc_start: 0.8033 (ptt180) cc_final: 0.7802 (ptt-90) REVERT: E 257 MET cc_start: 0.8332 (mtt) cc_final: 0.8025 (mtt) REVERT: E 264 GLN cc_start: 0.8569 (tp-100) cc_final: 0.8115 (tm-30) REVERT: E 402 MET cc_start: 0.6067 (tmm) cc_final: 0.4803 (tmm) REVERT: E 432 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8341 (t80) REVERT: E 739 TRP cc_start: 0.6724 (OUTLIER) cc_final: 0.5707 (t60) REVERT: E 1145 ARG cc_start: 0.8594 (ttp80) cc_final: 0.7827 (tmm160) REVERT: E 1191 GLN cc_start: 0.8208 (pp30) cc_final: 0.7980 (pp30) REVERT: E 1198 LEU cc_start: 0.9233 (tp) cc_final: 0.8977 (mt) REVERT: E 1229 GLU cc_start: 0.8242 (mp0) cc_final: 0.8009 (pm20) REVERT: E 1304 ASP cc_start: 0.9023 (t70) cc_final: 0.8743 (p0) REVERT: F 41 PHE cc_start: 0.8165 (m-80) cc_final: 0.7905 (m-80) REVERT: F 168 ARG cc_start: 0.5259 (mtt90) cc_final: 0.4551 (mtm-85) REVERT: F 248 ARG cc_start: 0.8029 (ptt180) cc_final: 0.7798 (ptt-90) REVERT: F 257 MET cc_start: 0.8335 (mtt) cc_final: 0.8100 (mtt) REVERT: F 264 GLN cc_start: 0.8557 (tp-100) cc_final: 0.8101 (tm-30) REVERT: F 432 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.8314 (t80) REVERT: F 739 TRP cc_start: 0.6689 (OUTLIER) cc_final: 0.5664 (t60) REVERT: F 1125 PHE cc_start: 0.7491 (t80) cc_final: 0.7270 (t80) REVERT: F 1191 GLN cc_start: 0.8199 (pp30) cc_final: 0.7967 (pp30) REVERT: F 1198 LEU cc_start: 0.9234 (tp) cc_final: 0.8965 (mt) REVERT: F 1230 TYR cc_start: 0.8778 (m-80) cc_final: 0.8567 (m-80) REVERT: G 41 PHE cc_start: 0.8107 (m-80) cc_final: 0.7884 (m-80) REVERT: G 168 ARG cc_start: 0.5595 (mtt90) cc_final: 0.5219 (mtm-85) REVERT: G 257 MET cc_start: 0.8319 (mtt) cc_final: 0.8113 (mtt) REVERT: G 264 GLN cc_start: 0.8584 (tp-100) cc_final: 0.8126 (tm-30) REVERT: G 402 MET cc_start: 0.5980 (tmm) cc_final: 0.4798 (tmm) REVERT: G 432 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8321 (t80) REVERT: G 739 TRP cc_start: 0.6690 (OUTLIER) cc_final: 0.5662 (t60) REVERT: G 1125 PHE cc_start: 0.7257 (t80) cc_final: 0.7048 (t80) REVERT: G 1145 ARG cc_start: 0.8829 (ttp80) cc_final: 0.8599 (ttp80) REVERT: G 1198 LEU cc_start: 0.9215 (tp) cc_final: 0.8972 (mt) REVERT: G 1253 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7792 (mm-30) REVERT: H 41 PHE cc_start: 0.8148 (m-80) cc_final: 0.7920 (m-80) REVERT: H 168 ARG cc_start: 0.5621 (mtt90) cc_final: 0.4980 (mtm-85) REVERT: H 264 GLN cc_start: 0.8583 (tp-100) cc_final: 0.8122 (tm-30) REVERT: H 402 MET cc_start: 0.6020 (tmm) cc_final: 0.4832 (tmm) REVERT: H 432 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8351 (t80) REVERT: H 445 ILE cc_start: 0.8682 (mm) cc_final: 0.8445 (mm) REVERT: H 739 TRP cc_start: 0.6664 (OUTLIER) cc_final: 0.5708 (t60) REVERT: H 1198 LEU cc_start: 0.9238 (tp) cc_final: 0.8978 (mt) REVERT: H 1253 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7639 (mm-30) outliers start: 174 outliers final: 131 residues processed: 1064 average time/residue: 0.2076 time to fit residues: 383.6809 Evaluate side-chains 1043 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 904 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 292 CYS Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 432 PHE Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 739 TRP Chi-restraints excluded: chain E residue 1133 ASP Chi-restraints excluded: chain E residue 1140 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1253 GLU Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 221 PHE Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 432 PHE Chi-restraints excluded: chain F residue 435 CYS Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 739 TRP Chi-restraints excluded: chain F residue 1129 CYS Chi-restraints excluded: chain F residue 1140 LEU Chi-restraints excluded: chain F residue 1175 CYS Chi-restraints excluded: chain F residue 1227 LEU Chi-restraints excluded: chain F residue 1272 LEU Chi-restraints excluded: chain F residue 1316 HIS Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 65 TRP Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 373 LEU Chi-restraints excluded: chain G residue 391 ILE Chi-restraints excluded: chain G residue 418 CYS Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 432 PHE Chi-restraints excluded: chain G residue 473 VAL Chi-restraints excluded: chain G residue 548 THR Chi-restraints excluded: chain G residue 739 TRP Chi-restraints excluded: chain G residue 1129 CYS Chi-restraints excluded: chain G residue 1140 LEU Chi-restraints excluded: chain G residue 1175 CYS Chi-restraints excluded: chain G residue 1202 SER Chi-restraints excluded: chain G residue 1227 LEU Chi-restraints excluded: chain G residue 1272 LEU Chi-restraints excluded: chain G residue 1316 HIS Chi-restraints excluded: chain H residue 44 PHE Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 292 CYS Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain H residue 361 LEU Chi-restraints excluded: chain H residue 391 ILE Chi-restraints excluded: chain H residue 418 CYS Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 432 PHE Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain H residue 473 VAL Chi-restraints excluded: chain H residue 548 THR Chi-restraints excluded: chain H residue 739 TRP Chi-restraints excluded: chain H residue 1175 CYS Chi-restraints excluded: chain H residue 1202 SER Chi-restraints excluded: chain H residue 1227 LEU Chi-restraints excluded: chain H residue 1258 CYS Chi-restraints excluded: chain H residue 1272 LEU Chi-restraints excluded: chain H residue 1316 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 643 optimal weight: 6.9990 chunk 463 optimal weight: 40.0000 chunk 554 optimal weight: 0.9990 chunk 264 optimal weight: 7.9990 chunk 173 optimal weight: 7.9990 chunk 502 optimal weight: 50.0000 chunk 592 optimal weight: 30.0000 chunk 449 optimal weight: 6.9990 chunk 524 optimal weight: 0.9990 chunk 330 optimal weight: 0.0770 chunk 488 optimal weight: 1.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 HIS ** C 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 444 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.135419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.106894 restraints weight = 122318.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.109715 restraints weight = 58467.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.111604 restraints weight = 35426.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.112840 restraints weight = 24894.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.113678 restraints weight = 19482.665| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.6365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 45740 Z= 0.145 Angle : 0.654 11.847 62732 Z= 0.326 Chirality : 0.045 0.411 7672 Planarity : 0.004 0.067 8064 Dihedral : 4.708 70.539 6896 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.10 % Allowed : 25.87 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.11), residues: 6464 helix: 2.15 (0.08), residues: 4052 sheet: -0.56 (0.23), residues: 512 loop : -0.59 (0.15), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H1145 TYR 0.025 0.001 TYR H1230 PHE 0.037 0.002 PHE B 168 TRP 0.017 0.001 TRP G 688 HIS 0.006 0.001 HIS G 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (45736) covalent geometry : angle 0.65386 / 0.33 (62724) SS BOND : bond 0.00126 / 0.06 ( 4) SS BOND : angle 1.67542 / 1.05 ( 8) hydrogen bonds : bond 0.04293 / 2.92 ( 3333) hydrogen bonds : angle 3.99078 / 2.92 ( 9783) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1038 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 892 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.9258 (mmtp) cc_final: 0.9027 (mmtm) REVERT: A 58 ASP cc_start: 0.7684 (t0) cc_final: 0.7207 (t0) REVERT: B 41 ASN cc_start: 0.8899 (t0) cc_final: 0.8626 (t0) REVERT: B 47 LYS cc_start: 0.9164 (mmtm) cc_final: 0.8939 (mmtp) REVERT: B 58 ASP cc_start: 0.7630 (t0) cc_final: 0.7181 (t0) REVERT: B 160 ASN cc_start: 0.8800 (m-40) cc_final: 0.8478 (t0) REVERT: B 328 VAL cc_start: 0.9299 (t) cc_final: 0.9082 (p) REVERT: C 41 ASN cc_start: 0.8846 (t0) cc_final: 0.8558 (t0) REVERT: C 58 ASP cc_start: 0.7710 (t0) cc_final: 0.7183 (t0) REVERT: C 160 ASN cc_start: 0.8788 (m-40) cc_final: 0.8460 (t0) REVERT: C 328 VAL cc_start: 0.9322 (t) cc_final: 0.9091 (p) REVERT: D 58 ASP cc_start: 0.7673 (t0) cc_final: 0.7226 (t0) REVERT: D 328 VAL cc_start: 0.9368 (t) cc_final: 0.9158 (p) REVERT: E 248 ARG cc_start: 0.8036 (ptt180) cc_final: 0.7797 (ptt-90) REVERT: E 257 MET cc_start: 0.8265 (mtt) cc_final: 0.8021 (mtt) REVERT: E 264 GLN cc_start: 0.8618 (tp-100) cc_final: 0.8158 (tm-30) REVERT: E 432 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.8364 (t80) REVERT: E 739 TRP cc_start: 0.6768 (OUTLIER) cc_final: 0.5683 (t60) REVERT: E 1145 ARG cc_start: 0.8646 (ttp80) cc_final: 0.7908 (tmm160) REVERT: E 1191 GLN cc_start: 0.8145 (pp30) cc_final: 0.7920 (pp30) REVERT: E 1198 LEU cc_start: 0.9256 (tp) cc_final: 0.8987 (mt) REVERT: E 1229 GLU cc_start: 0.8175 (mp0) cc_final: 0.7951 (pm20) REVERT: E 1304 ASP cc_start: 0.9025 (t70) cc_final: 0.8737 (p0) REVERT: F 96 ASP cc_start: 0.8405 (t0) cc_final: 0.8151 (t0) REVERT: F 168 ARG cc_start: 0.5457 (mtt90) cc_final: 0.4750 (mtm-85) REVERT: F 264 GLN cc_start: 0.8582 (tp-100) cc_final: 0.8331 (tm-30) REVERT: F 402 MET cc_start: 0.6383 (tmm) cc_final: 0.5111 (tmm) REVERT: F 432 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.8291 (t80) REVERT: F 739 TRP cc_start: 0.6754 (OUTLIER) cc_final: 0.5674 (t60) REVERT: F 1125 PHE cc_start: 0.7498 (t80) cc_final: 0.7265 (t80) REVERT: F 1145 ARG cc_start: 0.8738 (ttp80) cc_final: 0.7969 (tmm160) REVERT: F 1191 GLN cc_start: 0.8140 (pp30) cc_final: 0.7915 (pp30) REVERT: F 1198 LEU cc_start: 0.9256 (tp) cc_final: 0.8978 (mt) REVERT: F 1230 TYR cc_start: 0.8777 (m-80) cc_final: 0.8526 (m-80) REVERT: G 168 ARG cc_start: 0.5573 (mtt90) cc_final: 0.5153 (mtm-85) REVERT: G 257 MET cc_start: 0.8307 (mtt) cc_final: 0.8071 (mtt) REVERT: G 264 GLN cc_start: 0.8628 (tp-100) cc_final: 0.8163 (tm-30) REVERT: G 402 MET cc_start: 0.5959 (tmm) cc_final: 0.4818 (tmm) REVERT: G 432 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.8313 (t80) REVERT: G 739 TRP cc_start: 0.6748 (OUTLIER) cc_final: 0.5667 (t60) REVERT: G 1145 ARG cc_start: 0.8852 (ttp80) cc_final: 0.8640 (ttp80) REVERT: G 1198 LEU cc_start: 0.9189 (tp) cc_final: 0.8934 (mt) REVERT: G 1253 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7620 (mm-30) REVERT: G 1304 ASP cc_start: 0.8996 (t0) cc_final: 0.8789 (t70) REVERT: H 168 ARG cc_start: 0.5569 (mtt90) cc_final: 0.5153 (mtm-85) REVERT: H 257 MET cc_start: 0.8326 (mtt) cc_final: 0.8079 (mtt) REVERT: H 264 GLN cc_start: 0.8626 (tp-100) cc_final: 0.8161 (tm-30) REVERT: H 432 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.8319 (t80) REVERT: H 739 TRP cc_start: 0.6700 (OUTLIER) cc_final: 0.5701 (t60) REVERT: H 1145 ARG cc_start: 0.8660 (ttp80) cc_final: 0.7914 (tmm160) REVERT: H 1191 GLN cc_start: 0.8133 (pp30) cc_final: 0.7927 (pp30) REVERT: H 1198 LEU cc_start: 0.9259 (tp) cc_final: 0.8996 (mt) REVERT: H 1253 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7546 (mm-30) outliers start: 146 outliers final: 112 residues processed: 970 average time/residue: 0.2005 time to fit residues: 339.6816 Evaluate side-chains 993 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 873 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 432 PHE Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 739 TRP Chi-restraints excluded: chain E residue 1140 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1253 GLU Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 221 PHE Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 432 PHE Chi-restraints excluded: chain F residue 435 CYS Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 739 TRP Chi-restraints excluded: chain F residue 1140 LEU Chi-restraints excluded: chain F residue 1175 CYS Chi-restraints excluded: chain F residue 1227 LEU Chi-restraints excluded: chain F residue 1272 LEU Chi-restraints excluded: chain F residue 1316 HIS Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 65 TRP Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 418 CYS Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 432 PHE Chi-restraints excluded: chain G residue 548 THR Chi-restraints excluded: chain G residue 739 TRP Chi-restraints excluded: chain G residue 1129 CYS Chi-restraints excluded: chain G residue 1140 LEU Chi-restraints excluded: chain G residue 1175 CYS Chi-restraints excluded: chain G residue 1202 SER Chi-restraints excluded: chain G residue 1227 LEU Chi-restraints excluded: chain G residue 1272 LEU Chi-restraints excluded: chain G residue 1316 HIS Chi-restraints excluded: chain H residue 44 PHE Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain H residue 361 LEU Chi-restraints excluded: chain H residue 391 ILE Chi-restraints excluded: chain H residue 418 CYS Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 432 PHE Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain H residue 548 THR Chi-restraints excluded: chain H residue 739 TRP Chi-restraints excluded: chain H residue 1175 CYS Chi-restraints excluded: chain H residue 1202 SER Chi-restraints excluded: chain H residue 1227 LEU Chi-restraints excluded: chain H residue 1258 CYS Chi-restraints excluded: chain H residue 1272 LEU Chi-restraints excluded: chain H residue 1316 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 133 optimal weight: 10.0000 chunk 218 optimal weight: 2.9990 chunk 182 optimal weight: 20.0000 chunk 532 optimal weight: 0.8980 chunk 398 optimal weight: 0.9990 chunk 399 optimal weight: 5.9990 chunk 56 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 394 optimal weight: 0.9980 chunk 190 optimal weight: 0.8980 chunk 227 optimal weight: 9.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 HIS B 216 HIS E 72 ASN H 72 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.137460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.109361 restraints weight = 121908.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.112221 restraints weight = 58377.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.114120 restraints weight = 35181.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.115391 restraints weight = 24630.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.116200 restraints weight = 19151.167| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.6453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 45740 Z= 0.129 Angle : 0.641 11.563 62732 Z= 0.318 Chirality : 0.044 0.334 7672 Planarity : 0.004 0.057 8064 Dihedral : 4.551 66.759 6896 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.90 % Allowed : 25.90 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.89 (0.11), residues: 6464 helix: 2.28 (0.08), residues: 4072 sheet: -0.53 (0.23), residues: 500 loop : -0.50 (0.15), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 388 TYR 0.028 0.001 TYR H1230 PHE 0.040 0.001 PHE B 168 TRP 0.015 0.001 TRP F 430 HIS 0.005 0.001 HIS H 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (45736) covalent geometry : angle 0.64133 / 0.32 (62724) SS BOND : bond 0.00180 / 0.09 ( 4) SS BOND : angle 1.04966 / 0.63 ( 8) hydrogen bonds : bond 0.04056 / 2.76 ( 3333) hydrogen bonds : angle 3.85433 / 2.82 ( 9783) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10968.20 seconds wall clock time: 187 minutes 57.55 seconds (11277.55 seconds total)