Starting phenix.real_space_refine on Sat Oct 31 15:57:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6baa_7073/10_2026/6baa_7073.cif Found real_map, /net/cci-nas-00/data/ceres_data/6baa_7073/10_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6baa_7073/10_2026/6baa_7073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6baa_7073/10_2026/6baa_7073.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6baa_7073/10_2026/6baa_7073.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6baa_7073/10_2026/6baa_7073.cif" model { file = "/net/cci-nas-00/data/ceres_data/6baa_7073/10_2026/6baa_7073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6baa_7073/10_2026/6baa_7073.cif" } 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): 0.17s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/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: 13.50, per 1000 atoms: 0.30 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=8, 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 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 26 " distance=2.04 Simple disulfide: pdb=" SG CYS F 6 " - pdb=" SG CYS F 26 " distance=2.04 Simple disulfide: pdb=" SG CYS G 6 " - pdb=" SG CYS G 26 " distance=2.04 Simple disulfide: pdb=" SG CYS H 6 " - pdb=" SG CYS H 26 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.60 Conformation dependent library (CDL) restraints added in 2.0 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: 1.58 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: 11.62 Time building geometry restraints manager: 4.85 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: 976 33.12 - 49.68: 280 49.68 - 66.24: 68 66.24 - 82.80: 16 Dihedral angle restraints: 26644 sinusoidal: 7616 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 26641 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: 2.23 - 2.77: 8492 2.77 - 3.30: 47386 3.30 - 3.83: 76208 3.83 - 4.37: 83382 4.37 - 4.90: 139082 Nonbonded interactions: 354550 Sorted by model distance: nonbonded pdb=" O LEU F1192 " pdb=" OG1 THR F1196 " model vdw 2.235 3.040 nonbonded pdb=" O LEU E1192 " pdb=" OG1 THR E1196 " model vdw 2.235 3.040 nonbonded pdb=" O LEU H1192 " pdb=" OG1 THR H1196 " model vdw 2.235 3.040 nonbonded pdb=" O LEU G1192 " pdb=" OG1 THR G1196 " model vdw 2.235 3.040 nonbonded pdb=" O HIS E1203 " pdb=" OG1 THR E1207 " model vdw 2.244 3.040 ... (remaining 354545 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: 0.09 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: 1.550 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: 0.880 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 46.220 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.090 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.570 ------------------------------------------------------------------------------- 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 45744 Z= 0.449 Angle : 1.289 24.805 62740 Z= 0.847 Chirality : 0.073 0.468 7672 Planarity : 0.009 0.105 8064 Dihedral : 11.078 82.803 14236 Min Nonbonded Distance : 2.235 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 0.01119 / 0.61 ( 8) SS BOND : angle 1.27620 / 0.92 ( 16) 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 : 1.612 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: 0.2485 time to fit residues: 687.2815 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 : 1.677 ------------------------------------------------------------------------------- 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: [394, 430, 41, 265, 523, 497, 414, 310, 488, 366, 597] 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: 1.9990 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: 3.1990 ------------------------------------------------------------------------------- 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 = 0.4061 r_free = 0.4061 target = 0.140664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.113036 restraints weight = 122323.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.115850 restraints weight = 60878.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.117689 restraints weight = 37206.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.118878 restraints weight = 26178.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.119676 restraints weight = 20448.191| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 45744 Z= 0.183 Angle : 0.696 12.426 62740 Z= 0.356 Chirality : 0.045 0.160 7672 Planarity : 0.005 0.058 8064 Dihedral : 6.218 83.639 6928 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.24 % Allowed : 15.32 % Favored : 80.44 % 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: 1.12 (0.08), residues: 4012 sheet: -0.62 (0.21), residues: 512 loop : -0.61 (0.14), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 201 TYR 0.030 0.002 TYR H 179 PHE 0.023 0.002 PHE F 433 TRP 0.020 0.002 TRP E 688 HIS 0.006 0.001 HIS G 867 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (45736) covalent geometry : angle 0.69385 / 0.36 (62724) SS BOND : bond 0.01519 / 0.76 ( 8) SS BOND : angle 3.17636 / 1.95 ( 16) hydrogen bonds : bond 0.05133 / 3.49 ( 3333) hydrogen bonds : angle 4.51612 / 3.29 ( 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 1336 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 1185 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.9040 (mmtm) cc_final: 0.8805 (mmtp) REVERT: A 58 ASP cc_start: 0.7466 (t0) cc_final: 0.7139 (t0) REVERT: A 142 CYS cc_start: 0.5055 (m) cc_final: 0.4794 (m) REVERT: B 47 LYS cc_start: 0.9043 (mmtm) cc_final: 0.8815 (mmtp) REVERT: B 142 CYS cc_start: 0.5084 (m) cc_final: 0.4809 (m) REVERT: C 43 ASN cc_start: 0.8222 (t0) cc_final: 0.7854 (t0) REVERT: C 47 LYS cc_start: 0.9043 (mmtm) cc_final: 0.8816 (mmtp) REVERT: C 142 CYS cc_start: 0.5039 (m) cc_final: 0.4769 (m) REVERT: D 47 LYS cc_start: 0.8970 (mmtm) cc_final: 0.8713 (mmtm) REVERT: D 142 CYS cc_start: 0.5047 (m) cc_final: 0.4778 (m) REVERT: E 264 GLN cc_start: 0.8547 (tp-100) cc_final: 0.8140 (tm-30) REVERT: E 378 TYR cc_start: 0.8325 (t80) cc_final: 0.8021 (t80) REVERT: E 574 SER cc_start: 0.8184 (p) cc_final: 0.7859 (p) REVERT: E 602 LYS cc_start: 0.9083 (mttt) cc_final: 0.8877 (mmtt) REVERT: E 1125 PHE cc_start: 0.7826 (t80) cc_final: 0.7558 (t80) REVERT: E 1145 ARG cc_start: 0.8314 (ttp80) cc_final: 0.7783 (ttp80) REVERT: E 1149 LEU cc_start: 0.8854 (mt) cc_final: 0.8488 (mp) REVERT: E 1152 SER cc_start: 0.8898 (m) cc_final: 0.8630 (p) REVERT: E 1191 GLN cc_start: 0.8423 (pp30) cc_final: 0.8212 (pp30) REVERT: E 1224 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8464 (tp40) REVERT: E 1225 GLN cc_start: 0.9070 (mm-40) cc_final: 0.8661 (mm-40) REVERT: E 1230 TYR cc_start: 0.8960 (m-10) cc_final: 0.8738 (m-80) REVERT: E 1304 ASP cc_start: 0.9003 (t70) cc_final: 0.8771 (t70) REVERT: E 1496 PHE cc_start: 0.6197 (t80) cc_final: 0.5799 (t80) REVERT: F 264 GLN cc_start: 0.8546 (tp-100) cc_final: 0.8134 (tm-30) REVERT: F 574 SER cc_start: 0.8182 (p) cc_final: 0.7859 (p) REVERT: F 602 LYS cc_start: 0.9097 (mttt) cc_final: 0.8893 (mmtt) REVERT: F 1125 PHE cc_start: 0.7833 (t80) cc_final: 0.7557 (t80) REVERT: F 1145 ARG cc_start: 0.8291 (ttp80) cc_final: 0.7766 (ttp80) REVERT: F 1149 LEU cc_start: 0.8852 (mt) cc_final: 0.8490 (mp) REVERT: F 1152 SER cc_start: 0.8903 (m) cc_final: 0.8633 (p) REVERT: F 1191 GLN cc_start: 0.8414 (pp30) cc_final: 0.8198 (pp30) REVERT: F 1224 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8476 (tp40) REVERT: F 1230 TYR cc_start: 0.8969 (m-10) cc_final: 0.8756 (m-80) REVERT: F 1304 ASP cc_start: 0.9004 (t70) cc_final: 0.8775 (t70) REVERT: F 1496 PHE cc_start: 0.6202 (t80) cc_final: 0.5803 (t80) REVERT: G 264 GLN cc_start: 0.8541 (tp-100) cc_final: 0.8202 (tm-30) REVERT: G 370 ARG cc_start: 0.8311 (mmt-90) cc_final: 0.7820 (mpt-90) REVERT: G 378 TYR cc_start: 0.8322 (t80) cc_final: 0.8001 (t80) REVERT: G 574 SER cc_start: 0.8224 (p) cc_final: 0.7898 (p) REVERT: G 602 LYS cc_start: 0.9092 (mttt) cc_final: 0.8889 (mmtt) REVERT: G 1125 PHE cc_start: 0.7787 (t80) cc_final: 0.7502 (t80) REVERT: G 1145 ARG cc_start: 0.8279 (ttp80) cc_final: 0.7833 (ttp80) REVERT: G 1149 LEU cc_start: 0.8875 (mt) cc_final: 0.8543 (mm) REVERT: G 1152 SER cc_start: 0.8928 (m) cc_final: 0.8656 (p) REVERT: G 1191 GLN cc_start: 0.8414 (pp30) cc_final: 0.8161 (pp30) REVERT: G 1224 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8474 (tp40) REVERT: G 1225 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8647 (mm-40) REVERT: G 1230 TYR cc_start: 0.8960 (m-10) cc_final: 0.8728 (m-80) REVERT: G 1304 ASP cc_start: 0.9002 (t70) cc_final: 0.8772 (t70) REVERT: G 1496 PHE cc_start: 0.6137 (t80) cc_final: 0.5730 (t80) REVERT: H 264 GLN cc_start: 0.8559 (tp-100) cc_final: 0.8221 (tm-30) REVERT: H 378 TYR cc_start: 0.8321 (t80) cc_final: 0.8018 (t80) REVERT: H 574 SER cc_start: 0.8197 (p) cc_final: 0.7878 (p) REVERT: H 602 LYS cc_start: 0.9094 (mttt) cc_final: 0.8885 (mmtt) REVERT: H 1125 PHE cc_start: 0.7839 (t80) cc_final: 0.7554 (t80) REVERT: H 1145 ARG cc_start: 0.8296 (ttp80) cc_final: 0.7752 (ttp80) REVERT: H 1152 SER cc_start: 0.8902 (m) cc_final: 0.8637 (p) REVERT: H 1224 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8456 (tp40) REVERT: H 1225 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8651 (mm-40) REVERT: H 1230 TYR cc_start: 0.8970 (m-10) cc_final: 0.8744 (m-80) REVERT: H 1304 ASP cc_start: 0.9008 (t70) cc_final: 0.8774 (t70) REVERT: H 1496 PHE cc_start: 0.6139 (t80) cc_final: 0.5742 (t80) outliers start: 151 outliers final: 93 residues processed: 1279 average time/residue: 0.2408 time to fit residues: 522.1828 Evaluate side-chains 1074 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 977 time to evaluate : 1.690 ------------------------------------------------------------------------------- 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 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 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 1250 VAL Chi-restraints excluded: chain E residue 1285 LEU Chi-restraints excluded: chain E residue 1307 ILE 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 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 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 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 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 1250 VAL Chi-restraints excluded: chain G residue 1285 LEU Chi-restraints excluded: chain G residue 1307 ILE 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 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: [244, 8, 199, 19, 588, 465, 606, 6, 392, 318, 272] chunk 244 optimal weight: 50.0000 chunk 8 optimal weight: 9.9990 chunk 199 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 588 optimal weight: 0.0870 chunk 465 optimal weight: 40.0000 chunk 606 optimal weight: 40.0000 chunk 6 optimal weight: 0.9990 chunk 392 optimal weight: 0.8980 chunk 318 optimal weight: 30.0000 chunk 272 optimal weight: 1.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- 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 57 GLN D 173 GLN F 125 HIS G 125 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.140077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.112492 restraints weight = 119856.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.115405 restraints weight = 57680.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.117354 restraints weight = 34636.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.118615 restraints weight = 23990.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.119456 restraints weight = 18473.613| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 45744 Z= 0.143 Angle : 0.638 10.396 62740 Z= 0.320 Chirality : 0.044 0.169 7672 Planarity : 0.004 0.046 8064 Dihedral : 5.592 81.217 6906 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.55 % Allowed : 19.11 % Favored : 76.35 % 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: 1.69 (0.08), residues: 4020 sheet: -0.52 (0.21), residues: 556 loop : -0.57 (0.15), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 314 TYR 0.019 0.001 TYR H 179 PHE 0.030 0.002 PHE F 363 TRP 0.019 0.001 TRP E 232 HIS 0.015 0.001 HIS G 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (45736) covalent geometry : angle 0.63728 / 0.32 (62724) SS BOND : bond 0.00210 / 0.12 ( 8) SS BOND : angle 1.87530 / 1.14 ( 16) hydrogen bonds : bond 0.04589 / 3.12 ( 3333) hydrogen bonds : angle 4.15842 / 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 1225 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 1063 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.9025 (mmtm) cc_final: 0.8797 (mmtm) REVERT: A 142 CYS cc_start: 0.5073 (m) cc_final: 0.4826 (m) REVERT: B 47 LYS cc_start: 0.9054 (mmtm) cc_final: 0.8774 (mmtm) REVERT: B 142 CYS cc_start: 0.5074 (m) cc_final: 0.4865 (m) REVERT: C 47 LYS cc_start: 0.9044 (mmtm) cc_final: 0.8753 (mmtm) REVERT: C 142 CYS cc_start: 0.4923 (m) cc_final: 0.4651 (m) REVERT: D 47 LYS cc_start: 0.8939 (mmtm) cc_final: 0.8739 (mmtp) REVERT: D 142 CYS cc_start: 0.4985 (m) cc_final: 0.4732 (m) REVERT: E 71 HIS cc_start: 0.8571 (OUTLIER) cc_final: 0.7998 (p-80) REVERT: E 96 ASP cc_start: 0.8167 (t70) cc_final: 0.7905 (t0) REVERT: E 168 ARG cc_start: 0.8034 (ttm110) cc_final: 0.7692 (mtm-85) REVERT: E 183 LEU cc_start: 0.9064 (tp) cc_final: 0.8695 (tp) REVERT: E 248 ARG cc_start: 0.8064 (ptt180) cc_final: 0.7861 (ptt-90) REVERT: E 264 GLN cc_start: 0.8559 (tp-100) cc_final: 0.8304 (tm-30) REVERT: E 319 CYS cc_start: 0.8821 (m) cc_final: 0.8493 (m) REVERT: E 483 GLN cc_start: 0.7814 (mt0) cc_final: 0.7493 (mt0) REVERT: E 552 ILE cc_start: 0.8436 (mm) cc_final: 0.8122 (pt) REVERT: E 574 SER cc_start: 0.8030 (p) cc_final: 0.7687 (p) REVERT: E 601 VAL cc_start: 0.9042 (t) cc_final: 0.8833 (p) REVERT: E 1125 PHE cc_start: 0.7786 (t80) cc_final: 0.7514 (t80) REVERT: E 1230 TYR cc_start: 0.9006 (m-10) cc_final: 0.8736 (m-80) REVERT: E 1304 ASP cc_start: 0.9020 (t70) cc_final: 0.8734 (t0) REVERT: F 71 HIS cc_start: 0.8567 (OUTLIER) cc_final: 0.7999 (p-80) REVERT: F 96 ASP cc_start: 0.8180 (t70) cc_final: 0.7911 (t0) REVERT: F 168 ARG cc_start: 0.8028 (ttm110) cc_final: 0.7680 (mtm-85) REVERT: F 183 LEU cc_start: 0.9063 (tp) cc_final: 0.8679 (tp) REVERT: F 248 ARG cc_start: 0.8071 (ptt180) cc_final: 0.7869 (ptt-90) REVERT: F 264 GLN cc_start: 0.8556 (tp-100) cc_final: 0.8304 (tm-30) REVERT: F 319 CYS cc_start: 0.8816 (m) cc_final: 0.8497 (m) REVERT: F 432 PHE cc_start: 0.8714 (m-80) cc_final: 0.8461 (t80) REVERT: F 483 GLN cc_start: 0.7828 (mt0) cc_final: 0.7511 (mt0) REVERT: F 574 SER cc_start: 0.8039 (p) cc_final: 0.7701 (p) REVERT: F 601 VAL cc_start: 0.9051 (t) cc_final: 0.8842 (p) REVERT: F 1125 PHE cc_start: 0.7794 (t80) cc_final: 0.7520 (t80) REVERT: F 1206 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7898 (mt-10) REVERT: F 1226 LYS cc_start: 0.9058 (mttt) cc_final: 0.8729 (mttp) REVERT: F 1230 TYR cc_start: 0.9010 (m-10) cc_final: 0.8740 (m-80) REVERT: F 1304 ASP cc_start: 0.9021 (t70) cc_final: 0.8733 (t0) REVERT: G 71 HIS cc_start: 0.8555 (OUTLIER) cc_final: 0.8039 (p-80) REVERT: G 96 ASP cc_start: 0.8189 (t70) cc_final: 0.7888 (t0) REVERT: G 264 GLN cc_start: 0.8556 (tp-100) cc_final: 0.8289 (tm-30) REVERT: G 319 CYS cc_start: 0.8827 (m) cc_final: 0.8516 (m) REVERT: G 370 ARG cc_start: 0.8444 (mmt-90) cc_final: 0.8054 (mpt-90) REVERT: G 432 PHE cc_start: 0.8714 (m-80) cc_final: 0.8454 (t80) REVERT: G 574 SER cc_start: 0.8056 (p) cc_final: 0.7706 (p) REVERT: G 1125 PHE cc_start: 0.7825 (t80) cc_final: 0.7537 (t80) REVERT: G 1145 ARG cc_start: 0.8375 (ttp80) cc_final: 0.8175 (ttp80) REVERT: G 1225 GLN cc_start: 0.8962 (mm-40) cc_final: 0.8724 (mm-40) REVERT: G 1230 TYR cc_start: 0.8995 (m-10) cc_final: 0.8750 (m-80) REVERT: G 1304 ASP cc_start: 0.9037 (t70) cc_final: 0.8756 (t0) REVERT: H 168 ARG cc_start: 0.8052 (ttm110) cc_final: 0.7671 (mtm-85) REVERT: H 183 LEU cc_start: 0.9054 (tp) cc_final: 0.8687 (tp) REVERT: H 264 GLN cc_start: 0.8566 (tp-100) cc_final: 0.8307 (tm-30) REVERT: H 319 CYS cc_start: 0.8828 (m) cc_final: 0.8516 (m) REVERT: H 432 PHE cc_start: 0.8708 (m-80) cc_final: 0.8458 (t80) REVERT: H 483 GLN cc_start: 0.7829 (mt0) cc_final: 0.7603 (mt0) REVERT: H 574 SER cc_start: 0.8063 (p) cc_final: 0.7723 (p) REVERT: H 601 VAL cc_start: 0.9055 (t) cc_final: 0.8854 (p) REVERT: H 1125 PHE cc_start: 0.7789 (t80) cc_final: 0.7458 (t80) REVERT: H 1145 ARG cc_start: 0.8372 (ttp80) cc_final: 0.8166 (ttp80) REVERT: H 1230 TYR cc_start: 0.9008 (m-10) cc_final: 0.8742 (m-80) REVERT: H 1253 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7586 (mm-30) outliers start: 162 outliers final: 129 residues processed: 1154 average time/residue: 0.2220 time to fit residues: 447.9754 Evaluate side-chains 1086 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 954 time to evaluate : 1.542 ------------------------------------------------------------------------------- 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 236 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 297 THR 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 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 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 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 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 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 71 HIS Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 86 VAL 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 421 VAL Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1140 LEU Chi-restraints excluded: chain E residue 1146 SER Chi-restraints excluded: chain E residue 1171 LEU Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1250 VAL 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 71 HIS 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 440 THR Chi-restraints excluded: chain F residue 449 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 1146 SER Chi-restraints excluded: chain F residue 1171 LEU Chi-restraints excluded: chain F residue 1227 LEU 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 421 VAL Chi-restraints excluded: chain G residue 440 THR Chi-restraints excluded: chain G residue 449 VAL 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 366 LEU Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 440 THR Chi-restraints excluded: chain H residue 449 VAL 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 1171 LEU Chi-restraints excluded: chain H residue 1173 VAL 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 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: [145, 508, 112, 251, 539, 239, 445, 22, 358, 213, 267] chunk 145 optimal weight: 6.9990 chunk 508 optimal weight: 30.0000 chunk 112 optimal weight: 7.9990 chunk 251 optimal weight: 8.9990 chunk 539 optimal weight: 1.9990 chunk 239 optimal weight: 50.0000 chunk 445 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 358 optimal weight: 10.0000 chunk 213 optimal weight: 40.0000 chunk 267 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN B 57 GLN C 313 GLN D 313 GLN E 125 HIS E 326 HIS E 474 GLN F 223 ASN F 326 HIS F 474 GLN G 223 ASN G 326 HIS G 474 GLN G1224 GLN H 125 HIS H 326 HIS ** H 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 474 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.133068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.105041 restraints weight = 121687.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.107831 restraints weight = 58924.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.109641 restraints weight = 35564.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.110853 restraints weight = 25027.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.111644 restraints weight = 19501.905| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 45744 Z= 0.275 Angle : 0.736 9.633 62740 Z= 0.379 Chirality : 0.048 0.255 7672 Planarity : 0.004 0.038 8064 Dihedral : 5.586 67.402 6904 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 7.60 % Allowed : 18.18 % Favored : 74.21 % 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: 1.20 (0.11), residues: 6464 helix: 1.64 (0.08), residues: 4048 sheet: -0.69 (0.22), residues: 516 loop : -0.53 (0.15), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 201 TYR 0.020 0.002 TYR G 179 PHE 0.024 0.002 PHE H 363 TRP 0.035 0.002 TRP E 688 HIS 0.008 0.002 HIS E 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.27 (45736) covalent geometry : angle 0.73469 / 0.38 (62724) SS BOND : bond 0.00398 / 0.22 ( 8) SS BOND : angle 2.31686 / 1.48 ( 16) hydrogen bonds : bond 0.05056 / 3.42 ( 3333) hydrogen bonds : angle 4.42691 / 3.22 ( 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 1242 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 271 poor density : 971 time to evaluate : 1.734 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: 0.9202 (mmtm) cc_final: 0.8997 (mmtm) REVERT: A 58 ASP cc_start: 0.7750 (t0) cc_final: 0.7198 (t0) REVERT: B 47 LYS cc_start: 0.9164 (mmtm) cc_final: 0.8953 (mmtm) REVERT: B 58 ASP cc_start: 0.7751 (t0) cc_final: 0.7204 (t0) REVERT: B 211 ILE cc_start: 0.9453 (mm) cc_final: 0.9224 (mt) REVERT: C 47 LYS cc_start: 0.9157 (mmtm) cc_final: 0.8944 (mmtm) REVERT: C 58 ASP cc_start: 0.7763 (t0) cc_final: 0.7204 (t0) REVERT: C 211 ILE cc_start: 0.9429 (mm) cc_final: 0.9218 (mt) REVERT: D 58 ASP cc_start: 0.7746 (t0) cc_final: 0.7204 (t0) REVERT: D 211 ILE cc_start: 0.9426 (mm) cc_final: 0.9211 (mt) REVERT: E 96 ASP cc_start: 0.8325 (t70) cc_final: 0.7714 (t0) REVERT: E 226 SER cc_start: 0.8923 (m) cc_final: 0.8515 (p) REVERT: E 230 TYR cc_start: 0.9230 (m-80) cc_final: 0.8784 (m-80) REVERT: E 264 GLN cc_start: 0.8687 (tp-100) cc_final: 0.8289 (tm-30) REVERT: E 319 CYS cc_start: 0.8851 (m) cc_final: 0.8419 (m) REVERT: E 402 MET cc_start: 0.5497 (tmm) cc_final: 0.3808 (tmm) REVERT: E 432 PHE cc_start: 0.8797 (m-80) cc_final: 0.8422 (t80) REVERT: E 483 GLN cc_start: 0.7885 (mt0) cc_final: 0.7649 (mt0) REVERT: E 574 SER cc_start: 0.8216 (p) cc_final: 0.8004 (m) REVERT: E 601 VAL cc_start: 0.9141 (t) cc_final: 0.8934 (p) REVERT: E 739 TRP cc_start: 0.6408 (OUTLIER) cc_final: 0.5613 (t60) REVERT: E 1125 PHE cc_start: 0.7784 (t80) cc_final: 0.7428 (t80) REVERT: E 1206 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7712 (mt-10) REVERT: E 1226 LYS cc_start: 0.9034 (mttt) cc_final: 0.8786 (mttp) REVERT: E 1230 TYR cc_start: 0.9012 (m-10) cc_final: 0.8636 (m-80) REVERT: E 1304 ASP cc_start: 0.9009 (t70) cc_final: 0.8780 (t70) REVERT: F 96 ASP cc_start: 0.8339 (t70) cc_final: 0.7744 (t0) REVERT: F 230 TYR cc_start: 0.9222 (m-80) cc_final: 0.8771 (m-80) REVERT: F 264 GLN cc_start: 0.8672 (tp-100) cc_final: 0.8281 (tm-30) REVERT: F 402 MET cc_start: 0.5466 (tmm) cc_final: 0.3778 (tmm) REVERT: F 432 PHE cc_start: 0.8807 (m-80) cc_final: 0.8417 (t80) REVERT: F 483 GLN cc_start: 0.7880 (mt0) cc_final: 0.7642 (mt0) REVERT: F 574 SER cc_start: 0.8224 (p) cc_final: 0.8012 (m) REVERT: F 601 VAL cc_start: 0.9151 (t) cc_final: 0.8948 (p) REVERT: F 739 TRP cc_start: 0.6412 (OUTLIER) cc_final: 0.5609 (t60) REVERT: F 1125 PHE cc_start: 0.7743 (t80) cc_final: 0.7390 (t80) REVERT: F 1226 LYS cc_start: 0.9036 (mttt) cc_final: 0.8796 (mttp) REVERT: F 1230 TYR cc_start: 0.9007 (m-10) cc_final: 0.8632 (m-80) REVERT: F 1304 ASP cc_start: 0.8992 (t70) cc_final: 0.8767 (t70) REVERT: G 96 ASP cc_start: 0.8349 (t70) cc_final: 0.7750 (t0) REVERT: G 145 LEU cc_start: 0.9120 (tt) cc_final: 0.8848 (tp) REVERT: G 168 ARG cc_start: 0.5165 (mtt90) cc_final: 0.4738 (mtm-85) REVERT: G 230 TYR cc_start: 0.9215 (m-80) cc_final: 0.8807 (m-80) REVERT: G 264 GLN cc_start: 0.8683 (tp-100) cc_final: 0.8276 (tm-30) REVERT: G 319 CYS cc_start: 0.8882 (m) cc_final: 0.8493 (m) REVERT: G 370 ARG cc_start: 0.8536 (mmt-90) cc_final: 0.8112 (mmt90) REVERT: G 402 MET cc_start: 0.5423 (tmm) cc_final: 0.3673 (tmm) REVERT: G 432 PHE cc_start: 0.8810 (m-80) cc_final: 0.8420 (t80) REVERT: G 574 SER cc_start: 0.8234 (p) cc_final: 0.8017 (m) REVERT: G 739 TRP cc_start: 0.6416 (OUTLIER) cc_final: 0.5610 (t60) REVERT: G 1125 PHE cc_start: 0.7798 (t80) cc_final: 0.7435 (t80) REVERT: G 1142 CYS cc_start: 0.8602 (p) cc_final: 0.8360 (m) REVERT: G 1145 ARG cc_start: 0.8532 (ttp80) cc_final: 0.8285 (ttp80) REVERT: G 1198 LEU cc_start: 0.9313 (tp) cc_final: 0.9034 (mt) REVERT: G 1253 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7337 (mt-10) REVERT: G 1304 ASP cc_start: 0.9015 (t70) cc_final: 0.8791 (t70) REVERT: H 96 ASP cc_start: 0.8327 (t70) cc_final: 0.7730 (t0) REVERT: H 226 SER cc_start: 0.8887 (m) cc_final: 0.8490 (p) REVERT: H 230 TYR cc_start: 0.9211 (m-80) cc_final: 0.8798 (m-80) REVERT: H 264 GLN cc_start: 0.8677 (tp-100) cc_final: 0.8279 (tm-30) REVERT: H 319 CYS cc_start: 0.8866 (m) cc_final: 0.8433 (m) REVERT: H 402 MET cc_start: 0.5459 (tmm) cc_final: 0.3554 (tmm) REVERT: H 432 PHE cc_start: 0.8806 (m-80) cc_final: 0.8412 (t80) REVERT: H 483 GLN cc_start: 0.7883 (mt0) cc_final: 0.7556 (mt0) REVERT: H 574 SER cc_start: 0.8236 (p) cc_final: 0.8018 (m) REVERT: H 601 VAL cc_start: 0.9149 (t) cc_final: 0.8947 (p) REVERT: H 1125 PHE cc_start: 0.7712 (t80) cc_final: 0.7347 (t80) REVERT: H 1142 CYS cc_start: 0.8639 (p) cc_final: 0.8374 (m) REVERT: H 1145 ARG cc_start: 0.8535 (ttp80) cc_final: 0.8286 (ttp80) REVERT: H 1152 SER cc_start: 0.8906 (m) cc_final: 0.8625 (p) REVERT: H 1226 LYS cc_start: 0.9041 (mttt) cc_final: 0.8785 (mttp) REVERT: H 1230 TYR cc_start: 0.9013 (m-10) cc_final: 0.8626 (m-80) REVERT: H 1253 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7735 (mm-30) REVERT: H 1304 ASP cc_start: 0.9011 (t70) cc_final: 0.8782 (t70) outliers start: 271 outliers final: 205 residues processed: 1142 average time/residue: 0.2236 time to fit residues: 446.8723 Evaluate side-chains 1079 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 871 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 140 GLU 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 297 THR Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 139 THR 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 351 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 139 THR 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 351 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 139 THR 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 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 31 LEU 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 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 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 373 LEU Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 474 GLN Chi-restraints excluded: chain E residue 579 SER Chi-restraints excluded: chain E residue 739 TRP 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 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 1307 ILE Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain F residue 31 LEU 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 71 HIS Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 129 THR 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 198 PHE Chi-restraints excluded: chain F residue 221 PHE Chi-restraints excluded: chain F residue 223 ASN Chi-restraints excluded: chain F residue 268 VAL 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 373 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 474 GLN Chi-restraints excluded: chain F residue 739 TRP 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 1157 ILE 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 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 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 127 ILE Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 140 LEU 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 223 ASN Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 304 THR 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 373 LEU Chi-restraints excluded: chain G residue 421 VAL 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 474 GLN Chi-restraints excluded: chain G residue 739 TRP 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 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 1250 VAL 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 31 LEU 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 129 THR 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 304 THR 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 368 LEU Chi-restraints excluded: chain H residue 373 LEU Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain H residue 449 VAL 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 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 1157 ILE Chi-restraints excluded: chain H residue 1171 LEU Chi-restraints excluded: chain H residue 1173 VAL 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 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: [105, 121, 338, 465, 39, 443, 181, 9, 640, 565, 299] chunk 105 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 338 optimal weight: 30.0000 chunk 465 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 443 optimal weight: 6.9990 chunk 181 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 640 optimal weight: 40.0000 chunk 565 optimal weight: 6.9990 chunk 299 optimal weight: 20.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 166 GLN E1123 ASN E1270 ASN F 262 ASN F1270 ASN ** G 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 262 ASN G1270 ASN H 262 ASN ** H 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1123 ASN H1270 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.134806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.107501 restraints weight = 119574.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.111245 restraints weight = 62864.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.112493 restraints weight = 32433.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.113030 restraints weight = 23846.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.113332 restraints weight = 21333.453| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 45744 Z= 0.168 Angle : 0.652 9.774 62740 Z= 0.327 Chirality : 0.045 0.170 7672 Planarity : 0.004 0.037 8064 Dihedral : 5.310 68.093 6904 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 6.14 % Allowed : 19.44 % Favored : 74.41 % 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: 1.52 (0.11), residues: 6464 helix: 1.93 (0.08), residues: 4068 sheet: -0.72 (0.22), residues: 552 loop : -0.46 (0.15), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E1145 TYR 0.013 0.001 TYR D 330 PHE 0.028 0.002 PHE H 169 TRP 0.023 0.001 TRP E 688 HIS 0.006 0.001 HIS E 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (45736) covalent geometry : angle 0.65181 / 0.33 (62724) SS BOND : bond 0.00141 / 0.08 ( 8) SS BOND : angle 1.51517 / 0.91 ( 16) hydrogen bonds : bond 0.04603 / 3.12 ( 3333) hydrogen bonds : angle 4.14120 / 3.02 ( 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 1208 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 989 time to evaluate : 1.651 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: A 47 LYS cc_start: 0.9182 (mmtm) cc_final: 0.8927 (mmtm) REVERT: A 58 ASP cc_start: 0.7658 (t0) cc_final: 0.7119 (t0) REVERT: A 185 LYS cc_start: 0.8814 (ttmt) cc_final: 0.8449 (ttmm) REVERT: B 47 LYS cc_start: 0.9150 (mmtm) cc_final: 0.8888 (mmtm) REVERT: B 58 ASP cc_start: 0.7658 (t0) cc_final: 0.7121 (t0) REVERT: B 160 ASN cc_start: 0.8730 (m-40) cc_final: 0.8466 (t0) REVERT: B 185 LYS cc_start: 0.8808 (ttmt) cc_final: 0.8461 (ttmm) REVERT: C 47 LYS cc_start: 0.9145 (mmtm) cc_final: 0.8872 (mmtm) REVERT: C 58 ASP cc_start: 0.7652 (t0) cc_final: 0.7129 (t0) REVERT: C 160 ASN cc_start: 0.8720 (m-40) cc_final: 0.8400 (t0) REVERT: C 185 LYS cc_start: 0.8805 (ttmt) cc_final: 0.8451 (ttmm) REVERT: D 58 ASP cc_start: 0.7670 (t0) cc_final: 0.7129 (t0) REVERT: D 160 ASN cc_start: 0.8724 (m-40) cc_final: 0.8417 (t0) REVERT: D 185 LYS cc_start: 0.8802 (ttmt) cc_final: 0.8466 (ttmm) REVERT: E 41 PHE cc_start: 0.8258 (m-10) cc_final: 0.8049 (m-80) REVERT: E 226 SER cc_start: 0.8760 (m) cc_final: 0.8446 (p) REVERT: E 230 TYR cc_start: 0.9116 (m-80) cc_final: 0.8708 (m-80) REVERT: E 264 GLN cc_start: 0.8573 (tp-100) cc_final: 0.8203 (tm-30) REVERT: E 319 CYS cc_start: 0.8807 (m) cc_final: 0.8404 (m) REVERT: E 402 MET cc_start: 0.5414 (tmm) cc_final: 0.3800 (tmm) REVERT: E 432 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.8390 (t80) REVERT: E 483 GLN cc_start: 0.7858 (mt0) cc_final: 0.7527 (mt0) REVERT: E 601 VAL cc_start: 0.9137 (t) cc_final: 0.8927 (p) REVERT: E 739 TRP cc_start: 0.6483 (OUTLIER) cc_final: 0.5667 (t60) REVERT: E 1125 PHE cc_start: 0.7723 (t80) cc_final: 0.7419 (t80) REVERT: E 1226 LYS cc_start: 0.9024 (mttt) cc_final: 0.8761 (mttp) REVERT: E 1230 TYR cc_start: 0.8961 (m-10) cc_final: 0.8643 (m-80) REVERT: E 1294 TYR cc_start: 0.8809 (m-10) cc_final: 0.8461 (m-10) REVERT: E 1304 ASP cc_start: 0.9005 (t70) cc_final: 0.8520 (t0) REVERT: E 1306 GLU cc_start: 0.8571 (tm-30) cc_final: 0.7837 (tp30) REVERT: F 226 SER cc_start: 0.8826 (m) cc_final: 0.8549 (p) REVERT: F 230 TYR cc_start: 0.9106 (m-80) cc_final: 0.8718 (m-80) REVERT: F 264 GLN cc_start: 0.8555 (tp-100) cc_final: 0.8197 (tm-30) REVERT: F 402 MET cc_start: 0.5407 (tmm) cc_final: 0.3781 (tmm) REVERT: F 432 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8390 (t80) REVERT: F 483 GLN cc_start: 0.7851 (mt0) cc_final: 0.7525 (mt0) REVERT: F 601 VAL cc_start: 0.9151 (t) cc_final: 0.8944 (p) REVERT: F 739 TRP cc_start: 0.6459 (OUTLIER) cc_final: 0.5633 (t60) REVERT: F 1125 PHE cc_start: 0.7800 (t80) cc_final: 0.7454 (t80) REVERT: F 1226 LYS cc_start: 0.9003 (mttt) cc_final: 0.8773 (mttp) REVERT: F 1230 TYR cc_start: 0.8969 (m-10) cc_final: 0.8657 (m-80) REVERT: F 1294 TYR cc_start: 0.8808 (m-10) cc_final: 0.8461 (m-10) REVERT: F 1304 ASP cc_start: 0.9004 (t70) cc_final: 0.8515 (t0) REVERT: F 1306 GLU cc_start: 0.8567 (tm-30) cc_final: 0.7834 (tp30) REVERT: G 145 LEU cc_start: 0.8968 (tt) cc_final: 0.8707 (tp) REVERT: G 168 ARG cc_start: 0.5180 (mtt90) cc_final: 0.4514 (mtm-85) REVERT: G 226 SER cc_start: 0.8823 (m) cc_final: 0.8542 (p) REVERT: G 230 TYR cc_start: 0.9104 (m-80) cc_final: 0.8725 (m-80) REVERT: G 264 GLN cc_start: 0.8553 (tp-100) cc_final: 0.8243 (tm-30) REVERT: G 370 ARG cc_start: 0.8502 (mmt-90) cc_final: 0.7928 (mmt90) REVERT: G 402 MET cc_start: 0.5407 (tmm) cc_final: 0.3782 (tmm) REVERT: G 432 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.8389 (t80) REVERT: G 739 TRP cc_start: 0.6455 (OUTLIER) cc_final: 0.5640 (t60) REVERT: G 1125 PHE cc_start: 0.7805 (t80) cc_final: 0.7461 (t80) REVERT: G 1142 CYS cc_start: 0.8652 (p) cc_final: 0.8337 (m) REVERT: G 1198 LEU cc_start: 0.9266 (tp) cc_final: 0.9040 (mt) REVERT: G 1230 TYR cc_start: 0.8894 (m-80) cc_final: 0.8523 (m-80) REVERT: G 1253 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7309 (mt-10) REVERT: G 1292 SER cc_start: 0.8729 (m) cc_final: 0.8519 (p) REVERT: G 1304 ASP cc_start: 0.9009 (t70) cc_final: 0.8520 (t0) REVERT: G 1306 GLU cc_start: 0.8548 (tm-30) cc_final: 0.7805 (tp30) REVERT: H 226 SER cc_start: 0.8749 (m) cc_final: 0.8463 (p) REVERT: H 230 TYR cc_start: 0.9105 (m-80) cc_final: 0.8706 (m-80) REVERT: H 264 GLN cc_start: 0.8536 (tp-100) cc_final: 0.8128 (tm-30) REVERT: H 319 CYS cc_start: 0.8805 (m) cc_final: 0.8401 (m) REVERT: H 402 MET cc_start: 0.5443 (tmm) cc_final: 0.3751 (tmm) REVERT: H 432 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.8376 (t80) REVERT: H 483 GLN cc_start: 0.7846 (mt0) cc_final: 0.7503 (mt0) REVERT: H 601 VAL cc_start: 0.9136 (t) cc_final: 0.8932 (p) REVERT: H 739 TRP cc_start: 0.6445 (OUTLIER) cc_final: 0.5656 (t60) REVERT: H 1125 PHE cc_start: 0.7726 (t80) cc_final: 0.7431 (t80) REVERT: H 1142 CYS cc_start: 0.8663 (p) cc_final: 0.8328 (m) REVERT: H 1253 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7796 (mm-30) REVERT: H 1304 ASP cc_start: 0.9004 (t70) cc_final: 0.8767 (t70) REVERT: H 1306 GLU cc_start: 0.8580 (tm-30) cc_final: 0.7811 (tp30) outliers start: 219 outliers final: 157 residues processed: 1131 average time/residue: 0.2219 time to fit residues: 440.1131 Evaluate side-chains 1048 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 883 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 140 GLU 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 71 THR Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 140 GLU 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 71 THR Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain C residue 140 GLU 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 71 THR Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 97 HIS Chi-restraints excluded: chain D residue 140 GLU 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 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 223 ASN Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 304 THR 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 373 LEU Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 432 PHE Chi-restraints excluded: chain E residue 449 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 1171 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 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 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 223 ASN 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 432 PHE Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 739 TRP Chi-restraints excluded: chain F residue 1140 LEU Chi-restraints excluded: chain F residue 1146 SER Chi-restraints excluded: chain F residue 1171 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 1250 VAL 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 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 223 ASN Chi-restraints excluded: chain G residue 299 LEU 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 421 VAL Chi-restraints excluded: chain G residue 432 PHE Chi-restraints excluded: chain G residue 449 VAL Chi-restraints excluded: chain G residue 739 TRP Chi-restraints excluded: chain G residue 1140 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 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 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 223 ASN Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 368 LEU Chi-restraints excluded: chain H residue 373 LEU 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 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 1169 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 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: [168, 261, 513, 399, 567, 190, 96, 150, 5, 42, 27] chunk 168 optimal weight: 6.9990 chunk 261 optimal weight: 0.0980 chunk 513 optimal weight: 6.9990 chunk 399 optimal weight: 5.9990 chunk 567 optimal weight: 50.0000 chunk 190 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 150 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN E 474 GLN F 474 GLN ** G 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 474 GLN H 474 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.134337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.106793 restraints weight = 120524.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.110415 restraints weight = 62626.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.111526 restraints weight = 32813.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.112825 restraints weight = 23425.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.112814 restraints weight = 21002.065| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 45744 Z= 0.177 Angle : 0.647 9.850 62740 Z= 0.327 Chirality : 0.045 0.210 7672 Planarity : 0.004 0.037 8064 Dihedral : 5.145 69.031 6904 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 6.73 % Allowed : 19.87 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.63 (0.11), residues: 6464 helix: 2.02 (0.08), residues: 4056 sheet: -0.59 (0.23), residues: 512 loop : -0.46 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E1145 TYR 0.013 0.001 TYR C 330 PHE 0.031 0.002 PHE H 169 TRP 0.023 0.001 TRP E 688 HIS 0.007 0.001 HIS F 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (45736) covalent geometry : angle 0.64657 / 0.33 (62724) SS BOND : bond 0.00132 / 0.07 ( 8) SS BOND : angle 1.50174 / 0.93 ( 16) hydrogen bonds : bond 0.04529 / 3.06 ( 3333) hydrogen bonds : angle 4.07532 / 2.97 ( 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 1190 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 240 poor density : 950 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.9218 (mmtm) cc_final: 0.8919 (mmtm) REVERT: A 58 ASP cc_start: 0.7728 (t0) cc_final: 0.7173 (t0) REVERT: A 160 ASN cc_start: 0.8750 (m-40) cc_final: 0.8371 (t0) REVERT: A 185 LYS cc_start: 0.8861 (ttmt) cc_final: 0.8533 (ttmm) REVERT: B 47 LYS cc_start: 0.9161 (mmtm) cc_final: 0.8873 (mmtm) REVERT: B 58 ASP cc_start: 0.7737 (t0) cc_final: 0.7186 (t0) REVERT: B 160 ASN cc_start: 0.8760 (m-40) cc_final: 0.8492 (t0) REVERT: B 185 LYS cc_start: 0.8852 (ttmt) cc_final: 0.8530 (ttmm) REVERT: C 58 ASP cc_start: 0.7740 (t0) cc_final: 0.7189 (t0) REVERT: C 160 ASN cc_start: 0.8745 (m-40) cc_final: 0.8424 (t0) REVERT: C 185 LYS cc_start: 0.8843 (ttmt) cc_final: 0.8530 (ttmm) REVERT: D 47 LYS cc_start: 0.9193 (mmtm) cc_final: 0.8930 (mmtm) REVERT: D 58 ASP cc_start: 0.7740 (t0) cc_final: 0.7166 (t0) REVERT: D 141 GLU cc_start: 0.8566 (mp0) cc_final: 0.8345 (mp0) REVERT: D 160 ASN cc_start: 0.8753 (m-40) cc_final: 0.8432 (t0) REVERT: D 185 LYS cc_start: 0.8865 (ttmt) cc_final: 0.8543 (ttmm) REVERT: E 230 TYR cc_start: 0.9191 (m-80) cc_final: 0.8826 (m-80) REVERT: E 264 GLN cc_start: 0.8611 (tp-100) cc_final: 0.8210 (tm-30) REVERT: E 432 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8404 (t80) REVERT: E 480 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.7287 (tmtt) REVERT: E 483 GLN cc_start: 0.7817 (mt0) cc_final: 0.7510 (mt0) REVERT: E 601 VAL cc_start: 0.9130 (t) cc_final: 0.8921 (p) REVERT: E 739 TRP cc_start: 0.6596 (OUTLIER) cc_final: 0.5735 (t60) REVERT: E 1125 PHE cc_start: 0.7714 (t80) cc_final: 0.7423 (t80) REVERT: E 1198 LEU cc_start: 0.9286 (tp) cc_final: 0.8973 (mt) REVERT: E 1294 TYR cc_start: 0.8796 (m-10) cc_final: 0.8428 (m-10) REVERT: E 1304 ASP cc_start: 0.8987 (t70) cc_final: 0.8734 (p0) REVERT: F 41 PHE cc_start: 0.8157 (m-80) cc_final: 0.7910 (m-80) REVERT: F 145 LEU cc_start: 0.8998 (tt) cc_final: 0.8711 (tp) REVERT: F 226 SER cc_start: 0.9020 (m) cc_final: 0.8710 (p) REVERT: F 230 TYR cc_start: 0.9194 (m-80) cc_final: 0.8851 (m-80) REVERT: F 264 GLN cc_start: 0.8597 (tp-100) cc_final: 0.8174 (tm-30) REVERT: F 432 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8400 (t80) REVERT: F 480 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.7289 (tmtt) REVERT: F 483 GLN cc_start: 0.7807 (mt0) cc_final: 0.7494 (mt0) REVERT: F 601 VAL cc_start: 0.9136 (t) cc_final: 0.8925 (p) REVERT: F 739 TRP cc_start: 0.6601 (OUTLIER) cc_final: 0.5707 (t60) REVERT: F 1125 PHE cc_start: 0.7736 (t80) cc_final: 0.7439 (t80) REVERT: F 1226 LYS cc_start: 0.9033 (mttt) cc_final: 0.8819 (mttp) REVERT: F 1230 TYR cc_start: 0.9002 (m-10) cc_final: 0.8665 (m-80) REVERT: F 1294 TYR cc_start: 0.8786 (m-10) cc_final: 0.8419 (m-10) REVERT: F 1304 ASP cc_start: 0.8967 (t70) cc_final: 0.8719 (p0) REVERT: G 41 PHE cc_start: 0.8153 (m-80) cc_final: 0.7920 (m-80) REVERT: G 168 ARG cc_start: 0.5199 (mtt90) cc_final: 0.4373 (mtm-85) REVERT: G 226 SER cc_start: 0.9024 (m) cc_final: 0.8715 (p) REVERT: G 230 TYR cc_start: 0.9186 (m-80) cc_final: 0.8833 (m-80) REVERT: G 264 GLN cc_start: 0.8622 (tp-100) cc_final: 0.8186 (tm-30) REVERT: G 370 ARG cc_start: 0.8568 (mmt-90) cc_final: 0.8359 (mmt90) REVERT: G 432 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.8415 (t80) REVERT: G 739 TRP cc_start: 0.6592 (OUTLIER) cc_final: 0.5732 (t60) REVERT: G 1125 PHE cc_start: 0.7757 (t80) cc_final: 0.7470 (t80) REVERT: G 1198 LEU cc_start: 0.9240 (tp) cc_final: 0.8946 (mt) REVERT: G 1292 SER cc_start: 0.8707 (m) cc_final: 0.8183 (p) REVERT: G 1294 TYR cc_start: 0.8769 (m-10) cc_final: 0.8382 (m-10) REVERT: G 1304 ASP cc_start: 0.8994 (t70) cc_final: 0.8720 (p0) REVERT: H 41 PHE cc_start: 0.8176 (m-80) cc_final: 0.7930 (m-80) REVERT: H 230 TYR cc_start: 0.9194 (m-80) cc_final: 0.8809 (m-80) REVERT: H 264 GLN cc_start: 0.8618 (tp-100) cc_final: 0.8193 (tm-30) REVERT: H 432 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.8398 (t80) REVERT: H 480 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.7288 (tmtt) REVERT: H 483 GLN cc_start: 0.7791 (mt0) cc_final: 0.7458 (mt0) REVERT: H 601 VAL cc_start: 0.9131 (t) cc_final: 0.8922 (p) REVERT: H 739 TRP cc_start: 0.6565 (OUTLIER) cc_final: 0.5734 (t60) REVERT: H 1125 PHE cc_start: 0.7708 (t80) cc_final: 0.7430 (t80) REVERT: H 1145 ARG cc_start: 0.8315 (ttp80) cc_final: 0.7755 (tmm160) REVERT: H 1230 TYR cc_start: 0.8935 (m-80) cc_final: 0.8549 (m-80) REVERT: H 1253 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7713 (mm-30) REVERT: H 1294 TYR cc_start: 0.8762 (m-10) cc_final: 0.8435 (m-10) REVERT: H 1304 ASP cc_start: 0.9017 (t70) cc_final: 0.8720 (t0) outliers start: 240 outliers final: 183 residues processed: 1095 average time/residue: 0.2228 time to fit residues: 426.2015 Evaluate side-chains 1078 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 884 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 140 GLU 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 B residue 71 THR Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 138 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 C residue 71 THR Chi-restraints excluded: chain C residue 88 MET 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 D residue 71 THR Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 138 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 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 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 182 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 223 ASN Chi-restraints excluded: chain E residue 304 THR 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 373 LEU 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 1171 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 1261 LEU Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1283 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 176 VAL 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 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 432 PHE Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 474 GLN Chi-restraints excluded: chain F residue 480 LYS Chi-restraints excluded: chain F residue 739 TRP Chi-restraints excluded: chain F residue 1140 LEU Chi-restraints excluded: chain F residue 1169 LEU Chi-restraints excluded: chain F residue 1171 LEU Chi-restraints excluded: chain F residue 1175 CYS Chi-restraints excluded: chain F residue 1227 LEU Chi-restraints excluded: chain F residue 1229 GLU 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 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 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 223 ASN 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 421 VAL Chi-restraints excluded: chain G residue 432 PHE Chi-restraints excluded: chain G residue 449 VAL Chi-restraints excluded: chain G residue 474 GLN Chi-restraints excluded: chain G residue 581 SER Chi-restraints excluded: chain G residue 739 TRP 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 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 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 223 ASN Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 304 THR 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 373 LEU 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 474 GLN Chi-restraints excluded: chain H residue 480 LYS Chi-restraints excluded: chain H residue 739 TRP Chi-restraints excluded: chain H residue 1140 LEU Chi-restraints excluded: chain H residue 1146 SER Chi-restraints excluded: chain H residue 1169 LEU Chi-restraints excluded: chain H residue 1171 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 1285 LEU Chi-restraints excluded: chain H residue 1307 ILE 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: [354, 119, 450, 418, 23, 199, 5, 441, 120, 485, 218] chunk 354 optimal weight: 20.0000 chunk 119 optimal weight: 1.9990 chunk 450 optimal weight: 9.9990 chunk 418 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 199 optimal weight: 40.0000 chunk 5 optimal weight: 2.9990 chunk 441 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 485 optimal weight: 20.0000 chunk 218 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 173 GLN B 216 HIS E 72 ASN E 262 ASN E 386 ASN F 72 ASN G 72 ASN ** G 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.135336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.107623 restraints weight = 119771.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.110387 restraints weight = 57356.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.112216 restraints weight = 34770.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.113413 restraints weight = 24509.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.114206 restraints weight = 19169.702| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.5610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 45744 Z= 0.150 Angle : 0.640 9.879 62740 Z= 0.322 Chirality : 0.044 0.244 7672 Planarity : 0.004 0.103 8064 Dihedral : 5.011 68.041 6904 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 5.95 % Allowed : 21.60 % Favored : 72.45 % 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: 1.79 (0.11), residues: 6464 helix: 2.14 (0.08), residues: 4052 sheet: -0.50 (0.23), residues: 512 loop : -0.40 (0.15), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G1145 TYR 0.011 0.001 TYR G 396 PHE 0.031 0.002 PHE H 169 TRP 0.019 0.001 TRP E 688 HIS 0.006 0.001 HIS E 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (45736) covalent geometry : angle 0.64018 / 0.32 (62724) SS BOND : bond 0.00106 / 0.06 ( 8) SS BOND : angle 1.26120 / 0.77 ( 16) hydrogen bonds : bond 0.04395 / 2.97 ( 3333) hydrogen bonds : angle 3.99965 / 2.92 ( 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 1176 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 964 time to evaluate : 1.737 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 47 LYS cc_start: 0.9183 (mmtm) cc_final: 0.8973 (mmtm) REVERT: A 58 ASP cc_start: 0.7718 (t0) cc_final: 0.7162 (t0) REVERT: A 185 LYS cc_start: 0.8852 (ttmt) cc_final: 0.8535 (ttmm) REVERT: B 47 LYS cc_start: 0.9174 (mmtm) cc_final: 0.8973 (mmtm) REVERT: B 58 ASP cc_start: 0.7716 (t0) cc_final: 0.7151 (t0) REVERT: B 185 LYS cc_start: 0.8855 (ttmt) cc_final: 0.8540 (ttmm) REVERT: C 47 LYS cc_start: 0.9190 (mmtm) cc_final: 0.8941 (mmtm) REVERT: C 58 ASP cc_start: 0.7732 (t0) cc_final: 0.7172 (t0) REVERT: C 185 LYS cc_start: 0.8853 (ttmt) cc_final: 0.8541 (ttmm) REVERT: D 58 ASP cc_start: 0.7727 (t0) cc_final: 0.7161 (t0) REVERT: D 160 ASN cc_start: 0.8737 (m-40) cc_final: 0.8395 (t0) REVERT: D 185 LYS cc_start: 0.8870 (ttmt) cc_final: 0.8543 (ttmm) REVERT: D 328 VAL cc_start: 0.9484 (t) cc_final: 0.9248 (p) REVERT: E 181 MET cc_start: 0.7962 (tpt) cc_final: 0.7761 (mmt) REVERT: E 264 GLN cc_start: 0.8581 (tp-100) cc_final: 0.8298 (tm-30) REVERT: E 402 MET cc_start: 0.5995 (tmm) cc_final: 0.4076 (tmm) REVERT: E 432 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.8387 (t80) REVERT: E 483 GLN cc_start: 0.7824 (mt0) cc_final: 0.7499 (mt0) REVERT: E 601 VAL cc_start: 0.9121 (t) cc_final: 0.8907 (p) REVERT: E 739 TRP cc_start: 0.6505 (OUTLIER) cc_final: 0.5694 (t60) REVERT: E 1125 PHE cc_start: 0.7718 (t80) cc_final: 0.7498 (t80) REVERT: E 1191 GLN cc_start: 0.8297 (pp30) cc_final: 0.8036 (pp30) REVERT: E 1198 LEU cc_start: 0.9253 (tp) cc_final: 0.8926 (mt) REVERT: E 1225 GLN cc_start: 0.8843 (mm-40) cc_final: 0.7796 (mm-40) REVERT: E 1294 TYR cc_start: 0.8787 (m-10) cc_final: 0.8413 (m-10) REVERT: E 1306 GLU cc_start: 0.8473 (tm-30) cc_final: 0.7788 (tp30) REVERT: F 41 PHE cc_start: 0.8160 (m-80) cc_final: 0.7910 (m-80) REVERT: F 76 ILE cc_start: 0.9470 (pp) cc_final: 0.9139 (tp) REVERT: F 226 SER cc_start: 0.9041 (m) cc_final: 0.8757 (p) REVERT: F 264 GLN cc_start: 0.8574 (tp-100) cc_final: 0.8146 (tm-30) REVERT: F 402 MET cc_start: 0.6161 (tmm) cc_final: 0.4218 (tmm) REVERT: F 432 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8424 (t80) REVERT: F 483 GLN cc_start: 0.7812 (mt0) cc_final: 0.7482 (mt0) REVERT: F 601 VAL cc_start: 0.9128 (t) cc_final: 0.8912 (p) REVERT: F 739 TRP cc_start: 0.6503 (OUTLIER) cc_final: 0.5683 (t60) REVERT: F 1125 PHE cc_start: 0.7676 (t80) cc_final: 0.7274 (t80) REVERT: F 1191 GLN cc_start: 0.8238 (pp30) cc_final: 0.7977 (pp30) REVERT: F 1198 LEU cc_start: 0.9250 (tp) cc_final: 0.8907 (mt) REVERT: F 1230 TYR cc_start: 0.8971 (m-10) cc_final: 0.8621 (m-80) REVERT: F 1294 TYR cc_start: 0.8770 (m-10) cc_final: 0.8408 (m-10) REVERT: F 1306 GLU cc_start: 0.8468 (tm-30) cc_final: 0.7817 (tp30) REVERT: G 168 ARG cc_start: 0.5281 (mtt90) cc_final: 0.4693 (mtm-85) REVERT: G 226 SER cc_start: 0.8972 (m) cc_final: 0.8684 (p) REVERT: G 230 TYR cc_start: 0.9159 (m-80) cc_final: 0.8845 (m-80) REVERT: G 264 GLN cc_start: 0.8590 (tp-100) cc_final: 0.8158 (tm-30) REVERT: G 370 ARG cc_start: 0.8528 (mmt-90) cc_final: 0.8182 (mpt-90) REVERT: G 402 MET cc_start: 0.6117 (tmm) cc_final: 0.4261 (tmm) REVERT: G 432 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.8422 (t80) REVERT: G 1125 PHE cc_start: 0.7666 (t80) cc_final: 0.7351 (t80) REVERT: G 1143 LEU cc_start: 0.9135 (tt) cc_final: 0.8733 (tp) REVERT: G 1198 LEU cc_start: 0.9206 (tp) cc_final: 0.8952 (mt) REVERT: G 1225 GLN cc_start: 0.8839 (mm-40) cc_final: 0.7806 (mm-40) REVERT: G 1253 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7070 (mm-30) REVERT: G 1292 SER cc_start: 0.8731 (m) cc_final: 0.7321 (p) REVERT: G 1294 TYR cc_start: 0.8776 (m-10) cc_final: 0.8377 (m-10) REVERT: G 1306 GLU cc_start: 0.8453 (tm-30) cc_final: 0.7753 (tp30) REVERT: H 41 PHE cc_start: 0.8156 (m-80) cc_final: 0.7881 (m-80) REVERT: H 230 TYR cc_start: 0.9158 (m-80) cc_final: 0.8818 (m-80) REVERT: H 264 GLN cc_start: 0.8582 (tp-100) cc_final: 0.8170 (tm-30) REVERT: H 402 MET cc_start: 0.6063 (tmm) cc_final: 0.4206 (tmm) REVERT: H 432 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8355 (t80) REVERT: H 483 GLN cc_start: 0.7792 (mt0) cc_final: 0.7438 (mt0) REVERT: H 601 VAL cc_start: 0.9124 (t) cc_final: 0.8914 (p) REVERT: H 1125 PHE cc_start: 0.7724 (t80) cc_final: 0.7449 (t80) REVERT: H 1143 LEU cc_start: 0.9127 (tt) cc_final: 0.8698 (tp) REVERT: H 1198 LEU cc_start: 0.9240 (tp) cc_final: 0.8911 (mt) REVERT: H 1253 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7655 (mm-30) REVERT: H 1294 TYR cc_start: 0.8759 (m-10) cc_final: 0.8432 (m-10) REVERT: H 1306 GLU cc_start: 0.8409 (tm-30) cc_final: 0.7750 (tp30) outliers start: 212 outliers final: 180 residues processed: 1090 average time/residue: 0.2258 time to fit residues: 430.8803 Evaluate side-chains 1075 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 889 time to evaluate : 1.558 ------------------------------------------------------------------------------- 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 139 THR Chi-restraints excluded: chain A residue 140 GLU 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 B residue 71 THR 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 C residue 71 THR 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 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 71 THR 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 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 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 182 LEU Chi-restraints excluded: chain E residue 221 PHE 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 368 LEU 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 548 THR Chi-restraints excluded: chain E residue 739 TRP Chi-restraints excluded: chain E residue 1171 LEU 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 1250 VAL Chi-restraints excluded: chain E residue 1253 GLU Chi-restraints excluded: chain E residue 1261 LEU 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 176 VAL Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 221 PHE Chi-restraints excluded: chain F residue 223 ASN Chi-restraints excluded: chain F residue 299 LEU 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 391 ILE 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 548 THR Chi-restraints excluded: chain F residue 739 TRP Chi-restraints excluded: chain F residue 1171 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 1229 GLU 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 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 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 223 ASN 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 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 739 TRP Chi-restraints excluded: chain G residue 1140 LEU 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 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 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 176 VAL 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 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 373 LEU 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 739 TRP Chi-restraints excluded: chain H residue 1140 LEU Chi-restraints excluded: chain H residue 1169 LEU Chi-restraints excluded: chain H residue 1171 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: [473, 481, 262, 2, 329, 570, 579, 253, 186, 518, 346] chunk 473 optimal weight: 40.0000 chunk 481 optimal weight: 6.9990 chunk 262 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 329 optimal weight: 8.9990 chunk 570 optimal weight: 10.0000 chunk 579 optimal weight: 30.0000 chunk 253 optimal weight: 50.0000 chunk 186 optimal weight: 30.0000 chunk 518 optimal weight: 50.0000 chunk 346 optimal weight: 20.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN A 313 GLN B 313 GLN D 277 HIS ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 474 GLN F 103 HIS F 262 ASN F 474 GLN ** G 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 262 ASN G 474 GLN H 262 ASN H 474 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.129706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.101959 restraints weight = 121799.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.104605 restraints weight = 58830.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.106369 restraints weight = 35778.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.107523 restraints weight = 25287.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.108323 restraints weight = 19841.660| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.6163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 45744 Z= 0.321 Angle : 0.790 14.122 62740 Z= 0.409 Chirality : 0.049 0.269 7672 Planarity : 0.005 0.138 8064 Dihedral : 5.378 77.423 6904 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 7.30 % Allowed : 20.68 % Favored : 72.03 % 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: 1.11 (0.11), residues: 6464 helix: 1.62 (0.08), residues: 4020 sheet: -0.72 (0.22), residues: 516 loop : -0.67 (0.15), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 370 TYR 0.021 0.002 TYR C 304 PHE 0.037 0.003 PHE F 169 TRP 0.043 0.002 TRP E 688 HIS 0.008 0.002 HIS F 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00707 / 0.32 (45736) covalent geometry : angle 0.78952 / 0.41 (62724) SS BOND : bond 0.00318 / 0.17 ( 8) SS BOND : angle 2.11576 / 1.40 ( 16) hydrogen bonds : bond 0.05202 / 3.51 ( 3333) hydrogen bonds : angle 4.56303 / 3.33 ( 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 1095 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 260 poor density : 835 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.7896 (t0) cc_final: 0.7446 (t0) REVERT: B 58 ASP cc_start: 0.7887 (t0) cc_final: 0.7442 (t0) REVERT: C 58 ASP cc_start: 0.7895 (t0) cc_final: 0.7446 (t0) REVERT: C 185 LYS cc_start: 0.8958 (ttmt) cc_final: 0.8712 (ttmm) REVERT: D 58 ASP cc_start: 0.7897 (t0) cc_final: 0.7448 (t0) REVERT: D 185 LYS cc_start: 0.8977 (ttmt) cc_final: 0.8722 (ttmm) REVERT: E 41 PHE cc_start: 0.8226 (m-80) cc_final: 0.7931 (m-80) REVERT: E 264 GLN cc_start: 0.8737 (tp-100) cc_final: 0.8322 (tm-30) REVERT: E 402 MET cc_start: 0.5926 (tmm) cc_final: 0.4756 (tmm) REVERT: E 432 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.8471 (t80) REVERT: E 483 GLN cc_start: 0.7950 (mt0) cc_final: 0.7617 (mt0) REVERT: E 601 VAL cc_start: 0.9225 (t) cc_final: 0.9023 (p) REVERT: E 739 TRP cc_start: 0.6765 (OUTLIER) cc_final: 0.5678 (t60) REVERT: E 1145 ARG cc_start: 0.8558 (ttp80) cc_final: 0.7804 (tmm160) REVERT: E 1191 GLN cc_start: 0.8372 (pp30) cc_final: 0.8111 (pp30) REVERT: E 1229 GLU cc_start: 0.8276 (mp0) cc_final: 0.8020 (pm20) REVERT: E 1294 TYR cc_start: 0.8877 (m-10) cc_final: 0.8534 (m-10) REVERT: E 1306 GLU cc_start: 0.8444 (tm-30) cc_final: 0.7733 (tp30) REVERT: F 41 PHE cc_start: 0.8223 (m-80) cc_final: 0.7903 (m-80) REVERT: F 264 GLN cc_start: 0.8708 (tp-100) cc_final: 0.8359 (tm-30) REVERT: F 370 ARG cc_start: 0.8772 (mmt90) cc_final: 0.7946 (mmt-90) REVERT: F 402 MET cc_start: 0.5877 (tmm) cc_final: 0.4769 (tmm) REVERT: F 432 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.8496 (t80) REVERT: F 483 GLN cc_start: 0.7939 (mt0) cc_final: 0.7604 (mt0) REVERT: F 601 VAL cc_start: 0.9216 (t) cc_final: 0.8995 (p) REVERT: F 739 TRP cc_start: 0.6754 (OUTLIER) cc_final: 0.5644 (t60) REVERT: F 1145 ARG cc_start: 0.8560 (ttp80) cc_final: 0.7793 (tmm160) REVERT: F 1226 LYS cc_start: 0.9087 (mttt) cc_final: 0.8850 (mttp) REVERT: F 1230 TYR cc_start: 0.8967 (m-10) cc_final: 0.8506 (m-80) REVERT: F 1304 ASP cc_start: 0.9034 (t70) cc_final: 0.8827 (t0) REVERT: F 1306 GLU cc_start: 0.8413 (tm-30) cc_final: 0.7686 (tp30) REVERT: G 41 PHE cc_start: 0.8240 (m-80) cc_final: 0.7955 (m-80) REVERT: G 168 ARG cc_start: 0.5643 (mtt90) cc_final: 0.5246 (mtm-85) REVERT: G 264 GLN cc_start: 0.8729 (tp-100) cc_final: 0.8393 (tm-30) REVERT: G 370 ARG cc_start: 0.8554 (mmt-90) cc_final: 0.7719 (mpt-90) REVERT: G 402 MET cc_start: 0.5923 (tmm) cc_final: 0.4755 (tmm) REVERT: G 432 PHE cc_start: 0.8866 (OUTLIER) cc_final: 0.8473 (t80) REVERT: G 739 TRP cc_start: 0.6748 (OUTLIER) cc_final: 0.5671 (t60) REVERT: G 1145 ARG cc_start: 0.8538 (ttp80) cc_final: 0.7772 (tmm160) REVERT: G 1191 GLN cc_start: 0.8350 (pp30) cc_final: 0.8145 (pp30) REVERT: G 1198 LEU cc_start: 0.9260 (tp) cc_final: 0.9006 (mt) REVERT: G 1253 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7494 (mm-30) REVERT: G 1292 SER cc_start: 0.8679 (m) cc_final: 0.7967 (p) REVERT: G 1298 MET cc_start: 0.8526 (tmm) cc_final: 0.8204 (tmm) REVERT: G 1306 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7689 (tp30) REVERT: H 41 PHE cc_start: 0.8234 (m-80) cc_final: 0.7891 (m-80) REVERT: H 139 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.8994 (mp) REVERT: H 264 GLN cc_start: 0.8708 (tp-100) cc_final: 0.8385 (tm-30) REVERT: H 402 MET cc_start: 0.5990 (tmm) cc_final: 0.4806 (tmm) REVERT: H 432 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8436 (t80) REVERT: H 483 GLN cc_start: 0.7941 (mt0) cc_final: 0.7601 (mt0) REVERT: H 601 VAL cc_start: 0.9223 (t) cc_final: 0.9018 (p) REVERT: H 739 TRP cc_start: 0.6718 (OUTLIER) cc_final: 0.5676 (t60) REVERT: H 1142 CYS cc_start: 0.8612 (p) cc_final: 0.8340 (m) REVERT: H 1145 ARG cc_start: 0.8563 (ttp80) cc_final: 0.7823 (tmm160) REVERT: H 1253 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7754 (mm-30) REVERT: H 1290 MET cc_start: 0.8696 (mmp) cc_final: 0.8485 (mmp) REVERT: H 1294 TYR cc_start: 0.8869 (m-10) cc_final: 0.8562 (m-10) REVERT: H 1298 MET cc_start: 0.8528 (tmm) cc_final: 0.8206 (tmm) outliers start: 260 outliers final: 204 residues processed: 1004 average time/residue: 0.2255 time to fit residues: 394.5925 Evaluate side-chains 1033 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 820 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 140 GLU 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 297 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 88 MET 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 297 THR Chi-restraints excluded: chain C residue 88 MET 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 88 MET 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 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 121 VAL Chi-restraints excluded: chain E residue 129 THR 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 221 PHE Chi-restraints excluded: chain E residue 223 ASN 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 373 LEU Chi-restraints excluded: chain E residue 391 ILE 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 548 THR Chi-restraints excluded: chain E residue 739 TRP Chi-restraints excluded: chain E residue 1157 ILE Chi-restraints excluded: chain E residue 1171 LEU Chi-restraints excluded: chain E residue 1173 VAL 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 1250 VAL Chi-restraints excluded: chain E residue 1253 GLU Chi-restraints excluded: chain E residue 1261 LEU 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 121 VAL Chi-restraints excluded: chain F residue 139 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 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 221 PHE Chi-restraints excluded: chain F residue 223 ASN 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 432 PHE Chi-restraints excluded: chain F residue 449 VAL 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 1157 ILE Chi-restraints excluded: chain F residue 1171 LEU Chi-restraints excluded: chain F residue 1173 VAL Chi-restraints excluded: chain F residue 1175 CYS Chi-restraints excluded: chain F residue 1202 SER 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 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 121 VAL 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 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 373 LEU 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 1250 VAL Chi-restraints excluded: chain G residue 1261 LEU 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 121 VAL Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 139 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 177 ILE Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 198 PHE Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 223 ASN 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 373 LEU Chi-restraints excluded: chain H residue 391 ILE 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 1171 LEU Chi-restraints excluded: chain H residue 1173 VAL 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 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: [193, 151, 39, 80, 448, 76, 631, 490, 526, 551, 341] chunk 193 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 448 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 631 optimal weight: 50.0000 chunk 490 optimal weight: 0.9990 chunk 526 optimal weight: 2.9990 chunk 551 optimal weight: 0.9990 chunk 341 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN B 277 HIS D 173 GLN G 166 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.134231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.105656 restraints weight = 121854.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.108477 restraints weight = 57777.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.110358 restraints weight = 34888.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.111575 restraints weight = 24480.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.112381 restraints weight = 19199.205| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.6223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 45744 Z= 0.150 Angle : 0.661 12.133 62740 Z= 0.333 Chirality : 0.045 0.270 7672 Planarity : 0.004 0.105 8064 Dihedral : 4.911 72.359 6896 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 5.30 % Allowed : 23.37 % Favored : 71.32 % 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: 1.57 (0.11), residues: 6464 helix: 2.04 (0.08), residues: 4024 sheet: -0.67 (0.22), residues: 512 loop : -0.59 (0.15), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F1145 TYR 0.023 0.001 TYR G1230 PHE 0.031 0.002 PHE F 169 TRP 0.023 0.001 TRP E 688 HIS 0.007 0.001 HIS E 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (45736) covalent geometry : angle 0.66037 / 0.33 (62724) SS BOND : bond 0.00053 / 0.03 ( 8) SS BOND : angle 1.22858 / 0.74 ( 16) hydrogen bonds : bond 0.04455 / 3.01 ( 3333) hydrogen bonds : angle 4.10097 / 2.99 ( 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 1138 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 949 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.7635 (t0) cc_final: 0.7115 (t0) REVERT: A 229 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7452 (mm-30) REVERT: B 58 ASP cc_start: 0.7630 (t0) cc_final: 0.7115 (t0) REVERT: B 229 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7649 (mm-30) REVERT: B 328 VAL cc_start: 0.9390 (t) cc_final: 0.9134 (p) REVERT: C 58 ASP cc_start: 0.7647 (t0) cc_final: 0.7127 (t0) REVERT: C 229 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7671 (mm-30) REVERT: C 328 VAL cc_start: 0.9410 (t) cc_final: 0.9190 (p) REVERT: D 58 ASP cc_start: 0.7646 (t0) cc_final: 0.7122 (t0) REVERT: D 328 VAL cc_start: 0.9409 (t) cc_final: 0.9169 (p) REVERT: E 41 PHE cc_start: 0.8106 (m-80) cc_final: 0.7852 (m-80) REVERT: E 248 ARG cc_start: 0.8022 (ptt180) cc_final: 0.7788 (ptt-90) REVERT: E 264 GLN cc_start: 0.8638 (tp-100) cc_final: 0.8330 (tm-30) REVERT: E 402 MET cc_start: 0.5985 (tmm) cc_final: 0.4713 (tmm) REVERT: E 432 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.8393 (t80) REVERT: E 483 GLN cc_start: 0.7920 (mt0) cc_final: 0.7608 (mt0) REVERT: E 739 TRP cc_start: 0.6715 (OUTLIER) cc_final: 0.5707 (t60) REVERT: E 1191 GLN cc_start: 0.8224 (pp30) cc_final: 0.8002 (pp30) REVERT: E 1198 LEU cc_start: 0.9242 (tp) cc_final: 0.8978 (mt) REVERT: E 1229 GLU cc_start: 0.8267 (mp0) cc_final: 0.7990 (pm20) REVERT: E 1294 TYR cc_start: 0.8775 (m-10) cc_final: 0.8442 (m-10) REVERT: E 1304 ASP cc_start: 0.8925 (t70) cc_final: 0.8673 (p0) REVERT: E 1305 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8701 (mmm) REVERT: F 41 PHE cc_start: 0.8145 (m-80) cc_final: 0.7868 (m-80) REVERT: F 248 ARG cc_start: 0.8023 (ptt180) cc_final: 0.7797 (ptt-90) REVERT: F 264 GLN cc_start: 0.8612 (tp-100) cc_final: 0.8229 (tm-30) REVERT: F 306 ARG cc_start: 0.8582 (tpp80) cc_final: 0.8370 (tpt-90) REVERT: F 402 MET cc_start: 0.6013 (tmm) cc_final: 0.4752 (tmm) REVERT: F 432 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8396 (t80) REVERT: F 483 GLN cc_start: 0.7904 (mt0) cc_final: 0.7590 (mt0) REVERT: F 739 TRP cc_start: 0.6704 (OUTLIER) cc_final: 0.5694 (t60) REVERT: F 1198 LEU cc_start: 0.9244 (tp) cc_final: 0.8909 (mt) REVERT: F 1304 ASP cc_start: 0.9005 (t70) cc_final: 0.8708 (p0) REVERT: G 41 PHE cc_start: 0.8131 (m-80) cc_final: 0.7897 (m-80) REVERT: G 168 ARG cc_start: 0.5584 (mtt90) cc_final: 0.5223 (mtm-85) REVERT: G 264 GLN cc_start: 0.8641 (tp-100) cc_final: 0.8263 (tm-30) REVERT: G 402 MET cc_start: 0.6054 (tmm) cc_final: 0.4790 (tmm) REVERT: G 432 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.8394 (t80) REVERT: G 739 TRP cc_start: 0.6709 (OUTLIER) cc_final: 0.5712 (t60) REVERT: G 1198 LEU cc_start: 0.9206 (tp) cc_final: 0.8965 (mt) REVERT: G 1253 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7525 (mm-30) REVERT: G 1292 SER cc_start: 0.8717 (m) cc_final: 0.8118 (p) REVERT: G 1304 ASP cc_start: 0.8964 (t0) cc_final: 0.8470 (p0) REVERT: H 41 PHE cc_start: 0.8138 (m-80) cc_final: 0.7865 (m-80) REVERT: H 264 GLN cc_start: 0.8618 (tp-100) cc_final: 0.8154 (tm-30) REVERT: H 402 MET cc_start: 0.6058 (tmm) cc_final: 0.4803 (tmm) REVERT: H 432 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.8373 (t80) REVERT: H 483 GLN cc_start: 0.7912 (mt0) cc_final: 0.7583 (mt0) REVERT: H 739 TRP cc_start: 0.6694 (OUTLIER) cc_final: 0.5727 (t60) REVERT: H 1198 LEU cc_start: 0.9263 (tp) cc_final: 0.8923 (mt) REVERT: H 1253 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7647 (mm-30) REVERT: H 1294 TYR cc_start: 0.8778 (m-10) cc_final: 0.8470 (m-10) REVERT: H 1298 MET cc_start: 0.8470 (tmm) cc_final: 0.8169 (tmm) outliers start: 189 outliers final: 140 residues processed: 1050 average time/residue: 0.2261 time to fit residues: 413.5931 Evaluate side-chains 1026 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 877 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 155 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 A residue 236 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain B residue 88 MET 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 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 C residue 88 MET 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 215 ILE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 88 MET 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 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 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 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 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 391 ILE 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 1171 LEU 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 1272 LEU Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1285 LEU Chi-restraints excluded: chain E residue 1305 MET 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 299 LEU Chi-restraints excluded: chain F residue 304 THR 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 432 PHE 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 1171 LEU Chi-restraints excluded: chain F residue 1175 CYS Chi-restraints excluded: chain F residue 1202 SER Chi-restraints excluded: chain F residue 1229 GLU 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 65 TRP Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 86 VAL 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 183 LEU Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 304 THR 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 391 ILE 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 1139 THR 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 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 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 176 VAL Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 304 THR 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 373 LEU Chi-restraints excluded: chain H residue 391 ILE 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 1140 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 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: [643, 463, 554, 264, 173, 502, 592, 449, 524, 330, 488] chunk 643 optimal weight: 7.9990 chunk 463 optimal weight: 50.0000 chunk 554 optimal weight: 7.9990 chunk 264 optimal weight: 3.9990 chunk 173 optimal weight: 8.9990 chunk 502 optimal weight: 50.0000 chunk 592 optimal weight: 20.0000 chunk 449 optimal weight: 9.9990 chunk 524 optimal weight: 6.9990 chunk 330 optimal weight: 0.0070 chunk 488 optimal weight: 5.9990 overall best weight: 5.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 HIS ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.132570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.103978 restraints weight = 122489.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.106761 restraints weight = 58813.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.108573 restraints weight = 35709.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.109770 restraints weight = 25340.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.110573 restraints weight = 19981.156| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.6390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 45744 Z= 0.218 Angle : 0.703 11.919 62740 Z= 0.360 Chirality : 0.047 0.400 7672 Planarity : 0.004 0.100 8064 Dihedral : 4.963 73.014 6896 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.85 % Allowed : 24.05 % Favored : 71.10 % 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: 1.44 (0.11), residues: 6464 helix: 1.94 (0.08), residues: 4032 sheet: -0.72 (0.22), residues: 512 loop : -0.67 (0.15), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G1145 TYR 0.022 0.002 TYR G1230 PHE 0.034 0.002 PHE H 169 TRP 0.028 0.002 TRP F 688 HIS 0.007 0.001 HIS F 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.22 (45736) covalent geometry : angle 0.70238 / 0.36 (62724) SS BOND : bond 0.00176 / 0.09 ( 8) SS BOND : angle 1.64179 / 1.03 ( 16) hydrogen bonds : bond 0.04660 / 3.15 ( 3333) hydrogen bonds : angle 4.21131 / 3.08 ( 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 1031 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 858 time to evaluate : 1.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.7674 (t0) cc_final: 0.7259 (t0) REVERT: B 47 LYS cc_start: 0.9282 (mmtm) cc_final: 0.9055 (mmtp) REVERT: B 58 ASP cc_start: 0.7662 (t0) cc_final: 0.7244 (t0) REVERT: B 328 VAL cc_start: 0.9437 (t) cc_final: 0.9200 (p) REVERT: C 58 ASP cc_start: 0.7683 (t0) cc_final: 0.7284 (t0) REVERT: C 328 VAL cc_start: 0.9436 (t) cc_final: 0.9206 (p) REVERT: D 58 ASP cc_start: 0.7680 (t0) cc_final: 0.7267 (t0) REVERT: D 328 VAL cc_start: 0.9432 (t) cc_final: 0.9204 (p) REVERT: E 41 PHE cc_start: 0.8218 (m-80) cc_final: 0.7930 (m-80) REVERT: E 264 GLN cc_start: 0.8637 (tp-100) cc_final: 0.8338 (tm-30) REVERT: E 402 MET cc_start: 0.5980 (tmm) cc_final: 0.4860 (tmm) REVERT: E 432 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8420 (t80) REVERT: E 739 TRP cc_start: 0.6813 (OUTLIER) cc_final: 0.5619 (t60) REVERT: E 1145 ARG cc_start: 0.8586 (ttp80) cc_final: 0.7841 (tmm160) REVERT: E 1198 LEU cc_start: 0.9275 (tp) cc_final: 0.9011 (mt) REVERT: E 1229 GLU cc_start: 0.8216 (mp0) cc_final: 0.7960 (pm20) REVERT: E 1294 TYR cc_start: 0.8823 (m-10) cc_final: 0.8481 (m-10) REVERT: E 1304 ASP cc_start: 0.8966 (t70) cc_final: 0.8763 (p0) REVERT: E 1305 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8749 (mmm) REVERT: F 41 PHE cc_start: 0.8149 (m-80) cc_final: 0.7855 (m-80) REVERT: F 264 GLN cc_start: 0.8652 (tp-100) cc_final: 0.8271 (tm-30) REVERT: F 306 ARG cc_start: 0.8618 (tpp80) cc_final: 0.8354 (tpt-90) REVERT: F 432 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.8419 (t80) REVERT: F 739 TRP cc_start: 0.6795 (OUTLIER) cc_final: 0.5586 (t60) REVERT: F 1145 ARG cc_start: 0.8633 (ttp80) cc_final: 0.7895 (tmm160) REVERT: F 1230 TYR cc_start: 0.8896 (m-80) cc_final: 0.8514 (m-80) REVERT: F 1294 TYR cc_start: 0.8849 (m-10) cc_final: 0.8541 (m-10) REVERT: G 41 PHE cc_start: 0.8223 (m-80) cc_final: 0.7951 (m-80) REVERT: G 168 ARG cc_start: 0.5654 (mtt90) cc_final: 0.5299 (mtm-85) REVERT: G 264 GLN cc_start: 0.8685 (tp-100) cc_final: 0.8294 (tm-30) REVERT: G 402 MET cc_start: 0.6051 (tmm) cc_final: 0.4892 (tmm) REVERT: G 432 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.8417 (t80) REVERT: G 739 TRP cc_start: 0.6769 (OUTLIER) cc_final: 0.5613 (t60) REVERT: G 1145 ARG cc_start: 0.8656 (ttp80) cc_final: 0.7943 (tmm160) REVERT: G 1198 LEU cc_start: 0.9208 (tp) cc_final: 0.8953 (mt) REVERT: G 1253 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7529 (mm-30) REVERT: G 1292 SER cc_start: 0.8457 (m) cc_final: 0.8239 (p) REVERT: G 1294 TYR cc_start: 0.8826 (m-10) cc_final: 0.8499 (m-10) REVERT: H 41 PHE cc_start: 0.8144 (m-80) cc_final: 0.7842 (m-80) REVERT: H 264 GLN cc_start: 0.8670 (tp-100) cc_final: 0.8298 (tm-30) REVERT: H 402 MET cc_start: 0.5927 (tmm) cc_final: 0.4822 (tmm) REVERT: H 432 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8379 (t80) REVERT: H 739 TRP cc_start: 0.6761 (OUTLIER) cc_final: 0.5664 (t60) REVERT: H 1145 ARG cc_start: 0.8616 (ttp80) cc_final: 0.7875 (tmm160) REVERT: H 1198 LEU cc_start: 0.9284 (tp) cc_final: 0.8928 (mt) REVERT: H 1253 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7711 (mm-30) REVERT: H 1294 TYR cc_start: 0.8835 (m-10) cc_final: 0.8531 (m-10) REVERT: H 1298 MET cc_start: 0.8485 (tmm) cc_final: 0.8175 (tmm) outliers start: 173 outliers final: 150 residues processed: 949 average time/residue: 0.2256 time to fit residues: 374.0503 Evaluate side-chains 989 residues out of total 5700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 830 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 155 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 A residue 236 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain B residue 88 MET 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 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 C residue 88 MET 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 215 ILE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 88 MET 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 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 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 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 223 ASN 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 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 1171 LEU 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 1272 LEU Chi-restraints excluded: chain E residue 1285 LEU Chi-restraints excluded: chain E residue 1305 MET 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 108 MET 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 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 391 ILE Chi-restraints excluded: chain F residue 432 PHE 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 1171 LEU Chi-restraints excluded: chain F residue 1175 CYS Chi-restraints excluded: chain F residue 1202 SER Chi-restraints excluded: chain F residue 1229 GLU 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 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 108 MET 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 299 LEU Chi-restraints excluded: chain G residue 304 THR 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 391 ILE 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 1139 THR 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 1285 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 86 VAL Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 108 MET 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 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 373 LEU Chi-restraints excluded: chain H residue 391 ILE 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 1140 LEU Chi-restraints excluded: chain H residue 1171 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 1272 LEU Chi-restraints excluded: chain H residue 1285 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: [133, 218, 182, 532, 398, 399, 56, 0, 394, 190, 227] chunk 133 optimal weight: 4.9990 chunk 218 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 532 optimal weight: 0.7980 chunk 398 optimal weight: 0.8980 chunk 399 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 394 optimal weight: 5.9990 chunk 190 optimal weight: 20.0000 chunk 227 optimal weight: 9.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 ASN G 262 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.133619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.105342 restraints weight = 122118.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.109117 restraints weight = 62585.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.110180 restraints weight = 33189.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.110971 restraints weight = 24870.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.111115 restraints weight = 22584.605| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.6511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 45744 Z= 0.173 Angle : 0.680 11.950 62740 Z= 0.345 Chirality : 0.045 0.326 7672 Planarity : 0.004 0.085 8064 Dihedral : 4.875 72.732 6896 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.88 % Allowed : 24.02 % Favored : 71.10 % 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: 1.55 (0.11), residues: 6464 helix: 2.03 (0.08), residues: 4032 sheet: -0.72 (0.23), residues: 512 loop : -0.62 (0.15), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 388 TYR 0.024 0.001 TYR E1230 PHE 0.033 0.002 PHE E 169 TRP 0.025 0.001 TRP G 688 HIS 0.006 0.001 HIS F 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (45736) covalent geometry : angle 0.67983 / 0.35 (62724) SS BOND : bond 0.00148 / 0.07 ( 8) SS BOND : angle 1.24522 / 0.75 ( 16) hydrogen bonds : bond 0.04479 / 3.04 ( 3333) hydrogen bonds : angle 4.10458 / 2.99 ( 9783) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10891.91 seconds wall clock time: 186 minutes 25.52 seconds (11185.52 seconds total)