Starting phenix.real_space_refine on Sat Jul 4 14:25:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s60_24845/07_2026/7s60_24845.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s60_24845/07_2026/7s60_24845.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 { model { file = "/net/cci-nas-00/data/ceres_data/7s60_24845/07_2026/7s60_24845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s60_24845/07_2026/7s60_24845.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s60_24845/07_2026/7s60_24845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s60_24845/07_2026/7s60_24845.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7s60_24845/07_2026/7s60_24845.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s60_24845/07_2026/7s60_24845.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= 0.083 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 13635 2.51 5 N 3585 2.21 5 O 3737 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 125 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21086 Number of models: 1 Model: "" Number of chains: 6 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: "B" Number of atoms: 2527 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 321, 2519 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} Conformer: "B" Number of residues, atoms: 321, 2519 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} bond proxies already assigned to first conformer: 2567 Chain: "C" 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: "D" 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: 10942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1395, 10942 Classifications: {'peptide': 1395} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 42, 'TRANS': 1352} Chain breaks: 7 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} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AMET B 88 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET B 88 " occ=0.50 Time building chain proxies: 4.95, per 1000 atoms: 0.23 Number of scatterers: 21086 At special positions: 0 Unit cell: (140.4, 148.2, 139.1, 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 3737 8.00 N 3585 7.00 C 13635 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=2.04 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.04 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " distance=2.04 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS E 27 " distance=2.03 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: 1.70 Conformation dependent library (CDL) restraints added in 1.1 seconds 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5056 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 27 sheets defined 48.9% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 58 through 65 removed outlier: 4.086A pdb=" N THR A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 97 Processing helix chain 'A' and resid 116 through 129 removed outlier: 3.887A pdb=" N ALA A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 129 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 172 removed outlier: 3.701A pdb=" N ILE A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 180 removed outlier: 4.151A pdb=" N ARG A 176 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A 178 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 179 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 333 removed outlier: 3.763A pdb=" N PHE A 333 " --> pdb=" O TYR A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 330 through 333' Processing helix chain 'B' and resid 59 through 65 Processing helix chain 'B' and resid 67 through 97 removed outlier: 3.925A pdb=" N LEU B 73 " --> pdb=" O PRO B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 142 through 172 removed outlier: 3.895A pdb=" N ILE B 146 " --> pdb=" O CYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 179 removed outlier: 4.314A pdb=" N ARG B 176 " --> pdb=" O GLN B 173 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA B 178 " --> pdb=" O HIS B 175 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU B 179 " --> pdb=" O ARG B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 333 removed outlier: 3.723A pdb=" N PHE B 333 " --> pdb=" O TYR B 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 330 through 333' Processing helix chain 'C' and resid 59 through 65 Processing helix chain 'C' and resid 67 through 97 Processing helix chain 'C' and resid 117 through 129 removed outlier: 3.534A pdb=" N VAL C 129 " --> pdb=" O ILE C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 172 Processing helix chain 'C' and resid 176 through 179 removed outlier: 3.516A pdb=" N GLU C 179 " --> pdb=" O ARG C 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 176 through 179' Processing helix chain 'C' and resid 271 through 275 removed outlier: 3.539A pdb=" N LEU C 275 " --> pdb=" O PRO C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 333 removed outlier: 3.660A pdb=" N PHE C 333 " --> pdb=" O TYR C 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 330 through 333' Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'D' and resid 51 through 56 removed outlier: 3.974A pdb=" N ARG D 54 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE D 55 " --> pdb=" O GLN D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 65 removed outlier: 3.971A pdb=" N THR D 62 " --> pdb=" O ASP D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 97 Processing helix chain 'D' and resid 116 through 129 removed outlier: 3.612A pdb=" N ALA D 120 " --> pdb=" O SER D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 172 removed outlier: 3.524A pdb=" N ILE D 146 " --> pdb=" O CYS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 179 removed outlier: 3.616A pdb=" N GLU D 179 " --> pdb=" O ARG D 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 176 through 179' Processing helix chain 'D' and resid 271 through 275 removed outlier: 3.765A pdb=" N LEU D 275 " --> pdb=" O PRO D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 333 removed outlier: 3.839A pdb=" N PHE D 333 " --> pdb=" O TYR D 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 330 through 333' Processing helix chain 'E' and resid 25 through 52 removed outlier: 3.965A 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 Processing helix chain 'E' and resid 104 through 107 removed outlier: 3.838A 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 130 Processing helix chain 'E' and resid 137 through 161 removed outlier: 4.111A pdb=" N HIS E 161 " --> pdb=" O LYS E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 183 removed outlier: 3.907A pdb=" N CYS E 171 " --> pdb=" O GLN E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 191 removed outlier: 3.835A pdb=" N ASN E 189 " --> pdb=" O LEU E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 230 Processing helix chain 'E' and resid 233 through 240 removed outlier: 3.952A pdb=" N PHE E 237 " --> pdb=" O TRP E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 259 removed outlier: 3.673A pdb=" N ARG E 259 " --> pdb=" O ILE E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 270 Processing helix chain 'E' and resid 285 through 296 Processing helix chain 'E' and resid 296 through 310 removed outlier: 3.662A pdb=" N LEU E 302 " --> pdb=" O ARG E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 329 removed outlier: 3.908A pdb=" N ASP E 326 " --> pdb=" O PHE E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 353 Processing helix chain 'E' and resid 355 through 401 removed outlier: 3.540A pdb=" N LEU E 368 " --> pdb=" O PHE E 364 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU E 369 " --> pdb=" O LEU E 365 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLN E 375 " --> pdb=" O ARG E 371 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA E 381 " --> pdb=" O SER E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 435 removed outlier: 3.659A pdb=" N VAL E 422 " --> pdb=" O ILE E 418 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR E 426 " --> pdb=" O VAL E 422 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ASN E 427 " --> pdb=" O ALA E 423 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU E 435 " --> pdb=" O TRP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 440 removed outlier: 3.839A pdb=" N LEU E 439 " --> pdb=" O LEU E 435 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TRP E 440 " --> pdb=" O CYS E 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 435 through 440' Processing helix chain 'E' and resid 441 through 457 removed outlier: 4.156A pdb=" N ILE E 446 " --> pdb=" O MET E 442 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL E 448 " --> pdb=" O VAL E 444 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE E 456 " --> pdb=" O LEU E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 461 Processing helix chain 'E' and resid 464 through 469 removed outlier: 4.257A pdb=" N ILE E 468 " --> pdb=" O GLY E 464 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE E 469 " --> pdb=" O ALA E 465 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 464 through 469' Processing helix chain 'E' and resid 471 through 506 removed outlier: 4.402A pdb=" N SER E 488 " --> pdb=" O GLN E 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 513 Processing helix chain 'E' and resid 515 through 565 removed outlier: 3.939A pdb=" N SER E 533 " --> pdb=" O LYS E 529 " (cutoff:3.500A) Proline residue: E 552 - end of helix removed outlier: 4.011A pdb=" N VAL E 564 " --> pdb=" O PHE E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 589 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 616 removed outlier: 3.887A pdb=" N SER E 616 " --> pdb=" O SER E 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 721 through 728 Processing helix chain 'E' and resid 783 through 790 Processing helix chain 'E' and resid 795 through 807 removed outlier: 3.594A pdb=" N CYS E 806 " --> pdb=" O VAL E 802 " (cutoff:3.500A) Processing helix chain 'E' and resid 808 through 813 Processing helix chain 'E' and resid 817 through 821 removed outlier: 3.968A pdb=" N THR E 821 " --> pdb=" O GLY E 818 " (cutoff:3.500A) Processing helix chain 'E' and resid 832 through 841 removed outlier: 3.512A pdb=" N ARG E 837 " --> pdb=" O GLY E 833 " (cutoff:3.500A) Processing helix chain 'E' and resid 861 through 871 removed outlier: 3.529A pdb=" N ALA E 871 " --> pdb=" O HIS E 867 " (cutoff:3.500A) Processing helix chain 'E' and resid 890 through 894 removed outlier: 3.552A pdb=" N TYR E 893 " --> pdb=" O LYS E 890 " (cutoff:3.500A) Processing helix chain 'E' and resid 913 through 920 Processing helix chain 'E' and resid 922 through 932 Processing helix chain 'E' and resid 999 through 1009 Processing helix chain 'E' and resid 1009 through 1039 removed outlier: 4.160A pdb=" N LEU E1015 " --> pdb=" O LEU E1011 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER E1019 " --> pdb=" O LEU E1015 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN E1020 " --> pdb=" O LEU E1016 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LEU E1022 " --> pdb=" O PHE E1018 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR E1038 " --> pdb=" O LEU E1034 " (cutoff:3.500A) Processing helix chain 'E' and resid 1062 through 1097 removed outlier: 4.092A pdb=" N VAL E1067 " --> pdb=" O VAL E1063 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N PHE E1068 " --> pdb=" O TYR E1064 " (cutoff:3.500A) Processing helix chain 'E' and resid 1100 through 1106 Processing helix chain 'E' and resid 1109 through 1116 removed outlier: 3.578A pdb=" N PHE E1113 " --> pdb=" O PRO E1109 " (cutoff:3.500A) Processing helix chain 'E' and resid 1117 through 1124 removed outlier: 3.755A pdb=" N ILE E1121 " --> pdb=" O PRO E1117 " (cutoff:3.500A) Processing helix chain 'E' and resid 1126 through 1134 Processing helix chain 'E' and resid 1134 through 1160 removed outlier: 4.410A pdb=" N SER E1138 " --> pdb=" O GLN E1134 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR E1139 " --> pdb=" O HIS E1135 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER E1158 " --> pdb=" O LEU E1154 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR E1159 " --> pdb=" O ALA E1155 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL E1160 " --> pdb=" O VAL E1156 " (cutoff:3.500A) Processing helix chain 'E' and resid 1164 through 1210 removed outlier: 4.026A pdb=" N LEU E1169 " --> pdb=" O LEU E1165 " (cutoff:3.500A) Proline residue: E1170 - end of helix removed outlier: 4.634A pdb=" N ALA E1185 " --> pdb=" O TYR E1181 " (cutoff:3.500A) Proline residue: E1199 - end of helix removed outlier: 4.196A pdb=" N GLU E1209 " --> pdb=" O ALA E1205 " (cutoff:3.500A) Processing helix chain 'E' and resid 1210 through 1215 Processing helix chain 'E' and resid 1219 through 1270 Processing helix chain 'E' and resid 1278 through 1295 Processing helix chain 'E' and resid 1295 through 1320 removed outlier: 4.298A pdb=" N ALA E1311 " --> pdb=" O LEU E1307 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL E1312 " --> pdb=" O GLN E1308 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS E1320 " --> pdb=" O HIS E1316 " (cutoff:3.500A) Processing helix chain 'E' and resid 1384 through 1391 Processing helix chain 'E' and resid 1392 through 1394 No H-bonds generated for 'chain 'E' and resid 1392 through 1394' Processing helix chain 'E' and resid 1414 through 1422 removed outlier: 3.934A pdb=" N ARG E1421 " --> pdb=" O THR E1417 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU E1422 " --> pdb=" O LEU E1418 " (cutoff:3.500A) Processing helix chain 'E' and resid 1436 through 1441 Processing helix chain 'E' and resid 1447 through 1457 Processing helix chain 'E' and resid 1460 through 1466 removed outlier: 3.598A pdb=" N ALA E1466 " --> pdb=" O LEU E1462 " (cutoff:3.500A) Processing helix chain 'E' and resid 1483 through 1496 Processing helix chain 'E' and resid 1513 through 1528 removed outlier: 3.642A pdb=" N LYS E1522 " --> pdb=" O ASN E1518 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR E1526 " --> pdb=" O LYS E1522 " (cutoff:3.500A) Processing helix chain 'E' and resid 1539 through 1544 removed outlier: 3.512A pdb=" N ILE E1543 " --> pdb=" O ARG E1539 " (cutoff:3.500A) Processing helix chain 'E' and resid 1562 through 1569 Processing helix chain 'E' and resid 1572 through 1582 Processing sheet with id=AA1, first strand: chain 'A' and resid 256 through 260 removed outlier: 6.756A pdb=" N ALA A 187 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 230 through 238 removed outlier: 5.054A pdb=" N THR A 223 " --> pdb=" O PRO A 232 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG A 221 " --> pdb=" O HIS A 234 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA A 213 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLU A 288 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE A 215 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A 286 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N MET A 217 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE A 284 " --> pdb=" O MET A 217 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL A 219 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU A 282 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 313 through 315 Processing sheet with id=AA4, first strand: chain 'A' and resid 319 through 322 Processing sheet with id=AA5, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AA6, first strand: chain 'B' and resid 181 through 183 removed outlier: 6.299A pdb=" N ALA B 187 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 236 through 238 removed outlier: 4.614A pdb=" N MET B 217 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N SER B 212 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N VAL B 290 " --> pdb=" O SER B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 223 through 224 Processing sheet with id=AA9, first strand: chain 'B' and resid 313 through 315 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 Processing sheet with id=AB3, first strand: chain 'C' and resid 181 through 183 removed outlier: 6.499A pdb=" N ALA C 187 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 234 through 237 removed outlier: 3.577A pdb=" N ARG C 221 " --> pdb=" O HIS C 234 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA C 213 " --> pdb=" O ILE C 249 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 234 through 237 removed outlier: 3.577A pdb=" N ARG C 221 " --> pdb=" O HIS C 234 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N SER C 212 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL C 290 " --> pdb=" O SER C 212 " (cutoff:3.500A) 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 182 Processing sheet with id=AB8, first strand: chain 'D' and resid 256 through 260 removed outlier: 6.366A pdb=" N ALA D 187 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 230 through 238 removed outlier: 5.202A pdb=" N THR D 223 " --> pdb=" O PRO D 232 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG D 221 " --> pdb=" O HIS D 234 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N MET D 217 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N SER D 212 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N VAL D 290 " --> pdb=" O SER D 212 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 313 through 315 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: 3.520A pdb=" N CYS E 679 " --> pdb=" O ILE E 704 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE E 704 " --> pdb=" O CYS E 679 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 697 through 701 removed outlier: 7.192A pdb=" N SER E 698 " --> pdb=" O TYR E 686 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TYR E 686 " --> pdb=" O SER E 698 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ILE E 700 " --> pdb=" O GLY E 684 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 771 through 773 removed outlier: 6.483A pdb=" N ALA E 771 " --> pdb=" O PHE E 852 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU E 709 " --> pdb=" O TRP E 899 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ILE E 901 " --> pdb=" O LEU E 709 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N MET E 711 " --> pdb=" O ILE E 901 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N MET E 903 " --> pdb=" O MET E 711 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL E 713 " --> pdb=" O MET E 903 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 1345 through 1350 removed outlier: 5.330A pdb=" N VAL E1365 " --> pdb=" O ASN E1349 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 1352 through 1353 Processing sheet with id=AC8, first strand: chain 'E' and resid 1502 through 1505 removed outlier: 6.689A pdb=" N PHE E1503 " --> pdb=" O VAL E1534 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N ILE E1536 " --> pdb=" O PHE E1503 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N MET E1505 " --> pdb=" O ILE E1536 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLY E1376 " --> pdb=" O ILE E1550 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU E1552 " --> pdb=" O GLY E1376 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N CYS E1378 " --> pdb=" O LEU E1552 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP E1561 " --> pdb=" O VAL E1549 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU E1559 " --> pdb=" O VAL E1551 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS E1553 " --> pdb=" O ILE E1557 " (cutoff:3.500A) removed outlier: 5.511A 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 1045 hydrogen bonds defined for protein. 3040 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: 4.74 Time building geometry restraints manager: 2.33 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: 6321 1.34 - 1.46: 5281 1.46 - 1.59: 9741 1.59 - 1.71: 11 1.71 - 1.83: 196 Bond restraints: 21550 Sorted by residual: bond pdb=" C VAL E 35 " pdb=" N PRO E 36 " ideal model delta sigma weight residual 1.336 1.451 -0.116 1.25e-02 6.40e+03 8.55e+01 bond pdb=" C4 ATP E1604 " pdb=" C5 ATP E1604 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.65e+01 bond pdb=" C5 ATP E1604 " pdb=" N7 ATP E1604 " ideal model delta sigma weight residual 1.387 1.330 0.057 1.00e-02 1.00e+04 3.21e+01 bond pdb=" C5 ATP E1604 " pdb=" C6 ATP E1604 " ideal model delta sigma weight residual 1.409 1.461 -0.052 1.00e-02 1.00e+04 2.72e+01 bond pdb=" C4 ATP E1604 " pdb=" N9 ATP E1604 " ideal model delta sigma weight residual 1.374 1.326 0.048 1.00e-02 1.00e+04 2.33e+01 ... (remaining 21545 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.07: 28940 5.07 - 10.15: 311 10.15 - 15.22: 27 15.22 - 20.30: 5 20.30 - 25.37: 2 Bond angle restraints: 29285 Sorted by residual: angle pdb=" PA ATP E1604 " pdb=" O3A ATP E1604 " pdb=" PB ATP E1604 " ideal model delta sigma weight residual 136.83 118.92 17.91 1.00e+00 1.00e+00 3.21e+02 angle pdb=" PB ATP E1604 " pdb=" O3B ATP E1604 " pdb=" PG ATP E1604 " ideal model delta sigma weight residual 139.87 122.87 17.00 1.00e+00 1.00e+00 2.89e+02 angle pdb=" N SER E1158 " pdb=" CA SER E1158 " pdb=" C SER E1158 " ideal model delta sigma weight residual 114.62 104.51 10.11 1.14e+00 7.69e-01 7.86e+01 angle pdb=" C ASN E 263 " pdb=" N TYR E 264 " pdb=" CA TYR E 264 " ideal model delta sigma weight residual 121.54 137.59 -16.05 1.91e+00 2.74e-01 7.06e+01 angle pdb=" C5 ATP E1604 " pdb=" C4 ATP E1604 " pdb=" N3 ATP E1604 " ideal model delta sigma weight residual 126.80 119.23 7.57 1.00e+00 1.00e+00 5.73e+01 ... (remaining 29280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 11060 17.51 - 35.02: 1386 35.02 - 52.53: 261 52.53 - 70.04: 52 70.04 - 87.55: 15 Dihedral angle restraints: 12774 sinusoidal: 4991 harmonic: 7783 Sorted by residual: dihedral pdb=" CA HIS E 12 " pdb=" C HIS E 12 " pdb=" N SER E 13 " pdb=" CA SER E 13 " ideal model delta harmonic sigma weight residual -180.00 -111.89 -68.11 0 5.00e+00 4.00e-02 1.86e+02 dihedral pdb=" CA LYS E1499 " pdb=" C LYS E1499 " pdb=" N THR E1500 " pdb=" CA THR E1500 " ideal model delta harmonic sigma weight residual 180.00 123.82 56.18 0 5.00e+00 4.00e-02 1.26e+02 dihedral pdb=" CA ARG E1498 " pdb=" C ARG E1498 " pdb=" N LYS E1499 " pdb=" CA LYS E1499 " ideal model delta harmonic sigma weight residual 180.00 -135.19 -44.81 0 5.00e+00 4.00e-02 8.03e+01 ... (remaining 12771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2900 0.095 - 0.190: 464 0.190 - 0.285: 78 0.285 - 0.380: 15 0.380 - 0.475: 6 Chirality restraints: 3463 Sorted by residual: chirality pdb=" CG LEU E 40 " pdb=" CB LEU E 40 " pdb=" CD1 LEU E 40 " pdb=" CD2 LEU E 40 " both_signs ideal model delta sigma weight residual False -2.59 -2.12 -0.47 2.00e-01 2.50e+01 5.63e+00 chirality pdb=" CB VAL B 36 " pdb=" CA VAL B 36 " pdb=" CG1 VAL B 36 " pdb=" CG2 VAL B 36 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.23e+00 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 2.25 0.40 2.00e-01 2.50e+01 3.96e+00 ... (remaining 3460 not shown) Planarity restraints: 3641 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E1502 " -0.024 2.00e-02 2.50e+03 4.93e-02 2.43e+01 pdb=" C ILE E1502 " 0.085 2.00e-02 2.50e+03 pdb=" O ILE E1502 " -0.032 2.00e-02 2.50e+03 pdb=" N PHE E1503 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 110 " 0.021 2.00e-02 2.50e+03 4.34e-02 1.89e+01 pdb=" C CYS B 110 " -0.075 2.00e-02 2.50e+03 pdb=" O CYS B 110 " 0.029 2.00e-02 2.50e+03 pdb=" N VAL B 111 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 136 " 0.021 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C LEU E 136 " -0.074 2.00e-02 2.50e+03 pdb=" O LEU E 136 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU E 137 " 0.025 2.00e-02 2.50e+03 ... (remaining 3638 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 916 2.71 - 3.25: 18591 3.25 - 3.80: 34997 3.80 - 4.35: 42961 4.35 - 4.90: 72235 Nonbonded interactions: 169700 Sorted by model distance: nonbonded pdb="MG MG E1602 " pdb=" O3B ATP E1604 " model vdw 2.157 2.170 nonbonded pdb=" O3A ADP E1601 " pdb="MG MG E1603 " model vdw 2.159 2.170 nonbonded pdb=" OE1 GLN E 775 " pdb="MG MG E1602 " model vdw 2.160 2.170 nonbonded pdb="MG MG E1602 " pdb=" O2B ATP E1604 " model vdw 2.163 2.170 nonbonded pdb=" OG SER E1386 " pdb="MG MG E1603 " model vdw 2.175 2.170 ... (remaining 169695 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' and (resid 32 through 87 or resid 89 through 352)) selection = (chain 'B' and (resid 32 through 87 or resid 89 through 352)) selection = (chain 'C' and (resid 32 through 87 or resid 89 through 352)) selection = (chain 'D' and (resid 32 through 87 or resid 89 through 352)) } 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=0.50 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: 3.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.650 Find NCS groups from input model: 0.370 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 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 : 0.009 0.116 21555 Z= 0.441 Angle : 1.420 25.370 29293 Z= 0.800 Chirality : 0.075 0.475 3463 Planarity : 0.012 0.100 3641 Dihedral : 16.053 87.545 7706 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.27 % Favored : 94.61 % Rotamer: Outliers : 1.35 % Allowed : 12.07 % Favored : 86.58 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.66 % 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: -5.53 (0.11), residues: 2658 helix: -4.50 (0.06), residues: 1312 sheet: -1.77 (0.27), residues: 290 loop : -2.81 (0.15), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 314 TYR 0.030 0.003 TYR E 379 PHE 0.046 0.003 PHE E 222 TRP 0.028 0.003 TRP E1037 HIS 0.008 0.002 HIS D 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00913 / 0.44 (21550) covalent geometry : angle 1.41905 / 0.80 (29285) SS BOND : bond 0.00881 / 0.44 ( 4) SS BOND : angle 2.80409 / 1.60 ( 8) hydrogen bonds : bond 0.16168 / 10.61 ( 1038) hydrogen bonds : angle 8.31708 / 5.76 ( 3040) Misc. bond : bond 0.00060 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 489 time to evaluate : 0.862 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 74 ILE cc_start: 0.9467 (tp) cc_final: 0.9159 (tp) REVERT: A 152 GLN cc_start: 0.8120 (tt0) cc_final: 0.7795 (tm-30) REVERT: A 179 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7901 (mp0) REVERT: B 83 TRP cc_start: 0.9386 (m-10) cc_final: 0.9115 (m-10) REVERT: B 128 GLN cc_start: 0.8576 (tt0) cc_final: 0.8183 (tt0) REVERT: B 147 LEU cc_start: 0.8913 (tp) cc_final: 0.8531 (tp) REVERT: B 170 LYS cc_start: 0.9219 (tptt) cc_final: 0.8854 (tptm) REVERT: B 185 LYS cc_start: 0.9240 (ttpp) cc_final: 0.8933 (ttpp) REVERT: B 258 TYR cc_start: 0.9036 (p90) cc_final: 0.8715 (p90) REVERT: B 283 ILE cc_start: 0.9045 (mp) cc_final: 0.8831 (tp) REVERT: C 39 LYS cc_start: 0.9225 (mmtm) cc_final: 0.8964 (mmmm) REVERT: C 47 LYS cc_start: 0.9103 (mtmt) cc_final: 0.8866 (mttm) REVERT: C 52 GLN cc_start: 0.8805 (tp-100) cc_final: 0.8501 (tp-100) REVERT: C 65 ASP cc_start: 0.8277 (t70) cc_final: 0.7874 (t0) REVERT: C 144 LEU cc_start: 0.8871 (tp) cc_final: 0.8617 (tp) REVERT: C 160 ASN cc_start: 0.8845 (m-40) cc_final: 0.8594 (t0) REVERT: C 170 LYS cc_start: 0.9024 (tptt) cc_final: 0.8777 (tppt) REVERT: C 209 MET cc_start: 0.8768 (tpp) cc_final: 0.8552 (tpp) REVERT: C 240 MET cc_start: 0.8354 (tmm) cc_final: 0.8126 (ttt) REVERT: D 47 LYS cc_start: 0.9129 (mtpp) cc_final: 0.8829 (mtmm) REVERT: D 57 GLN cc_start: 0.8784 (mt0) cc_final: 0.8353 (mp10) REVERT: D 209 MET cc_start: 0.8753 (mmm) cc_final: 0.8543 (tpp) REVERT: D 251 LEU cc_start: 0.9089 (tp) cc_final: 0.8805 (tp) REVERT: D 290 VAL cc_start: 0.9398 (t) cc_final: 0.9145 (p) REVERT: D 332 LYS cc_start: 0.9228 (mttt) cc_final: 0.8952 (mtpt) REVERT: E 84 PHE cc_start: 0.8984 (t80) cc_final: 0.8709 (t80) REVERT: E 109 MET cc_start: 0.8408 (tpt) cc_final: 0.8169 (tpp) REVERT: E 153 ILE cc_start: 0.9366 (tp) cc_final: 0.9023 (tp) REVERT: E 189 ASN cc_start: 0.9023 (m-40) cc_final: 0.8500 (t0) REVERT: E 369 LEU cc_start: 0.9009 (tp) cc_final: 0.8798 (tt) REVERT: E 410 MET cc_start: 0.7613 (tpt) cc_final: 0.6947 (tmm) REVERT: E 546 PHE cc_start: 0.8882 (t80) cc_final: 0.8281 (t80) REVERT: E 919 ARG cc_start: 0.8387 (ttp-110) cc_final: 0.7990 (ptm-80) REVERT: E 1080 LEU cc_start: 0.9132 (tp) cc_final: 0.8764 (tp) REVERT: E 1141 GLU cc_start: 0.8816 (pp20) cc_final: 0.8501 (pp20) REVERT: E 1180 LYS cc_start: 0.8579 (mtpp) cc_final: 0.8352 (mtmt) REVERT: E 1248 LEU cc_start: 0.8966 (tp) cc_final: 0.8644 (tp) REVERT: E 1505 MET cc_start: 0.8588 (mtt) cc_final: 0.7767 (mmt) REVERT: E 1551 VAL cc_start: 0.9256 (t) cc_final: 0.9003 (p) outliers start: 30 outliers final: 10 residues processed: 512 average time/residue: 0.1495 time to fit residues: 118.8470 Evaluate side-chains 354 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 344 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 1082 THR Chi-restraints excluded: chain E residue 1535 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN B 218 GLN C 175 HIS C 234 HIS D 43 ASN D 264 ASN E 60 HIS E 375 GLN ** E 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 677 ASN E 708 GLN E 715 GLN E 797 GLN E 909 GLN E1234 ASN E1518 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.074562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.059913 restraints weight = 113162.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.062166 restraints weight = 46613.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.063705 restraints weight = 26168.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.064765 restraints weight = 17574.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.065420 restraints weight = 13311.396| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21555 Z= 0.190 Angle : 0.716 17.044 29293 Z= 0.370 Chirality : 0.044 0.189 3463 Planarity : 0.006 0.077 3641 Dihedral : 6.566 73.432 2885 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.92 % Favored : 95.97 % Rotamer: Outliers : 2.18 % Allowed : 19.17 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.84 (0.14), residues: 2658 helix: -1.67 (0.12), residues: 1309 sheet: -1.28 (0.29), residues: 290 loop : -2.16 (0.17), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E1222 TYR 0.024 0.002 TYR D 268 PHE 0.022 0.002 PHE E1182 TRP 0.015 0.001 TRP E1037 HIS 0.004 0.001 HIS E1203 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 (21550) covalent geometry : angle 0.71564 / 0.37 (29285) SS BOND : bond 0.00254 / 0.13 ( 4) SS BOND : angle 1.46113 / 0.82 ( 8) hydrogen bonds : bond 0.04494 / 3.01 ( 1038) hydrogen bonds : angle 4.73180 / 3.28 ( 3040) Misc. bond : bond 0.00048 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 358 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9519 (tp) cc_final: 0.9295 (tp) REVERT: A 179 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8218 (mp0) REVERT: B 77 MET cc_start: 0.7885 (tpp) cc_final: 0.7683 (tpt) REVERT: B 185 LYS cc_start: 0.9131 (ttpp) cc_final: 0.8908 (ttpp) REVERT: B 218 GLN cc_start: 0.8375 (mt0) cc_final: 0.8093 (mm110) REVERT: B 240 MET cc_start: 0.8827 (ttp) cc_final: 0.8358 (tmm) REVERT: B 257 ILE cc_start: 0.9338 (mt) cc_final: 0.9095 (tp) REVERT: C 47 LYS cc_start: 0.9092 (mtmt) cc_final: 0.8889 (mttp) REVERT: C 65 ASP cc_start: 0.8513 (t70) cc_final: 0.7968 (t0) REVERT: C 153 ASN cc_start: 0.9219 (m-40) cc_final: 0.9007 (m110) REVERT: C 268 TYR cc_start: 0.8986 (t80) cc_final: 0.8707 (t80) REVERT: C 330 TYR cc_start: 0.8364 (m-80) cc_final: 0.7868 (m-80) REVERT: D 57 GLN cc_start: 0.8675 (mt0) cc_final: 0.8368 (mp10) REVERT: D 92 LEU cc_start: 0.9333 (mt) cc_final: 0.8964 (mt) REVERT: D 128 GLN cc_start: 0.8366 (tt0) cc_final: 0.7995 (tm-30) REVERT: D 197 CYS cc_start: 0.8519 (m) cc_final: 0.7936 (m) REVERT: D 251 LEU cc_start: 0.9015 (tp) cc_final: 0.8644 (tp) REVERT: E 153 ILE cc_start: 0.9334 (tp) cc_final: 0.9096 (tp) REVERT: E 170 PHE cc_start: 0.8106 (t80) cc_final: 0.7791 (t80) REVERT: E 189 ASN cc_start: 0.8914 (m-40) cc_final: 0.8560 (t0) REVERT: E 309 LEU cc_start: 0.9591 (tp) cc_final: 0.9317 (tp) REVERT: E 369 LEU cc_start: 0.9273 (tp) cc_final: 0.8982 (tt) REVERT: E 410 MET cc_start: 0.7737 (tpt) cc_final: 0.6892 (tmm) REVERT: E 546 PHE cc_start: 0.8860 (t80) cc_final: 0.8312 (t80) REVERT: E 1080 LEU cc_start: 0.9258 (tp) cc_final: 0.8954 (tp) REVERT: E 1151 VAL cc_start: 0.9412 (m) cc_final: 0.9193 (p) REVERT: E 1180 LYS cc_start: 0.8739 (mtpp) cc_final: 0.8448 (mtmm) REVERT: E 1191 GLN cc_start: 0.8736 (tp40) cc_final: 0.8325 (mt0) REVERT: E 1229 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7889 (tm-30) REVERT: E 1234 ASN cc_start: 0.9336 (OUTLIER) cc_final: 0.9019 (t0) REVERT: E 1248 LEU cc_start: 0.9115 (tp) cc_final: 0.8909 (tp) REVERT: E 1318 LEU cc_start: 0.9238 (mt) cc_final: 0.9016 (tp) REVERT: E 1505 MET cc_start: 0.8620 (mtt) cc_final: 0.7899 (mmt) outliers start: 49 outliers final: 26 residues processed: 391 average time/residue: 0.1484 time to fit residues: 92.0649 Evaluate side-chains 331 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 304 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 559 THR Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1234 ASN Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1265 VAL Chi-restraints excluded: chain E residue 1535 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 31 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 213 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 227 optimal weight: 0.9980 chunk 224 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 265 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN B 160 ASN ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 ASN ** E 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 797 GLN ** E1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1427 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.074544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.060287 restraints weight = 99538.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.062441 restraints weight = 42817.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.063918 restraints weight = 24489.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.064928 restraints weight = 16678.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.065563 restraints weight = 12748.023| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21555 Z= 0.156 Angle : 0.666 17.646 29293 Z= 0.335 Chirality : 0.044 0.184 3463 Planarity : 0.004 0.066 3641 Dihedral : 6.063 71.729 2883 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.48 % Favored : 95.44 % Rotamer: Outliers : 2.35 % Allowed : 20.65 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -1.37 (0.15), residues: 2658 helix: -0.18 (0.14), residues: 1294 sheet: -1.01 (0.31), residues: 285 loop : -1.70 (0.17), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E1314 TYR 0.031 0.001 TYR D 258 PHE 0.030 0.001 PHE E1503 TRP 0.013 0.001 TRP E1037 HIS 0.003 0.001 HIS E 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 (21550) covalent geometry : angle 0.66551 / 0.33 (29285) SS BOND : bond 0.00219 / 0.11 ( 4) SS BOND : angle 1.13355 / 0.62 ( 8) hydrogen bonds : bond 0.04145 / 2.79 ( 1038) hydrogen bonds : angle 4.32019 / 2.99 ( 3040) Misc. bond : bond 0.00055 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 337 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9521 (tp) cc_final: 0.9275 (tp) REVERT: A 179 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8203 (mp0) REVERT: B 153 ASN cc_start: 0.9202 (m110) cc_final: 0.8949 (m110) REVERT: B 185 LYS cc_start: 0.9126 (ttpp) cc_final: 0.8897 (ttpp) REVERT: B 240 MET cc_start: 0.8855 (ttp) cc_final: 0.8478 (tmm) REVERT: B 338 LYS cc_start: 0.8952 (ttmm) cc_final: 0.8611 (ttmm) REVERT: C 65 ASP cc_start: 0.8430 (t70) cc_final: 0.7932 (t0) REVERT: C 330 TYR cc_start: 0.8500 (m-80) cc_final: 0.8119 (m-80) REVERT: D 49 ILE cc_start: 0.9186 (mt) cc_final: 0.8739 (tt) REVERT: D 57 GLN cc_start: 0.8630 (mt0) cc_final: 0.8378 (mp10) REVERT: D 77 MET cc_start: 0.8772 (mmm) cc_final: 0.8379 (mmm) REVERT: D 197 CYS cc_start: 0.8569 (m) cc_final: 0.8021 (m) REVERT: D 332 LYS cc_start: 0.9227 (mtpt) cc_final: 0.8633 (mtpt) REVERT: E 153 ILE cc_start: 0.9345 (tp) cc_final: 0.9105 (tp) REVERT: E 170 PHE cc_start: 0.8088 (t80) cc_final: 0.7684 (t80) REVERT: E 189 ASN cc_start: 0.8915 (m-40) cc_final: 0.8550 (t0) REVERT: E 309 LEU cc_start: 0.9595 (tp) cc_final: 0.9290 (tp) REVERT: E 369 LEU cc_start: 0.9282 (tp) cc_final: 0.9015 (tt) REVERT: E 401 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8652 (tpp) REVERT: E 410 MET cc_start: 0.7868 (tpt) cc_final: 0.7041 (tmm) REVERT: E 503 MET cc_start: 0.8836 (tpp) cc_final: 0.8607 (tpp) REVERT: E 546 PHE cc_start: 0.8893 (t80) cc_final: 0.8405 (t80) REVERT: E 1080 LEU cc_start: 0.9302 (tp) cc_final: 0.9005 (tp) REVERT: E 1151 VAL cc_start: 0.9390 (m) cc_final: 0.9164 (p) REVERT: E 1180 LYS cc_start: 0.8751 (mtpp) cc_final: 0.8450 (mtmm) REVERT: E 1229 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7917 (tm-30) REVERT: E 1254 TYR cc_start: 0.9014 (m-10) cc_final: 0.8790 (m-10) REVERT: E 1305 MET cc_start: 0.8958 (mmm) cc_final: 0.8658 (mmm) REVERT: E 1492 LEU cc_start: 0.9420 (mt) cc_final: 0.9187 (mm) REVERT: E 1505 MET cc_start: 0.8284 (mtt) cc_final: 0.7688 (mmt) outliers start: 53 outliers final: 36 residues processed: 374 average time/residue: 0.1436 time to fit residues: 85.3261 Evaluate side-chains 343 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 306 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 401 MET Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 547 MET Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 844 LEU Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 1082 THR Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1249 GLU Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1500 THR Chi-restraints excluded: chain E residue 1535 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 238 optimal weight: 3.9990 chunk 253 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 139 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 231 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 209 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN B 153 ASN C 153 ASN D 97 HIS D 242 ASN E 445 GLN ** E 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 867 HIS E1024 HIS E1234 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.074751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.060229 restraints weight = 113653.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.062483 restraints weight = 46297.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.064037 restraints weight = 25840.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.065030 restraints weight = 17255.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.065788 restraints weight = 13178.746| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21555 Z= 0.138 Angle : 0.646 18.738 29293 Z= 0.320 Chirality : 0.044 0.218 3463 Planarity : 0.004 0.060 3641 Dihedral : 5.731 65.432 2883 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.60 % Favored : 95.33 % Rotamer: Outliers : 3.22 % Allowed : 20.92 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 2658 helix: 0.55 (0.14), residues: 1299 sheet: -1.02 (0.30), residues: 300 loop : -1.31 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1246 TYR 0.024 0.001 TYR D 258 PHE 0.020 0.001 PHE E1182 TRP 0.012 0.001 TRP E1247 HIS 0.003 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (21550) covalent geometry : angle 0.64553 / 0.32 (29285) SS BOND : bond 0.00161 / 0.08 ( 4) SS BOND : angle 1.17680 / 0.64 ( 8) hydrogen bonds : bond 0.03921 / 2.65 ( 1038) hydrogen bonds : angle 4.10647 / 2.84 ( 3040) Misc. bond : bond 0.00057 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 328 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9509 (tp) cc_final: 0.9269 (tp) REVERT: A 179 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8175 (mp0) REVERT: A 197 CYS cc_start: 0.8543 (m) cc_final: 0.8211 (p) REVERT: B 185 LYS cc_start: 0.9151 (ttpp) cc_final: 0.8932 (ttpp) REVERT: B 338 LYS cc_start: 0.8894 (ttmm) cc_final: 0.8581 (ttmm) REVERT: C 56 LEU cc_start: 0.9154 (mt) cc_final: 0.8833 (pp) REVERT: C 65 ASP cc_start: 0.8529 (t70) cc_final: 0.7936 (t0) REVERT: D 49 ILE cc_start: 0.9152 (mt) cc_final: 0.8752 (tt) REVERT: D 77 MET cc_start: 0.8754 (mmm) cc_final: 0.8373 (mmm) REVERT: D 197 CYS cc_start: 0.8507 (m) cc_final: 0.7962 (m) REVERT: E 153 ILE cc_start: 0.9354 (tp) cc_final: 0.9126 (tp) REVERT: E 170 PHE cc_start: 0.8114 (t80) cc_final: 0.7779 (t80) REVERT: E 189 ASN cc_start: 0.8915 (m-40) cc_final: 0.8525 (t0) REVERT: E 234 MET cc_start: 0.8642 (mmm) cc_final: 0.8137 (mmm) REVERT: E 309 LEU cc_start: 0.9636 (tp) cc_final: 0.9348 (tp) REVERT: E 401 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8744 (tpp) REVERT: E 410 MET cc_start: 0.7835 (tpt) cc_final: 0.6991 (tmm) REVERT: E 503 MET cc_start: 0.8957 (tpp) cc_final: 0.8662 (tpp) REVERT: E 546 PHE cc_start: 0.8819 (t80) cc_final: 0.8451 (t80) REVERT: E 1080 LEU cc_start: 0.9317 (tp) cc_final: 0.9072 (tp) REVERT: E 1122 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9236 (mm) REVERT: E 1151 VAL cc_start: 0.9370 (m) cc_final: 0.9155 (p) REVERT: E 1191 GLN cc_start: 0.8657 (tp40) cc_final: 0.8251 (mt0) REVERT: E 1229 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7938 (tm-30) REVERT: E 1246 ARG cc_start: 0.8620 (mmp80) cc_final: 0.8399 (mmp80) REVERT: E 1305 MET cc_start: 0.8980 (mmm) cc_final: 0.8774 (mmm) outliers start: 73 outliers final: 36 residues processed: 381 average time/residue: 0.1418 time to fit residues: 86.5512 Evaluate side-chains 337 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 299 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 401 MET Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 1079 CYS Chi-restraints excluded: chain E residue 1082 THR Chi-restraints excluded: chain E residue 1122 LEU Chi-restraints excluded: chain E residue 1249 GLU Chi-restraints excluded: chain E residue 1500 THR Chi-restraints excluded: chain E residue 1535 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 115 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 97 optimal weight: 8.9990 chunk 12 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN B 153 ASN B 160 ASN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN D 41 ASN ** E 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 846 GLN ** 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 = 0.3220 r_free = 0.3220 target = 0.074735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.061170 restraints weight = 73365.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.063094 restraints weight = 35342.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.064416 restraints weight = 21606.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.065293 restraints weight = 15339.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.065919 restraints weight = 12188.990| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21555 Z= 0.139 Angle : 0.642 17.429 29293 Z= 0.317 Chirality : 0.044 0.277 3463 Planarity : 0.004 0.057 3641 Dihedral : 5.545 57.418 2883 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.56 % Favored : 95.37 % Rotamer: Outliers : 3.14 % Allowed : 21.70 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.17), residues: 2658 helix: 0.90 (0.15), residues: 1299 sheet: -0.88 (0.30), residues: 304 loop : -1.14 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1246 TYR 0.021 0.001 TYR D 258 PHE 0.024 0.001 PHE E1503 TRP 0.011 0.001 TRP E1247 HIS 0.003 0.001 HIS E1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (21550) covalent geometry : angle 0.64197 / 0.32 (29285) SS BOND : bond 0.00217 / 0.11 ( 4) SS BOND : angle 1.22374 / 0.66 ( 8) hydrogen bonds : bond 0.03879 / 2.62 ( 1038) hydrogen bonds : angle 4.03872 / 2.78 ( 3040) Misc. bond : bond 0.00060 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 321 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9514 (tp) cc_final: 0.9269 (tp) REVERT: A 179 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8186 (mp0) REVERT: A 288 GLU cc_start: 0.7813 (pp20) cc_final: 0.7559 (pp20) REVERT: B 169 MET cc_start: 0.8379 (ttm) cc_final: 0.8011 (ttm) REVERT: B 185 LYS cc_start: 0.9143 (ttpp) cc_final: 0.8926 (ttpp) REVERT: B 338 LYS cc_start: 0.8904 (ttmm) cc_final: 0.8567 (ttmm) REVERT: C 47 LYS cc_start: 0.9061 (mttm) cc_final: 0.8818 (mttp) REVERT: C 56 LEU cc_start: 0.9137 (mt) cc_final: 0.8840 (pp) REVERT: C 65 ASP cc_start: 0.8529 (t70) cc_final: 0.7916 (t0) REVERT: C 152 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8182 (tp40) REVERT: D 44 VAL cc_start: 0.9125 (OUTLIER) cc_final: 0.8878 (t) REVERT: D 49 ILE cc_start: 0.9141 (mt) cc_final: 0.8754 (tt) REVERT: D 77 MET cc_start: 0.8717 (mmm) cc_final: 0.8371 (mmm) REVERT: D 92 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9021 (mt) REVERT: D 197 CYS cc_start: 0.8502 (m) cc_final: 0.7967 (m) REVERT: D 240 MET cc_start: 0.8712 (tmm) cc_final: 0.8394 (tmm) REVERT: E 153 ILE cc_start: 0.9362 (tp) cc_final: 0.9139 (tp) REVERT: E 170 PHE cc_start: 0.8195 (t80) cc_final: 0.7886 (t80) REVERT: E 189 ASN cc_start: 0.8884 (m-40) cc_final: 0.8497 (t0) REVERT: E 309 LEU cc_start: 0.9609 (tp) cc_final: 0.9239 (tp) REVERT: E 410 MET cc_start: 0.7823 (tpt) cc_final: 0.6966 (tmm) REVERT: E 503 MET cc_start: 0.8972 (tpp) cc_final: 0.8671 (tpp) REVERT: E 546 PHE cc_start: 0.8804 (t80) cc_final: 0.8466 (t80) REVERT: E 731 MET cc_start: 0.8456 (mmm) cc_final: 0.7867 (mmm) REVERT: E 869 MET cc_start: 0.8560 (mmm) cc_final: 0.8223 (mmm) REVERT: E 1080 LEU cc_start: 0.9319 (tp) cc_final: 0.9072 (tp) REVERT: E 1122 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9319 (mm) REVERT: E 1151 VAL cc_start: 0.9387 (m) cc_final: 0.9182 (p) REVERT: E 1229 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7963 (tm-30) REVERT: E 1246 ARG cc_start: 0.8647 (mmp80) cc_final: 0.8335 (mmp80) REVERT: E 1305 MET cc_start: 0.8975 (mmm) cc_final: 0.8722 (mmm) outliers start: 71 outliers final: 45 residues processed: 377 average time/residue: 0.1375 time to fit residues: 83.9758 Evaluate side-chains 351 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 302 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 1079 CYS Chi-restraints excluded: chain E residue 1082 THR Chi-restraints excluded: chain E residue 1122 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1213 THR Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1467 LEU Chi-restraints excluded: chain E residue 1535 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 26 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 254 optimal weight: 2.9990 chunk 219 optimal weight: 0.3980 chunk 128 optimal weight: 6.9990 chunk 221 optimal weight: 0.0770 chunk 248 optimal weight: 3.9990 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN B 153 ASN C 152 GLN D 41 ASN E 189 ASN ** E 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 846 GLN ** 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 = 0.3233 r_free = 0.3233 target = 0.075334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.060421 restraints weight = 124963.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.062771 restraints weight = 49358.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.064397 restraints weight = 27119.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.065487 restraints weight = 17998.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.066182 restraints weight = 13552.916| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21555 Z= 0.125 Angle : 0.643 19.471 29293 Z= 0.312 Chirality : 0.044 0.261 3463 Planarity : 0.003 0.055 3641 Dihedral : 5.412 49.711 2883 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.63 % Favored : 95.29 % Rotamer: Outliers : 2.79 % Allowed : 22.48 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.05 (0.17), residues: 2658 helix: 1.02 (0.15), residues: 1320 sheet: -0.79 (0.30), residues: 304 loop : -1.13 (0.20), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1124 TYR 0.018 0.001 TYR D 258 PHE 0.020 0.001 PHE E1182 TRP 0.013 0.001 TRP E 144 HIS 0.002 0.000 HIS E 847 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (21550) covalent geometry : angle 0.64231 / 0.31 (29285) SS BOND : bond 0.00126 / 0.06 ( 4) SS BOND : angle 1.55135 / 0.84 ( 8) hydrogen bonds : bond 0.03813 / 2.57 ( 1038) hydrogen bonds : angle 3.96741 / 2.73 ( 3040) Misc. bond : bond 0.00059 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 334 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9516 (tp) cc_final: 0.9125 (tp) REVERT: A 147 LEU cc_start: 0.9288 (tt) cc_final: 0.8800 (tp) REVERT: A 179 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8187 (mp0) REVERT: A 288 GLU cc_start: 0.7790 (pp20) cc_final: 0.7501 (pp20) REVERT: B 169 MET cc_start: 0.8358 (ttm) cc_final: 0.7999 (ttm) REVERT: B 185 LYS cc_start: 0.9128 (ttpp) cc_final: 0.8918 (ttpp) REVERT: B 338 LYS cc_start: 0.8909 (ttmm) cc_final: 0.8566 (ttmm) REVERT: C 47 LYS cc_start: 0.9061 (mttm) cc_final: 0.8805 (mttp) REVERT: C 56 LEU cc_start: 0.9121 (mt) cc_final: 0.8836 (pp) REVERT: C 65 ASP cc_start: 0.8524 (t70) cc_final: 0.7937 (t0) REVERT: C 209 MET cc_start: 0.8577 (tpp) cc_final: 0.8329 (tpp) REVERT: D 44 VAL cc_start: 0.9142 (OUTLIER) cc_final: 0.8880 (t) REVERT: D 92 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9012 (mt) REVERT: D 197 CYS cc_start: 0.8660 (m) cc_final: 0.8025 (m) REVERT: D 209 MET cc_start: 0.8578 (mmm) cc_final: 0.8309 (tpp) REVERT: D 284 ILE cc_start: 0.9522 (pt) cc_final: 0.9235 (mt) REVERT: E 153 ILE cc_start: 0.9355 (tp) cc_final: 0.9147 (tp) REVERT: E 170 PHE cc_start: 0.8178 (t80) cc_final: 0.7900 (t80) REVERT: E 189 ASN cc_start: 0.8850 (OUTLIER) cc_final: 0.8442 (t0) REVERT: E 234 MET cc_start: 0.8456 (mmm) cc_final: 0.8055 (mmm) REVERT: E 309 LEU cc_start: 0.9621 (tp) cc_final: 0.9264 (tp) REVERT: E 410 MET cc_start: 0.7763 (tpt) cc_final: 0.6859 (tmm) REVERT: E 430 MET cc_start: 0.8040 (ttp) cc_final: 0.7832 (ttp) REVERT: E 503 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8595 (tpp) REVERT: E 546 PHE cc_start: 0.8827 (t80) cc_final: 0.8512 (t80) REVERT: E 731 MET cc_start: 0.8417 (mmm) cc_final: 0.7685 (mmm) REVERT: E 1080 LEU cc_start: 0.9309 (tp) cc_final: 0.9068 (tp) REVERT: E 1122 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9253 (mm) REVERT: E 1191 GLN cc_start: 0.8683 (tp40) cc_final: 0.8244 (mt0) REVERT: E 1229 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7933 (tm-30) REVERT: E 1305 MET cc_start: 0.9014 (mmm) cc_final: 0.8756 (mmm) outliers start: 63 outliers final: 43 residues processed: 382 average time/residue: 0.1383 time to fit residues: 85.6212 Evaluate side-chains 361 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 313 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 189 ASN Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 1079 CYS Chi-restraints excluded: chain E residue 1082 THR Chi-restraints excluded: chain E residue 1122 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1213 THR Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1260 VAL Chi-restraints excluded: chain E residue 1467 LEU Chi-restraints excluded: chain E residue 1535 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 150 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 225 optimal weight: 0.0570 chunk 157 optimal weight: 6.9990 chunk 236 optimal weight: 0.7980 chunk 121 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 chunk 246 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 158 optimal weight: 0.4980 overall best weight: 1.0500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN B 160 ASN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 ASN ** E 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 846 GLN ** 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 = 0.3230 r_free = 0.3230 target = 0.075266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.061352 restraints weight = 88702.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.063412 restraints weight = 39698.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.064838 restraints weight = 23273.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.065807 restraints weight = 16054.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.066416 restraints weight = 12372.684| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21555 Z= 0.132 Angle : 0.644 19.185 29293 Z= 0.313 Chirality : 0.045 0.322 3463 Planarity : 0.003 0.055 3641 Dihedral : 5.307 44.271 2883 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.78 % Favored : 95.14 % Rotamer: Outliers : 2.96 % Allowed : 22.88 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.06 (0.17), residues: 2658 helix: 1.11 (0.15), residues: 1323 sheet: -0.74 (0.30), residues: 304 loop : -1.08 (0.20), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E1124 TYR 0.018 0.001 TYR D 258 PHE 0.028 0.001 PHE E1164 TRP 0.015 0.001 TRP A 90 HIS 0.003 0.001 HIS E 847 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (21550) covalent geometry : angle 0.64353 / 0.31 (29285) SS BOND : bond 0.00180 / 0.09 ( 4) SS BOND : angle 1.37654 / 0.76 ( 8) hydrogen bonds : bond 0.03805 / 2.57 ( 1038) hydrogen bonds : angle 3.95241 / 2.72 ( 3040) Misc. bond : bond 0.00063 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 318 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9511 (tp) cc_final: 0.9137 (tp) REVERT: A 147 LEU cc_start: 0.9289 (tt) cc_final: 0.8941 (tp) REVERT: A 179 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8182 (mp0) REVERT: A 288 GLU cc_start: 0.7767 (pp20) cc_final: 0.7484 (pp20) REVERT: B 169 MET cc_start: 0.8375 (ttm) cc_final: 0.7997 (ttm) REVERT: B 240 MET cc_start: 0.8928 (ttp) cc_final: 0.8282 (ttt) REVERT: B 338 LYS cc_start: 0.8921 (ttmm) cc_final: 0.8569 (ttmm) REVERT: C 47 LYS cc_start: 0.9056 (mttm) cc_final: 0.8790 (mttp) REVERT: C 56 LEU cc_start: 0.9127 (mt) cc_final: 0.8845 (pp) REVERT: C 65 ASP cc_start: 0.8557 (t70) cc_final: 0.7893 (t0) REVERT: C 152 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8421 (tp40) REVERT: C 209 MET cc_start: 0.8497 (tpp) cc_final: 0.8203 (tpp) REVERT: C 211 ILE cc_start: 0.9558 (mp) cc_final: 0.9149 (mt) REVERT: D 44 VAL cc_start: 0.9102 (OUTLIER) cc_final: 0.8839 (t) REVERT: D 49 ILE cc_start: 0.9141 (mt) cc_final: 0.8755 (tt) REVERT: D 197 CYS cc_start: 0.8536 (m) cc_final: 0.7966 (m) REVERT: D 209 MET cc_start: 0.8575 (mmm) cc_final: 0.8318 (tpp) REVERT: D 284 ILE cc_start: 0.9505 (pt) cc_final: 0.9255 (mt) REVERT: E 170 PHE cc_start: 0.8197 (t80) cc_final: 0.7933 (t80) REVERT: E 189 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8453 (t0) REVERT: E 234 MET cc_start: 0.8531 (mmm) cc_final: 0.8164 (mmm) REVERT: E 309 LEU cc_start: 0.9567 (tp) cc_final: 0.9238 (tp) REVERT: E 410 MET cc_start: 0.7746 (tpt) cc_final: 0.6835 (tmm) REVERT: E 503 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8603 (tpp) REVERT: E 546 PHE cc_start: 0.8807 (t80) cc_final: 0.8513 (t80) REVERT: E 731 MET cc_start: 0.8502 (mmm) cc_final: 0.7685 (mmm) REVERT: E 1080 LEU cc_start: 0.9328 (tp) cc_final: 0.9120 (tp) REVERT: E 1122 LEU cc_start: 0.9566 (OUTLIER) cc_final: 0.9301 (mm) REVERT: E 1229 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7899 (tm-30) REVERT: E 1305 MET cc_start: 0.9014 (mmm) cc_final: 0.8749 (mmm) outliers start: 67 outliers final: 49 residues processed: 374 average time/residue: 0.1317 time to fit residues: 79.6183 Evaluate side-chains 367 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 313 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 189 ASN Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 1079 CYS Chi-restraints excluded: chain E residue 1082 THR Chi-restraints excluded: chain E residue 1122 LEU Chi-restraints excluded: chain E residue 1123 ASN Chi-restraints excluded: chain E residue 1163 VAL Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1177 PHE Chi-restraints excluded: chain E residue 1213 THR Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1339 TRP Chi-restraints excluded: chain E residue 1467 LEU Chi-restraints excluded: chain E residue 1535 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 12 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 212 optimal weight: 0.8980 chunk 143 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 241 optimal weight: 9.9990 chunk 236 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN A 264 ASN B 153 ASN E 189 ASN E 428 GLN ** E 846 GLN ** 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 = 0.3236 r_free = 0.3236 target = 0.075548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.061418 restraints weight = 93173.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.063554 restraints weight = 40956.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.065028 restraints weight = 23694.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.066014 restraints weight = 16208.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.066629 restraints weight = 12471.948| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21555 Z= 0.131 Angle : 0.662 20.115 29293 Z= 0.318 Chirality : 0.044 0.268 3463 Planarity : 0.003 0.054 3641 Dihedral : 5.245 44.447 2882 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.63 % Favored : 95.25 % Rotamer: Outliers : 2.96 % Allowed : 23.27 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.14 (0.17), residues: 2658 helix: 1.18 (0.15), residues: 1323 sheet: -0.68 (0.30), residues: 304 loop : -1.05 (0.20), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E1124 TYR 0.023 0.001 TYR E 231 PHE 0.021 0.001 PHE E1164 TRP 0.017 0.001 TRP A 90 HIS 0.005 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (21550) covalent geometry : angle 0.66190 / 0.32 (29285) SS BOND : bond 0.00193 / 0.10 ( 4) SS BOND : angle 1.26317 / 0.70 ( 8) hydrogen bonds : bond 0.03785 / 2.56 ( 1038) hydrogen bonds : angle 3.95111 / 2.73 ( 3040) Misc. bond : bond 0.00066 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 320 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9513 (tp) cc_final: 0.9145 (tp) REVERT: A 147 LEU cc_start: 0.9309 (tt) cc_final: 0.8957 (tp) REVERT: A 179 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8182 (mp0) REVERT: A 288 GLU cc_start: 0.7745 (pp20) cc_final: 0.7349 (pp20) REVERT: B 151 VAL cc_start: 0.9634 (t) cc_final: 0.9428 (p) REVERT: B 169 MET cc_start: 0.8374 (ttm) cc_final: 0.7998 (ttm) REVERT: B 240 MET cc_start: 0.8929 (ttp) cc_final: 0.8275 (ttt) REVERT: B 338 LYS cc_start: 0.8936 (ttmm) cc_final: 0.8568 (ttmm) REVERT: C 47 LYS cc_start: 0.9061 (mttm) cc_final: 0.8786 (mttp) REVERT: C 56 LEU cc_start: 0.9117 (mt) cc_final: 0.8845 (pp) REVERT: C 65 ASP cc_start: 0.8491 (t70) cc_final: 0.7810 (t0) REVERT: C 152 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8138 (tp40) REVERT: C 209 MET cc_start: 0.8479 (tpp) cc_final: 0.8195 (tpp) REVERT: C 211 ILE cc_start: 0.9544 (mp) cc_final: 0.9188 (mt) REVERT: D 44 VAL cc_start: 0.9084 (OUTLIER) cc_final: 0.8819 (t) REVERT: D 197 CYS cc_start: 0.8520 (m) cc_final: 0.7959 (m) REVERT: E 80 PHE cc_start: 0.8661 (m-80) cc_final: 0.8266 (m-80) REVERT: E 170 PHE cc_start: 0.8191 (t80) cc_final: 0.7946 (t80) REVERT: E 189 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8294 (t0) REVERT: E 234 MET cc_start: 0.8490 (mmm) cc_final: 0.8187 (mmm) REVERT: E 309 LEU cc_start: 0.9539 (tp) cc_final: 0.9188 (tp) REVERT: E 410 MET cc_start: 0.7635 (tpt) cc_final: 0.6842 (tmm) REVERT: E 503 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8653 (tpp) REVERT: E 546 PHE cc_start: 0.8799 (t80) cc_final: 0.8520 (t80) REVERT: E 731 MET cc_start: 0.8498 (mmm) cc_final: 0.7654 (mmm) REVERT: E 1080 LEU cc_start: 0.9324 (tp) cc_final: 0.9124 (tp) REVERT: E 1122 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9281 (mm) REVERT: E 1191 GLN cc_start: 0.8773 (tp40) cc_final: 0.8263 (mt0) REVERT: E 1229 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7909 (tm-30) REVERT: E 1305 MET cc_start: 0.8949 (mmm) cc_final: 0.8699 (mmm) outliers start: 67 outliers final: 53 residues processed: 371 average time/residue: 0.1354 time to fit residues: 81.4848 Evaluate side-chains 369 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 311 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 189 ASN Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 1079 CYS Chi-restraints excluded: chain E residue 1082 THR Chi-restraints excluded: chain E residue 1122 LEU Chi-restraints excluded: chain E residue 1123 ASN Chi-restraints excluded: chain E residue 1163 VAL Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1177 PHE Chi-restraints excluded: chain E residue 1213 THR Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1260 VAL Chi-restraints excluded: chain E residue 1339 TRP Chi-restraints excluded: chain E residue 1467 LEU Chi-restraints excluded: chain E residue 1535 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 97 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 chunk 230 optimal weight: 1.9990 chunk 255 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN A 264 ASN B 153 ASN B 160 ASN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 GLN ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 ASN ** E 846 GLN ** 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 = 0.3236 r_free = 0.3236 target = 0.075467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.061322 restraints weight = 101813.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.063526 restraints weight = 43124.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.065020 restraints weight = 24476.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.065978 restraints weight = 16529.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.066723 restraints weight = 12693.546| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21555 Z= 0.130 Angle : 0.671 19.901 29293 Z= 0.321 Chirality : 0.045 0.310 3463 Planarity : 0.003 0.053 3641 Dihedral : 5.192 44.578 2882 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.52 % Favored : 95.40 % Rotamer: Outliers : 2.66 % Allowed : 23.88 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.17), residues: 2658 helix: 1.24 (0.15), residues: 1320 sheet: -0.61 (0.30), residues: 304 loop : -1.03 (0.20), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E1124 TYR 0.030 0.001 TYR E1159 PHE 0.019 0.001 PHE E1164 TRP 0.019 0.001 TRP A 90 HIS 0.004 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (21550) covalent geometry : angle 0.67096 / 0.32 (29285) SS BOND : bond 0.00191 / 0.10 ( 4) SS BOND : angle 1.25211 / 0.70 ( 8) hydrogen bonds : bond 0.03769 / 2.54 ( 1038) hydrogen bonds : angle 3.93237 / 2.72 ( 3040) Misc. bond : bond 0.00066 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 322 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9501 (tp) cc_final: 0.9145 (tp) REVERT: A 147 LEU cc_start: 0.9293 (tt) cc_final: 0.8940 (tp) REVERT: A 179 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8193 (mp0) REVERT: A 288 GLU cc_start: 0.7705 (pp20) cc_final: 0.7322 (pp20) REVERT: B 169 MET cc_start: 0.8381 (ttm) cc_final: 0.7999 (ttm) REVERT: B 240 MET cc_start: 0.8922 (ttp) cc_final: 0.8256 (ttt) REVERT: B 241 GLU cc_start: 0.8480 (tp30) cc_final: 0.8087 (tp30) REVERT: B 338 LYS cc_start: 0.9054 (ttmm) cc_final: 0.8623 (ttmm) REVERT: C 47 LYS cc_start: 0.9063 (mttm) cc_final: 0.8778 (mttp) REVERT: C 56 LEU cc_start: 0.9077 (mt) cc_final: 0.8818 (pp) REVERT: C 65 ASP cc_start: 0.8462 (t70) cc_final: 0.7804 (t0) REVERT: C 152 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.8234 (tp40) REVERT: C 209 MET cc_start: 0.8472 (tpp) cc_final: 0.8192 (tpp) REVERT: C 211 ILE cc_start: 0.9541 (mp) cc_final: 0.9174 (mt) REVERT: D 44 VAL cc_start: 0.9064 (OUTLIER) cc_final: 0.8805 (t) REVERT: D 47 LYS cc_start: 0.9191 (mtmt) cc_final: 0.8902 (mtmt) REVERT: D 197 CYS cc_start: 0.8520 (m) cc_final: 0.7964 (m) REVERT: E 170 PHE cc_start: 0.8189 (t80) cc_final: 0.7953 (t80) REVERT: E 234 MET cc_start: 0.8487 (mmm) cc_final: 0.8215 (mmm) REVERT: E 309 LEU cc_start: 0.9529 (tp) cc_final: 0.9123 (tp) REVERT: E 410 MET cc_start: 0.7541 (tpt) cc_final: 0.6869 (tmm) REVERT: E 503 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8639 (tpp) REVERT: E 546 PHE cc_start: 0.8789 (t80) cc_final: 0.8514 (t80) REVERT: E 1080 LEU cc_start: 0.9311 (tp) cc_final: 0.9081 (tp) REVERT: E 1122 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9263 (mm) REVERT: E 1188 ASP cc_start: 0.7947 (m-30) cc_final: 0.7680 (m-30) REVERT: E 1191 GLN cc_start: 0.8838 (tp40) cc_final: 0.8342 (mt0) REVERT: E 1229 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7919 (tm-30) REVERT: E 1305 MET cc_start: 0.8943 (mmm) cc_final: 0.8687 (mmm) outliers start: 60 outliers final: 49 residues processed: 368 average time/residue: 0.1424 time to fit residues: 84.5185 Evaluate side-chains 366 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 313 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 1079 CYS Chi-restraints excluded: chain E residue 1082 THR Chi-restraints excluded: chain E residue 1122 LEU Chi-restraints excluded: chain E residue 1123 ASN Chi-restraints excluded: chain E residue 1163 VAL Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1177 PHE Chi-restraints excluded: chain E residue 1213 THR Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1260 VAL Chi-restraints excluded: chain E residue 1339 TRP Chi-restraints excluded: chain E residue 1467 LEU Chi-restraints excluded: chain E residue 1535 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 50 optimal weight: 0.9980 chunk 265 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 240 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 194 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN A 264 ASN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 846 GLN ** 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 = 0.3240 r_free = 0.3240 target = 0.075638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.061405 restraints weight = 102719.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.063594 restraints weight = 43395.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.065115 restraints weight = 24680.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.066140 restraints weight = 16664.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.066771 restraints weight = 12668.443| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21555 Z= 0.130 Angle : 0.681 19.703 29293 Z= 0.325 Chirality : 0.045 0.357 3463 Planarity : 0.003 0.053 3641 Dihedral : 5.135 45.288 2881 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.71 % Favored : 95.22 % Rotamer: Outliers : 2.40 % Allowed : 24.40 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.17), residues: 2658 helix: 1.26 (0.15), residues: 1321 sheet: -0.60 (0.30), residues: 304 loop : -0.98 (0.20), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E1124 TYR 0.027 0.001 TYR E1159 PHE 0.019 0.001 PHE E1182 TRP 0.022 0.001 TRP A 90 HIS 0.004 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (21550) covalent geometry : angle 0.68113 / 0.33 (29285) SS BOND : bond 0.00208 / 0.11 ( 4) SS BOND : angle 1.20632 / 0.67 ( 8) hydrogen bonds : bond 0.03769 / 2.55 ( 1038) hydrogen bonds : angle 3.93038 / 2.71 ( 3040) Misc. bond : bond 0.00068 / 0.04 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 321 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8608 (t0) cc_final: 0.7950 (t0) REVERT: A 74 ILE cc_start: 0.9506 (tp) cc_final: 0.9144 (tp) REVERT: A 147 LEU cc_start: 0.9288 (tt) cc_final: 0.8923 (tp) REVERT: A 179 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8192 (mp0) REVERT: A 288 GLU cc_start: 0.7709 (pp20) cc_final: 0.7327 (pp20) REVERT: B 169 MET cc_start: 0.8370 (ttm) cc_final: 0.7991 (ttm) REVERT: B 240 MET cc_start: 0.8899 (ttp) cc_final: 0.8262 (ttt) REVERT: B 241 GLU cc_start: 0.8467 (tp30) cc_final: 0.8085 (tp30) REVERT: B 338 LYS cc_start: 0.9056 (ttmm) cc_final: 0.8625 (ttmm) REVERT: C 47 LYS cc_start: 0.8985 (mttm) cc_final: 0.8721 (mttp) REVERT: C 56 LEU cc_start: 0.9069 (mt) cc_final: 0.8816 (pp) REVERT: C 65 ASP cc_start: 0.8488 (t70) cc_final: 0.7784 (t0) REVERT: C 152 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8413 (tp40) REVERT: C 209 MET cc_start: 0.8467 (tpp) cc_final: 0.8193 (tpp) REVERT: C 211 ILE cc_start: 0.9537 (mp) cc_final: 0.9173 (mt) REVERT: D 44 VAL cc_start: 0.9054 (OUTLIER) cc_final: 0.8799 (t) REVERT: D 47 LYS cc_start: 0.9186 (mtmt) cc_final: 0.8878 (mtmt) REVERT: D 197 CYS cc_start: 0.8531 (m) cc_final: 0.7980 (m) REVERT: E 170 PHE cc_start: 0.8170 (t80) cc_final: 0.7941 (t80) REVERT: E 234 MET cc_start: 0.8480 (mmm) cc_final: 0.8220 (mmm) REVERT: E 309 LEU cc_start: 0.9537 (tp) cc_final: 0.9136 (tp) REVERT: E 410 MET cc_start: 0.7583 (tpt) cc_final: 0.6916 (tmm) REVERT: E 442 MET cc_start: 0.7407 (ttt) cc_final: 0.7122 (tmm) REVERT: E 503 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8647 (tpp) REVERT: E 546 PHE cc_start: 0.8809 (t80) cc_final: 0.8528 (t80) REVERT: E 731 MET cc_start: 0.8338 (mmm) cc_final: 0.7794 (mmm) REVERT: E 1080 LEU cc_start: 0.9308 (tp) cc_final: 0.9085 (tp) REVERT: E 1122 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9254 (mm) REVERT: E 1191 GLN cc_start: 0.8847 (tp40) cc_final: 0.8322 (mt0) REVERT: E 1229 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7916 (tm-30) REVERT: E 1305 MET cc_start: 0.8939 (mmm) cc_final: 0.8679 (mmm) outliers start: 54 outliers final: 50 residues processed: 364 average time/residue: 0.1415 time to fit residues: 82.8554 Evaluate side-chains 364 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 310 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 1079 CYS Chi-restraints excluded: chain E residue 1122 LEU Chi-restraints excluded: chain E residue 1123 ASN Chi-restraints excluded: chain E residue 1163 VAL Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1177 PHE Chi-restraints excluded: chain E residue 1213 THR Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1260 VAL Chi-restraints excluded: chain E residue 1339 TRP Chi-restraints excluded: chain E residue 1467 LEU Chi-restraints excluded: chain E residue 1535 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 232 optimal weight: 3.9990 chunk 72 optimal weight: 0.0020 chunk 151 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 200 optimal weight: 6.9990 chunk 262 optimal weight: 7.9990 chunk 213 optimal weight: 8.9990 chunk 249 optimal weight: 7.9990 chunk 133 optimal weight: 0.8980 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 ASN B 160 ASN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 846 GLN ** 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 = 0.3258 r_free = 0.3258 target = 0.076593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.062019 restraints weight = 113209.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.064313 restraints weight = 46035.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.065908 restraints weight = 25688.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.066973 restraints weight = 17125.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.067636 restraints weight = 12896.604| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21555 Z= 0.122 Angle : 0.671 19.496 29293 Z= 0.320 Chirality : 0.045 0.363 3463 Planarity : 0.003 0.053 3641 Dihedral : 5.058 43.947 2881 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.41 % Favored : 95.56 % Rotamer: Outliers : 2.53 % Allowed : 24.27 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.17), residues: 2658 helix: 1.30 (0.15), residues: 1321 sheet: -0.55 (0.29), residues: 316 loop : -1.02 (0.20), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E1124 TYR 0.026 0.001 TYR E1159 PHE 0.019 0.001 PHE E1182 TRP 0.023 0.001 TRP A 90 HIS 0.004 0.000 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (21550) covalent geometry : angle 0.67116 / 0.32 (29285) SS BOND : bond 0.00181 / 0.09 ( 4) SS BOND : angle 1.17524 / 0.66 ( 8) hydrogen bonds : bond 0.03728 / 2.51 ( 1038) hydrogen bonds : angle 3.89827 / 2.69 ( 3040) Misc. bond : bond 0.00066 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3861.79 seconds wall clock time: 67 minutes 40.75 seconds (4060.75 seconds total)