Starting phenix.real_space_refine on Thu Mar 5 10:29:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s5x_24842/03_2026/7s5x_24842.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s5x_24842/03_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_24842/03_2026/7s5x_24842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s5x_24842/03_2026/7s5x_24842.map" model { file = "/net/cci-nas-00/data/ceres_data/7s5x_24842/03_2026/7s5x_24842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s5x_24842/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 4.36, per 1000 atoms: 0.21 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: 1.79 Conformation dependent library (CDL) restraints added in 1.2 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: 0.73 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: 4.99 Time building geometry restraints manager: 2.52 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: 12435 35.58 - 71.15: 437 71.15 - 106.73: 18 106.73 - 142.30: 1 142.30 - 177.88: 1 Dihedral angle restraints: 12892 sinusoidal: 5063 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 12889 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: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.030 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 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 : 17.259 177.881 7794 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 covalent geometry : bond 0.00965 (21680) covalent geometry : angle 1.39396 (29463) SS BOND : bond 0.01137 ( 4) SS BOND : angle 2.53051 ( 8) hydrogen bonds : bond 0.15466 ( 1070) hydrogen bonds : angle 8.08570 ( 3123) Misc. bond : bond 0.00025 ( 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 : 0.743 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: 0.1443 time to fit residues: 143.2222 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 : 0.834 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.079514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.065649 restraints weight = 70122.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.067769 restraints weight = 32990.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.069194 restraints weight = 19883.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.070192 restraints weight = 14023.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.070820 restraints weight = 10938.027| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2322 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= 0.137 Angle : 0.654 9.951 29471 Z= 0.339 Chirality : 0.044 0.175 3482 Planarity : 0.006 0.076 3667 Dihedral : 8.610 166.229 2987 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.59 % Allowed : 17.23 % Favored : 79.18 % 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: -2.74 (0.14), residues: 2674 helix: -1.51 (0.12), residues: 1304 sheet: -0.61 (0.33), residues: 260 loop : -2.40 (0.16), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 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 E1024 Details of bonding type rmsd covalent geometry : bond 0.00285 (21680) covalent geometry : angle 0.65320 (29463) SS BOND : bond 0.00420 ( 4) SS BOND : angle 1.52569 ( 8) hydrogen bonds : bond 0.04481 ( 1070) hydrogen bonds : angle 4.81431 ( 3123) Misc. bond : bond 0.00075 ( 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 493 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 410 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8663 (mtpp) cc_final: 0.8308 (mmmt) REVERT: A 48 ASN cc_start: 0.8269 (m110) cc_final: 0.7815 (m110) REVERT: A 54 ARG cc_start: 0.8210 (mtt90) cc_final: 0.7793 (mtp85) REVERT: A 84 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9079 (mt) REVERT: A 153 ASN cc_start: 0.9034 (m-40) cc_final: 0.8731 (m110) REVERT: A 160 ASN cc_start: 0.8677 (m-40) cc_final: 0.8057 (m110) REVERT: A 179 GLU cc_start: 0.8424 (mp0) cc_final: 0.8197 (mp0) REVERT: A 207 LYS cc_start: 0.9172 (tptt) cc_final: 0.8949 (tppt) REVERT: A 217 MET cc_start: 0.8760 (mtm) cc_final: 0.8488 (mtm) REVERT: A 288 GLU cc_start: 0.7636 (pm20) cc_final: 0.7135 (pm20) REVERT: A 304 TYR cc_start: 0.8732 (m-80) cc_final: 0.8316 (m-80) REVERT: B 60 PHE cc_start: 0.9049 (t80) cc_final: 0.8695 (t80) REVERT: B 137 MET cc_start: 0.8823 (ptt) cc_final: 0.8418 (ptt) REVERT: B 169 MET cc_start: 0.8794 (ttm) cc_final: 0.8542 (mtp) REVERT: B 179 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8434 (mt-10) REVERT: B 237 ASP cc_start: 0.8512 (t0) cc_final: 0.8204 (t0) REVERT: B 304 TYR cc_start: 0.8894 (m-80) cc_final: 0.8535 (m-80) REVERT: C 39 LYS cc_start: 0.8627 (mmmm) cc_final: 0.8394 (mmmm) REVERT: C 160 ASN cc_start: 0.8859 (m-40) cc_final: 0.8632 (m-40) REVERT: C 170 LYS cc_start: 0.9215 (ttmm) cc_final: 0.8968 (ttmm) REVERT: C 173 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.8426 (pm20) REVERT: C 199 MET cc_start: 0.8169 (mtm) cc_final: 0.7908 (mtm) REVERT: C 303 SER cc_start: 0.9364 (t) cc_final: 0.8918 (p) REVERT: C 304 TYR cc_start: 0.8670 (m-80) cc_final: 0.7989 (m-80) REVERT: C 327 SER cc_start: 0.8977 (OUTLIER) cc_final: 0.8551 (p) REVERT: D 57 GLN cc_start: 0.7996 (mt0) cc_final: 0.6485 (tp40) REVERT: D 137 MET cc_start: 0.8953 (ptt) cc_final: 0.8514 (ptm) REVERT: D 140 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8058 (mp0) REVERT: D 141 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7299 (tt0) REVERT: D 163 MET cc_start: 0.8922 (mmt) cc_final: 0.8518 (mmp) REVERT: D 167 ILE cc_start: 0.9075 (tp) cc_final: 0.8841 (tp) REVERT: D 184 SER cc_start: 0.9424 (OUTLIER) cc_final: 0.9179 (m) REVERT: D 185 LYS cc_start: 0.9164 (mmmt) cc_final: 0.8938 (tptt) REVERT: D 197 CYS cc_start: 0.8703 (m) cc_final: 0.8087 (m) REVERT: D 222 LYS cc_start: 0.8982 (ttmt) cc_final: 0.8642 (tttm) REVERT: D 327 SER cc_start: 0.8811 (OUTLIER) cc_final: 0.8363 (p) REVERT: E 95 LEU cc_start: 0.9088 (mt) cc_final: 0.8743 (mt) REVERT: E 178 ILE cc_start: 0.9057 (mm) cc_final: 0.8811 (mm) REVERT: E 209 GLU cc_start: 0.8510 (mp0) cc_final: 0.8284 (mp0) REVERT: E 225 LEU cc_start: 0.9354 (tp) cc_final: 0.9109 (tp) REVERT: E 243 LYS cc_start: 0.8296 (mmtt) cc_final: 0.7927 (mptt) REVERT: E 388 LEU cc_start: 0.9498 (tp) cc_final: 0.9296 (tp) REVERT: E 587 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8698 (mt) REVERT: E 731 MET cc_start: 0.6991 (tpp) cc_final: 0.6594 (tpp) REVERT: E 855 ASP cc_start: 0.8578 (t0) cc_final: 0.8377 (t0) REVERT: E 1141 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8455 (tm-30) REVERT: E 1190 GLN cc_start: 0.8465 (tm-30) cc_final: 0.7830 (tm-30) REVERT: E 1194 ASP cc_start: 0.8117 (m-30) cc_final: 0.7642 (m-30) REVERT: E 1225 GLN cc_start: 0.7892 (tm-30) cc_final: 0.7444 (tm-30) REVERT: E 1229 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7684 (mt-10) REVERT: E 1242 THR cc_start: 0.9141 (m) cc_final: 0.8554 (m) REVERT: E 1246 ARG cc_start: 0.8481 (mmp80) cc_final: 0.8022 (mmp80) REVERT: E 1248 LEU cc_start: 0.9171 (tp) cc_final: 0.8925 (tp) REVERT: E 1262 ILE cc_start: 0.9276 (tp) cc_final: 0.9062 (tp) REVERT: E 1298 MET cc_start: 0.8807 (tmm) cc_final: 0.8595 (tmm) REVERT: E 1505 MET cc_start: 0.7114 (mpp) cc_final: 0.6795 (mpp) outliers start: 83 outliers final: 30 residues processed: 474 average time/residue: 0.1497 time to fit residues: 111.5699 Evaluate side-chains 373 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 334 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 84 LEU Chi-restraints excluded: chain A residue 260 VAL 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 313 GLN 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 222 PHE Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 369 LEU 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 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: 0.0980 chunk 241 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 245 optimal weight: 5.9990 chunk 165 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 47 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN C 279 GLN D 128 GLN D 160 ASN D 335 ASN E 224 ASN E 438 ASN E 563 HIS E 836 GLN ** E 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1020 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.078880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.064986 restraints weight = 70769.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.067119 restraints weight = 33300.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.068588 restraints weight = 20062.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.069515 restraints weight = 14020.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.070241 restraints weight = 11057.056| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2916 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= 0.127 Angle : 0.619 13.878 29471 Z= 0.312 Chirality : 0.043 0.185 3482 Planarity : 0.004 0.060 3667 Dihedral : 7.223 147.255 2942 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.94 % Allowed : 19.05 % Favored : 77.01 % 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: -1.29 (0.15), residues: 2674 helix: -0.05 (0.14), residues: 1308 sheet: -0.27 (0.33), residues: 264 loop : -1.97 (0.17), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 54 TYR 0.026 0.001 TYR D 268 PHE 0.018 0.001 PHE E 614 TRP 0.009 0.001 TRP D 90 HIS 0.003 0.001 HIS E1024 Details of bonding type rmsd covalent geometry : bond 0.00274 (21680) covalent geometry : angle 0.61743 (29463) SS BOND : bond 0.00250 ( 4) SS BOND : angle 2.60777 ( 8) hydrogen bonds : bond 0.04041 ( 1070) hydrogen bonds : angle 4.24690 ( 3123) Misc. bond : bond 0.00190 ( 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 457 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 366 time to evaluate : 0.826 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: 0.8729 (mtpp) cc_final: 0.8339 (mmmt) REVERT: A 48 ASN cc_start: 0.8425 (m110) cc_final: 0.7926 (m110) REVERT: A 54 ARG cc_start: 0.8167 (mtt90) cc_final: 0.7800 (mtp85) REVERT: A 84 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.8950 (mm) REVERT: A 153 ASN cc_start: 0.9015 (m-40) cc_final: 0.8651 (m110) REVERT: A 179 GLU cc_start: 0.8531 (mp0) cc_final: 0.8262 (mp0) REVERT: A 288 GLU cc_start: 0.7804 (pm20) cc_final: 0.7489 (pm20) REVERT: B 47 LYS cc_start: 0.9090 (mtpt) cc_final: 0.8781 (mtmt) REVERT: B 137 MET cc_start: 0.8768 (ptt) cc_final: 0.8331 (ptt) REVERT: B 144 LEU cc_start: 0.9209 (tp) cc_final: 0.8975 (tp) REVERT: B 169 MET cc_start: 0.8797 (ttm) cc_final: 0.8541 (mtp) REVERT: B 170 LYS cc_start: 0.9259 (tptp) cc_final: 0.8976 (tttm) REVERT: B 179 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8291 (mp0) REVERT: B 237 ASP cc_start: 0.8571 (t0) cc_final: 0.8318 (t0) REVERT: B 288 GLU cc_start: 0.7623 (pm20) cc_final: 0.7124 (pm20) REVERT: C 170 LYS cc_start: 0.9262 (ttmm) cc_final: 0.8992 (ttmm) REVERT: C 173 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8501 (pm20) REVERT: C 199 MET cc_start: 0.8164 (mtm) cc_final: 0.7940 (mtm) REVERT: C 288 GLU cc_start: 0.8204 (pt0) cc_final: 0.7946 (pt0) REVERT: C 303 SER cc_start: 0.9259 (t) cc_final: 0.8988 (t) REVERT: C 304 TYR cc_start: 0.8819 (m-80) cc_final: 0.8137 (m-80) REVERT: D 137 MET cc_start: 0.8905 (ptt) cc_final: 0.8535 (ptm) REVERT: D 141 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7175 (tt0) REVERT: D 152 GLN cc_start: 0.8954 (tt0) cc_final: 0.8526 (tm-30) REVERT: D 163 MET cc_start: 0.8921 (mmt) cc_final: 0.8375 (mmp) REVERT: D 170 LYS cc_start: 0.9190 (tppt) cc_final: 0.8973 (tptt) REVERT: D 197 CYS cc_start: 0.8716 (m) cc_final: 0.8011 (m) REVERT: D 222 LYS cc_start: 0.8947 (ttmt) cc_final: 0.8607 (tttm) REVERT: D 268 TYR cc_start: 0.8492 (t80) cc_final: 0.8213 (t80) REVERT: D 335 ASN cc_start: 0.9076 (m110) cc_final: 0.8846 (m110) REVERT: E 178 ILE cc_start: 0.9101 (mm) cc_final: 0.8858 (mm) REVERT: E 179 LEU cc_start: 0.8994 (tp) cc_final: 0.8737 (tp) REVERT: E 209 GLU cc_start: 0.8496 (mp0) cc_final: 0.8288 (mp0) REVERT: E 225 LEU cc_start: 0.9317 (tp) cc_final: 0.9078 (tp) REVERT: E 243 LYS cc_start: 0.8255 (mmtt) cc_final: 0.7794 (mptt) REVERT: E 304 SER cc_start: 0.9324 (t) cc_final: 0.8765 (p) REVERT: E 388 LEU cc_start: 0.9539 (tp) cc_final: 0.9269 (tp) REVERT: E 433 PHE cc_start: 0.9347 (m-10) cc_final: 0.9116 (m-10) REVERT: E 731 MET cc_start: 0.6990 (tpp) cc_final: 0.6522 (tpp) REVERT: E 855 ASP cc_start: 0.8565 (t0) cc_final: 0.8342 (t0) REVERT: E 1141 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8657 (tm-30) REVERT: E 1190 GLN cc_start: 0.8444 (tm-30) cc_final: 0.7777 (tm-30) REVERT: E 1194 ASP cc_start: 0.8127 (m-30) cc_final: 0.7559 (m-30) REVERT: E 1225 GLN cc_start: 0.7695 (tm-30) cc_final: 0.7078 (tm-30) REVERT: E 1246 ARG cc_start: 0.8415 (mmp80) cc_final: 0.8012 (mmp80) REVERT: E 1253 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7446 (tp30) REVERT: E 1298 MET cc_start: 0.8793 (tmm) cc_final: 0.8550 (tmm) REVERT: E 1392 PHE cc_start: 0.7966 (m-80) cc_final: 0.7594 (m-80) REVERT: E 1552 LEU cc_start: 0.8377 (tp) cc_final: 0.8155 (tp) outliers start: 91 outliers final: 49 residues processed: 434 average time/residue: 0.1369 time to fit residues: 94.5305 Evaluate side-chains 384 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 330 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 287 LEU 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 251 LEU 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 142 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 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 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 557 LEU Chi-restraints excluded: chain E residue 725 LEU Chi-restraints excluded: chain E residue 770 VAL 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 1227 LEU Chi-restraints excluded: chain E residue 1253 GLU Chi-restraints excluded: chain E residue 1281 VAL 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: 0.9990 chunk 146 optimal weight: 0.7980 chunk 219 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 229 optimal weight: 0.9980 chunk 259 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 233 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 HIS C 97 HIS C 160 ASN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN E 242 HIS E 847 HIS ** E 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1020 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.078846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.064940 restraints weight = 70217.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.067055 restraints weight = 33162.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.068504 restraints weight = 19997.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.069505 restraints weight = 14082.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.070177 restraints weight = 10983.853| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21685 Z= 0.123 Angle : 0.603 12.210 29471 Z= 0.300 Chirality : 0.043 0.245 3482 Planarity : 0.004 0.055 3667 Dihedral : 6.703 142.387 2935 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.42 % Allowed : 19.44 % Favored : 76.15 % 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: -0.59 (0.16), residues: 2674 helix: 0.57 (0.14), residues: 1315 sheet: -0.03 (0.33), residues: 264 loop : -1.67 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 54 TYR 0.017 0.001 TYR E1287 PHE 0.019 0.001 PHE E1182 TRP 0.014 0.001 TRP B 83 HIS 0.003 0.000 HIS D 175 Details of bonding type rmsd covalent geometry : bond 0.00268 (21680) covalent geometry : angle 0.60215 (29463) SS BOND : bond 0.00194 ( 4) SS BOND : angle 2.05530 ( 8) hydrogen bonds : bond 0.03900 ( 1070) hydrogen bonds : angle 3.99380 ( 3123) Misc. bond : bond 0.00177 ( 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 463 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 361 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9125 (tptt) cc_final: 0.8708 (tppt) REVERT: A 47 LYS cc_start: 0.8651 (mtpp) cc_final: 0.8160 (mmmt) REVERT: A 48 ASN cc_start: 0.8529 (m110) cc_final: 0.8004 (m110) REVERT: A 54 ARG cc_start: 0.8159 (mtt90) cc_final: 0.7818 (mtp85) REVERT: A 84 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8948 (mm) REVERT: A 137 MET cc_start: 0.8822 (ptm) cc_final: 0.8508 (ptm) REVERT: A 153 ASN cc_start: 0.9005 (m-40) cc_final: 0.8597 (m110) REVERT: A 160 ASN cc_start: 0.8751 (m-40) cc_final: 0.8429 (m110) REVERT: A 175 HIS cc_start: 0.8848 (OUTLIER) cc_final: 0.8369 (p-80) REVERT: A 199 MET cc_start: 0.8407 (mtt) cc_final: 0.8194 (mtp) REVERT: A 217 MET cc_start: 0.8829 (mtp) cc_final: 0.8541 (mtm) REVERT: A 288 GLU cc_start: 0.7880 (pm20) cc_final: 0.7506 (pm20) REVERT: B 39 LYS cc_start: 0.8369 (tmtt) cc_final: 0.7831 (ttpt) REVERT: B 47 LYS cc_start: 0.9143 (mtpt) cc_final: 0.8817 (mtmt) REVERT: B 50 ARG cc_start: 0.7418 (mmt180) cc_final: 0.7193 (mmp-170) REVERT: B 137 MET cc_start: 0.8714 (ptt) cc_final: 0.8216 (ptm) REVERT: B 169 MET cc_start: 0.8771 (ttm) cc_final: 0.8545 (mtp) REVERT: B 170 LYS cc_start: 0.9275 (tptp) cc_final: 0.8980 (tttm) REVERT: B 179 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8359 (mp0) REVERT: B 237 ASP cc_start: 0.8600 (t0) cc_final: 0.8350 (t0) REVERT: B 288 GLU cc_start: 0.7623 (pm20) cc_final: 0.7098 (pm20) REVERT: C 170 LYS cc_start: 0.9263 (ttmm) cc_final: 0.9011 (ttmm) REVERT: C 173 GLN cc_start: 0.9202 (OUTLIER) cc_final: 0.8541 (pm20) REVERT: C 185 LYS cc_start: 0.9156 (ttpt) cc_final: 0.8926 (tppt) REVERT: C 216 HIS cc_start: 0.7592 (OUTLIER) cc_final: 0.7316 (m170) REVERT: C 217 MET cc_start: 0.8896 (mtm) cc_final: 0.8649 (mtm) REVERT: C 303 SER cc_start: 0.9192 (t) cc_final: 0.8870 (t) REVERT: C 304 TYR cc_start: 0.8870 (m-80) cc_final: 0.8169 (m-80) REVERT: D 137 MET cc_start: 0.8882 (ptt) cc_final: 0.8561 (ptm) REVERT: D 141 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6825 (tt0) REVERT: D 163 MET cc_start: 0.8940 (mmt) cc_final: 0.8435 (mmp) REVERT: D 197 CYS cc_start: 0.8706 (m) cc_final: 0.8043 (m) REVERT: D 222 LYS cc_start: 0.8928 (ttmt) cc_final: 0.8601 (tttm) REVERT: D 268 TYR cc_start: 0.8613 (t80) cc_final: 0.8405 (t80) REVERT: D 335 ASN cc_start: 0.9057 (m110) cc_final: 0.8836 (m110) REVERT: E 178 ILE cc_start: 0.9132 (mm) cc_final: 0.8870 (mm) REVERT: E 179 LEU cc_start: 0.9023 (tp) cc_final: 0.8803 (tp) REVERT: E 209 GLU cc_start: 0.8474 (mp0) cc_final: 0.8239 (mp0) REVERT: E 243 LYS cc_start: 0.8385 (mmtt) cc_final: 0.7990 (mmtt) REVERT: E 304 SER cc_start: 0.9206 (OUTLIER) cc_final: 0.8539 (p) REVERT: E 388 LEU cc_start: 0.9548 (tp) cc_final: 0.9257 (tp) REVERT: E 433 PHE cc_start: 0.9316 (m-10) cc_final: 0.9050 (m-10) REVERT: E 731 MET cc_start: 0.6997 (tpp) cc_final: 0.6644 (tpp) REVERT: E 855 ASP cc_start: 0.8570 (t0) cc_final: 0.8276 (t0) REVERT: E 1141 GLU cc_start: 0.9052 (tm-30) cc_final: 0.8801 (tm-30) REVERT: E 1190 GLN cc_start: 0.8447 (tm-30) cc_final: 0.7792 (tm-30) REVERT: E 1194 ASP cc_start: 0.8188 (m-30) cc_final: 0.7634 (m-30) REVERT: E 1225 GLN cc_start: 0.7688 (tm-30) cc_final: 0.7069 (tm-30) REVERT: E 1246 ARG cc_start: 0.8250 (mmp80) cc_final: 0.7948 (mmp80) REVERT: E 1248 LEU cc_start: 0.9305 (tp) cc_final: 0.9079 (tp) REVERT: E 1253 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7457 (tp30) REVERT: E 1298 MET cc_start: 0.8799 (tmm) cc_final: 0.8570 (tmm) REVERT: E 1392 PHE cc_start: 0.7940 (m-80) cc_final: 0.7574 (m-80) REVERT: E 1552 LEU cc_start: 0.8427 (tp) cc_final: 0.8181 (tp) outliers start: 102 outliers final: 51 residues processed: 434 average time/residue: 0.1344 time to fit residues: 93.1451 Evaluate side-chains 381 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 322 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 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 173 GLN Chi-restraints excluded: chain C residue 184 SER 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 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 300 LEU Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 369 LEU 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 1025 MET 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 1253 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 139 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 267 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 57 GLN A 152 GLN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN C 216 HIS ** E 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1020 GLN ** E1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.078111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.064223 restraints weight = 70193.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.066330 restraints weight = 33236.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.067729 restraints weight = 20109.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.068744 restraints weight = 14212.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.069366 restraints weight = 11077.249| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21685 Z= 0.133 Angle : 0.605 11.801 29471 Z= 0.300 Chirality : 0.043 0.217 3482 Planarity : 0.004 0.053 3667 Dihedral : 6.419 140.323 2933 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.11 % Allowed : 20.30 % 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: -0.18 (0.16), residues: 2674 helix: 0.90 (0.14), residues: 1318 sheet: 0.27 (0.34), residues: 244 loop : -1.47 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 54 TYR 0.017 0.001 TYR E1287 PHE 0.023 0.001 PHE B 168 TRP 0.014 0.001 TRP B 83 HIS 0.004 0.000 HIS D 175 Details of bonding type rmsd covalent geometry : bond 0.00293 (21680) covalent geometry : angle 0.60468 (29463) SS BOND : bond 0.00154 ( 4) SS BOND : angle 1.74474 ( 8) hydrogen bonds : bond 0.03908 ( 1070) hydrogen bonds : angle 3.92478 ( 3123) Misc. bond : bond 0.00157 ( 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 438 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 343 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8688 (mtpp) cc_final: 0.8180 (mmmt) REVERT: A 48 ASN cc_start: 0.8632 (m110) cc_final: 0.8149 (m110) REVERT: A 54 ARG cc_start: 0.8174 (mtt90) cc_final: 0.7838 (mtp85) REVERT: A 84 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9043 (mm) REVERT: A 137 MET cc_start: 0.8713 (ptm) cc_final: 0.8378 (ptm) REVERT: A 153 ASN cc_start: 0.9009 (m-40) cc_final: 0.8618 (m110) REVERT: A 160 ASN cc_start: 0.8757 (m-40) cc_final: 0.8438 (m110) REVERT: A 175 HIS cc_start: 0.8827 (OUTLIER) cc_final: 0.8310 (p-80) REVERT: A 199 MET cc_start: 0.8565 (mtt) cc_final: 0.8361 (mtp) REVERT: A 217 MET cc_start: 0.8823 (mtp) cc_final: 0.8540 (mtm) REVERT: A 222 LYS cc_start: 0.8549 (ttmm) cc_final: 0.8214 (ttmm) REVERT: A 288 GLU cc_start: 0.7926 (pm20) cc_final: 0.7538 (pm20) REVERT: A 304 TYR cc_start: 0.8744 (m-80) cc_final: 0.8480 (m-80) REVERT: B 39 LYS cc_start: 0.8399 (tmtt) cc_final: 0.7867 (ttpt) REVERT: B 47 LYS cc_start: 0.9147 (mtpt) cc_final: 0.8819 (mtmt) REVERT: B 88 MET cc_start: 0.8485 (tpp) cc_final: 0.8248 (ttp) REVERT: B 137 MET cc_start: 0.8742 (ptt) cc_final: 0.8237 (ptm) REVERT: B 170 LYS cc_start: 0.9277 (tptp) cc_final: 0.9047 (tttm) REVERT: B 179 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8344 (mp0) REVERT: B 237 ASP cc_start: 0.8623 (t0) cc_final: 0.8379 (t0) REVERT: B 240 MET cc_start: 0.8638 (tmm) cc_final: 0.8289 (tmm) REVERT: B 256 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8973 (mt) REVERT: B 288 GLU cc_start: 0.7647 (pm20) cc_final: 0.7083 (pm20) REVERT: C 170 LYS cc_start: 0.9268 (ttmm) cc_final: 0.8908 (ttmm) REVERT: C 173 GLN cc_start: 0.9299 (OUTLIER) cc_final: 0.8918 (pm20) REVERT: C 185 LYS cc_start: 0.9149 (ttpt) cc_final: 0.8911 (tppt) REVERT: C 199 MET cc_start: 0.8250 (mtm) cc_final: 0.8045 (mtm) REVERT: C 217 MET cc_start: 0.8906 (mtm) cc_final: 0.8669 (mtm) REVERT: C 303 SER cc_start: 0.9215 (t) cc_final: 0.8918 (t) REVERT: C 304 TYR cc_start: 0.8972 (m-80) cc_final: 0.8336 (m-80) REVERT: D 137 MET cc_start: 0.8948 (ptt) cc_final: 0.8523 (ptm) REVERT: D 141 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6868 (tt0) REVERT: D 163 MET cc_start: 0.8891 (mmt) cc_final: 0.8582 (mmp) REVERT: D 170 LYS cc_start: 0.9142 (tppt) cc_final: 0.8842 (tptt) REVERT: D 197 CYS cc_start: 0.8762 (m) cc_final: 0.8059 (m) REVERT: D 222 LYS cc_start: 0.8898 (ttmt) cc_final: 0.8542 (tttm) REVERT: D 251 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8855 (tt) REVERT: D 268 TYR cc_start: 0.8753 (t80) cc_final: 0.8542 (t80) REVERT: D 335 ASN cc_start: 0.9056 (m110) cc_final: 0.8854 (m110) REVERT: E 179 LEU cc_start: 0.9013 (tp) cc_final: 0.8738 (tp) REVERT: E 209 GLU cc_start: 0.8453 (mp0) cc_final: 0.8192 (mp0) REVERT: E 243 LYS cc_start: 0.8310 (mmtt) cc_final: 0.7887 (mmtt) REVERT: E 304 SER cc_start: 0.9258 (t) cc_final: 0.8738 (p) REVERT: E 731 MET cc_start: 0.7091 (tpp) cc_final: 0.6658 (tpp) REVERT: E 785 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7918 (pm20) REVERT: E 1141 GLU cc_start: 0.9095 (tm-30) cc_final: 0.8866 (tm-30) REVERT: E 1190 GLN cc_start: 0.8332 (tm-30) cc_final: 0.7818 (tm-30) REVERT: E 1194 ASP cc_start: 0.8256 (m-30) cc_final: 0.7654 (m-30) REVERT: E 1229 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7889 (mt-10) REVERT: E 1246 ARG cc_start: 0.8269 (mmp80) cc_final: 0.7998 (mmp80) REVERT: E 1248 LEU cc_start: 0.9193 (tp) cc_final: 0.8966 (tp) REVERT: E 1253 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7534 (tp30) REVERT: E 1298 MET cc_start: 0.8809 (tmm) cc_final: 0.8586 (tmm) REVERT: E 1392 PHE cc_start: 0.8017 (m-80) cc_final: 0.7637 (m-80) REVERT: E 1483 SER cc_start: 0.7945 (OUTLIER) cc_final: 0.7562 (t) REVERT: E 1552 LEU cc_start: 0.8414 (tp) cc_final: 0.8141 (tp) outliers start: 95 outliers final: 57 residues processed: 409 average time/residue: 0.1494 time to fit residues: 96.7065 Evaluate side-chains 384 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 317 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 260 VAL Chi-restraints excluded: chain A residue 286 ILE 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 236 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 256 ILE 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 349 LEU Chi-restraints excluded: chain D residue 56 LEU 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 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 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 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 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 728 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 785 GLU 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 1168 LEU Chi-restraints excluded: chain E residue 1189 LEU Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1253 GLU 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: 0.9980 chunk 101 optimal weight: 4.9990 chunk 249 optimal weight: 2.9990 chunk 196 optimal weight: 0.5980 chunk 230 optimal weight: 0.1980 chunk 89 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 236 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN C 216 HIS E 263 ASN E 265 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.078938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.065073 restraints weight = 69861.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.067177 restraints weight = 33054.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.068569 restraints weight = 20023.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.069579 restraints weight = 14203.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.070201 restraints weight = 11095.729| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3709 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= 0.115 Angle : 0.603 12.099 29471 Z= 0.293 Chirality : 0.043 0.176 3482 Planarity : 0.003 0.050 3667 Dihedral : 6.213 138.325 2930 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.42 % Allowed : 20.91 % Favored : 74.68 % 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: 0.13 (0.16), residues: 2674 helix: 1.21 (0.15), residues: 1285 sheet: 0.23 (0.33), residues: 256 loop : -1.27 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 54 TYR 0.016 0.001 TYR E1287 PHE 0.020 0.001 PHE B 168 TRP 0.007 0.001 TRP B 83 HIS 0.005 0.000 HIS D 175 Details of bonding type rmsd covalent geometry : bond 0.00250 (21680) covalent geometry : angle 0.60284 (29463) SS BOND : bond 0.00348 ( 4) SS BOND : angle 1.64955 ( 8) hydrogen bonds : bond 0.03793 ( 1070) hydrogen bonds : angle 3.85583 ( 3123) Misc. bond : bond 0.00154 ( 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 445 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 343 time to evaluate : 0.790 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: 0.8704 (mtpp) cc_final: 0.8174 (mmmt) REVERT: A 48 ASN cc_start: 0.8690 (m110) cc_final: 0.8133 (m110) REVERT: A 54 ARG cc_start: 0.8200 (mtt90) cc_final: 0.7871 (mtp85) REVERT: A 84 LEU cc_start: 0.9318 (mt) cc_final: 0.9058 (mm) REVERT: A 137 MET cc_start: 0.8711 (ptm) cc_final: 0.8310 (ptm) REVERT: A 153 ASN cc_start: 0.9017 (m-40) cc_final: 0.8602 (m110) REVERT: A 160 ASN cc_start: 0.8645 (m-40) cc_final: 0.8348 (m110) REVERT: A 175 HIS cc_start: 0.8799 (OUTLIER) cc_final: 0.8438 (p-80) REVERT: A 199 MET cc_start: 0.8523 (mtt) cc_final: 0.8320 (mtp) REVERT: A 288 GLU cc_start: 0.8022 (pm20) cc_final: 0.7566 (pm20) REVERT: A 304 TYR cc_start: 0.8779 (m-80) cc_final: 0.8450 (m-80) REVERT: B 39 LYS cc_start: 0.8410 (tmtt) cc_final: 0.7862 (ttpt) REVERT: B 47 LYS cc_start: 0.9168 (mtpt) cc_final: 0.8880 (mtmt) REVERT: B 88 MET cc_start: 0.8458 (tpp) cc_final: 0.8199 (ttp) REVERT: B 137 MET cc_start: 0.8743 (ptt) cc_final: 0.8234 (ptm) REVERT: B 169 MET cc_start: 0.8795 (ttm) cc_final: 0.8410 (mtp) REVERT: B 170 LYS cc_start: 0.9259 (tptp) cc_final: 0.9010 (tttm) REVERT: B 179 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8398 (mp0) REVERT: B 237 ASP cc_start: 0.8625 (t0) cc_final: 0.8386 (t0) REVERT: B 288 GLU cc_start: 0.7607 (pm20) cc_final: 0.7130 (pm20) REVERT: C 170 LYS cc_start: 0.9274 (ttmm) cc_final: 0.8998 (ttmm) REVERT: C 173 GLN cc_start: 0.9298 (OUTLIER) cc_final: 0.8925 (pm20) REVERT: C 185 LYS cc_start: 0.9179 (ttpt) cc_final: 0.8881 (tppt) REVERT: C 303 SER cc_start: 0.9198 (t) cc_final: 0.8894 (t) REVERT: C 304 TYR cc_start: 0.8951 (m-80) cc_final: 0.8746 (m-80) REVERT: D 48 ASN cc_start: 0.8955 (m-40) cc_final: 0.8718 (t0) REVERT: D 137 MET cc_start: 0.8929 (ptt) cc_final: 0.8580 (ptm) REVERT: D 141 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6840 (tt0) REVERT: D 197 CYS cc_start: 0.8735 (m) cc_final: 0.8010 (m) REVERT: D 222 LYS cc_start: 0.8927 (ttmt) cc_final: 0.8581 (tttm) REVERT: D 268 TYR cc_start: 0.8680 (t80) cc_final: 0.8443 (t80) REVERT: E 179 LEU cc_start: 0.8963 (tp) cc_final: 0.8760 (tp) REVERT: E 209 GLU cc_start: 0.8446 (mp0) cc_final: 0.8186 (mp0) REVERT: E 243 LYS cc_start: 0.8292 (mmtt) cc_final: 0.7822 (mmtt) REVERT: E 304 SER cc_start: 0.9195 (OUTLIER) cc_final: 0.8511 (p) REVERT: E 445 GLN cc_start: 0.9123 (tt0) cc_final: 0.8837 (tt0) REVERT: E 591 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8100 (mt) REVERT: E 731 MET cc_start: 0.7079 (tpp) cc_final: 0.6609 (tpp) REVERT: E 785 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7893 (pm20) REVERT: E 804 GLU cc_start: 0.8821 (mp0) cc_final: 0.8619 (mm-30) REVERT: E 903 MET cc_start: 0.7395 (mtp) cc_final: 0.7193 (ptp) REVERT: E 1141 GLU cc_start: 0.9097 (tm-30) cc_final: 0.8868 (tm-30) REVERT: E 1190 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7817 (tm-30) REVERT: E 1194 ASP cc_start: 0.8206 (m-30) cc_final: 0.7602 (m-30) REVERT: E 1229 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7879 (mt-10) REVERT: E 1253 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7508 (tp30) REVERT: E 1298 MET cc_start: 0.8951 (tmm) cc_final: 0.8649 (tmm) REVERT: E 1348 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7943 (tm-30) REVERT: E 1392 PHE cc_start: 0.8061 (m-80) cc_final: 0.7676 (m-80) REVERT: E 1483 SER cc_start: 0.7727 (OUTLIER) cc_final: 0.7388 (t) REVERT: E 1552 LEU cc_start: 0.8443 (tp) cc_final: 0.8141 (tp) outliers start: 102 outliers final: 63 residues processed: 422 average time/residue: 0.1482 time to fit residues: 98.9967 Evaluate side-chains 393 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 320 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 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 277 HIS 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 115 HIS Chi-restraints excluded: chain B residue 125 ILE 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 303 SER 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 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 80 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 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 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 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 534 LEU Chi-restraints excluded: chain E residue 591 LEU Chi-restraints excluded: chain E residue 680 VAL Chi-restraints excluded: chain E residue 728 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 1025 MET 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 1253 GLU Chi-restraints excluded: chain E residue 1281 VAL Chi-restraints excluded: chain E residue 1337 LYS Chi-restraints excluded: chain E residue 1348 GLN 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: 0.8980 chunk 55 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 256 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 219 optimal weight: 2.9990 chunk 245 optimal weight: 0.8980 chunk 237 optimal weight: 0.6980 chunk 231 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN C 216 HIS ** E 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 445 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.077105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.063259 restraints weight = 70263.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.065334 restraints weight = 33393.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.066764 restraints weight = 20210.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.067664 restraints weight = 14282.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.068336 restraints weight = 11338.438| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21685 Z= 0.156 Angle : 0.626 11.223 29471 Z= 0.310 Chirality : 0.044 0.343 3482 Planarity : 0.004 0.050 3667 Dihedral : 6.133 139.732 2929 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.72 % Allowed : 21.43 % Favored : 73.85 % 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: 0.22 (0.17), residues: 2674 helix: 1.33 (0.15), residues: 1277 sheet: 0.19 (0.33), residues: 259 loop : -1.25 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E1246 TYR 0.018 0.001 TYR E1287 PHE 0.018 0.001 PHE C 86 TRP 0.019 0.001 TRP E 52 HIS 0.005 0.001 HIS D 175 Details of bonding type rmsd covalent geometry : bond 0.00346 (21680) covalent geometry : angle 0.62591 (29463) SS BOND : bond 0.00140 ( 4) SS BOND : angle 1.64095 ( 8) hydrogen bonds : bond 0.03941 ( 1070) hydrogen bonds : angle 3.89194 ( 3123) Misc. bond : bond 0.00159 ( 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 435 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 326 time to evaluate : 0.848 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: 0.8757 (OUTLIER) cc_final: 0.8264 (mmmt) REVERT: A 48 ASN cc_start: 0.8661 (m110) cc_final: 0.8152 (m110) REVERT: A 54 ARG cc_start: 0.8227 (mtt90) cc_final: 0.7937 (mtp85) REVERT: A 84 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9117 (mm) REVERT: A 137 MET cc_start: 0.8755 (ptm) cc_final: 0.8456 (ptm) REVERT: A 153 ASN cc_start: 0.9039 (m-40) cc_final: 0.8661 (m110) REVERT: A 160 ASN cc_start: 0.8689 (m-40) cc_final: 0.8401 (m110) REVERT: A 175 HIS cc_start: 0.8791 (OUTLIER) cc_final: 0.8511 (p-80) REVERT: A 288 GLU cc_start: 0.8024 (pm20) cc_final: 0.7608 (pm20) REVERT: A 304 TYR cc_start: 0.8847 (m-80) cc_final: 0.8479 (m-80) REVERT: B 39 LYS cc_start: 0.8508 (tmtt) cc_final: 0.8000 (ttpt) REVERT: B 47 LYS cc_start: 0.9177 (mtpt) cc_final: 0.8893 (mtmt) REVERT: B 137 MET cc_start: 0.8759 (ptt) cc_final: 0.8271 (ptm) REVERT: B 170 LYS cc_start: 0.9285 (tptp) cc_final: 0.8993 (tttm) REVERT: B 179 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8359 (mp0) REVERT: B 201 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8755 (ttm-80) REVERT: B 288 GLU cc_start: 0.7659 (pm20) cc_final: 0.7018 (pm20) REVERT: C 170 LYS cc_start: 0.9312 (ttmm) cc_final: 0.8954 (ttmm) REVERT: C 173 GLN cc_start: 0.9324 (OUTLIER) cc_final: 0.8943 (pm20) REVERT: C 185 LYS cc_start: 0.9198 (ttpt) cc_final: 0.8911 (tppt) REVERT: C 303 SER cc_start: 0.9246 (t) cc_final: 0.8975 (t) REVERT: C 304 TYR cc_start: 0.9017 (m-80) cc_final: 0.8290 (m-80) REVERT: D 137 MET cc_start: 0.9024 (ptt) cc_final: 0.8623 (ptm) REVERT: D 141 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6896 (tt0) REVERT: D 170 LYS cc_start: 0.9156 (tppt) cc_final: 0.8846 (tptt) REVERT: D 197 CYS cc_start: 0.8700 (m) cc_final: 0.8008 (m) REVERT: D 222 LYS cc_start: 0.9035 (ttmt) cc_final: 0.8705 (tttm) REVERT: D 268 TYR cc_start: 0.8804 (t80) cc_final: 0.8576 (t80) REVERT: E 132 ASN cc_start: 0.9094 (t0) cc_final: 0.8849 (t0) REVERT: E 179 LEU cc_start: 0.8968 (tp) cc_final: 0.8687 (tp) REVERT: E 209 GLU cc_start: 0.8462 (mp0) cc_final: 0.8174 (mp0) REVERT: E 243 LYS cc_start: 0.8213 (mmtt) cc_final: 0.7659 (mmtt) REVERT: E 304 SER cc_start: 0.9309 (t) cc_final: 0.8776 (p) REVERT: E 712 ILE cc_start: 0.9222 (mm) cc_final: 0.8899 (mm) REVERT: E 785 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7828 (pm20) REVERT: E 903 MET cc_start: 0.7430 (mtp) cc_final: 0.7125 (ptp) REVERT: E 1141 GLU cc_start: 0.9139 (tm-30) cc_final: 0.8935 (tm-30) REVERT: E 1190 GLN cc_start: 0.8264 (tm-30) cc_final: 0.7808 (tm-30) REVERT: E 1194 ASP cc_start: 0.8151 (m-30) cc_final: 0.7527 (m-30) REVERT: E 1229 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7880 (mt-10) REVERT: E 1298 MET cc_start: 0.8997 (tmm) cc_final: 0.8748 (tmm) REVERT: E 1392 PHE cc_start: 0.8083 (m-80) cc_final: 0.7681 (m-80) REVERT: E 1428 ASP cc_start: 0.8631 (t70) cc_final: 0.8289 (t0) REVERT: E 1483 SER cc_start: 0.8091 (OUTLIER) cc_final: 0.7727 (t) REVERT: E 1552 LEU cc_start: 0.8449 (tp) cc_final: 0.8160 (tp) outliers start: 109 outliers final: 71 residues processed: 409 average time/residue: 0.1433 time to fit residues: 92.8260 Evaluate side-chains 398 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 318 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 47 LYS 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 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 125 ILE 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 201 ARG 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 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 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 290 VAL 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 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 38 VAL Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 301 VAL 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 444 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 728 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 808 LEU Chi-restraints excluded: chain E residue 828 ILE Chi-restraints excluded: chain E residue 911 GLU Chi-restraints excluded: chain E residue 1025 MET 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 1262 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 139 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 167 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 221 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 249 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 157 optimal weight: 0.7980 chunk 154 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN C 216 HIS D 173 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.077063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.063115 restraints weight = 70705.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.065190 restraints weight = 33480.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.066609 restraints weight = 20239.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.067518 restraints weight = 14329.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.068192 restraints weight = 11364.958| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21685 Z= 0.155 Angle : 0.633 11.327 29471 Z= 0.312 Chirality : 0.044 0.455 3482 Planarity : 0.004 0.049 3667 Dihedral : 6.084 139.527 2929 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.24 % Allowed : 21.95 % Favored : 73.81 % 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: 0.32 (0.17), residues: 2674 helix: 1.39 (0.15), residues: 1281 sheet: 0.28 (0.33), residues: 259 loop : -1.20 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1246 TYR 0.018 0.001 TYR E1287 PHE 0.017 0.001 PHE E1182 TRP 0.015 0.001 TRP B 83 HIS 0.007 0.001 HIS D 175 Details of bonding type rmsd covalent geometry : bond 0.00345 (21680) covalent geometry : angle 0.63275 (29463) SS BOND : bond 0.00136 ( 4) SS BOND : angle 1.58377 ( 8) hydrogen bonds : bond 0.03925 ( 1070) hydrogen bonds : angle 3.90518 ( 3123) Misc. bond : bond 0.00161 ( 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 429 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 331 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8246 (mmmt) REVERT: A 48 ASN cc_start: 0.8667 (m110) cc_final: 0.8168 (m110) REVERT: A 54 ARG cc_start: 0.8271 (mtt90) cc_final: 0.7967 (mtp85) REVERT: A 67 LYS cc_start: 0.6584 (tptt) cc_final: 0.6348 (tptt) REVERT: A 73 LEU cc_start: 0.8983 (mt) cc_final: 0.8698 (tp) REVERT: A 84 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9084 (mm) REVERT: A 137 MET cc_start: 0.8723 (ptm) cc_final: 0.8417 (ptm) REVERT: A 153 ASN cc_start: 0.9040 (m-40) cc_final: 0.8642 (m110) REVERT: A 160 ASN cc_start: 0.8695 (m-40) cc_final: 0.8405 (m110) REVERT: A 175 HIS cc_start: 0.8814 (OUTLIER) cc_final: 0.8569 (p-80) REVERT: A 288 GLU cc_start: 0.8052 (pm20) cc_final: 0.7611 (pm20) REVERT: A 304 TYR cc_start: 0.8885 (m-80) cc_final: 0.8493 (m-80) REVERT: B 39 LYS cc_start: 0.8551 (tmtt) cc_final: 0.8062 (ttpt) REVERT: B 47 LYS cc_start: 0.9188 (mtpt) cc_final: 0.8906 (mtmt) REVERT: B 137 MET cc_start: 0.8790 (ptt) cc_final: 0.8461 (ptt) REVERT: B 170 LYS cc_start: 0.9288 (tptp) cc_final: 0.8980 (tttm) REVERT: B 179 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8356 (mp0) REVERT: B 201 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8736 (ttm-80) REVERT: B 288 GLU cc_start: 0.7620 (pm20) cc_final: 0.6963 (pm20) REVERT: C 170 LYS cc_start: 0.9308 (ttmm) cc_final: 0.8990 (ttmm) REVERT: C 173 GLN cc_start: 0.9351 (OUTLIER) cc_final: 0.8975 (pm20) REVERT: C 185 LYS cc_start: 0.9215 (ttpt) cc_final: 0.8913 (tppt) REVERT: C 277 HIS cc_start: 0.8275 (OUTLIER) cc_final: 0.7604 (m-70) REVERT: C 303 SER cc_start: 0.9262 (t) cc_final: 0.9000 (t) REVERT: C 304 TYR cc_start: 0.9013 (m-80) cc_final: 0.8288 (m-80) REVERT: D 137 MET cc_start: 0.9024 (ptt) cc_final: 0.8636 (ptm) REVERT: D 141 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7003 (tt0) REVERT: D 170 LYS cc_start: 0.9124 (tppt) cc_final: 0.8794 (tptt) REVERT: D 197 CYS cc_start: 0.8739 (m) cc_final: 0.8013 (m) REVERT: D 222 LYS cc_start: 0.9079 (ttmt) cc_final: 0.8698 (tttm) REVERT: D 268 TYR cc_start: 0.8852 (t80) cc_final: 0.8592 (t80) REVERT: E 179 LEU cc_start: 0.8904 (tp) cc_final: 0.8610 (tp) REVERT: E 209 GLU cc_start: 0.8399 (mp0) cc_final: 0.8099 (mp0) REVERT: E 222 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.7969 (p90) REVERT: E 243 LYS cc_start: 0.8145 (mmtt) cc_final: 0.7672 (mmtt) REVERT: E 258 MET cc_start: 0.8716 (pmm) cc_final: 0.8451 (pmm) REVERT: E 304 SER cc_start: 0.9315 (t) cc_final: 0.8772 (p) REVERT: E 425 ASP cc_start: 0.8054 (m-30) cc_final: 0.7658 (m-30) REVERT: E 591 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8179 (mt) REVERT: E 903 MET cc_start: 0.7445 (mtp) cc_final: 0.7139 (ptp) REVERT: E 1141 GLU cc_start: 0.9182 (tm-30) cc_final: 0.8974 (tm-30) REVERT: E 1190 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7830 (tm-30) REVERT: E 1194 ASP cc_start: 0.8203 (m-30) cc_final: 0.7546 (m-30) REVERT: E 1229 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7911 (mt-10) REVERT: E 1298 MET cc_start: 0.8997 (tmm) cc_final: 0.8714 (tmm) REVERT: E 1392 PHE cc_start: 0.8086 (m-80) cc_final: 0.7634 (m-80) REVERT: E 1483 SER cc_start: 0.7834 (OUTLIER) cc_final: 0.7553 (t) REVERT: E 1552 LEU cc_start: 0.8449 (tp) cc_final: 0.8153 (tp) outliers start: 98 outliers final: 70 residues processed: 408 average time/residue: 0.1417 time to fit residues: 91.0009 Evaluate side-chains 398 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 317 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 47 LYS 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 214 THR 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 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 125 ILE 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 201 ARG 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 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 111 VAL 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 277 HIS 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 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 236 VAL Chi-restraints excluded: chain D residue 251 LEU 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 38 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 300 LEU Chi-restraints excluded: chain E residue 301 VAL 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 444 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 725 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 808 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 259 optimal weight: 0.9980 chunk 166 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 136 optimal weight: 0.6980 chunk 181 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN C 216 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.077176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.063247 restraints weight = 70351.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.065321 restraints weight = 33295.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.066734 restraints weight = 20161.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.067676 restraints weight = 14289.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.068318 restraints weight = 11289.073| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21685 Z= 0.145 Angle : 0.639 11.174 29471 Z= 0.313 Chirality : 0.044 0.442 3482 Planarity : 0.004 0.050 3667 Dihedral : 6.025 138.771 2929 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.33 % Allowed : 22.21 % Favored : 73.46 % 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: 1.41 (0.15), residues: 1278 sheet: 0.34 (0.33), residues: 259 loop : -1.14 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 249 TYR 0.026 0.001 TYR E 799 PHE 0.038 0.001 PHE D 35 TRP 0.013 0.001 TRP B 83 HIS 0.007 0.001 HIS D 175 Details of bonding type rmsd covalent geometry : bond 0.00320 (21680) covalent geometry : angle 0.63867 (29463) SS BOND : bond 0.00134 ( 4) SS BOND : angle 1.53399 ( 8) hydrogen bonds : bond 0.03984 ( 1070) hydrogen bonds : angle 3.91894 ( 3123) Misc. bond : bond 0.00155 ( 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 425 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 325 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8250 (mmmt) REVERT: A 48 ASN cc_start: 0.8641 (m110) cc_final: 0.8152 (m110) REVERT: A 54 ARG cc_start: 0.8264 (mtt90) cc_final: 0.7975 (mtp85) REVERT: A 67 LYS cc_start: 0.6628 (tptt) cc_final: 0.6408 (tptt) REVERT: A 73 LEU cc_start: 0.8988 (mt) cc_final: 0.8706 (tp) REVERT: A 84 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9100 (mm) REVERT: A 137 MET cc_start: 0.8722 (ptm) cc_final: 0.8386 (ptm) REVERT: A 153 ASN cc_start: 0.9035 (m-40) cc_final: 0.8643 (m110) REVERT: A 160 ASN cc_start: 0.8698 (m-40) cc_final: 0.8411 (m110) REVERT: A 175 HIS cc_start: 0.8715 (OUTLIER) cc_final: 0.8461 (p-80) REVERT: A 240 MET cc_start: 0.8188 (ttp) cc_final: 0.7950 (ptm) REVERT: A 288 GLU cc_start: 0.8037 (pm20) cc_final: 0.7610 (pm20) REVERT: A 304 TYR cc_start: 0.8888 (m-80) cc_final: 0.8473 (m-80) REVERT: B 39 LYS cc_start: 0.8560 (tmtt) cc_final: 0.8079 (ttpt) REVERT: B 47 LYS cc_start: 0.9172 (mtpt) cc_final: 0.8919 (mtmt) REVERT: B 137 MET cc_start: 0.8784 (ptt) cc_final: 0.8522 (ptt) REVERT: B 170 LYS cc_start: 0.9286 (tptp) cc_final: 0.8986 (tttm) REVERT: B 179 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8347 (mp0) REVERT: B 256 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.9017 (mt) REVERT: B 288 GLU cc_start: 0.7609 (pm20) cc_final: 0.7086 (pm20) REVERT: C 170 LYS cc_start: 0.9302 (ttmm) cc_final: 0.8991 (ttmm) REVERT: C 173 GLN cc_start: 0.9352 (OUTLIER) cc_final: 0.8999 (pm20) REVERT: C 185 LYS cc_start: 0.9193 (ttpt) cc_final: 0.8909 (tppt) REVERT: C 303 SER cc_start: 0.9243 (t) cc_final: 0.8983 (t) REVERT: C 304 TYR cc_start: 0.9006 (m-80) cc_final: 0.8286 (m-80) REVERT: D 137 MET cc_start: 0.9054 (ptt) cc_final: 0.8699 (ptm) REVERT: D 141 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6969 (tt0) REVERT: D 170 LYS cc_start: 0.9125 (tppt) cc_final: 0.8811 (tptt) REVERT: D 197 CYS cc_start: 0.8699 (m) cc_final: 0.7991 (m) REVERT: D 222 LYS cc_start: 0.9089 (ttmt) cc_final: 0.8722 (tttm) REVERT: D 268 TYR cc_start: 0.8846 (t80) cc_final: 0.8576 (t80) REVERT: E 1 MET cc_start: 0.6854 (mmm) cc_final: 0.6440 (tpp) REVERT: E 179 LEU cc_start: 0.8903 (tp) cc_final: 0.8625 (tp) REVERT: E 209 GLU cc_start: 0.8375 (mp0) cc_final: 0.8081 (mp0) REVERT: E 222 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.7886 (p90) REVERT: E 243 LYS cc_start: 0.8132 (mmtt) cc_final: 0.7660 (mmtt) REVERT: E 258 MET cc_start: 0.8697 (pmm) cc_final: 0.8440 (pmm) REVERT: E 425 ASP cc_start: 0.8030 (m-30) cc_final: 0.7618 (m-30) REVERT: E 442 MET cc_start: 0.8738 (mmm) cc_final: 0.8404 (tpt) REVERT: E 591 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8299 (mt) REVERT: E 712 ILE cc_start: 0.9215 (mm) cc_final: 0.8964 (mm) REVERT: E 785 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7981 (pm20) REVERT: E 1190 GLN cc_start: 0.8274 (tm-30) cc_final: 0.7823 (tm-30) REVERT: E 1194 ASP cc_start: 0.8201 (m-30) cc_final: 0.7534 (m-30) REVERT: E 1229 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7906 (mt-10) REVERT: E 1248 LEU cc_start: 0.9298 (tp) cc_final: 0.8989 (tp) REVERT: E 1298 MET cc_start: 0.8964 (tmm) cc_final: 0.8678 (tmm) REVERT: E 1428 ASP cc_start: 0.8641 (t70) cc_final: 0.8303 (t0) REVERT: E 1483 SER cc_start: 0.7576 (OUTLIER) cc_final: 0.7155 (t) REVERT: E 1505 MET cc_start: 0.7387 (mpp) cc_final: 0.7071 (mmp) REVERT: E 1552 LEU cc_start: 0.8422 (tp) cc_final: 0.8121 (tp) outliers start: 100 outliers final: 72 residues processed: 404 average time/residue: 0.1456 time to fit residues: 93.1750 Evaluate side-chains 396 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 313 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 214 THR 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 118 SER Chi-restraints excluded: chain B residue 125 ILE 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 256 ILE 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 343 LEU 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 290 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 236 VAL Chi-restraints excluded: chain D residue 251 LEU 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 183 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 311 ASP 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 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 808 LEU 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 1025 MET 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 1242 THR 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: 0.2980 chunk 144 optimal weight: 4.9990 chunk 167 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 252 optimal weight: 0.0670 chunk 137 optimal weight: 0.8980 chunk 235 optimal weight: 3.9990 chunk 236 optimal weight: 2.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN C 216 HIS E 132 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.079389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.065153 restraints weight = 70440.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.067284 restraints weight = 33360.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.068746 restraints weight = 20230.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.069745 restraints weight = 14238.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.070345 restraints weight = 11164.094| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4167 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= 0.117 Angle : 0.640 11.498 29471 Z= 0.310 Chirality : 0.044 0.402 3482 Planarity : 0.004 0.049 3667 Dihedral : 5.933 137.611 2929 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.42 % Allowed : 23.51 % Favored : 73.07 % 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: 0.47 (0.17), residues: 2674 helix: 1.41 (0.15), residues: 1289 sheet: 0.41 (0.33), residues: 259 loop : -1.02 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 249 TYR 0.016 0.001 TYR B 304 PHE 0.034 0.001 PHE D 35 TRP 0.017 0.001 TRP B 83 HIS 0.007 0.000 HIS D 175 Details of bonding type rmsd covalent geometry : bond 0.00254 (21680) covalent geometry : angle 0.63932 (29463) SS BOND : bond 0.00129 ( 4) SS BOND : angle 1.35573 ( 8) hydrogen bonds : bond 0.03847 ( 1070) hydrogen bonds : angle 3.88599 ( 3123) Misc. bond : bond 0.00145 ( 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 420 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 341 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8743 (mtpp) cc_final: 0.8230 (mmmt) REVERT: A 48 ASN cc_start: 0.8643 (m110) cc_final: 0.8163 (m110) REVERT: A 54 ARG cc_start: 0.8271 (mtt90) cc_final: 0.7965 (mtp85) REVERT: A 67 LYS cc_start: 0.6401 (tptt) cc_final: 0.6173 (tptt) REVERT: A 73 LEU cc_start: 0.8951 (mt) cc_final: 0.8684 (tp) REVERT: A 84 LEU cc_start: 0.9316 (mt) cc_final: 0.9108 (mm) REVERT: A 137 MET cc_start: 0.8690 (ptm) cc_final: 0.8371 (ptm) REVERT: A 153 ASN cc_start: 0.9048 (m-40) cc_final: 0.8640 (m110) REVERT: A 160 ASN cc_start: 0.8649 (m-40) cc_final: 0.8247 (m110) REVERT: A 175 HIS cc_start: 0.8613 (OUTLIER) cc_final: 0.8354 (p-80) REVERT: A 240 MET cc_start: 0.8142 (ttp) cc_final: 0.7912 (ptm) REVERT: A 288 GLU cc_start: 0.7964 (pm20) cc_final: 0.7536 (pm20) REVERT: A 304 TYR cc_start: 0.8856 (m-80) cc_final: 0.8428 (m-80) REVERT: B 39 LYS cc_start: 0.8468 (tmtt) cc_final: 0.7930 (ttpt) REVERT: B 47 LYS cc_start: 0.9204 (mtpt) cc_final: 0.8974 (mtmt) REVERT: B 137 MET cc_start: 0.8775 (ptt) cc_final: 0.8449 (ptt) REVERT: B 170 LYS cc_start: 0.9243 (tptp) cc_final: 0.8898 (tttm) REVERT: B 179 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8333 (mp0) REVERT: B 256 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8972 (mt) REVERT: B 288 GLU cc_start: 0.7514 (pm20) cc_final: 0.6967 (pm20) REVERT: C 170 LYS cc_start: 0.9276 (ttmm) cc_final: 0.8997 (ttmm) REVERT: C 173 GLN cc_start: 0.9297 (OUTLIER) cc_final: 0.8949 (pm20) REVERT: C 185 LYS cc_start: 0.9202 (ttpt) cc_final: 0.8875 (tppt) REVERT: C 204 ASP cc_start: 0.7507 (t70) cc_final: 0.7045 (p0) REVERT: C 277 HIS cc_start: 0.8210 (OUTLIER) cc_final: 0.7494 (m-70) REVERT: C 303 SER cc_start: 0.9220 (t) cc_final: 0.8937 (t) REVERT: C 344 CYS cc_start: 0.8491 (p) cc_final: 0.8219 (p) REVERT: D 47 LYS cc_start: 0.9143 (mtpp) cc_final: 0.8911 (tptt) REVERT: D 137 MET cc_start: 0.8936 (ptt) cc_final: 0.8626 (ptm) REVERT: D 163 MET cc_start: 0.8842 (mmt) cc_final: 0.8473 (mmm) REVERT: D 170 LYS cc_start: 0.9148 (tppt) cc_final: 0.8762 (tptt) REVERT: D 197 CYS cc_start: 0.8711 (m) cc_final: 0.7977 (m) REVERT: D 222 LYS cc_start: 0.9043 (ttmt) cc_final: 0.8722 (tttm) REVERT: D 268 TYR cc_start: 0.8888 (t80) cc_final: 0.8607 (t80) REVERT: E 1 MET cc_start: 0.6845 (mmm) cc_final: 0.6417 (tpp) REVERT: E 179 LEU cc_start: 0.8842 (tp) cc_final: 0.8587 (tp) REVERT: E 209 GLU cc_start: 0.8411 (mp0) cc_final: 0.8118 (mp0) REVERT: E 222 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.7746 (p90) REVERT: E 243 LYS cc_start: 0.8061 (mmtt) cc_final: 0.7577 (mmtt) REVERT: E 258 MET cc_start: 0.8660 (pmm) cc_final: 0.8450 (pmm) REVERT: E 304 SER cc_start: 0.9262 (t) cc_final: 0.8736 (p) REVERT: E 388 LEU cc_start: 0.9528 (tp) cc_final: 0.9316 (tp) REVERT: E 433 PHE cc_start: 0.9320 (m-10) cc_final: 0.9004 (m-10) REVERT: E 442 MET cc_start: 0.8866 (mmm) cc_final: 0.8629 (tpt) REVERT: E 591 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8222 (mt) REVERT: E 594 LEU cc_start: 0.8390 (mm) cc_final: 0.7377 (tt) REVERT: E 785 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8056 (pm20) REVERT: E 1190 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7791 (tm-30) REVERT: E 1194 ASP cc_start: 0.8073 (m-30) cc_final: 0.7437 (m-30) REVERT: E 1229 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7879 (mt-10) REVERT: E 1248 LEU cc_start: 0.9354 (tp) cc_final: 0.9072 (tp) REVERT: E 1298 MET cc_start: 0.8974 (tmm) cc_final: 0.8761 (tmm) REVERT: E 1392 PHE cc_start: 0.7965 (m-80) cc_final: 0.7615 (m-80) REVERT: E 1428 ASP cc_start: 0.8642 (t70) cc_final: 0.8292 (t0) REVERT: E 1483 SER cc_start: 0.7296 (OUTLIER) cc_final: 0.7026 (t) REVERT: E 1505 MET cc_start: 0.7413 (mpp) cc_final: 0.7080 (mmp) REVERT: E 1552 LEU cc_start: 0.8478 (tp) cc_final: 0.8219 (tp) outliers start: 79 outliers final: 56 residues processed: 403 average time/residue: 0.1392 time to fit residues: 88.9954 Evaluate side-chains 387 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 322 time to evaluate : 1.383 ------------------------------------------------------------------------------- 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 115 HIS Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 214 THR 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 115 HIS Chi-restraints excluded: chain B residue 118 SER 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 256 ILE 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 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 169 MET 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 277 HIS Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 81 CYS 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 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 301 VAL Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 420 ASN Chi-restraints excluded: chain E residue 444 VAL Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 591 LEU Chi-restraints excluded: chain E residue 725 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 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 1425 ILE Chi-restraints excluded: chain E residue 1483 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 246 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 59 optimal weight: 0.0470 chunk 88 optimal weight: 30.0000 chunk 67 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 255 optimal weight: 0.1980 chunk 197 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN C 216 HIS ** E 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1273 HIS ** 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 = 0.3378 r_free = 0.3378 target = 0.079926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.065685 restraints weight = 70333.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.067824 restraints weight = 33409.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.069301 restraints weight = 20240.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.070297 restraints weight = 14194.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.070897 restraints weight = 11125.244| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.4303 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= 0.117 Angle : 0.648 11.352 29471 Z= 0.313 Chirality : 0.044 0.381 3482 Planarity : 0.003 0.049 3667 Dihedral : 5.861 137.904 2929 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.16 % Allowed : 23.98 % 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: 0.51 (0.17), residues: 2674 helix: 1.43 (0.15), residues: 1294 sheet: 0.48 (0.33), residues: 259 loop : -1.00 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 249 TYR 0.020 0.001 TYR C 304 PHE 0.031 0.001 PHE D 35 TRP 0.025 0.001 TRP B 83 HIS 0.007 0.000 HIS D 175 Details of bonding type rmsd covalent geometry : bond 0.00254 (21680) covalent geometry : angle 0.64755 (29463) SS BOND : bond 0.00117 ( 4) SS BOND : angle 1.27765 ( 8) hydrogen bonds : bond 0.03794 ( 1070) hydrogen bonds : angle 3.87315 ( 3123) Misc. bond : bond 0.00146 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3578.94 seconds wall clock time: 62 minutes 45.18 seconds (3765.18 seconds total)