Starting phenix.real_space_refine on Sat Jul 4 14:46:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s5x_24842/07_2026/7s5x_24842.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s5x_24842/07_2026/7s5x_24842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s5x_24842/07_2026/7s5x_24842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s5x_24842/07_2026/7s5x_24842.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7s5x_24842/07_2026/7s5x_24842.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s5x_24842/07_2026/7s5x_24842.cif" model { file = "/net/cci-nas-00/data/ceres_data/7s5x_24842/07_2026/7s5x_24842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s5x_24842/07_2026/7s5x_24842.cif" } resolution = 3.7 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= -0.005 sd= 0.085 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 5 5.49 5 Mg 2 5.21 5 S 122 5.16 5 C 13714 2.51 5 N 3607 2.21 5 O 3763 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 121 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21213 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2519 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain: "E" Number of atoms: 11077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1412, 11077 Classifications: {'peptide': 1412} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 46, 'TRANS': 1365} Chain breaks: 6 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 1, 'ASP:plan': 3, 'GLU:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 53 Chain: "E" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: B, C, D Time building chain proxies: 4.99, per 1000 atoms: 0.24 Number of scatterers: 21213 At special positions: 0 Unit cell: (135.2, 154.7, 137.8, 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) S 122 16.00 P 5 15.00 Mg 2 11.99 O 3763 8.00 N 3607 7.00 C 13714 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.02 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 142 " distance=2.02 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.02 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 1.1 seconds 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5086 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 27 sheets defined 49.1% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 59 through 65 Processing helix chain 'A' and resid 67 through 97 Processing helix chain 'A' and resid 116 through 129 removed outlier: 3.674A pdb=" N ALA A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 129 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 172 removed outlier: 3.566A pdb=" N ILE A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 removed outlier: 4.271A pdb=" N ARG A 176 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A 178 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 179 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 275 removed outlier: 4.065A pdb=" N LEU A 275 " --> pdb=" O PRO A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 351 removed outlier: 3.758A pdb=" N GLU A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 65 Processing helix chain 'B' and resid 67 through 97 Processing helix chain 'B' and resid 116 through 129 removed outlier: 3.674A pdb=" N ALA B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 129 " --> pdb=" O ILE B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 172 removed outlier: 3.566A pdb=" N ILE B 146 " --> pdb=" O CYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 179 removed outlier: 4.271A pdb=" N ARG B 176 " --> pdb=" O GLN B 173 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA B 178 " --> pdb=" O HIS B 175 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU B 179 " --> pdb=" O ARG B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 275 removed outlier: 4.065A pdb=" N LEU B 275 " --> pdb=" O PRO B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 351 removed outlier: 3.758A pdb=" N GLU B 351 " --> pdb=" O ARG B 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 65 Processing helix chain 'C' and resid 67 through 97 Processing helix chain 'C' and resid 116 through 129 removed outlier: 3.673A pdb=" N ALA C 120 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL C 129 " --> pdb=" O ILE C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 172 removed outlier: 3.567A pdb=" N ILE C 146 " --> pdb=" O CYS C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 179 removed outlier: 4.271A pdb=" N ARG C 176 " --> pdb=" O GLN C 173 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA C 178 " --> pdb=" O HIS C 175 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU C 179 " --> pdb=" O ARG C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 275 removed outlier: 4.065A pdb=" N LEU C 275 " --> pdb=" O PRO C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 351 removed outlier: 3.759A pdb=" N GLU C 351 " --> pdb=" O ARG C 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 65 Processing helix chain 'D' and resid 67 through 97 Processing helix chain 'D' and resid 116 through 129 removed outlier: 3.674A pdb=" N ALA D 120 " --> pdb=" O SER D 116 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL D 129 " --> pdb=" O ILE D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 172 removed outlier: 3.567A pdb=" N ILE D 146 " --> pdb=" O CYS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 179 removed outlier: 4.271A pdb=" N ARG D 176 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA D 178 " --> pdb=" O HIS D 175 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU D 179 " --> pdb=" O ARG D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 275 removed outlier: 4.066A pdb=" N LEU D 275 " --> pdb=" O PRO D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 351 removed outlier: 3.759A pdb=" N GLU D 351 " --> pdb=" O ARG D 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 52 removed outlier: 3.785A pdb=" N VAL E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL E 35 " --> pdb=" O ALA E 31 " (cutoff:3.500A) Proline residue: E 36 - end of helix Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 71 through 98 removed outlier: 3.676A pdb=" N GLY E 98 " --> pdb=" O ILE E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 107 removed outlier: 3.778A pdb=" N LEU E 107 " --> pdb=" O HIS E 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 104 through 107' Processing helix chain 'E' and resid 108 through 131 Processing helix chain 'E' and resid 137 through 161 Processing helix chain 'E' and resid 167 through 183 removed outlier: 4.053A pdb=" N CYS E 171 " --> pdb=" O GLN E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 191 Processing helix chain 'E' and resid 224 through 230 removed outlier: 3.584A pdb=" N GLY E 229 " --> pdb=" O LEU E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 242 removed outlier: 3.715A pdb=" N PHE E 237 " --> pdb=" O TRP E 233 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 272 Processing helix chain 'E' and resid 285 through 296 Processing helix chain 'E' and resid 297 through 310 Processing helix chain 'E' and resid 316 through 330 removed outlier: 4.106A pdb=" N ASP E 326 " --> pdb=" O PHE E 322 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS E 330 " --> pdb=" O ASP E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 353 Processing helix chain 'E' and resid 355 through 401 Processing helix chain 'E' and resid 402 through 404 No H-bonds generated for 'chain 'E' and resid 402 through 404' Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.103A pdb=" N MET E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 425 removed outlier: 3.807A pdb=" N VAL E 422 " --> pdb=" O ILE E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 457 Proline residue: E 437 - end of helix Proline residue: E 443 - end of helix Processing helix chain 'E' and resid 460 through 470 removed outlier: 4.165A pdb=" N GLY E 464 " --> pdb=" O SER E 460 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA E 466 " --> pdb=" O LEU E 462 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL E 467 " --> pdb=" O ILE E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 505 removed outlier: 4.822A pdb=" N VAL E 478 " --> pdb=" O VAL E 474 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA E 479 " --> pdb=" O GLN E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 513 Processing helix chain 'E' and resid 515 through 565 Proline residue: E 552 - end of helix removed outlier: 3.842A pdb=" N LEU E 557 " --> pdb=" O ILE E 553 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL E 564 " --> pdb=" O PHE E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 589 removed outlier: 3.700A pdb=" N ALA E 577 " --> pdb=" O SER E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 590 through 592 No H-bonds generated for 'chain 'E' and resid 590 through 592' Processing helix chain 'E' and resid 593 through 615 Processing helix chain 'E' and resid 719 through 728 removed outlier: 3.756A pdb=" N LEU E 724 " --> pdb=" O LYS E 720 " (cutoff:3.500A) Processing helix chain 'E' and resid 783 through 790 Processing helix chain 'E' and resid 795 through 807 removed outlier: 3.742A pdb=" N CYS E 806 " --> pdb=" O VAL E 802 " (cutoff:3.500A) Processing helix chain 'E' and resid 808 through 814 Processing helix chain 'E' and resid 817 through 821 removed outlier: 3.971A pdb=" N THR E 821 " --> pdb=" O GLY E 818 " (cutoff:3.500A) Processing helix chain 'E' and resid 832 through 843 removed outlier: 3.795A pdb=" N GLN E 836 " --> pdb=" O GLY E 832 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG E 837 " --> pdb=" O GLY E 833 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA E 843 " --> pdb=" O SER E 839 " (cutoff:3.500A) Processing helix chain 'E' and resid 861 through 871 removed outlier: 3.586A pdb=" N SER E 865 " --> pdb=" O ASP E 861 " (cutoff:3.500A) Processing helix chain 'E' and resid 875 through 880 removed outlier: 3.716A pdb=" N ASP E 879 " --> pdb=" O GLU E 875 " (cutoff:3.500A) Processing helix chain 'E' and resid 913 through 920 Processing helix chain 'E' and resid 921 through 933 removed outlier: 3.606A pdb=" N ASN E 933 " --> pdb=" O LYS E 929 " (cutoff:3.500A) Processing helix chain 'E' and resid 998 through 1009 removed outlier: 4.073A pdb=" N ALA E1002 " --> pdb=" O TRP E 998 " (cutoff:3.500A) Processing helix chain 'E' and resid 1010 through 1038 removed outlier: 3.956A pdb=" N LEU E1015 " --> pdb=" O LEU E1011 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN E1020 " --> pdb=" O LEU E1016 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU E1027 " --> pdb=" O LYS E1023 " (cutoff:3.500A) Processing helix chain 'E' and resid 1063 through 1097 Processing helix chain 'E' and resid 1101 through 1106 Processing helix chain 'E' and resid 1109 through 1116 removed outlier: 3.689A pdb=" N PHE E1113 " --> pdb=" O PRO E1109 " (cutoff:3.500A) Processing helix chain 'E' and resid 1117 through 1134 removed outlier: 3.709A pdb=" N ILE E1121 " --> pdb=" O PRO E1117 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP E1128 " --> pdb=" O ARG E1124 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N CYS E1129 " --> pdb=" O PHE E1125 " (cutoff:3.500A) Processing helix chain 'E' and resid 1134 through 1161 removed outlier: 4.547A pdb=" N SER E1138 " --> pdb=" O GLN E1134 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR E1139 " --> pdb=" O HIS E1135 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL E1160 " --> pdb=" O VAL E1156 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR E1161 " --> pdb=" O ILE E1157 " (cutoff:3.500A) Processing helix chain 'E' and resid 1162 through 1166 removed outlier: 3.597A pdb=" N VAL E1166 " --> pdb=" O VAL E1163 " (cutoff:3.500A) Processing helix chain 'E' and resid 1167 through 1210 removed outlier: 3.884A pdb=" N LEU E1171 " --> pdb=" O ALA E1167 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA E1185 " --> pdb=" O TYR E1181 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASP E1188 " --> pdb=" O VAL E1184 " (cutoff:3.500A) Proline residue: E1199 - end of helix removed outlier: 3.556A pdb=" N GLU E1209 " --> pdb=" O ALA E1205 " (cutoff:3.500A) Processing helix chain 'E' and resid 1219 through 1271 removed outlier: 3.507A pdb=" N PHE E1223 " --> pdb=" O TYR E1219 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU E1249 " --> pdb=" O ASN E1245 " (cutoff:3.500A) Processing helix chain 'E' and resid 1278 through 1320 removed outlier: 3.541A pdb=" N SER E1292 " --> pdb=" O ALA E1288 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ASN E1296 " --> pdb=" O SER E1292 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N TRP E1297 " --> pdb=" O ASN E1293 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA E1311 " --> pdb=" O LEU E1307 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL E1312 " --> pdb=" O GLN E1308 " (cutoff:3.500A) Processing helix chain 'E' and resid 1384 through 1392 removed outlier: 3.791A pdb=" N SER E1389 " --> pdb=" O LYS E1385 " (cutoff:3.500A) Processing helix chain 'E' and resid 1414 through 1421 removed outlier: 3.570A pdb=" N ARG E1421 " --> pdb=" O THR E1417 " (cutoff:3.500A) Processing helix chain 'E' and resid 1436 through 1441 removed outlier: 3.568A pdb=" N ASP E1441 " --> pdb=" O ARG E1437 " (cutoff:3.500A) Processing helix chain 'E' and resid 1447 through 1457 Processing helix chain 'E' and resid 1460 through 1467 removed outlier: 3.606A pdb=" N VAL E1464 " --> pdb=" O LEU E1460 " (cutoff:3.500A) Processing helix chain 'E' and resid 1483 through 1496 Processing helix chain 'E' and resid 1513 through 1528 Processing helix chain 'E' and resid 1562 through 1568 Processing helix chain 'E' and resid 1572 through 1582 Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 183 removed outlier: 3.514A pdb=" N VAL A 202 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183 removed outlier: 6.608A pdb=" N ALA A 187 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 236 through 237 removed outlier: 5.236A pdb=" N SER A 212 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N VAL A 290 " --> pdb=" O SER A 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 224 Processing sheet with id=AA5, first strand: chain 'A' and resid 319 through 322 Processing sheet with id=AA6, first strand: chain 'B' and resid 181 through 183 removed outlier: 3.515A pdb=" N VAL B 202 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 181 through 183 removed outlier: 6.607A pdb=" N ALA B 187 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 236 through 237 removed outlier: 5.237A pdb=" N SER B 212 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N VAL B 290 " --> pdb=" O SER B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 223 through 224 Processing sheet with id=AB1, first strand: chain 'B' and resid 319 through 322 Processing sheet with id=AB2, first strand: chain 'C' and resid 181 through 183 removed outlier: 3.515A pdb=" N VAL C 202 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 181 through 183 removed outlier: 6.607A pdb=" N ALA C 187 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 236 through 237 removed outlier: 5.237A pdb=" N SER C 212 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL C 290 " --> pdb=" O SER C 212 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 223 through 224 Processing sheet with id=AB6, first strand: chain 'C' and resid 319 through 322 Processing sheet with id=AB7, first strand: chain 'D' and resid 181 through 183 removed outlier: 3.515A pdb=" N VAL D 202 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 181 through 183 removed outlier: 6.606A pdb=" N ALA D 187 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 236 through 237 removed outlier: 5.237A pdb=" N SER D 212 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N VAL D 290 " --> pdb=" O SER D 212 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 223 through 224 Processing sheet with id=AC2, first strand: chain 'D' and resid 319 through 322 Processing sheet with id=AC3, first strand: chain 'E' and resid 678 through 680 removed outlier: 6.445A pdb=" N ILE E 704 " --> pdb=" O CYS E 679 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 697 through 701 removed outlier: 3.738A pdb=" N ASN E 699 " --> pdb=" O GLY E 685 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLY E 685 " --> pdb=" O ASN E 699 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR E 701 " --> pdb=" O MET E 683 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N MET E 683 " --> pdb=" O THR E 701 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLY E 684 " --> pdb=" O GLY E 736 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY E 736 " --> pdb=" O GLY E 684 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TYR E 686 " --> pdb=" O VAL E 734 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR E 688 " --> pdb=" O GLN E 732 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN E 732 " --> pdb=" O THR E 688 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 770 through 773 removed outlier: 5.938A pdb=" N ALA E 771 " --> pdb=" O PHE E 852 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ASP E 854 " --> pdb=" O ALA E 771 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA E 773 " --> pdb=" O ASP E 854 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL E 887 " --> pdb=" O LEU E 853 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR E 710 " --> pdb=" O LEU E 886 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N MET E 711 " --> pdb=" O ILE E 901 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N MET E 903 " --> pdb=" O MET E 711 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL E 713 " --> pdb=" O MET E 903 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG E 910 " --> pdb=" O ALA E 902 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LYS E 904 " --> pdb=" O ILE E 908 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE E 908 " --> pdb=" O LYS E 904 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 1365 through 1368 removed outlier: 5.239A pdb=" N VAL E1365 " --> pdb=" O ASN E1349 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU E1400 " --> pdb=" O SER E1351 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ARG E1353 " --> pdb=" O THR E1398 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N THR E1398 " --> pdb=" O ARG E1353 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 1365 through 1368 removed outlier: 5.239A pdb=" N VAL E1365 " --> pdb=" O ASN E1349 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 1502 through 1505 removed outlier: 7.036A pdb=" N GLY E1376 " --> pdb=" O ILE E1550 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU E1552 " --> pdb=" O GLY E1376 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N CYS E1378 " --> pdb=" O LEU E1552 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP E1561 " --> pdb=" O VAL E1549 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU E1559 " --> pdb=" O VAL E1551 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LYS E1553 " --> pdb=" O ILE E1557 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ILE E1557 " --> pdb=" O LYS E1553 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 1434 through 1435 1081 hydrogen bonds defined for protein. 3123 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: 4.76 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6243 1.34 - 1.46: 4868 1.46 - 1.58: 10355 1.58 - 1.70: 18 1.70 - 1.82: 196 Bond restraints: 21680 Sorted by residual: bond pdb=" C4 ATP E1604 " pdb=" C5 ATP E1604 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.50e+01 bond pdb=" C5 ATP E1604 " pdb=" C6 ATP E1604 " ideal model delta sigma weight residual 1.409 1.469 -0.060 1.00e-02 1.00e+04 3.64e+01 bond pdb=" C5 ATP E1604 " pdb=" N7 ATP E1604 " ideal model delta sigma weight residual 1.387 1.337 0.050 1.00e-02 1.00e+04 2.54e+01 bond pdb=" C4 ATP E1604 " pdb=" N9 ATP E1604 " ideal model delta sigma weight residual 1.374 1.324 0.050 1.00e-02 1.00e+04 2.54e+01 bond pdb=" C8 ATP E1604 " pdb=" N7 ATP E1604 " ideal model delta sigma weight residual 1.310 1.352 -0.042 1.00e-02 1.00e+04 1.78e+01 ... (remaining 21675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.83: 28766 3.83 - 7.66: 595 7.66 - 11.49: 77 11.49 - 15.32: 17 15.32 - 19.16: 8 Bond angle restraints: 29463 Sorted by residual: angle pdb=" PB ATP E1604 " pdb=" O3B ATP E1604 " pdb=" PG ATP E1604 " ideal model delta sigma weight residual 139.87 122.49 17.38 1.00e+00 1.00e+00 3.02e+02 angle pdb=" PA ATP E1604 " pdb=" O3A ATP E1604 " pdb=" PB ATP E1604 " ideal model delta sigma weight residual 136.83 119.81 17.02 1.00e+00 1.00e+00 2.90e+02 angle pdb=" C5 ATP E1604 " pdb=" C4 ATP E1604 " pdb=" N3 ATP E1604 " ideal model delta sigma weight residual 126.80 119.57 7.23 1.00e+00 1.00e+00 5.23e+01 angle pdb=" C ILE E 191 " pdb=" N ARG E 192 " pdb=" CA ARG E 192 " ideal model delta sigma weight residual 121.54 135.31 -13.77 1.91e+00 2.74e-01 5.20e+01 angle pdb=" N3 ATP E1604 " pdb=" C4 ATP E1604 " pdb=" N9 ATP E1604 " ideal model delta sigma weight residual 127.04 134.79 -7.75 1.15e+00 7.59e-01 4.56e+01 ... (remaining 29458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 12406 35.58 - 71.15: 435 71.15 - 106.73: 18 106.73 - 142.30: 1 142.30 - 177.88: 1 Dihedral angle restraints: 12861 sinusoidal: 5032 harmonic: 7829 Sorted by residual: dihedral pdb=" CA ALA E 250 " pdb=" C ALA E 250 " pdb=" N ILE E 251 " pdb=" CA ILE E 251 " ideal model delta harmonic sigma weight residual 180.00 143.62 36.38 0 5.00e+00 4.00e-02 5.29e+01 dihedral pdb=" O1B ADP E1601 " pdb=" O3A ADP E1601 " pdb=" PB ADP E1601 " pdb=" PA ADP E1601 " ideal model delta sinusoidal sigma weight residual 300.00 122.12 177.88 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" CA ASN E 11 " pdb=" C ASN E 11 " pdb=" N HIS E 12 " pdb=" CA HIS E 12 " ideal model delta harmonic sigma weight residual 180.00 145.55 34.45 0 5.00e+00 4.00e-02 4.75e+01 ... (remaining 12858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2707 0.081 - 0.162: 597 0.162 - 0.243: 114 0.243 - 0.324: 48 0.324 - 0.405: 16 Chirality restraints: 3482 Sorted by residual: chirality pdb=" CB ILE E1403 " pdb=" CA ILE E1403 " pdb=" CG1 ILE E1403 " pdb=" CG2 ILE E1403 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CB VAL E 325 " pdb=" CA VAL E 325 " pdb=" CG1 VAL E 325 " pdb=" CG2 VAL E 325 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" CG LEU E 453 " pdb=" CB LEU E 453 " pdb=" CD1 LEU E 453 " pdb=" CD2 LEU E 453 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 3479 not shown) Planarity restraints: 3667 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 894 " 0.073 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO E 895 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO E 895 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO E 895 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL E1250 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C VAL E1250 " 0.056 2.00e-02 2.50e+03 pdb=" O VAL E1250 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG E1251 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E1291 " 0.016 2.00e-02 2.50e+03 3.17e-02 1.00e+01 pdb=" C VAL E1291 " -0.055 2.00e-02 2.50e+03 pdb=" O VAL E1291 " 0.020 2.00e-02 2.50e+03 pdb=" N SER E1292 " 0.019 2.00e-02 2.50e+03 ... (remaining 3664 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1024 2.71 - 3.26: 19168 3.26 - 3.81: 36502 3.81 - 4.35: 42785 4.35 - 4.90: 72415 Nonbonded interactions: 171894 Sorted by model distance: nonbonded pdb=" O2A ADP E1601 " pdb="MG MG E1603 " model vdw 2.165 2.170 nonbonded pdb=" OG SER E1386 " pdb="MG MG E1603 " model vdw 2.178 2.170 nonbonded pdb=" OE1 GLN E 775 " pdb="MG MG E1602 " model vdw 2.185 2.170 nonbonded pdb=" OG SER E 721 " pdb="MG MG E1602 " model vdw 2.194 2.170 nonbonded pdb=" O1B ADP E1601 " pdb="MG MG E1603 " model vdw 2.206 2.170 ... (remaining 171889 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 3.690 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.990 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.098 21685 Z= 0.454 Angle : 1.394 19.155 29471 Z= 0.770 Chirality : 0.079 0.405 3482 Planarity : 0.012 0.110 3667 Dihedral : 17.239 177.881 7763 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 6.10 % Allowed : 11.08 % Favored : 82.81 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -5.19 (0.11), residues: 2674 helix: -4.23 (0.06), residues: 1298 sheet: -1.33 (0.32), residues: 237 loop : -2.73 (0.15), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 522 TYR 0.026 0.003 TYR E 397 PHE 0.031 0.003 PHE E 578 TRP 0.022 0.003 TRP E 144 HIS 0.012 0.002 HIS E 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00965 / 0.45 (21680) covalent geometry : angle 1.39396 / 0.77 (29463) SS BOND : bond 0.01137 / 0.57 ( 4) SS BOND : angle 2.53051 / 1.52 ( 8) hydrogen bonds : bond 0.15466 / 10.18 ( 1070) hydrogen bonds : angle 8.08570 / 5.68 ( 3123) Misc. bond : bond 0.00025 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 539 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 VAL cc_start: 0.7883 (OUTLIER) cc_final: 0.7632 (m) REVERT: A 47 LYS cc_start: 0.8587 (mtpp) cc_final: 0.8357 (mmmt) REVERT: A 48 ASN cc_start: 0.8097 (m-40) cc_final: 0.7784 (m-40) REVERT: A 207 LYS cc_start: 0.9046 (tptt) cc_final: 0.8816 (tppt) REVERT: A 217 MET cc_start: 0.8828 (mtm) cc_final: 0.8599 (mtm) REVERT: A 222 LYS cc_start: 0.8633 (ttmt) cc_final: 0.8424 (ttmm) REVERT: A 283 ILE cc_start: 0.9218 (mt) cc_final: 0.8823 (tt) REVERT: A 288 GLU cc_start: 0.7951 (pm20) cc_final: 0.7544 (pm20) REVERT: A 304 TYR cc_start: 0.8718 (m-80) cc_final: 0.8449 (m-80) REVERT: B 137 MET cc_start: 0.8557 (ptt) cc_final: 0.8253 (ptt) REVERT: B 144 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8469 (tp) REVERT: B 148 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.9073 (tp) REVERT: B 169 MET cc_start: 0.8759 (ttm) cc_final: 0.8539 (mtp) REVERT: B 170 LYS cc_start: 0.8844 (tptt) cc_final: 0.8617 (tptp) REVERT: B 179 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8337 (mt-10) REVERT: B 184 SER cc_start: 0.9429 (OUTLIER) cc_final: 0.9093 (t) REVERT: B 200 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8580 (pt) REVERT: B 224 THR cc_start: 0.8738 (OUTLIER) cc_final: 0.8495 (p) REVERT: B 240 MET cc_start: 0.8973 (tmm) cc_final: 0.8503 (tmm) REVERT: B 304 TYR cc_start: 0.8824 (m-80) cc_final: 0.8477 (m-80) REVERT: B 332 LYS cc_start: 0.8683 (mtpt) cc_final: 0.8431 (ttpt) REVERT: B 343 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8258 (tt) REVERT: C 144 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8369 (tt) REVERT: C 214 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.7998 (p) REVERT: C 288 GLU cc_start: 0.8190 (pm20) cc_final: 0.7814 (pm20) REVERT: C 303 SER cc_start: 0.9301 (OUTLIER) cc_final: 0.8987 (t) REVERT: C 327 SER cc_start: 0.8677 (OUTLIER) cc_final: 0.8075 (p) REVERT: D 39 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8146 (ttpt) REVERT: D 47 LYS cc_start: 0.8858 (mtpp) cc_final: 0.8435 (mmmt) REVERT: D 118 SER cc_start: 0.8952 (OUTLIER) cc_final: 0.8572 (p) REVERT: D 126 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8589 (mt-10) REVERT: D 137 MET cc_start: 0.8733 (ptt) cc_final: 0.8335 (ptm) REVERT: D 144 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8655 (tp) REVERT: D 167 ILE cc_start: 0.9423 (tp) cc_final: 0.9201 (tp) REVERT: D 184 SER cc_start: 0.9213 (OUTLIER) cc_final: 0.8891 (m) REVERT: D 222 LYS cc_start: 0.8844 (ttmt) cc_final: 0.8580 (tttm) REVERT: D 268 TYR cc_start: 0.8328 (t80) cc_final: 0.8090 (t80) REVERT: D 304 TYR cc_start: 0.9030 (m-80) cc_final: 0.8826 (m-80) REVERT: D 327 SER cc_start: 0.8564 (OUTLIER) cc_final: 0.8152 (p) REVERT: E 74 LEU cc_start: 0.8963 (tp) cc_final: 0.8498 (tp) REVERT: E 89 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7539 (tm-30) REVERT: E 178 ILE cc_start: 0.8964 (mm) cc_final: 0.8562 (mm) REVERT: E 209 GLU cc_start: 0.8226 (mp0) cc_final: 0.7970 (mp0) REVERT: E 309 LEU cc_start: 0.9138 (mt) cc_final: 0.8818 (mt) REVERT: E 311 ASP cc_start: 0.7978 (p0) cc_final: 0.7659 (p0) REVERT: E 367 LEU cc_start: 0.9550 (mm) cc_final: 0.9318 (mm) REVERT: E 388 LEU cc_start: 0.9450 (tp) cc_final: 0.9186 (tp) REVERT: E 1016 LEU cc_start: 0.9184 (tp) cc_final: 0.8874 (tp) REVERT: E 1141 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7978 (tm-30) REVERT: E 1143 LEU cc_start: 0.9245 (tp) cc_final: 0.8993 (tp) REVERT: E 1190 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7745 (tm-30) REVERT: E 1191 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8163 (tm-30) REVERT: E 1192 LEU cc_start: 0.9373 (tp) cc_final: 0.9042 (tt) REVERT: E 1200 LEU cc_start: 0.9263 (tt) cc_final: 0.8965 (tt) REVERT: E 1225 GLN cc_start: 0.7893 (tm-30) cc_final: 0.6784 (tm-30) REVERT: E 1229 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7146 (mm-30) REVERT: E 1246 ARG cc_start: 0.8462 (mmp80) cc_final: 0.8194 (mmp80) REVERT: E 1262 ILE cc_start: 0.9397 (tp) cc_final: 0.9161 (tp) REVERT: E 1402 HIS cc_start: 0.8045 (m90) cc_final: 0.7306 (m90) outliers start: 141 outliers final: 31 residues processed: 627 average time/residue: 0.1339 time to fit residues: 133.4365 Evaluate side-chains 396 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 348 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 41 ASN Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 770 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.0670 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN A 48 ASN A 276 HIS A 277 HIS ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 HIS B 277 HIS C 276 HIS C 335 ASN D 48 ASN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 HIS D 277 HIS E 167 GLN E 375 GLN ** E 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 438 ASN E 609 GLN E 699 ASN E 708 GLN E 732 GLN E 787 ASN E 795 ASN E 820 GLN E 863 HIS E 889 HIS E 935 GLN E 937 GLN ** E1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1316 HIS E1348 GLN E1373 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.079547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.065678 restraints weight = 70078.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.067815 restraints weight = 33078.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.069243 restraints weight = 19919.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.070256 restraints weight = 14022.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.070880 restraints weight = 10911.476| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21685 Z= 0.139 Angle : 0.650 9.906 29471 Z= 0.337 Chirality : 0.043 0.178 3482 Planarity : 0.006 0.076 3667 Dihedral : 8.226 165.630 2956 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.64 % Allowed : 17.49 % Favored : 78.87 % 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: -2.72 (0.14), residues: 2674 helix: -1.47 (0.12), residues: 1306 sheet: -0.64 (0.32), residues: 260 loop : -2.40 (0.16), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 54 TYR 0.014 0.001 TYR E1287 PHE 0.020 0.001 PHE E1182 TRP 0.011 0.001 TRP E1297 HIS 0.004 0.001 HIS E 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (21680) covalent geometry : angle 0.64975 / 0.34 (29463) SS BOND : bond 0.01488 / 0.78 ( 4) SS BOND : angle 1.37145 / 0.98 ( 8) hydrogen bonds : bond 0.04429 / 2.98 ( 1070) hydrogen bonds : angle 4.75845 / 3.32 ( 3123) Misc. bond : bond 0.00068 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 412 time to evaluate : 0.835 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: 0.8660 (mtpp) cc_final: 0.8307 (mmmt) REVERT: A 48 ASN cc_start: 0.8271 (m110) cc_final: 0.7814 (m110) REVERT: A 54 ARG cc_start: 0.8224 (mtt90) cc_final: 0.7806 (mtp85) REVERT: A 153 ASN cc_start: 0.9038 (m-40) cc_final: 0.8734 (m110) REVERT: A 160 ASN cc_start: 0.8676 (m-40) cc_final: 0.8043 (m110) REVERT: A 207 LYS cc_start: 0.9178 (tptt) cc_final: 0.8940 (tppt) REVERT: A 217 MET cc_start: 0.8683 (mtm) cc_final: 0.8370 (mtm) REVERT: A 288 GLU cc_start: 0.7657 (pm20) cc_final: 0.7161 (pm20) REVERT: A 304 TYR cc_start: 0.8741 (m-80) cc_final: 0.8318 (m-80) REVERT: B 60 PHE cc_start: 0.9046 (t80) cc_final: 0.8694 (t80) REVERT: B 137 MET cc_start: 0.8825 (ptt) cc_final: 0.8424 (ptt) REVERT: B 169 MET cc_start: 0.8793 (ttm) cc_final: 0.8543 (mtp) REVERT: B 179 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8418 (mt-10) REVERT: B 237 ASP cc_start: 0.8513 (t0) cc_final: 0.8199 (t0) REVERT: B 304 TYR cc_start: 0.8932 (m-80) cc_final: 0.8584 (m-80) REVERT: C 39 LYS cc_start: 0.8644 (mmmm) cc_final: 0.8395 (mmmm) REVERT: C 170 LYS cc_start: 0.9230 (ttmm) cc_final: 0.8989 (ttmm) REVERT: C 173 GLN cc_start: 0.9183 (OUTLIER) cc_final: 0.8452 (pm20) REVERT: C 185 LYS cc_start: 0.9074 (ttpt) cc_final: 0.8868 (tppt) REVERT: C 199 MET cc_start: 0.8189 (mtm) cc_final: 0.7934 (mtm) REVERT: C 304 TYR cc_start: 0.8682 (m-80) cc_final: 0.8096 (m-80) REVERT: C 327 SER cc_start: 0.8994 (OUTLIER) cc_final: 0.8572 (p) REVERT: D 57 GLN cc_start: 0.7982 (mt0) cc_final: 0.6477 (tp40) REVERT: D 137 MET cc_start: 0.8960 (ptt) cc_final: 0.8505 (ptm) REVERT: D 140 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8073 (mp0) REVERT: D 141 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.7066 (tt0) REVERT: D 163 MET cc_start: 0.8925 (mmt) cc_final: 0.8524 (mmp) REVERT: D 167 ILE cc_start: 0.9075 (tp) cc_final: 0.8857 (tp) REVERT: D 184 SER cc_start: 0.9431 (OUTLIER) cc_final: 0.9195 (m) REVERT: D 185 LYS cc_start: 0.9191 (mmmt) cc_final: 0.8951 (tptt) REVERT: D 197 CYS cc_start: 0.8691 (m) cc_final: 0.8077 (m) REVERT: D 222 LYS cc_start: 0.8962 (ttmt) cc_final: 0.8586 (tttm) REVERT: D 327 SER cc_start: 0.8825 (OUTLIER) cc_final: 0.8369 (p) REVERT: E 95 LEU cc_start: 0.9120 (mt) cc_final: 0.8794 (mt) REVERT: E 178 ILE cc_start: 0.9083 (mm) cc_final: 0.8868 (mm) REVERT: E 209 GLU cc_start: 0.8514 (mp0) cc_final: 0.8292 (mp0) REVERT: E 225 LEU cc_start: 0.9339 (tp) cc_final: 0.9098 (tp) REVERT: E 243 LYS cc_start: 0.8292 (mmtt) cc_final: 0.7925 (mptt) REVERT: E 367 LEU cc_start: 0.9388 (mm) cc_final: 0.9117 (mm) REVERT: E 370 GLN cc_start: 0.9141 (tm-30) cc_final: 0.8794 (tm-30) REVERT: E 371 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8444 (mmt-90) REVERT: E 388 LEU cc_start: 0.9499 (tp) cc_final: 0.9293 (tp) REVERT: E 587 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8696 (mt) REVERT: E 731 MET cc_start: 0.6981 (tpp) cc_final: 0.6580 (tpp) REVERT: E 855 ASP cc_start: 0.8565 (t0) cc_final: 0.8361 (t0) REVERT: E 1141 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8460 (tm-30) REVERT: E 1190 GLN cc_start: 0.8411 (tm-30) cc_final: 0.7755 (tm-30) REVERT: E 1191 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8358 (tp-100) REVERT: E 1194 ASP cc_start: 0.8099 (m-30) cc_final: 0.7622 (m-30) REVERT: E 1225 GLN cc_start: 0.7893 (tm-30) cc_final: 0.7415 (tm-30) REVERT: E 1229 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7674 (mt-10) REVERT: E 1242 THR cc_start: 0.9144 (m) cc_final: 0.8578 (m) REVERT: E 1246 ARG cc_start: 0.8476 (mmp80) cc_final: 0.8022 (mmp80) REVERT: E 1248 LEU cc_start: 0.9173 (tp) cc_final: 0.8931 (tp) REVERT: E 1262 ILE cc_start: 0.9276 (tp) cc_final: 0.9062 (tp) REVERT: E 1298 MET cc_start: 0.8810 (tmm) cc_final: 0.8606 (tmm) REVERT: E 1306 GLU cc_start: 0.8947 (tt0) cc_final: 0.8561 (pt0) REVERT: E 1505 MET cc_start: 0.7122 (mpp) cc_final: 0.6815 (mpp) outliers start: 84 outliers final: 30 residues processed: 477 average time/residue: 0.1383 time to fit residues: 104.0555 Evaluate side-chains 380 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 341 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 81 CYS Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 371 ARG Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 808 LEU Chi-restraints excluded: chain E residue 1091 LEU Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain E residue 1168 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 152 optimal weight: 0.5980 chunk 241 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 245 optimal weight: 30.0000 chunk 165 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 188 optimal weight: 0.4980 chunk 112 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 GLN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN C 160 ASN C 279 GLN D 128 GLN D 160 ASN D 335 ASN ** E 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 563 HIS E 836 GLN ** E 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.079435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.065512 restraints weight = 70623.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.067663 restraints weight = 33266.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.069132 restraints weight = 20034.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.070117 restraints weight = 14019.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.070735 restraints weight = 10951.896| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21685 Z= 0.122 Angle : 0.617 13.621 29471 Z= 0.310 Chirality : 0.043 0.213 3482 Planarity : 0.004 0.061 3667 Dihedral : 6.805 146.596 2911 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.94 % Allowed : 18.92 % Favored : 77.14 % 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: -1.34 (0.15), residues: 2674 helix: -0.09 (0.14), residues: 1313 sheet: -0.14 (0.33), residues: 256 loop : -2.05 (0.17), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1437 TYR 0.023 0.001 TYR D 268 PHE 0.018 0.001 PHE E 614 TRP 0.008 0.001 TRP D 90 HIS 0.004 0.001 HIS E 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (21680) covalent geometry : angle 0.61500 / 0.31 (29463) SS BOND : bond 0.00547 / 0.27 ( 4) SS BOND : angle 3.11547 / 2.13 ( 8) hydrogen bonds : bond 0.04025 / 2.72 ( 1070) hydrogen bonds : angle 4.24308 / 2.96 ( 3123) Misc. bond : bond 0.00134 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 376 time to evaluate : 0.867 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 54 ARG cc_start: 0.8166 (mtt90) cc_final: 0.7801 (mtp85) REVERT: A 84 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8926 (mm) REVERT: A 153 ASN cc_start: 0.9018 (m-40) cc_final: 0.8671 (m110) REVERT: A 179 GLU cc_start: 0.8395 (mp0) cc_final: 0.7829 (pm20) REVERT: A 288 GLU cc_start: 0.7796 (pm20) cc_final: 0.7486 (pm20) REVERT: B 47 LYS cc_start: 0.9090 (mtpt) cc_final: 0.8788 (mtmt) REVERT: B 137 MET cc_start: 0.8767 (ptt) cc_final: 0.8339 (ptt) REVERT: B 144 LEU cc_start: 0.9177 (tp) cc_final: 0.8879 (tp) REVERT: B 169 MET cc_start: 0.8781 (ttm) cc_final: 0.8524 (mtp) REVERT: B 170 LYS cc_start: 0.9245 (tptp) cc_final: 0.8956 (tttm) REVERT: B 179 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8317 (mp0) REVERT: B 237 ASP cc_start: 0.8570 (t0) cc_final: 0.8316 (t0) REVERT: B 288 GLU cc_start: 0.7711 (pm20) cc_final: 0.7251 (pm20) REVERT: B 304 TYR cc_start: 0.8999 (m-80) cc_final: 0.8786 (m-80) REVERT: C 170 LYS cc_start: 0.9257 (ttmm) cc_final: 0.8981 (ttmm) REVERT: C 173 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.8484 (pm20) REVERT: C 199 MET cc_start: 0.8175 (mtm) cc_final: 0.7947 (mtm) REVERT: C 288 GLU cc_start: 0.8236 (pt0) cc_final: 0.7984 (pt0) REVERT: C 303 SER cc_start: 0.9261 (t) cc_final: 0.8999 (t) REVERT: C 304 TYR cc_start: 0.8792 (m-80) cc_final: 0.8157 (m-80) REVERT: D 57 GLN cc_start: 0.8023 (mt0) cc_final: 0.7530 (mt0) REVERT: D 137 MET cc_start: 0.8899 (ptt) cc_final: 0.8532 (ptm) REVERT: D 141 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7208 (tt0) REVERT: D 152 GLN cc_start: 0.8945 (tt0) cc_final: 0.8542 (tm-30) REVERT: D 163 MET cc_start: 0.8900 (mmt) cc_final: 0.8322 (mmp) REVERT: D 197 CYS cc_start: 0.8722 (m) cc_final: 0.7995 (m) REVERT: D 222 LYS cc_start: 0.8942 (ttmt) cc_final: 0.8601 (tttm) REVERT: D 335 ASN cc_start: 0.9068 (m110) cc_final: 0.8841 (m110) REVERT: E 178 ILE cc_start: 0.9117 (mm) cc_final: 0.8835 (mm) REVERT: E 179 LEU cc_start: 0.8984 (tp) cc_final: 0.8719 (tp) REVERT: E 209 GLU cc_start: 0.8513 (mp0) cc_final: 0.8291 (mp0) REVERT: E 225 LEU cc_start: 0.9290 (tp) cc_final: 0.9056 (tp) REVERT: E 232 TRP cc_start: 0.7642 (OUTLIER) cc_final: 0.7346 (t-100) REVERT: E 243 LYS cc_start: 0.8246 (mmtt) cc_final: 0.7784 (mptt) REVERT: E 304 SER cc_start: 0.9305 (t) cc_final: 0.8744 (p) REVERT: E 388 LEU cc_start: 0.9510 (tp) cc_final: 0.9223 (tp) REVERT: E 433 PHE cc_start: 0.9339 (m-10) cc_final: 0.9104 (m-10) REVERT: E 722 SER cc_start: 0.9315 (m) cc_final: 0.8860 (p) REVERT: E 731 MET cc_start: 0.6957 (tpp) cc_final: 0.6492 (tpp) REVERT: E 855 ASP cc_start: 0.8538 (t0) cc_final: 0.8334 (t0) REVERT: E 1141 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8651 (tm-30) REVERT: E 1190 GLN cc_start: 0.8519 (tm-30) cc_final: 0.7794 (tm-30) REVERT: E 1191 GLN cc_start: 0.8753 (tm-30) cc_final: 0.8334 (tp-100) REVERT: E 1192 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8873 (tt) REVERT: E 1194 ASP cc_start: 0.8187 (m-30) cc_final: 0.7617 (m-30) REVERT: E 1225 GLN cc_start: 0.7668 (tm-30) cc_final: 0.7161 (tm-30) REVERT: E 1229 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7615 (mt-10) REVERT: E 1246 ARG cc_start: 0.8409 (mmp80) cc_final: 0.8040 (mmp80) REVERT: E 1248 LEU cc_start: 0.9091 (tp) cc_final: 0.8889 (tp) REVERT: E 1298 MET cc_start: 0.8792 (tmm) cc_final: 0.8557 (tmm) REVERT: E 1392 PHE cc_start: 0.7944 (m-80) cc_final: 0.7567 (m-80) REVERT: E 1552 LEU cc_start: 0.8300 (tp) cc_final: 0.8071 (tp) outliers start: 91 outliers final: 47 residues processed: 441 average time/residue: 0.1421 time to fit residues: 98.9268 Evaluate side-chains 388 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 335 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 81 CYS Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 371 ARG Chi-restraints excluded: chain E residue 386 ILE Chi-restraints excluded: chain E residue 420 ASN Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 444 VAL Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 725 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 1091 LEU Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1122 LEU Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1281 VAL Chi-restraints excluded: chain E residue 1402 HIS Chi-restraints excluded: chain E residue 1425 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 165 optimal weight: 3.9990 chunk 156 optimal weight: 0.7980 chunk 146 optimal weight: 0.5980 chunk 219 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 126 optimal weight: 0.3980 chunk 229 optimal weight: 10.0000 chunk 259 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 233 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 GLN A 173 GLN B 70 HIS ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN ** E 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 847 HIS ** E 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.079600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.065722 restraints weight = 70251.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.067868 restraints weight = 33207.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.069327 restraints weight = 19899.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.070251 restraints weight = 13951.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.070984 restraints weight = 10964.855| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21685 Z= 0.116 Angle : 0.598 12.165 29471 Z= 0.297 Chirality : 0.043 0.192 3482 Planarity : 0.004 0.056 3667 Dihedral : 6.237 141.608 2904 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.37 % Allowed : 19.78 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.16), residues: 2674 helix: 0.54 (0.14), residues: 1317 sheet: -0.05 (0.33), residues: 264 loop : -1.67 (0.18), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 371 TYR 0.040 0.001 TYR D 268 PHE 0.013 0.001 PHE E 49 TRP 0.014 0.001 TRP B 83 HIS 0.003 0.000 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (21680) covalent geometry : angle 0.59701 / 0.30 (29463) SS BOND : bond 0.00176 / 0.09 ( 4) SS BOND : angle 2.00550 / 1.52 ( 8) hydrogen bonds : bond 0.03863 / 2.62 ( 1070) hydrogen bonds : angle 3.98365 / 2.78 ( 3123) Misc. bond : bond 0.00163 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 371 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7820 (m110) cc_final: 0.7367 (m110) REVERT: A 54 ARG cc_start: 0.8135 (mtt90) cc_final: 0.7773 (mtp85) REVERT: A 84 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8936 (mm) REVERT: A 137 MET cc_start: 0.8815 (ptm) cc_final: 0.8500 (ptm) REVERT: A 153 ASN cc_start: 0.9004 (m-40) cc_final: 0.8597 (m110) REVERT: A 160 ASN cc_start: 0.8732 (m-40) cc_final: 0.8409 (m110) REVERT: A 173 GLN cc_start: 0.8791 (pt0) cc_final: 0.7976 (pt0) REVERT: A 175 HIS cc_start: 0.8865 (OUTLIER) cc_final: 0.8365 (p-80) REVERT: A 179 GLU cc_start: 0.8406 (mp0) cc_final: 0.8100 (pm20) REVERT: A 217 MET cc_start: 0.8820 (mtp) cc_final: 0.8542 (mtm) REVERT: A 288 GLU cc_start: 0.7895 (pm20) cc_final: 0.7544 (pm20) REVERT: A 304 TYR cc_start: 0.8782 (m-80) cc_final: 0.8548 (m-80) REVERT: B 39 LYS cc_start: 0.8351 (tmtt) cc_final: 0.7811 (ttpt) REVERT: B 47 LYS cc_start: 0.9146 (mtpt) cc_final: 0.8820 (mtmt) REVERT: B 137 MET cc_start: 0.8753 (ptt) cc_final: 0.8294 (ptm) REVERT: B 169 MET cc_start: 0.8749 (ttm) cc_final: 0.8524 (mtp) REVERT: B 170 LYS cc_start: 0.9266 (tptp) cc_final: 0.8983 (tttm) REVERT: B 179 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8306 (mp0) REVERT: B 237 ASP cc_start: 0.8596 (t0) cc_final: 0.8332 (t0) REVERT: B 288 GLU cc_start: 0.7634 (pm20) cc_final: 0.7123 (pm20) REVERT: C 170 LYS cc_start: 0.9261 (ttmm) cc_final: 0.9000 (ttmm) REVERT: C 173 GLN cc_start: 0.9173 (OUTLIER) cc_final: 0.8498 (pm20) REVERT: C 216 HIS cc_start: 0.7600 (OUTLIER) cc_final: 0.7340 (m170) REVERT: C 303 SER cc_start: 0.9161 (t) cc_final: 0.8852 (t) REVERT: C 304 TYR cc_start: 0.8837 (m-80) cc_final: 0.8195 (m-80) REVERT: D 137 MET cc_start: 0.8826 (ptt) cc_final: 0.8520 (ptm) REVERT: D 141 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6801 (tt0) REVERT: D 163 MET cc_start: 0.8926 (mmt) cc_final: 0.8430 (mmp) REVERT: D 197 CYS cc_start: 0.8688 (m) cc_final: 0.8008 (m) REVERT: D 222 LYS cc_start: 0.8913 (ttmt) cc_final: 0.8575 (tttm) REVERT: D 268 TYR cc_start: 0.8053 (t80) cc_final: 0.7848 (t80) REVERT: D 335 ASN cc_start: 0.9053 (m110) cc_final: 0.8831 (m110) REVERT: E 178 ILE cc_start: 0.9116 (mm) cc_final: 0.8840 (mm) REVERT: E 179 LEU cc_start: 0.9014 (tp) cc_final: 0.8797 (tp) REVERT: E 209 GLU cc_start: 0.8470 (mp0) cc_final: 0.8240 (mp0) REVERT: E 226 LEU cc_start: 0.9153 (tt) cc_final: 0.8887 (tp) REVERT: E 232 TRP cc_start: 0.7601 (OUTLIER) cc_final: 0.7307 (t-100) REVERT: E 243 LYS cc_start: 0.8300 (mmtt) cc_final: 0.7912 (mmtt) REVERT: E 304 SER cc_start: 0.9165 (OUTLIER) cc_final: 0.8502 (p) REVERT: E 388 LEU cc_start: 0.9546 (tp) cc_final: 0.9250 (tp) REVERT: E 433 PHE cc_start: 0.9330 (m-10) cc_final: 0.9087 (m-10) REVERT: E 731 MET cc_start: 0.6942 (tpp) cc_final: 0.6376 (tpp) REVERT: E 855 ASP cc_start: 0.8532 (t0) cc_final: 0.8297 (t0) REVERT: E 1016 LEU cc_start: 0.9246 (tp) cc_final: 0.9034 (tp) REVERT: E 1141 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8796 (tm-30) REVERT: E 1190 GLN cc_start: 0.8474 (tm-30) cc_final: 0.7765 (tm-30) REVERT: E 1191 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8378 (tp-100) REVERT: E 1192 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8763 (tt) REVERT: E 1194 ASP cc_start: 0.8189 (m-30) cc_final: 0.7624 (m-30) REVERT: E 1225 GLN cc_start: 0.7657 (tm-30) cc_final: 0.7147 (tm-30) REVERT: E 1229 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7539 (mt-10) REVERT: E 1246 ARG cc_start: 0.8300 (mmp80) cc_final: 0.7973 (mmp80) REVERT: E 1298 MET cc_start: 0.8787 (tmm) cc_final: 0.8550 (tmm) REVERT: E 1305 MET cc_start: 0.8712 (tpp) cc_final: 0.8467 (tpp) REVERT: E 1392 PHE cc_start: 0.7926 (m-80) cc_final: 0.7551 (m-80) REVERT: E 1483 SER cc_start: 0.7643 (OUTLIER) cc_final: 0.7392 (t) REVERT: E 1505 MET cc_start: 0.7224 (mpp) cc_final: 0.6784 (mpp) REVERT: E 1552 LEU cc_start: 0.8429 (tp) cc_final: 0.8184 (tp) outliers start: 101 outliers final: 50 residues processed: 443 average time/residue: 0.1422 time to fit residues: 99.2522 Evaluate side-chains 385 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 325 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 142 CYS Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 81 CYS Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 371 ARG Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 420 ASN Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 444 VAL Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 591 LEU Chi-restraints excluded: chain E residue 680 VAL Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 828 ILE Chi-restraints excluded: chain E residue 1122 LEU Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1281 VAL Chi-restraints excluded: chain E residue 1425 ILE Chi-restraints excluded: chain E residue 1483 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 139 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 189 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 229 optimal weight: 2.9990 chunk 267 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 GLN A 152 GLN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 HIS C 160 ASN C 216 HIS D 52 GLN E 242 HIS E 265 GLN ** E 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.078084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.064093 restraints weight = 70524.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.066207 restraints weight = 33424.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.067611 restraints weight = 20249.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.068619 restraints weight = 14345.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.069238 restraints weight = 11207.055| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21685 Z= 0.146 Angle : 0.612 11.580 29471 Z= 0.305 Chirality : 0.043 0.265 3482 Planarity : 0.004 0.053 3667 Dihedral : 6.004 140.523 2899 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.24 % Allowed : 20.17 % Favored : 75.58 % 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: -0.20 (0.16), residues: 2674 helix: 0.90 (0.15), residues: 1315 sheet: 0.21 (0.34), residues: 246 loop : -1.47 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1251 TYR 0.025 0.001 TYR D 268 PHE 0.020 0.001 PHE E1182 TRP 0.015 0.001 TRP B 83 HIS 0.004 0.001 HIS D 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (21680) covalent geometry : angle 0.61147 / 0.30 (29463) SS BOND : bond 0.00173 / 0.09 ( 4) SS BOND : angle 1.83365 / 1.38 ( 8) hydrogen bonds : bond 0.03943 / 2.69 ( 1070) hydrogen bonds : angle 3.91608 / 2.73 ( 3123) Misc. bond : bond 0.00159 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 336 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8244 (m110) cc_final: 0.7823 (m110) REVERT: A 54 ARG cc_start: 0.8190 (mtt90) cc_final: 0.7833 (mtp85) REVERT: A 84 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9050 (mm) REVERT: A 137 MET cc_start: 0.8816 (ptm) cc_final: 0.8482 (ptm) REVERT: A 153 ASN cc_start: 0.8998 (m-40) cc_final: 0.8601 (m110) REVERT: A 160 ASN cc_start: 0.8685 (m-40) cc_final: 0.8398 (m110) REVERT: A 173 GLN cc_start: 0.8658 (pt0) cc_final: 0.7871 (pt0) REVERT: A 175 HIS cc_start: 0.8731 (OUTLIER) cc_final: 0.8271 (p-80) REVERT: A 217 MET cc_start: 0.8906 (mtp) cc_final: 0.8634 (mtm) REVERT: A 222 LYS cc_start: 0.8457 (ttmm) cc_final: 0.8138 (ttmm) REVERT: A 258 TYR cc_start: 0.8564 (p90) cc_final: 0.8147 (p90) REVERT: A 288 GLU cc_start: 0.8058 (pm20) cc_final: 0.7611 (pm20) REVERT: B 39 LYS cc_start: 0.8401 (tmtt) cc_final: 0.7876 (ttpt) REVERT: B 47 LYS cc_start: 0.9120 (mtpt) cc_final: 0.8776 (mtmt) REVERT: B 137 MET cc_start: 0.8748 (ptt) cc_final: 0.8258 (ptm) REVERT: B 169 MET cc_start: 0.8800 (ttm) cc_final: 0.8561 (mtp) REVERT: B 170 LYS cc_start: 0.9265 (tptp) cc_final: 0.8996 (tttm) REVERT: B 179 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8351 (mp0) REVERT: B 237 ASP cc_start: 0.8632 (t0) cc_final: 0.8376 (t0) REVERT: B 288 GLU cc_start: 0.7639 (pm20) cc_final: 0.7084 (pm20) REVERT: B 304 TYR cc_start: 0.9018 (m-80) cc_final: 0.8777 (m-80) REVERT: C 170 LYS cc_start: 0.9288 (ttmm) cc_final: 0.8918 (ttmm) REVERT: C 173 GLN cc_start: 0.9311 (OUTLIER) cc_final: 0.8930 (pm20) REVERT: C 185 LYS cc_start: 0.9093 (ttpt) cc_final: 0.8886 (tppt) REVERT: C 199 MET cc_start: 0.8259 (mtm) cc_final: 0.8055 (mtm) REVERT: C 217 MET cc_start: 0.8903 (mtm) cc_final: 0.8649 (mtm) REVERT: C 303 SER cc_start: 0.9204 (t) cc_final: 0.8921 (t) REVERT: D 137 MET cc_start: 0.8929 (ptt) cc_final: 0.8535 (ptm) REVERT: D 141 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6867 (tt0) REVERT: D 163 MET cc_start: 0.8915 (mmt) cc_final: 0.8516 (mmm) REVERT: D 197 CYS cc_start: 0.8744 (m) cc_final: 0.8098 (m) REVERT: D 222 LYS cc_start: 0.8901 (ttmt) cc_final: 0.8545 (tttm) REVERT: D 251 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8923 (tt) REVERT: D 335 ASN cc_start: 0.9057 (m110) cc_final: 0.8853 (m110) REVERT: E 179 LEU cc_start: 0.9013 (tp) cc_final: 0.8741 (tp) REVERT: E 209 GLU cc_start: 0.8451 (mp0) cc_final: 0.8191 (mp0) REVERT: E 243 LYS cc_start: 0.8308 (mmtt) cc_final: 0.7827 (mmtt) REVERT: E 304 SER cc_start: 0.9262 (t) cc_final: 0.8743 (p) REVERT: E 731 MET cc_start: 0.7085 (tpp) cc_final: 0.6649 (tpp) REVERT: E 785 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7936 (pm20) REVERT: E 1141 GLU cc_start: 0.9099 (tm-30) cc_final: 0.8886 (tm-30) REVERT: E 1190 GLN cc_start: 0.8425 (tm-30) cc_final: 0.7860 (tm-30) REVERT: E 1194 ASP cc_start: 0.8141 (m-30) cc_final: 0.7516 (m-30) REVERT: E 1229 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7888 (mt-10) REVERT: E 1246 ARG cc_start: 0.8295 (mmp80) cc_final: 0.8026 (mmp80) REVERT: E 1248 LEU cc_start: 0.9296 (tp) cc_final: 0.9046 (tp) REVERT: E 1298 MET cc_start: 0.8789 (tmm) cc_final: 0.8547 (tmm) REVERT: E 1305 MET cc_start: 0.8724 (tpp) cc_final: 0.8451 (tpp) REVERT: E 1392 PHE cc_start: 0.8022 (m-80) cc_final: 0.7637 (m-80) REVERT: E 1483 SER cc_start: 0.7719 (OUTLIER) cc_final: 0.7458 (t) REVERT: E 1552 LEU cc_start: 0.8438 (tp) cc_final: 0.8168 (tp) outliers start: 98 outliers final: 64 residues processed: 409 average time/residue: 0.1380 time to fit residues: 89.7139 Evaluate side-chains 382 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 310 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 81 CYS Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 371 ARG Chi-restraints excluded: chain E residue 400 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 420 ASN Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 444 VAL Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 591 LEU Chi-restraints excluded: chain E residue 680 VAL Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 828 ILE Chi-restraints excluded: chain E residue 1091 LEU Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1122 LEU Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1281 VAL Chi-restraints excluded: chain E residue 1337 LYS Chi-restraints excluded: chain E residue 1402 HIS Chi-restraints excluded: chain E residue 1425 ILE Chi-restraints excluded: chain E residue 1483 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 209 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 249 optimal weight: 1.9990 chunk 196 optimal weight: 5.9990 chunk 230 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 236 optimal weight: 3.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 GLN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 HIS E 563 HIS ** E 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.078541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.064656 restraints weight = 70045.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.066772 restraints weight = 33232.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.068170 restraints weight = 20098.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.069164 restraints weight = 14230.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.069767 restraints weight = 11136.027| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21685 Z= 0.128 Angle : 0.607 11.623 29471 Z= 0.298 Chirality : 0.043 0.224 3482 Planarity : 0.004 0.051 3667 Dihedral : 5.893 139.187 2899 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.24 % Allowed : 20.74 % Favored : 75.02 % 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: 0.09 (0.16), residues: 2674 helix: 1.19 (0.15), residues: 1286 sheet: 0.11 (0.33), residues: 262 loop : -1.29 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 54 TYR 0.023 0.001 TYR D 268 PHE 0.017 0.001 PHE E1182 TRP 0.007 0.001 TRP B 83 HIS 0.004 0.000 HIS D 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (21680) covalent geometry : angle 0.60679 / 0.30 (29463) SS BOND : bond 0.00131 / 0.07 ( 4) SS BOND : angle 1.59641 / 1.22 ( 8) hydrogen bonds : bond 0.03862 / 2.65 ( 1070) hydrogen bonds : angle 3.89024 / 2.72 ( 3123) Misc. bond : bond 0.00158 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 342 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7937 (tppt) cc_final: 0.7683 (tppt) REVERT: A 48 ASN cc_start: 0.8317 (m110) cc_final: 0.7757 (m110) REVERT: A 54 ARG cc_start: 0.8212 (mtt90) cc_final: 0.7866 (mtp85) REVERT: A 84 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9072 (mm) REVERT: A 137 MET cc_start: 0.8734 (ptm) cc_final: 0.8426 (ptm) REVERT: A 153 ASN cc_start: 0.9012 (m-40) cc_final: 0.8603 (m110) REVERT: A 160 ASN cc_start: 0.8680 (m-40) cc_final: 0.8384 (m110) REVERT: A 217 MET cc_start: 0.8779 (mtp) cc_final: 0.8504 (mtm) REVERT: A 262 ASP cc_start: 0.7854 (p0) cc_final: 0.7648 (p0) REVERT: A 288 GLU cc_start: 0.8049 (pm20) cc_final: 0.7675 (pm20) REVERT: A 304 TYR cc_start: 0.8785 (m-80) cc_final: 0.8522 (m-80) REVERT: B 39 LYS cc_start: 0.8415 (tmtt) cc_final: 0.7884 (ttpt) REVERT: B 47 LYS cc_start: 0.9165 (mtpt) cc_final: 0.8885 (mtmt) REVERT: B 88 MET cc_start: 0.8495 (tpp) cc_final: 0.8259 (ttp) REVERT: B 137 MET cc_start: 0.8740 (ptt) cc_final: 0.8236 (ptm) REVERT: B 169 MET cc_start: 0.8760 (ttm) cc_final: 0.8524 (mtp) REVERT: B 170 LYS cc_start: 0.9274 (tptp) cc_final: 0.9054 (tttm) REVERT: B 179 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8466 (mp0) REVERT: B 237 ASP cc_start: 0.8632 (t0) cc_final: 0.8396 (t0) REVERT: B 288 GLU cc_start: 0.7621 (pm20) cc_final: 0.7140 (pm20) REVERT: C 170 LYS cc_start: 0.9293 (ttmm) cc_final: 0.8999 (ttmm) REVERT: C 173 GLN cc_start: 0.9330 (OUTLIER) cc_final: 0.8978 (pm20) REVERT: C 185 LYS cc_start: 0.9092 (ttpt) cc_final: 0.8853 (tppt) REVERT: C 217 MET cc_start: 0.8896 (mtm) cc_final: 0.8642 (mtm) REVERT: C 303 SER cc_start: 0.9250 (t) cc_final: 0.8958 (t) REVERT: C 304 TYR cc_start: 0.8587 (m-80) cc_final: 0.8071 (m-80) REVERT: D 48 ASN cc_start: 0.8950 (m-40) cc_final: 0.8750 (t0) REVERT: D 137 MET cc_start: 0.8919 (ptt) cc_final: 0.8503 (ptm) REVERT: D 141 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6870 (tt0) REVERT: D 163 MET cc_start: 0.8848 (mmt) cc_final: 0.8474 (mmm) REVERT: D 197 CYS cc_start: 0.8721 (m) cc_final: 0.8049 (m) REVERT: D 222 LYS cc_start: 0.8956 (ttmt) cc_final: 0.8586 (tttm) REVERT: E 113 MET cc_start: 0.8261 (mtt) cc_final: 0.8017 (mtp) REVERT: E 179 LEU cc_start: 0.9011 (tp) cc_final: 0.8737 (tp) REVERT: E 209 GLU cc_start: 0.8363 (mp0) cc_final: 0.8075 (mp0) REVERT: E 243 LYS cc_start: 0.8247 (mmtt) cc_final: 0.7797 (mmtt) REVERT: E 304 SER cc_start: 0.9239 (OUTLIER) cc_final: 0.8715 (p) REVERT: E 731 MET cc_start: 0.7106 (tpp) cc_final: 0.6646 (tpp) REVERT: E 785 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7837 (pm20) REVERT: E 903 MET cc_start: 0.7531 (mtp) cc_final: 0.7196 (ptp) REVERT: E 1141 GLU cc_start: 0.9104 (tm-30) cc_final: 0.8885 (tm-30) REVERT: E 1190 GLN cc_start: 0.8353 (tm-30) cc_final: 0.7828 (tm-30) REVERT: E 1194 ASP cc_start: 0.8097 (m-30) cc_final: 0.7496 (m-30) REVERT: E 1229 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7847 (mt-10) REVERT: E 1246 ARG cc_start: 0.8274 (mmp80) cc_final: 0.8058 (mmp80) REVERT: E 1248 LEU cc_start: 0.9169 (tp) cc_final: 0.8925 (tp) REVERT: E 1298 MET cc_start: 0.8811 (tmm) cc_final: 0.8579 (tmm) REVERT: E 1392 PHE cc_start: 0.8068 (m-80) cc_final: 0.7684 (m-80) REVERT: E 1483 SER cc_start: 0.7676 (OUTLIER) cc_final: 0.7401 (t) REVERT: E 1505 MET cc_start: 0.7409 (mpp) cc_final: 0.6746 (mpp) REVERT: E 1552 LEU cc_start: 0.8460 (tp) cc_final: 0.8156 (tp) outliers start: 98 outliers final: 65 residues processed: 418 average time/residue: 0.1319 time to fit residues: 87.4185 Evaluate side-chains 383 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 311 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 81 CYS Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 371 ARG Chi-restraints excluded: chain E residue 400 ILE Chi-restraints excluded: chain E residue 420 ASN Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 444 VAL Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 680 VAL Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 828 ILE Chi-restraints excluded: chain E residue 911 GLU Chi-restraints excluded: chain E residue 1091 LEU Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1122 LEU Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain E residue 1166 VAL Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1189 LEU Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1281 VAL Chi-restraints excluded: chain E residue 1402 HIS Chi-restraints excluded: chain E residue 1425 ILE Chi-restraints excluded: chain E residue 1483 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 71 optimal weight: 0.2980 chunk 256 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 219 optimal weight: 1.9990 chunk 245 optimal weight: 5.9990 chunk 237 optimal weight: 0.9980 chunk 231 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 GLN A 173 GLN A 175 HIS C 160 ASN C 216 HIS E 263 ASN ** E 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1123 ASN ** E1541 HIS ** 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 = 0.3367 r_free = 0.3367 target = 0.079056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.065124 restraints weight = 70116.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.067245 restraints weight = 33247.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.068697 restraints weight = 20055.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.069654 restraints weight = 14111.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.070331 restraints weight = 11124.680| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21685 Z= 0.120 Angle : 0.613 11.718 29471 Z= 0.299 Chirality : 0.043 0.237 3482 Planarity : 0.003 0.049 3667 Dihedral : 5.822 138.196 2898 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.37 % Allowed : 21.52 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.21 (0.17), residues: 2674 helix: 1.32 (0.15), residues: 1288 sheet: 0.14 (0.33), residues: 267 loop : -1.28 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E1251 TYR 0.022 0.001 TYR D 268 PHE 0.017 0.001 PHE C 86 TRP 0.007 0.001 TRP B 83 HIS 0.004 0.000 HIS D 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (21680) covalent geometry : angle 0.61312 / 0.30 (29463) SS BOND : bond 0.00481 / 0.24 ( 4) SS BOND : angle 1.29959 / 0.88 ( 8) hydrogen bonds : bond 0.03834 / 2.63 ( 1070) hydrogen bonds : angle 3.83006 / 2.68 ( 3123) Misc. bond : bond 0.00153 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 331 time to evaluate : 0.581 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: 0.7982 (tppt) cc_final: 0.7705 (tppt) REVERT: A 48 ASN cc_start: 0.8382 (m110) cc_final: 0.7789 (m110) REVERT: A 54 ARG cc_start: 0.8221 (mtt90) cc_final: 0.7909 (mtp85) REVERT: A 73 LEU cc_start: 0.8983 (mt) cc_final: 0.8706 (tp) REVERT: A 137 MET cc_start: 0.8734 (ptm) cc_final: 0.8321 (ptm) REVERT: A 153 ASN cc_start: 0.9031 (m-40) cc_final: 0.8644 (m110) REVERT: A 160 ASN cc_start: 0.8670 (m-40) cc_final: 0.8381 (m110) REVERT: A 173 GLN cc_start: 0.8777 (pt0) cc_final: 0.8277 (pt0) REVERT: A 175 HIS cc_start: 0.8675 (OUTLIER) cc_final: 0.8472 (p90) REVERT: A 288 GLU cc_start: 0.8123 (pm20) cc_final: 0.7688 (pm20) REVERT: A 304 TYR cc_start: 0.8786 (m-80) cc_final: 0.8435 (m-80) REVERT: B 39 LYS cc_start: 0.8424 (tmtt) cc_final: 0.7879 (ttpt) REVERT: B 47 LYS cc_start: 0.9177 (mtpt) cc_final: 0.8894 (mtmt) REVERT: B 137 MET cc_start: 0.8731 (ptt) cc_final: 0.8244 (ptm) REVERT: B 169 MET cc_start: 0.8757 (ttm) cc_final: 0.8541 (mtp) REVERT: B 170 LYS cc_start: 0.9278 (tptp) cc_final: 0.9008 (tttm) REVERT: B 179 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8454 (mp0) REVERT: B 237 ASP cc_start: 0.8575 (t0) cc_final: 0.8340 (t0) REVERT: B 288 GLU cc_start: 0.7583 (pm20) cc_final: 0.7073 (pm20) REVERT: B 304 TYR cc_start: 0.8970 (m-80) cc_final: 0.8645 (m-80) REVERT: C 170 LYS cc_start: 0.9291 (ttmm) cc_final: 0.8953 (ttmm) REVERT: C 173 GLN cc_start: 0.9311 (OUTLIER) cc_final: 0.8939 (pm20) REVERT: C 185 LYS cc_start: 0.9086 (ttpt) cc_final: 0.8848 (tppt) REVERT: C 217 MET cc_start: 0.8886 (mtm) cc_final: 0.8651 (mtm) REVERT: C 303 SER cc_start: 0.9204 (t) cc_final: 0.8891 (t) REVERT: C 304 TYR cc_start: 0.8705 (m-80) cc_final: 0.8242 (m-80) REVERT: D 137 MET cc_start: 0.8930 (ptt) cc_final: 0.8550 (ptm) REVERT: D 141 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7246 (tt0) REVERT: D 163 MET cc_start: 0.8810 (mmt) cc_final: 0.8427 (mmm) REVERT: D 197 CYS cc_start: 0.8637 (m) cc_final: 0.7974 (m) REVERT: D 222 LYS cc_start: 0.8946 (ttmt) cc_final: 0.8607 (tttm) REVERT: E 113 MET cc_start: 0.8239 (mtt) cc_final: 0.8003 (mtp) REVERT: E 132 ASN cc_start: 0.9022 (t0) cc_final: 0.8660 (t0) REVERT: E 179 LEU cc_start: 0.8997 (tp) cc_final: 0.8717 (tp) REVERT: E 209 GLU cc_start: 0.8433 (mp0) cc_final: 0.8170 (mp0) REVERT: E 243 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7631 (mmtt) REVERT: E 304 SER cc_start: 0.9223 (OUTLIER) cc_final: 0.8698 (p) REVERT: E 594 LEU cc_start: 0.8498 (mm) cc_final: 0.7522 (tt) REVERT: E 731 MET cc_start: 0.7225 (tpp) cc_final: 0.6549 (tpp) REVERT: E 785 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7939 (pm20) REVERT: E 903 MET cc_start: 0.7482 (mtp) cc_final: 0.7162 (ptp) REVERT: E 1141 GLU cc_start: 0.9115 (tm-30) cc_final: 0.8912 (tm-30) REVERT: E 1190 GLN cc_start: 0.8310 (tm-30) cc_final: 0.7878 (tm-30) REVERT: E 1194 ASP cc_start: 0.8217 (m-30) cc_final: 0.7622 (m-30) REVERT: E 1229 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7842 (mt-10) REVERT: E 1246 ARG cc_start: 0.8304 (mmp80) cc_final: 0.8083 (mmp80) REVERT: E 1248 LEU cc_start: 0.9140 (tp) cc_final: 0.8922 (tp) REVERT: E 1298 MET cc_start: 0.8836 (tmm) cc_final: 0.8622 (tmm) REVERT: E 1392 PHE cc_start: 0.8062 (m-80) cc_final: 0.7670 (m-80) REVERT: E 1428 ASP cc_start: 0.8603 (t70) cc_final: 0.8254 (t0) REVERT: E 1455 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8812 (pp) REVERT: E 1483 SER cc_start: 0.7685 (OUTLIER) cc_final: 0.7390 (t) REVERT: E 1552 LEU cc_start: 0.8448 (tp) cc_final: 0.8139 (tp) outliers start: 101 outliers final: 64 residues processed: 409 average time/residue: 0.1411 time to fit residues: 91.0012 Evaluate side-chains 386 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 314 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 277 HIS Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 371 ARG Chi-restraints excluded: chain E residue 420 ASN Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 680 VAL Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 828 ILE Chi-restraints excluded: chain E residue 911 GLU Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1122 LEU Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain E residue 1166 VAL Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1189 LEU Chi-restraints excluded: chain E residue 1201 LEU Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1281 VAL Chi-restraints excluded: chain E residue 1337 LYS Chi-restraints excluded: chain E residue 1402 HIS Chi-restraints excluded: chain E residue 1425 ILE Chi-restraints excluded: chain E residue 1455 LEU Chi-restraints excluded: chain E residue 1483 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 139 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 221 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 249 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 157 optimal weight: 0.7980 chunk 154 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN C 216 HIS ** E 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.077960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.064023 restraints weight = 70630.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.066113 restraints weight = 33404.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.067517 restraints weight = 20212.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.068507 restraints weight = 14326.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.069158 restraints weight = 11237.699| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21685 Z= 0.145 Angle : 0.631 10.990 29471 Z= 0.308 Chirality : 0.044 0.272 3482 Planarity : 0.004 0.053 3667 Dihedral : 5.828 139.031 2898 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.03 % Allowed : 22.47 % Favored : 73.51 % 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: 0.29 (0.17), residues: 2674 helix: 1.41 (0.15), residues: 1286 sheet: 0.27 (0.33), residues: 267 loop : -1.29 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 177 TYR 0.018 0.001 TYR E1287 PHE 0.031 0.001 PHE B 168 TRP 0.018 0.001 TRP B 83 HIS 0.006 0.001 HIS D 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (21680) covalent geometry : angle 0.63008 / 0.31 (29463) SS BOND : bond 0.00109 / 0.05 ( 4) SS BOND : angle 1.72230 / 1.32 ( 8) hydrogen bonds : bond 0.03859 / 2.64 ( 1070) hydrogen bonds : angle 3.84894 / 2.70 ( 3123) Misc. bond : bond 0.00158 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 321 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7911 (tppt) cc_final: 0.7674 (tppt) REVERT: A 48 ASN cc_start: 0.8524 (m110) cc_final: 0.7883 (m110) REVERT: A 54 ARG cc_start: 0.8236 (mtt90) cc_final: 0.7917 (mtp85) REVERT: A 73 LEU cc_start: 0.8991 (mt) cc_final: 0.8708 (tp) REVERT: A 137 MET cc_start: 0.8757 (ptm) cc_final: 0.8421 (ptm) REVERT: A 153 ASN cc_start: 0.9036 (m-40) cc_final: 0.8653 (m110) REVERT: A 160 ASN cc_start: 0.8691 (m-40) cc_final: 0.8282 (m110) REVERT: A 173 GLN cc_start: 0.8664 (pt0) cc_final: 0.7883 (pt0) REVERT: A 175 HIS cc_start: 0.8682 (OUTLIER) cc_final: 0.8241 (p-80) REVERT: A 288 GLU cc_start: 0.8175 (pm20) cc_final: 0.7729 (pm20) REVERT: A 304 TYR cc_start: 0.8832 (m-80) cc_final: 0.8444 (m-80) REVERT: B 39 LYS cc_start: 0.8525 (tmtt) cc_final: 0.8007 (ttpt) REVERT: B 47 LYS cc_start: 0.9168 (mtpt) cc_final: 0.8905 (mtmt) REVERT: B 137 MET cc_start: 0.8738 (ptt) cc_final: 0.8244 (ptm) REVERT: B 170 LYS cc_start: 0.9297 (tptp) cc_final: 0.9018 (tttm) REVERT: B 179 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8351 (mp0) REVERT: B 237 ASP cc_start: 0.8581 (t0) cc_final: 0.8347 (t0) REVERT: B 288 GLU cc_start: 0.7591 (pm20) cc_final: 0.7060 (pm20) REVERT: C 170 LYS cc_start: 0.9316 (ttmm) cc_final: 0.8984 (ttmm) REVERT: C 173 GLN cc_start: 0.9338 (OUTLIER) cc_final: 0.8980 (pm20) REVERT: C 185 LYS cc_start: 0.9113 (ttpt) cc_final: 0.8869 (tppt) REVERT: C 217 MET cc_start: 0.8887 (mtm) cc_final: 0.8627 (mtm) REVERT: C 303 SER cc_start: 0.9225 (t) cc_final: 0.8936 (t) REVERT: D 137 MET cc_start: 0.9038 (ptt) cc_final: 0.8692 (ptm) REVERT: D 141 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7296 (tt0) REVERT: D 163 MET cc_start: 0.8810 (mmt) cc_final: 0.8441 (mmm) REVERT: D 170 LYS cc_start: 0.9067 (tptt) cc_final: 0.8820 (tptt) REVERT: D 197 CYS cc_start: 0.8701 (m) cc_final: 0.7996 (m) REVERT: D 222 LYS cc_start: 0.8953 (ttmt) cc_final: 0.8640 (tttm) REVERT: D 251 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8772 (tt) REVERT: E 179 LEU cc_start: 0.8991 (tp) cc_final: 0.8701 (tp) REVERT: E 209 GLU cc_start: 0.8401 (mp0) cc_final: 0.8119 (mp0) REVERT: E 222 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7944 (p90) REVERT: E 243 LYS cc_start: 0.8107 (mmtt) cc_final: 0.7635 (mmtt) REVERT: E 304 SER cc_start: 0.9263 (OUTLIER) cc_final: 0.8751 (p) REVERT: E 442 MET cc_start: 0.8653 (tpt) cc_final: 0.8301 (mmm) REVERT: E 591 LEU cc_start: 0.7905 (mm) cc_final: 0.7570 (mm) REVERT: E 594 LEU cc_start: 0.8598 (mm) cc_final: 0.7815 (tt) REVERT: E 712 ILE cc_start: 0.9231 (mm) cc_final: 0.8972 (mm) REVERT: E 785 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7972 (pm20) REVERT: E 903 MET cc_start: 0.7533 (mtp) cc_final: 0.7153 (ptp) REVERT: E 1190 GLN cc_start: 0.8347 (tm-30) cc_final: 0.7851 (tm-30) REVERT: E 1194 ASP cc_start: 0.8202 (m-30) cc_final: 0.7606 (m-30) REVERT: E 1229 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7868 (mt-10) REVERT: E 1246 ARG cc_start: 0.8388 (mmp80) cc_final: 0.8124 (mmp80) REVERT: E 1248 LEU cc_start: 0.9156 (tp) cc_final: 0.8939 (tp) REVERT: E 1298 MET cc_start: 0.9034 (tmm) cc_final: 0.8722 (tmm) REVERT: E 1305 MET cc_start: 0.8785 (tpp) cc_final: 0.8525 (tpp) REVERT: E 1392 PHE cc_start: 0.8063 (m-80) cc_final: 0.7630 (m-80) REVERT: E 1483 SER cc_start: 0.7747 (OUTLIER) cc_final: 0.7451 (t) REVERT: E 1552 LEU cc_start: 0.8467 (tp) cc_final: 0.8157 (tp) outliers start: 93 outliers final: 68 residues processed: 394 average time/residue: 0.1472 time to fit residues: 91.2374 Evaluate side-chains 393 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 316 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 277 HIS Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 81 CYS Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 81 CYS Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 420 ASN Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 828 ILE Chi-restraints excluded: chain E residue 911 GLU Chi-restraints excluded: chain E residue 1022 LEU Chi-restraints excluded: chain E residue 1091 LEU Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1122 LEU Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain E residue 1166 VAL Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1189 LEU Chi-restraints excluded: chain E residue 1201 LEU Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1281 VAL Chi-restraints excluded: chain E residue 1402 HIS Chi-restraints excluded: chain E residue 1425 ILE Chi-restraints excluded: chain E residue 1483 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 259 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 136 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 102 optimal weight: 0.0170 chunk 103 optimal weight: 1.9990 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 GLN C 160 ASN C 216 HIS ** E 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.079231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.065423 restraints weight = 70168.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.067545 restraints weight = 32990.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.068986 restraints weight = 19828.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.069967 restraints weight = 13864.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.070553 restraints weight = 10792.171| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21685 Z= 0.117 Angle : 0.633 11.452 29471 Z= 0.303 Chirality : 0.044 0.211 3482 Planarity : 0.003 0.053 3667 Dihedral : 5.747 137.772 2898 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.46 % Allowed : 23.25 % Favored : 73.29 % 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: 0.37 (0.17), residues: 2674 helix: 1.49 (0.15), residues: 1283 sheet: 0.21 (0.32), residues: 277 loop : -1.24 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E1251 TYR 0.026 0.001 TYR E 799 PHE 0.027 0.001 PHE B 168 TRP 0.016 0.001 TRP B 83 HIS 0.005 0.001 HIS D 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (21680) covalent geometry : angle 0.63242 / 0.30 (29463) SS BOND : bond 0.00168 / 0.08 ( 4) SS BOND : angle 1.34120 / 0.98 ( 8) hydrogen bonds : bond 0.03785 / 2.59 ( 1070) hydrogen bonds : angle 3.82939 / 2.68 ( 3123) Misc. bond : bond 0.00150 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 333 time to evaluate : 0.866 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: 0.7823 (tppt) cc_final: 0.7619 (tppt) REVERT: A 48 ASN cc_start: 0.8532 (m110) cc_final: 0.7866 (m110) REVERT: A 54 ARG cc_start: 0.8209 (mtt90) cc_final: 0.7917 (mtp85) REVERT: A 67 LYS cc_start: 0.6798 (tptt) cc_final: 0.6503 (tptt) REVERT: A 73 LEU cc_start: 0.8963 (mt) cc_final: 0.8690 (tp) REVERT: A 137 MET cc_start: 0.8737 (ptm) cc_final: 0.8381 (ptm) REVERT: A 153 ASN cc_start: 0.9045 (m-40) cc_final: 0.8670 (m110) REVERT: A 160 ASN cc_start: 0.8651 (m-40) cc_final: 0.8256 (m110) REVERT: A 173 GLN cc_start: 0.8491 (pt0) cc_final: 0.8236 (pt0) REVERT: A 258 TYR cc_start: 0.8563 (p90) cc_final: 0.8152 (p90) REVERT: A 288 GLU cc_start: 0.8139 (pm20) cc_final: 0.7669 (pm20) REVERT: A 304 TYR cc_start: 0.8852 (m-80) cc_final: 0.8439 (m-80) REVERT: B 39 LYS cc_start: 0.8462 (tmtt) cc_final: 0.8208 (ttpt) REVERT: B 47 LYS cc_start: 0.9194 (mtpt) cc_final: 0.8966 (mtmt) REVERT: B 137 MET cc_start: 0.8750 (ptt) cc_final: 0.8252 (ptm) REVERT: B 170 LYS cc_start: 0.9206 (tptp) cc_final: 0.8873 (tttm) REVERT: B 179 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8462 (mp0) REVERT: B 237 ASP cc_start: 0.8592 (t0) cc_final: 0.8336 (t0) REVERT: B 288 GLU cc_start: 0.7523 (pm20) cc_final: 0.6979 (pm20) REVERT: C 170 LYS cc_start: 0.9296 (ttmm) cc_final: 0.8990 (ttmm) REVERT: C 173 GLN cc_start: 0.9307 (OUTLIER) cc_final: 0.8925 (pm20) REVERT: C 185 LYS cc_start: 0.9120 (ttpt) cc_final: 0.8856 (tppt) REVERT: C 286 ILE cc_start: 0.9575 (OUTLIER) cc_final: 0.9173 (pt) REVERT: C 303 SER cc_start: 0.9204 (t) cc_final: 0.8860 (t) REVERT: C 304 TYR cc_start: 0.8572 (m-80) cc_final: 0.8064 (m-80) REVERT: D 137 MET cc_start: 0.9010 (ptt) cc_final: 0.8696 (ptm) REVERT: D 141 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7238 (tt0) REVERT: D 163 MET cc_start: 0.8799 (mmt) cc_final: 0.8409 (mmm) REVERT: D 197 CYS cc_start: 0.8692 (m) cc_final: 0.7962 (m) REVERT: D 222 LYS cc_start: 0.8945 (ttmt) cc_final: 0.8630 (tttm) REVERT: E 1 MET cc_start: 0.6777 (mmm) cc_final: 0.6348 (tpp) REVERT: E 113 MET cc_start: 0.8215 (mtt) cc_final: 0.7981 (mtp) REVERT: E 179 LEU cc_start: 0.8926 (tp) cc_final: 0.8633 (tp) REVERT: E 209 GLU cc_start: 0.8400 (mp0) cc_final: 0.8068 (mp0) REVERT: E 222 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7862 (p90) REVERT: E 232 TRP cc_start: 0.7649 (OUTLIER) cc_final: 0.7252 (t-100) REVERT: E 243 LYS cc_start: 0.8026 (mmtt) cc_final: 0.7537 (mmtt) REVERT: E 304 SER cc_start: 0.9237 (OUTLIER) cc_final: 0.8721 (p) REVERT: E 309 LEU cc_start: 0.9426 (mt) cc_final: 0.9121 (mt) REVERT: E 442 MET cc_start: 0.8681 (tpt) cc_final: 0.8357 (mmm) REVERT: E 594 LEU cc_start: 0.8688 (mm) cc_final: 0.7846 (tt) REVERT: E 785 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8018 (pm20) REVERT: E 903 MET cc_start: 0.7457 (mtp) cc_final: 0.7254 (ptp) REVERT: E 1190 GLN cc_start: 0.8281 (tm-30) cc_final: 0.7849 (tm-30) REVERT: E 1194 ASP cc_start: 0.8210 (m-30) cc_final: 0.7619 (m-30) REVERT: E 1229 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7861 (mt-10) REVERT: E 1298 MET cc_start: 0.9039 (tmm) cc_final: 0.8746 (tmm) REVERT: E 1305 MET cc_start: 0.8760 (tpp) cc_final: 0.8512 (tpp) REVERT: E 1428 ASP cc_start: 0.8614 (t70) cc_final: 0.8266 (t0) REVERT: E 1483 SER cc_start: 0.7592 (OUTLIER) cc_final: 0.7316 (t) REVERT: E 1505 MET cc_start: 0.7373 (mpp) cc_final: 0.7039 (mmp) REVERT: E 1552 LEU cc_start: 0.8437 (tp) cc_final: 0.8155 (tp) outliers start: 80 outliers final: 59 residues processed: 397 average time/residue: 0.1450 time to fit residues: 91.1584 Evaluate side-chains 383 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 315 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 81 CYS Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 420 ASN Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 1022 LEU Chi-restraints excluded: chain E residue 1091 LEU Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1122 LEU Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain E residue 1166 VAL Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1189 LEU Chi-restraints excluded: chain E residue 1201 LEU Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1281 VAL Chi-restraints excluded: chain E residue 1425 ILE Chi-restraints excluded: chain E residue 1483 SER Chi-restraints excluded: chain E residue 1535 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 140 optimal weight: 0.5980 chunk 144 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 184 optimal weight: 0.1980 chunk 99 optimal weight: 0.6980 chunk 252 optimal weight: 0.1980 chunk 137 optimal weight: 1.9990 chunk 235 optimal weight: 4.9990 chunk 236 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 160 ASN C 216 HIS ** E 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.079586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.065580 restraints weight = 70653.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.067705 restraints weight = 33475.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.069166 restraints weight = 20153.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.070163 restraints weight = 14166.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.070760 restraints weight = 11057.821| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21685 Z= 0.120 Angle : 0.650 11.405 29471 Z= 0.312 Chirality : 0.044 0.397 3482 Planarity : 0.004 0.052 3667 Dihedral : 5.720 137.920 2898 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.38 % Allowed : 23.77 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.17), residues: 2674 helix: 1.49 (0.15), residues: 1283 sheet: 0.27 (0.32), residues: 275 loop : -1.18 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E1246 TYR 0.018 0.001 TYR C 304 PHE 0.025 0.001 PHE B 168 TRP 0.017 0.001 TRP B 83 HIS 0.005 0.000 HIS D 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (21680) covalent geometry : angle 0.64988 / 0.31 (29463) SS BOND : bond 0.00158 / 0.08 ( 4) SS BOND : angle 1.27516 / 0.90 ( 8) hydrogen bonds : bond 0.03804 / 2.59 ( 1070) hydrogen bonds : angle 3.85269 / 2.69 ( 3123) Misc. bond : bond 0.00150 / 0.08 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5348 Ramachandran restraints generated. 2674 Oldfield, 0 Emsley, 2674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 329 time to evaluate : 0.866 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: 0.7787 (tppt) cc_final: 0.7587 (tppt) REVERT: A 48 ASN cc_start: 0.8597 (m110) cc_final: 0.7923 (m110) REVERT: A 54 ARG cc_start: 0.8228 (mtt90) cc_final: 0.7940 (mtp85) REVERT: A 67 LYS cc_start: 0.6734 (tptt) cc_final: 0.6489 (tptt) REVERT: A 73 LEU cc_start: 0.8985 (mt) cc_final: 0.8684 (tp) REVERT: A 137 MET cc_start: 0.8747 (ptm) cc_final: 0.8381 (ptm) REVERT: A 153 ASN cc_start: 0.9034 (m-40) cc_final: 0.8660 (m110) REVERT: A 160 ASN cc_start: 0.8655 (m-40) cc_final: 0.8258 (m110) REVERT: A 173 GLN cc_start: 0.8529 (pt0) cc_final: 0.8239 (pt0) REVERT: A 288 GLU cc_start: 0.8088 (pm20) cc_final: 0.7715 (pm20) REVERT: A 304 TYR cc_start: 0.8874 (m-80) cc_final: 0.8467 (m-80) REVERT: A 332 LYS cc_start: 0.8416 (mtmm) cc_final: 0.8154 (mtmm) REVERT: B 39 LYS cc_start: 0.8428 (tmtt) cc_final: 0.8174 (ttpt) REVERT: B 47 LYS cc_start: 0.9187 (mtpt) cc_final: 0.8962 (mtmt) REVERT: B 137 MET cc_start: 0.8748 (ptt) cc_final: 0.8251 (ptm) REVERT: B 170 LYS cc_start: 0.9186 (tptp) cc_final: 0.8858 (tttm) REVERT: B 179 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8451 (mp0) REVERT: B 237 ASP cc_start: 0.8581 (t0) cc_final: 0.8324 (t0) REVERT: B 288 GLU cc_start: 0.7521 (pm20) cc_final: 0.6979 (pm20) REVERT: C 170 LYS cc_start: 0.9319 (ttmm) cc_final: 0.8981 (ttmm) REVERT: C 173 GLN cc_start: 0.9333 (OUTLIER) cc_final: 0.9004 (pm20) REVERT: C 185 LYS cc_start: 0.9111 (ttpt) cc_final: 0.8857 (tppt) REVERT: C 240 MET cc_start: 0.7830 (tmm) cc_final: 0.7511 (tmm) REVERT: C 277 HIS cc_start: 0.8091 (OUTLIER) cc_final: 0.7388 (m-70) REVERT: C 303 SER cc_start: 0.9196 (t) cc_final: 0.8858 (t) REVERT: C 304 TYR cc_start: 0.8547 (m-80) cc_final: 0.8078 (m-80) REVERT: D 47 LYS cc_start: 0.9221 (mtpp) cc_final: 0.8966 (tptt) REVERT: D 137 MET cc_start: 0.9021 (ptt) cc_final: 0.8681 (ptm) REVERT: D 141 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7359 (tt0) REVERT: D 163 MET cc_start: 0.8791 (mmt) cc_final: 0.8429 (mmm) REVERT: D 170 LYS cc_start: 0.9067 (tptt) cc_final: 0.8820 (tptt) REVERT: D 197 CYS cc_start: 0.8669 (m) cc_final: 0.7911 (m) REVERT: D 222 LYS cc_start: 0.8879 (ttmt) cc_final: 0.8596 (tttm) REVERT: D 251 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8829 (tt) REVERT: E 1 MET cc_start: 0.6786 (mmm) cc_final: 0.6350 (tpp) REVERT: E 113 MET cc_start: 0.8209 (mtt) cc_final: 0.7962 (mtp) REVERT: E 179 LEU cc_start: 0.8939 (tp) cc_final: 0.8638 (tp) REVERT: E 209 GLU cc_start: 0.8345 (mp0) cc_final: 0.8053 (mp0) REVERT: E 222 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.7847 (p90) REVERT: E 232 TRP cc_start: 0.7631 (OUTLIER) cc_final: 0.7248 (t-100) REVERT: E 243 LYS cc_start: 0.8017 (mmtt) cc_final: 0.7527 (mmtt) REVERT: E 304 SER cc_start: 0.9219 (OUTLIER) cc_final: 0.8703 (p) REVERT: E 309 LEU cc_start: 0.9411 (mt) cc_final: 0.9133 (mt) REVERT: E 442 MET cc_start: 0.8707 (tpt) cc_final: 0.8408 (mmm) REVERT: E 594 LEU cc_start: 0.8689 (mm) cc_final: 0.7842 (tt) REVERT: E 785 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8019 (pm20) REVERT: E 1190 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7812 (tm-30) REVERT: E 1194 ASP cc_start: 0.8206 (m-30) cc_final: 0.7608 (m-30) REVERT: E 1229 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7859 (mt-10) REVERT: E 1298 MET cc_start: 0.9002 (tmm) cc_final: 0.8747 (tmm) REVERT: E 1305 MET cc_start: 0.8760 (tpp) cc_final: 0.8521 (tpp) REVERT: E 1392 PHE cc_start: 0.7931 (m-80) cc_final: 0.7579 (m-80) REVERT: E 1428 ASP cc_start: 0.8607 (t70) cc_final: 0.8260 (t0) REVERT: E 1483 SER cc_start: 0.7595 (OUTLIER) cc_final: 0.7316 (t) REVERT: E 1505 MET cc_start: 0.7403 (mpp) cc_final: 0.7082 (mmp) REVERT: E 1552 LEU cc_start: 0.8422 (tp) cc_final: 0.8141 (tp) outliers start: 78 outliers final: 59 residues processed: 390 average time/residue: 0.1481 time to fit residues: 91.4581 Evaluate side-chains 384 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 315 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 277 HIS Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 277 HIS Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 81 CYS Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 420 ASN Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 828 ILE Chi-restraints excluded: chain E residue 1022 LEU Chi-restraints excluded: chain E residue 1091 LEU Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1122 LEU Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain E residue 1166 VAL Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1189 LEU Chi-restraints excluded: chain E residue 1201 LEU Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1425 ILE Chi-restraints excluded: chain E residue 1483 SER Chi-restraints excluded: chain E residue 1535 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 246 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 59 optimal weight: 0.0670 chunk 88 optimal weight: 30.0000 chunk 67 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 255 optimal weight: 0.6980 chunk 197 optimal weight: 0.0170 chunk 174 optimal weight: 0.8980 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 160 ASN C 216 HIS E 935 GLN ** E1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1273 HIS E1541 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.080898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.066846 restraints weight = 70520.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.069006 restraints weight = 33341.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.070439 restraints weight = 20107.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.071370 restraints weight = 14176.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.072093 restraints weight = 11181.377| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21685 Z= 0.114 Angle : 0.655 12.776 29471 Z= 0.312 Chirality : 0.044 0.444 3482 Planarity : 0.004 0.050 3667 Dihedral : 5.677 137.765 2898 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.07 % Allowed : 24.11 % Favored : 72.81 % 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: 0.48 (0.17), residues: 2674 helix: 1.52 (0.15), residues: 1287 sheet: 0.31 (0.33), residues: 275 loop : -1.13 (0.19), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E1246 TYR 0.018 0.001 TYR E 799 PHE 0.025 0.001 PHE B 168 TRP 0.023 0.001 TRP C 68 HIS 0.005 0.000 HIS E1273 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (21680) covalent geometry : angle 0.65454 / 0.31 (29463) SS BOND : bond 0.00151 / 0.08 ( 4) SS BOND : angle 1.18154 / 0.82 ( 8) hydrogen bonds : bond 0.03765 / 2.56 ( 1070) hydrogen bonds : angle 3.85763 / 2.69 ( 3123) Misc. bond : bond 0.00146 / 0.08 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3593.13 seconds wall clock time: 63 minutes 4.30 seconds (3784.30 seconds total)