Starting phenix.real_space_refine on Thu Mar 5 10:16:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s60_24845/03_2026/7s60_24845.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s60_24845/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7s60_24845/03_2026/7s60_24845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s60_24845/03_2026/7s60_24845.map" model { file = "/net/cci-nas-00/data/ceres_data/7s60_24845/03_2026/7s60_24845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s60_24845/03_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-5986/lib/python3.9/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: 5.05, per 1000 atoms: 0.24 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: 1.33 Conformation dependent library (CDL) restraints added in 974.8 milliseconds 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: 0.76 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: 4.90 Time building geometry restraints manager: 1.87 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: 11075 17.51 - 35.02: 1399 35.02 - 52.53: 264 52.53 - 70.04: 52 70.04 - 87.55: 15 Dihedral angle restraints: 12805 sinusoidal: 5022 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 12802 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: 3.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.050 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 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 : 16.091 87.545 7737 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 covalent geometry : bond 0.00913 (21550) covalent geometry : angle 1.41905 (29285) SS BOND : bond 0.00881 ( 4) SS BOND : angle 2.80409 ( 8) hydrogen bonds : bond 0.16168 ( 1038) hydrogen bonds : angle 8.31708 ( 3040) Misc. bond : bond 0.00060 ( 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 : 0.561 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: 0.1413 time to fit residues: 111.3415 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 : 0.757 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.074582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.059788 restraints weight = 113472.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.062066 restraints weight = 46725.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.063596 restraints weight = 26386.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.064604 restraints weight = 17799.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.065392 restraints weight = 13619.327| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21555 Z= 0.187 Angle : 0.714 17.501 29293 Z= 0.371 Chirality : 0.044 0.184 3463 Planarity : 0.006 0.079 3641 Dihedral : 7.126 75.907 2916 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.80 % Favored : 96.08 % Rotamer: Outliers : 2.22 % Allowed : 18.95 % Favored : 78.82 % 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: -2.88 (0.14), residues: 2658 helix: -1.71 (0.12), residues: 1305 sheet: -1.31 (0.29), residues: 290 loop : -2.17 (0.17), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E1222 TYR 0.027 0.002 TYR D 268 PHE 0.021 0.002 PHE E1182 TRP 0.016 0.001 TRP E1037 HIS 0.004 0.001 HIS E1203 Details of bonding type rmsd covalent geometry : bond 0.00395 (21550) covalent geometry : angle 0.71416 (29285) SS BOND : bond 0.00285 ( 4) SS BOND : angle 1.45036 ( 8) hydrogen bonds : bond 0.04476 ( 1038) hydrogen bonds : angle 4.77945 ( 3040) Misc. bond : bond 0.00053 ( 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 405 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 355 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9520 (tp) cc_final: 0.9294 (tp) REVERT: A 179 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8176 (mp0) REVERT: B 77 MET cc_start: 0.7900 (tpp) cc_final: 0.7682 (tpt) REVERT: B 185 LYS cc_start: 0.9133 (ttpp) cc_final: 0.8917 (ttpp) REVERT: B 218 GLN cc_start: 0.8369 (mt0) cc_final: 0.8113 (mm110) REVERT: B 240 MET cc_start: 0.8836 (ttp) cc_final: 0.8122 (tmm) REVERT: C 65 ASP cc_start: 0.8497 (t70) cc_final: 0.7954 (t0) REVERT: C 268 TYR cc_start: 0.8963 (t80) cc_final: 0.8665 (t80) REVERT: C 330 TYR cc_start: 0.8355 (m-80) cc_final: 0.7863 (m-80) REVERT: D 57 GLN cc_start: 0.8669 (mt0) cc_final: 0.8368 (mp10) REVERT: D 92 LEU cc_start: 0.9341 (mt) cc_final: 0.8962 (mt) REVERT: D 128 GLN cc_start: 0.8357 (tt0) cc_final: 0.7985 (tm-30) REVERT: D 197 CYS cc_start: 0.8591 (m) cc_final: 0.8034 (m) REVERT: D 251 LEU cc_start: 0.9030 (tp) cc_final: 0.8663 (tp) REVERT: E 153 ILE cc_start: 0.9337 (tp) cc_final: 0.9097 (tp) REVERT: E 170 PHE cc_start: 0.8105 (t80) cc_final: 0.7729 (t80) REVERT: E 189 ASN cc_start: 0.8905 (m-40) cc_final: 0.8553 (t0) REVERT: E 309 LEU cc_start: 0.9504 (tp) cc_final: 0.9229 (tp) REVERT: E 369 LEU cc_start: 0.9265 (tp) cc_final: 0.8982 (tt) REVERT: E 410 MET cc_start: 0.7744 (tpt) cc_final: 0.6892 (tmm) REVERT: E 546 PHE cc_start: 0.8837 (t80) cc_final: 0.8305 (t80) REVERT: E 1080 LEU cc_start: 0.9249 (tp) cc_final: 0.8941 (tp) REVERT: E 1151 VAL cc_start: 0.9392 (m) cc_final: 0.9169 (p) REVERT: E 1180 LYS cc_start: 0.8736 (mtpp) cc_final: 0.8454 (mtmm) REVERT: E 1191 GLN cc_start: 0.8737 (tp40) cc_final: 0.8329 (mt0) REVERT: E 1229 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7907 (tm-30) REVERT: E 1234 ASN cc_start: 0.9251 (OUTLIER) cc_final: 0.9011 (t0) REVERT: E 1318 LEU cc_start: 0.9237 (mt) cc_final: 0.9011 (tp) REVERT: E 1425 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7932 (tt) REVERT: E 1492 LEU cc_start: 0.9388 (mt) cc_final: 0.9162 (mm) REVERT: E 1505 MET cc_start: 0.8615 (mtt) cc_final: 0.7882 (mmt) outliers start: 50 outliers final: 24 residues processed: 390 average time/residue: 0.1329 time to fit residues: 82.2016 Evaluate side-chains 326 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 300 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 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 1425 ILE 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: 0.8980 chunk 34 optimal weight: 5.9990 chunk 213 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 227 optimal weight: 1.9990 chunk 224 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 265 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 235 GLN B 160 ASN C 153 ASN D 335 ASN E 797 GLN ** E1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1427 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.075159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.061038 restraints weight = 99088.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.063160 restraints weight = 42788.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.064610 restraints weight = 24552.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.065625 restraints weight = 16757.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.066258 restraints weight = 12785.187| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 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 = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2410 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= 0.142 Angle : 0.655 14.924 29293 Z= 0.331 Chirality : 0.044 0.186 3463 Planarity : 0.004 0.067 3641 Dihedral : 6.684 89.265 2914 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.41 % Favored : 95.52 % Rotamer: Outliers : 2.35 % Allowed : 20.44 % Favored : 77.21 % 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: -1.48 (0.15), residues: 2658 helix: -0.32 (0.14), residues: 1317 sheet: -1.11 (0.29), residues: 303 loop : -1.70 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 194 TYR 0.015 0.001 TYR D 268 PHE 0.030 0.001 PHE E1503 TRP 0.012 0.001 TRP E1037 HIS 0.003 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00305 (21550) covalent geometry : angle 0.65461 (29285) SS BOND : bond 0.00189 ( 4) SS BOND : angle 1.09568 ( 8) hydrogen bonds : bond 0.04127 ( 1038) hydrogen bonds : angle 4.32212 ( 3040) Misc. bond : bond 0.00053 ( 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 396 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 343 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9489 (tp) cc_final: 0.9237 (tp) REVERT: A 179 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8196 (mp0) REVERT: B 153 ASN cc_start: 0.9242 (m110) cc_final: 0.9003 (m110) REVERT: B 185 LYS cc_start: 0.9162 (ttpp) cc_final: 0.8882 (ttpp) REVERT: B 240 MET cc_start: 0.8888 (ttp) cc_final: 0.8489 (tmm) REVERT: B 338 LYS cc_start: 0.8988 (ttmm) cc_final: 0.8632 (ttmm) REVERT: C 56 LEU cc_start: 0.9183 (mt) cc_final: 0.8828 (pp) REVERT: C 65 ASP cc_start: 0.8561 (t70) cc_final: 0.8010 (t0) REVERT: C 330 TYR cc_start: 0.8504 (m-80) cc_final: 0.8096 (m-80) REVERT: D 57 GLN cc_start: 0.8667 (mt0) cc_final: 0.8377 (mp10) REVERT: D 77 MET cc_start: 0.8811 (mmm) cc_final: 0.8450 (mmm) REVERT: D 197 CYS cc_start: 0.8578 (m) cc_final: 0.8032 (m) REVERT: D 332 LYS cc_start: 0.9253 (mtpt) cc_final: 0.8666 (mtpt) REVERT: E 153 ILE cc_start: 0.9335 (tp) cc_final: 0.9103 (tp) REVERT: E 170 PHE cc_start: 0.8053 (t80) cc_final: 0.7609 (t80) REVERT: E 189 ASN cc_start: 0.8962 (m-40) cc_final: 0.8585 (t0) REVERT: E 309 LEU cc_start: 0.9596 (tp) cc_final: 0.9285 (tp) REVERT: E 401 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8672 (tpp) REVERT: E 410 MET cc_start: 0.7912 (tpt) cc_final: 0.7035 (tmm) REVERT: E 546 PHE cc_start: 0.8907 (t80) cc_final: 0.8419 (t80) REVERT: E 1080 LEU cc_start: 0.9286 (tp) cc_final: 0.8997 (tp) REVERT: E 1151 VAL cc_start: 0.9402 (m) cc_final: 0.9180 (p) REVERT: E 1180 LYS cc_start: 0.8747 (mtpp) cc_final: 0.8434 (mtmm) REVERT: E 1188 ASP cc_start: 0.8127 (m-30) cc_final: 0.7869 (m-30) REVERT: E 1191 GLN cc_start: 0.8760 (tp40) cc_final: 0.7950 (pp30) REVERT: E 1229 GLU cc_start: 0.8227 (tm-30) cc_final: 0.8015 (tm-30) REVERT: E 1254 TYR cc_start: 0.9030 (m-10) cc_final: 0.8804 (m-10) REVERT: E 1305 MET cc_start: 0.8951 (mmm) cc_final: 0.8640 (mmm) REVERT: E 1492 LEU cc_start: 0.9420 (mt) cc_final: 0.9191 (mm) REVERT: E 1505 MET cc_start: 0.8280 (mtt) cc_final: 0.7646 (mmt) outliers start: 53 outliers final: 31 residues processed: 379 average time/residue: 0.1329 time to fit residues: 80.0341 Evaluate side-chains 346 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 314 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 C residue 115 HIS 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 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 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 887 VAL Chi-restraints excluded: chain E residue 1082 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 238 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 231 optimal weight: 2.9990 chunk 95 optimal weight: 0.0060 chunk 209 optimal weight: 1.9990 chunk 223 optimal weight: 4.9990 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 264 ASN B 153 ASN C 153 ASN ** E 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 867 HIS E1024 HIS ** E1234 ASN ** 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 = 0.3215 r_free = 0.3215 target = 0.074508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.059898 restraints weight = 113942.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.062155 restraints weight = 46466.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.063705 restraints weight = 26030.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.064755 restraints weight = 17445.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.065463 restraints weight = 13259.151| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 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 = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2695 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= 0.149 Angle : 0.649 17.801 29293 Z= 0.324 Chirality : 0.044 0.203 3463 Planarity : 0.004 0.060 3641 Dihedral : 6.372 73.365 2914 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.60 % Favored : 95.33 % Rotamer: Outliers : 3.09 % Allowed : 20.96 % Favored : 75.95 % 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: -0.67 (0.16), residues: 2658 helix: 0.47 (0.14), residues: 1299 sheet: -1.01 (0.30), residues: 300 loop : -1.35 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1124 TYR 0.014 0.001 TYR A 304 PHE 0.021 0.001 PHE E1182 TRP 0.013 0.001 TRP E1247 HIS 0.003 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00324 (21550) covalent geometry : angle 0.64884 (29285) SS BOND : bond 0.00206 ( 4) SS BOND : angle 1.17002 ( 8) hydrogen bonds : bond 0.03954 ( 1038) hydrogen bonds : angle 4.14783 ( 3040) Misc. bond : bond 0.00060 ( 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 393 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 323 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9509 (tp) cc_final: 0.9247 (tp) REVERT: A 179 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8190 (mp0) REVERT: B 153 ASN cc_start: 0.9219 (m-40) cc_final: 0.8947 (m110) REVERT: B 185 LYS cc_start: 0.9116 (ttpp) cc_final: 0.8889 (ttpp) REVERT: B 338 LYS cc_start: 0.8895 (ttmm) cc_final: 0.8584 (ttmm) REVERT: C 56 LEU cc_start: 0.9179 (mt) cc_final: 0.8829 (pp) REVERT: C 65 ASP cc_start: 0.8535 (t70) cc_final: 0.7943 (t0) REVERT: C 152 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8291 (tp40) REVERT: C 321 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8306 (mt-10) REVERT: D 49 ILE cc_start: 0.9156 (mt) cc_final: 0.8746 (tt) REVERT: D 77 MET cc_start: 0.8767 (mmm) cc_final: 0.8383 (mmm) REVERT: D 197 CYS cc_start: 0.8528 (m) cc_final: 0.7865 (m) REVERT: E 153 ILE cc_start: 0.9354 (tp) cc_final: 0.9125 (tp) REVERT: E 170 PHE cc_start: 0.8141 (t80) cc_final: 0.7800 (t80) REVERT: E 189 ASN cc_start: 0.8910 (m-40) cc_final: 0.8534 (t0) REVERT: E 309 LEU cc_start: 0.9635 (tp) cc_final: 0.9262 (tp) REVERT: E 401 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8715 (tpp) REVERT: E 410 MET cc_start: 0.7857 (tpt) cc_final: 0.7011 (tmm) REVERT: E 503 MET cc_start: 0.8918 (tpt) cc_final: 0.8701 (tpt) REVERT: E 546 PHE cc_start: 0.8854 (t80) cc_final: 0.8491 (t80) REVERT: E 1080 LEU cc_start: 0.9315 (tp) cc_final: 0.9067 (tp) REVERT: E 1122 LEU cc_start: 0.9572 (OUTLIER) cc_final: 0.9284 (mm) REVERT: E 1151 VAL cc_start: 0.9372 (m) cc_final: 0.9156 (p) REVERT: E 1229 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7987 (tm-30) REVERT: E 1246 ARG cc_start: 0.8642 (mmp80) cc_final: 0.8404 (mmp80) outliers start: 70 outliers final: 36 residues processed: 376 average time/residue: 0.1277 time to fit residues: 77.1573 Evaluate side-chains 339 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 299 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 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 C residue 321 GLU Chi-restraints excluded: chain C residue 349 LEU 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 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 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 844 LEU 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: 8.9990 chunk 170 optimal weight: 0.0370 chunk 68 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 overall best weight: 0.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 264 ASN B 160 ASN C 152 GLN D 41 ASN D 97 HIS ** E 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1234 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.075687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.062115 restraints weight = 72942.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.064063 restraints weight = 35157.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.065392 restraints weight = 21383.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.066213 restraints weight = 15189.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.066837 restraints weight = 12124.596| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 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 = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2934 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= 0.119 Angle : 0.640 19.040 29293 Z= 0.314 Chirality : 0.044 0.234 3463 Planarity : 0.004 0.057 3641 Dihedral : 6.185 67.331 2914 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.29 % Favored : 95.63 % Rotamer: Outliers : 2.92 % Allowed : 21.61 % Favored : 75.47 % 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: -0.26 (0.17), residues: 2658 helix: 0.84 (0.15), residues: 1304 sheet: -0.92 (0.29), residues: 321 loop : -1.15 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1124 TYR 0.013 0.001 TYR E 379 PHE 0.027 0.001 PHE E1503 TRP 0.012 0.001 TRP E1247 HIS 0.003 0.000 HIS E1024 Details of bonding type rmsd covalent geometry : bond 0.00253 (21550) covalent geometry : angle 0.63950 (29285) SS BOND : bond 0.00194 ( 4) SS BOND : angle 1.13545 ( 8) hydrogen bonds : bond 0.03822 ( 1038) hydrogen bonds : angle 4.03488 ( 3040) Misc. bond : bond 0.00057 ( 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 404 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 338 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9502 (tp) cc_final: 0.9254 (tp) REVERT: A 179 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8186 (mp0) REVERT: A 197 CYS cc_start: 0.8493 (m) cc_final: 0.8273 (m) REVERT: A 288 GLU cc_start: 0.7812 (pp20) cc_final: 0.7540 (pp20) REVERT: B 185 LYS cc_start: 0.9141 (ttpp) cc_final: 0.8914 (ttpp) REVERT: B 209 MET cc_start: 0.8097 (mmm) cc_final: 0.7862 (tpp) REVERT: B 338 LYS cc_start: 0.8879 (ttmm) cc_final: 0.8563 (ttmm) REVERT: C 47 LYS cc_start: 0.9068 (mttm) cc_final: 0.8822 (mttp) REVERT: C 56 LEU cc_start: 0.9125 (mt) cc_final: 0.8817 (pp) REVERT: C 65 ASP cc_start: 0.8499 (t70) cc_final: 0.7909 (t0) REVERT: C 152 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8200 (tp40) REVERT: C 209 MET cc_start: 0.8603 (tpp) cc_final: 0.8335 (tpp) REVERT: D 47 LYS cc_start: 0.9207 (mtmt) cc_final: 0.8955 (mtmt) REVERT: D 49 ILE cc_start: 0.9139 (mt) cc_final: 0.8741 (tt) REVERT: D 77 MET cc_start: 0.8709 (mmm) cc_final: 0.8350 (mmm) REVERT: D 88 MET cc_start: 0.8137 (ttp) cc_final: 0.7904 (tmm) REVERT: D 92 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9003 (mt) REVERT: D 152 GLN cc_start: 0.9148 (tt0) cc_final: 0.8797 (tm-30) REVERT: D 197 CYS cc_start: 0.8477 (m) cc_final: 0.7791 (m) REVERT: D 240 MET cc_start: 0.8777 (tmm) cc_final: 0.8492 (tmm) REVERT: E 153 ILE cc_start: 0.9352 (tp) cc_final: 0.9127 (tp) REVERT: E 170 PHE cc_start: 0.8074 (t80) cc_final: 0.7770 (t80) REVERT: E 189 ASN cc_start: 0.8861 (m-40) cc_final: 0.8486 (t0) REVERT: E 234 MET cc_start: 0.8451 (mmm) cc_final: 0.8040 (mmm) REVERT: E 309 LEU cc_start: 0.9560 (tp) cc_final: 0.9201 (tp) REVERT: E 401 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8800 (tpp) REVERT: E 410 MET cc_start: 0.7787 (tpt) cc_final: 0.6941 (tmm) REVERT: E 413 MET cc_start: 0.7611 (ptp) cc_final: 0.7367 (ptp) REVERT: E 503 MET cc_start: 0.8976 (tpt) cc_final: 0.8665 (tpt) REVERT: E 546 PHE cc_start: 0.8809 (t80) cc_final: 0.8457 (t80) REVERT: E 869 MET cc_start: 0.8541 (mmm) cc_final: 0.8215 (mmm) REVERT: E 1080 LEU cc_start: 0.9314 (tp) cc_final: 0.9081 (tp) REVERT: E 1122 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9221 (mm) REVERT: E 1151 VAL cc_start: 0.9376 (m) cc_final: 0.9171 (p) REVERT: E 1191 GLN cc_start: 0.8643 (tp40) cc_final: 0.8235 (mt0) REVERT: E 1229 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7943 (tm-30) REVERT: E 1246 ARG cc_start: 0.8612 (mmp80) cc_final: 0.8395 (mmp80) REVERT: E 1305 MET cc_start: 0.8992 (mmm) cc_final: 0.8667 (mmm) outliers start: 66 outliers final: 41 residues processed: 386 average time/residue: 0.1260 time to fit residues: 78.3930 Evaluate side-chains 350 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 305 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 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 152 GLN 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 41 ASN 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 12 HIS Chi-restraints excluded: chain E residue 74 LEU 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 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 1175 CYS Chi-restraints excluded: chain E residue 1213 THR Chi-restraints excluded: chain E residue 1228 LEU 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: 4.9990 chunk 215 optimal weight: 0.9980 chunk 75 optimal weight: 0.3980 chunk 93 optimal weight: 0.9980 chunk 254 optimal weight: 0.0770 chunk 219 optimal weight: 4.9990 chunk 128 optimal weight: 0.0980 chunk 221 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 276 HIS ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN D 41 ASN ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 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 = 0.3252 r_free = 0.3252 target = 0.076455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.061455 restraints weight = 124512.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.063840 restraints weight = 49047.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.065488 restraints weight = 26933.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.066605 restraints weight = 17834.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.067352 restraints weight = 13341.029| |-----------------------------------------------------------------------------| 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 = 0.22 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 = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 21555 Z= 0.114 Angle : 0.641 19.576 29293 Z= 0.310 Chirality : 0.044 0.303 3463 Planarity : 0.003 0.055 3641 Dihedral : 6.051 66.350 2914 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.52 % Favored : 95.40 % Rotamer: Outliers : 2.88 % Allowed : 22.18 % Favored : 74.95 % 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: -0.09 (0.17), residues: 2658 helix: 1.00 (0.15), residues: 1318 sheet: -0.70 (0.30), residues: 313 loop : -1.20 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E1124 TYR 0.012 0.001 TYR E 379 PHE 0.025 0.001 PHE E1164 TRP 0.013 0.001 TRP E1247 HIS 0.002 0.000 HIS E 847 Details of bonding type rmsd covalent geometry : bond 0.00242 (21550) covalent geometry : angle 0.64088 (29285) SS BOND : bond 0.00472 ( 4) SS BOND : angle 1.48824 ( 8) hydrogen bonds : bond 0.03759 ( 1038) hydrogen bonds : angle 3.93972 ( 3040) Misc. bond : bond 0.00061 ( 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 401 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 336 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9507 (tp) cc_final: 0.9258 (tp) REVERT: A 179 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8199 (mp0) REVERT: A 197 CYS cc_start: 0.8508 (m) cc_final: 0.8303 (m) REVERT: A 288 GLU cc_start: 0.7769 (pp20) cc_final: 0.7498 (pp20) REVERT: B 126 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7704 (mt-10) REVERT: B 185 LYS cc_start: 0.9146 (ttpp) cc_final: 0.8924 (ttpp) REVERT: B 338 LYS cc_start: 0.9024 (ttmm) cc_final: 0.8638 (ttmm) REVERT: C 47 LYS cc_start: 0.9065 (mttm) cc_final: 0.8811 (mttp) REVERT: C 56 LEU cc_start: 0.9093 (mt) cc_final: 0.8804 (pp) REVERT: C 65 ASP cc_start: 0.8516 (t70) cc_final: 0.7878 (t0) REVERT: C 152 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8567 (tp40) REVERT: C 209 MET cc_start: 0.8493 (tpp) cc_final: 0.8198 (tpp) REVERT: C 211 ILE cc_start: 0.9568 (mp) cc_final: 0.9217 (mt) REVERT: D 44 VAL cc_start: 0.9089 (OUTLIER) cc_final: 0.8843 (t) REVERT: D 47 LYS cc_start: 0.9186 (mtmt) cc_final: 0.8920 (mtmt) REVERT: D 88 MET cc_start: 0.8101 (ttp) cc_final: 0.7851 (tmm) REVERT: D 92 LEU cc_start: 0.9295 (mt) cc_final: 0.8987 (mt) REVERT: D 197 CYS cc_start: 0.8440 (m) cc_final: 0.7756 (m) REVERT: E 80 PHE cc_start: 0.8626 (m-80) cc_final: 0.8281 (m-80) REVERT: E 170 PHE cc_start: 0.8058 (t80) cc_final: 0.7766 (t80) REVERT: E 189 ASN cc_start: 0.8849 (m-40) cc_final: 0.8451 (t0) REVERT: E 234 MET cc_start: 0.8447 (mmm) cc_final: 0.8137 (mmm) REVERT: E 309 LEU cc_start: 0.9562 (tp) cc_final: 0.9178 (tp) REVERT: E 410 MET cc_start: 0.7719 (tpt) cc_final: 0.6819 (tmm) REVERT: E 413 MET cc_start: 0.7454 (ptp) cc_final: 0.7203 (ptt) REVERT: E 546 PHE cc_start: 0.8800 (t80) cc_final: 0.8458 (t80) REVERT: E 731 MET cc_start: 0.8375 (mmm) cc_final: 0.7494 (mmm) REVERT: E 1080 LEU cc_start: 0.9270 (tp) cc_final: 0.9011 (tp) REVERT: E 1122 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9141 (mm) REVERT: E 1151 VAL cc_start: 0.9365 (m) cc_final: 0.9158 (p) REVERT: E 1191 GLN cc_start: 0.8808 (tp40) cc_final: 0.8322 (mt0) REVERT: E 1229 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7841 (tm-30) outliers start: 65 outliers final: 43 residues processed: 388 average time/residue: 0.1270 time to fit residues: 80.3466 Evaluate side-chains 360 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 314 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 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 219 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 44 VAL 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 305 LEU 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 175 LEU 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 474 VAL 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 1339 TRP 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: 4.9990 chunk 115 optimal weight: 7.9990 chunk 225 optimal weight: 0.5980 chunk 157 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 114 optimal weight: 0.3980 chunk 246 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 160 ASN C 173 GLN ** 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 = 0.3236 r_free = 0.3236 target = 0.075441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.061458 restraints weight = 88633.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.063541 restraints weight = 39742.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.064977 restraints weight = 23260.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.065945 restraints weight = 16053.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.066542 restraints weight = 12421.954| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 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 = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3264 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= 0.142 Angle : 0.657 18.435 29293 Z= 0.318 Chirality : 0.044 0.325 3463 Planarity : 0.003 0.054 3641 Dihedral : 5.951 58.880 2913 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.48 % Favored : 95.44 % Rotamer: Outliers : 2.88 % Allowed : 23.14 % Favored : 73.99 % 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: 0.08 (0.17), residues: 2658 helix: 1.12 (0.15), residues: 1322 sheet: -0.65 (0.30), residues: 313 loop : -1.08 (0.20), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E1246 TYR 0.013 0.001 TYR B 304 PHE 0.019 0.001 PHE E1182 TRP 0.017 0.001 TRP A 90 HIS 0.003 0.001 HIS E 847 Details of bonding type rmsd covalent geometry : bond 0.00313 (21550) covalent geometry : angle 0.65680 (29285) SS BOND : bond 0.00228 ( 4) SS BOND : angle 1.38945 ( 8) hydrogen bonds : bond 0.03781 ( 1038) hydrogen bonds : angle 3.94648 ( 3040) Misc. bond : bond 0.00067 ( 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 383 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 318 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9521 (tp) cc_final: 0.9143 (tp) REVERT: A 179 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8205 (mp0) REVERT: A 185 LYS cc_start: 0.8843 (mtpp) cc_final: 0.8565 (tppp) REVERT: A 197 CYS cc_start: 0.8537 (m) cc_final: 0.8316 (m) REVERT: A 288 GLU cc_start: 0.7762 (pp20) cc_final: 0.7479 (pp20) REVERT: B 169 MET cc_start: 0.8125 (ttm) cc_final: 0.7856 (ttm) REVERT: B 240 MET cc_start: 0.8920 (ttp) cc_final: 0.8353 (ttp) REVERT: B 241 GLU cc_start: 0.8388 (tp30) cc_final: 0.7970 (tp30) REVERT: B 338 LYS cc_start: 0.8938 (ttmm) cc_final: 0.8592 (ttmm) REVERT: C 47 LYS cc_start: 0.9069 (mttm) cc_final: 0.8802 (mttp) REVERT: C 56 LEU cc_start: 0.9123 (mt) cc_final: 0.8842 (pp) REVERT: C 65 ASP cc_start: 0.8587 (t70) cc_final: 0.7903 (t0) REVERT: C 152 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8282 (tp40) REVERT: C 209 MET cc_start: 0.8509 (tpp) cc_final: 0.8233 (tpp) REVERT: D 44 VAL cc_start: 0.9093 (OUTLIER) cc_final: 0.8833 (t) REVERT: D 47 LYS cc_start: 0.9184 (mtmt) cc_final: 0.8960 (mtmt) REVERT: D 92 LEU cc_start: 0.9315 (mt) cc_final: 0.8998 (mt) REVERT: D 197 CYS cc_start: 0.8468 (m) cc_final: 0.7795 (m) REVERT: E 153 ILE cc_start: 0.9358 (tp) cc_final: 0.9128 (tp) REVERT: E 170 PHE cc_start: 0.8194 (t80) cc_final: 0.7914 (t80) REVERT: E 189 ASN cc_start: 0.8853 (m-40) cc_final: 0.8448 (t0) REVERT: E 234 MET cc_start: 0.8503 (mmm) cc_final: 0.8289 (mmm) REVERT: E 309 LEU cc_start: 0.9562 (tp) cc_final: 0.9191 (tp) REVERT: E 410 MET cc_start: 0.7752 (tpt) cc_final: 0.6914 (tmm) REVERT: E 413 MET cc_start: 0.7617 (ptp) cc_final: 0.7354 (ptt) REVERT: E 546 PHE cc_start: 0.8816 (t80) cc_final: 0.8517 (t80) REVERT: E 731 MET cc_start: 0.8463 (mmm) cc_final: 0.7347 (mmm) REVERT: E 1080 LEU cc_start: 0.9298 (tp) cc_final: 0.9078 (tp) REVERT: E 1122 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9112 (mm) REVERT: E 1229 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7938 (tm-30) REVERT: E 1305 MET cc_start: 0.9000 (mmm) cc_final: 0.8748 (mmm) outliers start: 65 outliers final: 49 residues processed: 363 average time/residue: 0.1239 time to fit residues: 72.9915 Evaluate side-chains 358 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 306 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 209 MET 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 345 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 137 MET 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 C residue 349 LEU Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 44 VAL 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 305 LEU Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 34 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 175 LEU Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 365 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 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 1163 VAL 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 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: 0.7980 chunk 153 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 212 optimal weight: 8.9990 chunk 143 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 241 optimal weight: 9.9990 chunk 236 optimal weight: 8.9990 chunk 180 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN C 152 GLN ** E 73 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.075919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.061746 restraints weight = 93169.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.063899 restraints weight = 41156.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.065369 restraints weight = 23895.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.066367 restraints weight = 16379.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.066977 restraints weight = 12600.371| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 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 = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3371 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 : 0.654 19.684 29293 Z= 0.314 Chirality : 0.044 0.349 3463 Planarity : 0.003 0.054 3641 Dihedral : 5.914 58.629 2913 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.48 % Favored : 95.44 % Rotamer: Outliers : 2.44 % Allowed : 23.79 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.19 (0.17), residues: 2658 helix: 1.20 (0.15), residues: 1323 sheet: -0.58 (0.30), residues: 304 loop : -1.02 (0.20), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1246 TYR 0.021 0.001 TYR E 231 PHE 0.019 0.001 PHE E1182 TRP 0.018 0.001 TRP A 90 HIS 0.003 0.001 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00274 (21550) covalent geometry : angle 0.65336 (29285) SS BOND : bond 0.00170 ( 4) SS BOND : angle 1.23031 ( 8) hydrogen bonds : bond 0.03756 ( 1038) hydrogen bonds : angle 3.91214 ( 3040) Misc. bond : bond 0.00065 ( 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 374 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 319 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9510 (tp) cc_final: 0.9143 (tp) REVERT: A 179 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8203 (mp0) REVERT: A 185 LYS cc_start: 0.8837 (mtpp) cc_final: 0.8558 (tppp) REVERT: A 197 CYS cc_start: 0.8530 (m) cc_final: 0.8286 (m) REVERT: A 288 GLU cc_start: 0.7747 (pp20) cc_final: 0.7468 (pp20) REVERT: B 169 MET cc_start: 0.8149 (ttm) cc_final: 0.7872 (ttm) REVERT: B 240 MET cc_start: 0.8903 (ttp) cc_final: 0.8288 (ttp) REVERT: B 338 LYS cc_start: 0.8926 (ttmm) cc_final: 0.8586 (ttmm) REVERT: C 47 LYS cc_start: 0.9060 (mttm) cc_final: 0.8790 (mttp) REVERT: C 56 LEU cc_start: 0.9078 (mt) cc_final: 0.8814 (pp) REVERT: C 65 ASP cc_start: 0.8449 (t70) cc_final: 0.7779 (t0) REVERT: C 152 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.8310 (tp40) REVERT: C 209 MET cc_start: 0.8475 (tpp) cc_final: 0.8183 (tpp) REVERT: C 211 ILE cc_start: 0.9542 (mp) cc_final: 0.9170 (mt) REVERT: D 44 VAL cc_start: 0.9062 (OUTLIER) cc_final: 0.8808 (t) REVERT: D 47 LYS cc_start: 0.9169 (mtmt) cc_final: 0.8945 (mtmt) REVERT: D 92 LEU cc_start: 0.9326 (mt) cc_final: 0.8988 (mt) REVERT: D 197 CYS cc_start: 0.8440 (m) cc_final: 0.7770 (m) REVERT: E 153 ILE cc_start: 0.9352 (tp) cc_final: 0.9123 (tp) REVERT: E 170 PHE cc_start: 0.8166 (t80) cc_final: 0.7913 (t80) REVERT: E 189 ASN cc_start: 0.8850 (m-40) cc_final: 0.8448 (t0) REVERT: E 309 LEU cc_start: 0.9555 (tp) cc_final: 0.9194 (tp) REVERT: E 410 MET cc_start: 0.7527 (tpt) cc_final: 0.6877 (tmm) REVERT: E 413 MET cc_start: 0.7565 (ptp) cc_final: 0.7337 (ptt) REVERT: E 442 MET cc_start: 0.7384 (ttt) cc_final: 0.7102 (tmm) REVERT: E 546 PHE cc_start: 0.8815 (t80) cc_final: 0.8532 (t80) REVERT: E 1080 LEU cc_start: 0.9309 (tp) cc_final: 0.9107 (tp) REVERT: E 1122 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9104 (mm) REVERT: E 1191 GLN cc_start: 0.8819 (tp40) cc_final: 0.8331 (mt0) REVERT: E 1229 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7881 (tm-30) REVERT: E 1305 MET cc_start: 0.8975 (mmm) cc_final: 0.8654 (mmm) outliers start: 55 outliers final: 43 residues processed: 364 average time/residue: 0.1259 time to fit residues: 74.0379 Evaluate side-chains 360 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 314 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 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 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 115 HIS Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 175 HIS 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 113 MET Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 365 LEU 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 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 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 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: 3.9990 chunk 112 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 230 optimal weight: 2.9990 chunk 255 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 147 optimal weight: 0.1980 chunk 84 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 160 ASN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN ** E 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.076451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.062175 restraints weight = 101376.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.064403 restraints weight = 42900.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.065920 restraints weight = 24378.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.066875 restraints weight = 16484.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.067624 restraints weight = 12667.215| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3469 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= 0.120 Angle : 0.663 19.568 29293 Z= 0.316 Chirality : 0.045 0.393 3463 Planarity : 0.003 0.054 3641 Dihedral : 5.863 58.919 2913 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.33 % Favored : 95.63 % Rotamer: Outliers : 2.22 % Allowed : 24.40 % Favored : 73.38 % 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: 0.24 (0.17), residues: 2658 helix: 1.22 (0.15), residues: 1323 sheet: -0.54 (0.30), residues: 304 loop : -0.97 (0.20), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E1246 TYR 0.028 0.001 TYR E1159 PHE 0.019 0.001 PHE E1182 TRP 0.018 0.001 TRP A 90 HIS 0.003 0.000 HIS E 847 Details of bonding type rmsd covalent geometry : bond 0.00262 (21550) covalent geometry : angle 0.66277 (29285) SS BOND : bond 0.00189 ( 4) SS BOND : angle 1.16107 ( 8) hydrogen bonds : bond 0.03760 ( 1038) hydrogen bonds : angle 3.90485 ( 3040) Misc. bond : bond 0.00066 ( 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 371 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 321 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.9400 (ttpp) cc_final: 0.9134 (tppt) REVERT: A 74 ILE cc_start: 0.9503 (tp) cc_final: 0.9137 (tp) REVERT: A 179 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8209 (mp0) REVERT: A 197 CYS cc_start: 0.8537 (m) cc_final: 0.8291 (m) REVERT: A 288 GLU cc_start: 0.7710 (pp20) cc_final: 0.7329 (pp20) REVERT: B 169 MET cc_start: 0.8148 (ttm) cc_final: 0.7867 (ttm) REVERT: B 222 LYS cc_start: 0.9012 (tptm) cc_final: 0.8794 (tptp) REVERT: B 240 MET cc_start: 0.8883 (ttp) cc_final: 0.8194 (ttt) REVERT: B 241 GLU cc_start: 0.8399 (tp30) cc_final: 0.8022 (tp30) REVERT: B 338 LYS cc_start: 0.9037 (ttmm) cc_final: 0.8640 (ttmm) REVERT: C 47 LYS cc_start: 0.9076 (mttm) cc_final: 0.8808 (mttp) REVERT: C 56 LEU cc_start: 0.9057 (mt) cc_final: 0.8801 (pp) REVERT: C 65 ASP cc_start: 0.8517 (t70) cc_final: 0.7874 (t0) REVERT: C 152 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8593 (tp40) REVERT: C 209 MET cc_start: 0.8462 (tpp) cc_final: 0.8154 (tpp) REVERT: C 211 ILE cc_start: 0.9530 (mp) cc_final: 0.9152 (mt) REVERT: D 44 VAL cc_start: 0.9034 (OUTLIER) cc_final: 0.8800 (t) REVERT: D 47 LYS cc_start: 0.9165 (mtmt) cc_final: 0.8926 (mtmt) REVERT: D 92 LEU cc_start: 0.9318 (mt) cc_final: 0.8969 (mt) REVERT: D 197 CYS cc_start: 0.8424 (m) cc_final: 0.7760 (m) REVERT: E 153 ILE cc_start: 0.9339 (tp) cc_final: 0.9109 (tp) REVERT: E 170 PHE cc_start: 0.8137 (t80) cc_final: 0.7906 (t80) REVERT: E 189 ASN cc_start: 0.8834 (m-40) cc_final: 0.8428 (t0) REVERT: E 309 LEU cc_start: 0.9554 (tp) cc_final: 0.9194 (tp) REVERT: E 410 MET cc_start: 0.7490 (tpt) cc_final: 0.6848 (tmm) REVERT: E 413 MET cc_start: 0.7691 (ptp) cc_final: 0.7469 (ptt) REVERT: E 442 MET cc_start: 0.7402 (ttt) cc_final: 0.7104 (tmm) REVERT: E 546 PHE cc_start: 0.8799 (t80) cc_final: 0.8528 (t80) REVERT: E 731 MET cc_start: 0.8325 (mmm) cc_final: 0.7776 (mmm) REVERT: E 1080 LEU cc_start: 0.9274 (tp) cc_final: 0.9056 (tp) REVERT: E 1122 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9024 (mm) REVERT: E 1191 GLN cc_start: 0.8850 (tp40) cc_final: 0.8289 (mt0) REVERT: E 1229 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7879 (tm-30) REVERT: E 1236 ILE cc_start: 0.9382 (tp) cc_final: 0.9156 (tp) REVERT: E 1287 TYR cc_start: 0.8536 (m-80) cc_final: 0.8158 (m-10) REVERT: E 1305 MET cc_start: 0.8990 (mmm) cc_final: 0.8648 (mmm) outliers start: 50 outliers final: 42 residues processed: 361 average time/residue: 0.1239 time to fit residues: 72.2230 Evaluate side-chains 358 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 313 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 137 MET 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 219 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain D residue 44 VAL 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 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 248 LEU Chi-restraints excluded: chain E residue 365 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 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 1122 LEU 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 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: 5.9990 chunk 265 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 194 optimal weight: 0.0170 chunk 155 optimal weight: 0.9980 chunk 133 optimal weight: 0.6980 chunk 119 optimal weight: 0.0980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN D 173 GLN D 175 HIS ** 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 = 0.3274 r_free = 0.3274 target = 0.077341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.062921 restraints weight = 102090.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.065174 restraints weight = 43325.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.066715 restraints weight = 24559.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.067748 restraints weight = 16583.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.068472 restraints weight = 12625.451| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 21555 Z= 0.114 Angle : 0.672 19.519 29293 Z= 0.318 Chirality : 0.045 0.367 3463 Planarity : 0.003 0.055 3641 Dihedral : 5.773 60.790 2912 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.26 % Favored : 95.67 % Rotamer: Outliers : 2.09 % Allowed : 24.71 % 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: 0.30 (0.17), residues: 2658 helix: 1.32 (0.15), residues: 1311 sheet: -0.48 (0.30), residues: 304 loop : -1.00 (0.20), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1246 TYR 0.026 0.001 TYR E1159 PHE 0.021 0.001 PHE B 117 TRP 0.020 0.001 TRP A 90 HIS 0.002 0.000 HIS E1024 Details of bonding type rmsd covalent geometry : bond 0.00247 (21550) covalent geometry : angle 0.67169 (29285) SS BOND : bond 0.00188 ( 4) SS BOND : angle 1.06662 ( 8) hydrogen bonds : bond 0.03692 ( 1038) hydrogen bonds : angle 3.89960 ( 3040) Misc. bond : bond 0.00069 ( 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 379 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 332 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.9399 (ttpp) cc_final: 0.9136 (tppt) REVERT: A 48 ASN cc_start: 0.8592 (t0) cc_final: 0.8008 (t0) REVERT: A 74 ILE cc_start: 0.9489 (tp) cc_final: 0.9131 (tp) REVERT: A 147 LEU cc_start: 0.9265 (tt) cc_final: 0.8745 (tp) REVERT: A 179 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8201 (mp0) REVERT: A 197 CYS cc_start: 0.8508 (m) cc_final: 0.8266 (m) REVERT: A 288 GLU cc_start: 0.7699 (pp20) cc_final: 0.7343 (pp20) REVERT: B 169 MET cc_start: 0.8130 (ttm) cc_final: 0.7853 (ttm) REVERT: B 222 LYS cc_start: 0.8988 (tptm) cc_final: 0.8767 (tptp) REVERT: B 240 MET cc_start: 0.8854 (ttp) cc_final: 0.8141 (ttt) REVERT: B 241 GLU cc_start: 0.8370 (tp30) cc_final: 0.7993 (tp30) REVERT: B 338 LYS cc_start: 0.9025 (ttmm) cc_final: 0.8626 (ttmm) REVERT: C 47 LYS cc_start: 0.8960 (mttm) cc_final: 0.8691 (mttp) REVERT: C 56 LEU cc_start: 0.9005 (mt) cc_final: 0.8754 (pp) REVERT: C 65 ASP cc_start: 0.8452 (t70) cc_final: 0.7710 (t0) REVERT: C 152 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8344 (tp40) REVERT: C 160 ASN cc_start: 0.8879 (m-40) cc_final: 0.8672 (m-40) REVERT: C 240 MET cc_start: 0.7650 (tmm) cc_final: 0.7060 (tmm) REVERT: D 44 VAL cc_start: 0.8987 (OUTLIER) cc_final: 0.8781 (t) REVERT: D 47 LYS cc_start: 0.9142 (mtmt) cc_final: 0.8898 (mtmt) REVERT: D 92 LEU cc_start: 0.9300 (mt) cc_final: 0.8952 (mt) REVERT: D 197 CYS cc_start: 0.8406 (m) cc_final: 0.7756 (m) REVERT: E 80 PHE cc_start: 0.8539 (m-80) cc_final: 0.8059 (m-80) REVERT: E 153 ILE cc_start: 0.9311 (tp) cc_final: 0.9091 (tp) REVERT: E 170 PHE cc_start: 0.8119 (t80) cc_final: 0.7886 (t80) REVERT: E 189 ASN cc_start: 0.8819 (m-40) cc_final: 0.8408 (t0) REVERT: E 309 LEU cc_start: 0.9519 (tp) cc_final: 0.9123 (tp) REVERT: E 410 MET cc_start: 0.7468 (tpt) cc_final: 0.6791 (tmm) REVERT: E 442 MET cc_start: 0.7383 (ttt) cc_final: 0.7079 (tmm) REVERT: E 546 PHE cc_start: 0.8771 (t80) cc_final: 0.8506 (t80) REVERT: E 731 MET cc_start: 0.8263 (mmm) cc_final: 0.7696 (mmm) REVERT: E 1080 LEU cc_start: 0.9245 (tp) cc_final: 0.9027 (tp) REVERT: E 1122 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9032 (mm) REVERT: E 1191 GLN cc_start: 0.8842 (tp40) cc_final: 0.8264 (mt0) REVERT: E 1229 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7884 (tm-30) REVERT: E 1287 TYR cc_start: 0.8533 (m-80) cc_final: 0.8143 (m-10) REVERT: E 1305 MET cc_start: 0.8982 (mmm) cc_final: 0.8766 (mmm) outliers start: 47 outliers final: 41 residues processed: 371 average time/residue: 0.1244 time to fit residues: 74.3794 Evaluate side-chains 361 residues out of total 2315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 317 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 137 MET 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 219 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 88 MET 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 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 365 LEU 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 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 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 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: 2.9990 chunk 72 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 8 optimal weight: 0.0000 chunk 130 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 262 optimal weight: 0.7980 chunk 213 optimal weight: 8.9990 chunk 249 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 264 ASN B 160 ASN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 846 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.077287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.062456 restraints weight = 113352.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.064771 restraints weight = 46414.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.066370 restraints weight = 25979.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.067438 restraints weight = 17417.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.068162 restraints weight = 13196.998| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3638 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= 0.123 Angle : 0.688 19.250 29293 Z= 0.325 Chirality : 0.045 0.368 3463 Planarity : 0.003 0.055 3641 Dihedral : 5.734 59.765 2912 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.18 % Allowed : 24.75 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.17), residues: 2658 helix: 1.33 (0.15), residues: 1312 sheet: -0.48 (0.30), residues: 304 loop : -0.96 (0.20), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1246 TYR 0.027 0.001 TYR E1159 PHE 0.020 0.001 PHE E1182 TRP 0.023 0.001 TRP A 90 HIS 0.013 0.001 HIS D 175 Details of bonding type rmsd covalent geometry : bond 0.00273 (21550) covalent geometry : angle 0.68793 (29285) SS BOND : bond 0.00191 ( 4) SS BOND : angle 1.12473 ( 8) hydrogen bonds : bond 0.03712 ( 1038) hydrogen bonds : angle 3.91783 ( 3040) Misc. bond : bond 0.00069 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3513.38 seconds wall clock time: 61 minutes 30.51 seconds (3690.51 seconds total)