Starting phenix.real_space_refine on Sat Jul 4 11:39:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7u2x_26321/07_2026/7u2x_26321.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u2x_26321/07_2026/7u2x_26321.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7u2x_26321/07_2026/7u2x_26321.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7u2x_26321/07_2026/7u2x_26321.cif" model { file = "/net/cci-nas-00/data/ceres_data/7u2x_26321/07_2026/7u2x_26321.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u2x_26321/07_2026/7u2x_26321.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u2x_26321/07_2026/7u2x_26321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u2x_26321/07_2026/7u2x_26321.map" } resolution = 4.1 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians P 17 5.49 5 S 76 5.16 5 C 12633 2.51 5 N 3345 2.21 5 O 3409 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19480 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2381 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 14, 'TRANS': 333} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 455 Unresolved non-hydrogen dihedrals: 293 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'ARG:plan': 13, 'GLU:plan': 19, 'TYR:plan': 1, 'ASP:plan': 12, 'ASN:plan1': 2, 'GLN:plan1': 4, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 221 Chain: "E" Number of atoms: 9709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1427, 9709 Classifications: {'peptide': 1427} Incomplete info: {'truncation_to_alanine': 466} Link IDs: {'PTRANS': 48, 'TRANS': 1378} Chain breaks: 6 Unresolved non-hydrogen bonds: 1596 Unresolved non-hydrogen angles: 1992 Unresolved non-hydrogen dihedrals: 1277 Unresolved non-hydrogen chiralities: 165 Planarities with less than four sites: {'GLU:plan': 46, 'ASP:plan': 40, 'PHE:plan': 21, 'GLN:plan1': 28, 'HIS:plan': 6, 'ARG:plan': 32, 'ASN:plan1': 12, 'TRP:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 807 Chain: "B" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2277 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 13, 'TRANS': 312} Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ARG:plan': 6, 'ASN:plan1': 3, 'GLU:plan': 14, 'GLN:plan1': 6, 'ASP:plan': 13, 'HIS:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 185 Chain: "C" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2282 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 13, 'TRANS': 312} Unresolved non-hydrogen bonds: 286 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ARG:plan': 7, 'ASN:plan1': 2, 'GLU:plan': 14, 'GLN:plan1': 5, 'PHE:plan': 1, 'ASP:plan': 13, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 182 Chain: "D" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2296 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 13, 'TRANS': 312} Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 338 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ARG:plan': 8, 'ASN:plan1': 2, 'GLU:plan': 13, 'GLN:plan1': 5, 'PHE:plan': 1, 'ASP:plan': 13, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 178 Chain: "A" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 132 Unusual residues: {'POV': 1, 'PTY': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 231 Unusual residues: {'ATP': 1, 'NAG': 1, 'POV': 1, 'PTY': 3} Classifications: {'peptide': 1, 'undetermined': 6} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 68 Unusual residues: {'POV': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 68 Unusual residues: {'POV': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 4.85, per 1000 atoms: 0.25 Number of scatterers: 19480 At special positions: 0 Unit cell: (165.87, 109.44, 148.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 P 17 15.00 O 3409 8.00 N 3345 7.00 C 12633 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " 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=0, symmetry=0 Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 865.5 milliseconds 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5188 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 32 sheets defined 52.9% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 55 through 66 removed outlier: 3.809A pdb=" N VAL A 59 " --> pdb=" O PHE A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 97 Processing helix chain 'A' and resid 116 through 129 Processing helix chain 'A' and resid 142 through 175 removed outlier: 4.222A pdb=" N HIS A 175 " --> pdb=" O THR A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 removed outlier: 3.847A pdb=" N ASP A 269 " --> pdb=" O PRO A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 345 through 356 Processing helix chain 'E' and resid 8 through 16 removed outlier: 3.845A pdb=" N HIS E 11 " --> pdb=" O THR E 8 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ALA E 14 " --> pdb=" O HIS E 11 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR E 15 " --> pdb=" O SER E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 23 removed outlier: 3.558A pdb=" N ASN E 23 " --> pdb=" O GLY E 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 20 through 23' Processing helix chain 'E' and resid 24 through 49 removed outlier: 3.747A pdb=" N VAL E 33 " --> pdb=" O ASP E 29 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) Proline residue: E 35 - end of helix Proline residue: E 45 - end of helix Processing helix chain 'E' and resid 71 through 96 removed outlier: 3.748A pdb=" N TRP E 75 " --> pdb=" O HIS E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 106 Processing helix chain 'E' and resid 107 through 130 removed outlier: 4.288A pdb=" N SER E 130 " --> pdb=" O ASN E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 135 Processing helix chain 'E' and resid 136 through 160 removed outlier: 3.649A pdb=" N ILE E 141 " --> pdb=" O ILE E 137 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TYR E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS E 150 " --> pdb=" O ALA E 146 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE E 157 " --> pdb=" O LYS E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 194 removed outlier: 3.516A pdb=" N CYS E 170 " --> pdb=" O GLN E 166 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE E 177 " --> pdb=" O GLY E 173 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL E 185 " --> pdb=" O MET E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 212 removed outlier: 4.004A pdb=" N ASP E 212 " --> pdb=" O GLU E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 230 Processing helix chain 'E' and resid 231 through 243 removed outlier: 4.271A pdb=" N ALA E 235 " --> pdb=" O TRP E 231 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE E 236 " --> pdb=" O TRP E 232 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS E 241 " --> pdb=" O ILE E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 257 Processing helix chain 'E' and resid 258 through 276 Processing helix chain 'E' and resid 283 through 328 removed outlier: 6.118A pdb=" N ARG E 297 " --> pdb=" O HIS E 293 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ARG E 298 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA E 315 " --> pdb=" O LEU E 311 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY E 316 " --> pdb=" O LEU E 312 " (cutoff:3.500A) Proline residue: E 317 - end of helix Processing helix chain 'E' and resid 347 through 352 Processing helix chain 'E' and resid 354 through 401 removed outlier: 3.707A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 411 removed outlier: 3.681A pdb=" N GLU E 411 " --> pdb=" O LEU E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 457 Proline residue: E 436 - end of helix Proline residue: E 442 - end of helix Processing helix chain 'E' and resid 458 through 505 removed outlier: 4.139A pdb=" N ILE E 462 " --> pdb=" O VAL E 458 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA E 465 " --> pdb=" O LEU E 461 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL E 466 " --> pdb=" O ILE E 462 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE E 467 " --> pdb=" O GLY E 463 " (cutoff:3.500A) Proline residue: E 472 - end of helix removed outlier: 3.864A pdb=" N GLY E 505 " --> pdb=" O GLU E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 513 Processing helix chain 'E' and resid 514 through 564 removed outlier: 3.581A pdb=" N PHE E 518 " --> pdb=" O TRP E 514 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER E 532 " --> pdb=" O LYS E 528 " (cutoff:3.500A) Proline residue: E 551 - end of helix Processing helix chain 'E' and resid 572 through 615 removed outlier: 3.723A pdb=" N THR E 588 " --> pdb=" O HIS E 584 " (cutoff:3.500A) Proline residue: E 589 - end of helix removed outlier: 4.786A pdb=" N SER E 594 " --> pdb=" O LEU E 590 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N SER E 595 " --> pdb=" O PHE E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 718 through 728 removed outlier: 3.626A pdb=" N LEU E 722 " --> pdb=" O GLY E 718 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU E 723 " --> pdb=" O LYS E 719 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY E 728 " --> pdb=" O LEU E 724 " (cutoff:3.500A) Processing helix chain 'E' and resid 783 through 790 Processing helix chain 'E' and resid 795 through 806 Processing helix chain 'E' and resid 808 through 815 Processing helix chain 'E' and resid 831 through 847 removed outlier: 4.229A pdb=" N GLN E 847 " --> pdb=" O ALA E 843 " (cutoff:3.500A) Processing helix chain 'E' and resid 856 through 860 removed outlier: 4.058A pdb=" N ALA E 859 " --> pdb=" O PRO E 856 " (cutoff:3.500A) Processing helix chain 'E' and resid 864 through 880 removed outlier: 3.872A pdb=" N LEU E 868 " --> pdb=" O LEU E 864 " (cutoff:3.500A) Processing helix chain 'E' and resid 916 through 919 removed outlier: 3.729A pdb=" N ARG E 919 " --> pdb=" O ASP E 916 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 916 through 919' Processing helix chain 'E' and resid 920 through 931 removed outlier: 3.733A pdb=" N LEU E 924 " --> pdb=" O SER E 920 " (cutoff:3.500A) Processing helix chain 'E' and resid 987 through 993 Processing helix chain 'E' and resid 996 through 1009 removed outlier: 4.077A pdb=" N ALA E1000 " --> pdb=" O ILE E 996 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR E1002 " --> pdb=" O TRP E 998 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS E1003 " --> pdb=" O ARG E 999 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY E1009 " --> pdb=" O LEU E1005 " (cutoff:3.500A) Processing helix chain 'E' and resid 1010 through 1042 removed outlier: 3.802A pdb=" N SER E1014 " --> pdb=" O ILE E1010 " (cutoff:3.500A) Processing helix chain 'E' and resid 1064 through 1107 removed outlier: 3.591A pdb=" N ARG E1099 " --> pdb=" O LYS E1095 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N SER E1100 " --> pdb=" O ARG E1096 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU E1107 " --> pdb=" O ASN E1103 " (cutoff:3.500A) Processing helix chain 'E' and resid 1109 through 1116 removed outlier: 3.713A pdb=" N PHE E1113 " --> pdb=" O PRO E1109 " (cutoff:3.500A) Processing helix chain 'E' and resid 1117 through 1135 removed outlier: 3.815A pdb=" N ILE E1121 " --> pdb=" O PRO E1117 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ASP E1128 " --> pdb=" O ARG E1124 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N CYS E1129 " --> pdb=" O PHE E1125 " (cutoff:3.500A) Processing helix chain 'E' and resid 1135 through 1161 removed outlier: 4.119A pdb=" N ILE E1157 " --> pdb=" O ALA E1153 " (cutoff:3.500A) Processing helix chain 'E' and resid 1161 through 1210 removed outlier: 3.658A pdb=" N LEU E1165 " --> pdb=" O THR E1161 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU E1169 " --> pdb=" O LEU E1165 " (cutoff:3.500A) Proline residue: E1170 - end of helix removed outlier: 3.981A pdb=" N ASP E1188 " --> pdb=" O VAL E1184 " (cutoff:3.500A) Proline residue: E1199 - end of helix Processing helix chain 'E' and resid 1210 through 1217 Processing helix chain 'E' and resid 1219 through 1273 removed outlier: 3.645A pdb=" N ALA E1237 " --> pdb=" O SER E1233 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS E1273 " --> pdb=" O SER E1269 " (cutoff:3.500A) Processing helix chain 'E' and resid 1277 through 1319 removed outlier: 3.625A pdb=" N MET E1290 " --> pdb=" O THR E1286 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER E1292 " --> pdb=" O ALA E1288 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASN E1293 " --> pdb=" O LEU E1289 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY E1310 " --> pdb=" O GLU E1306 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA E1311 " --> pdb=" O ILE E1307 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL E1312 " --> pdb=" O GLN E1308 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU E1318 " --> pdb=" O ARG E1314 " (cutoff:3.500A) Processing helix chain 'E' and resid 1386 through 1392 removed outlier: 3.868A pdb=" N LEU E1390 " --> pdb=" O SER E1386 " (cutoff:3.500A) Processing helix chain 'E' and resid 1414 through 1421 removed outlier: 4.488A pdb=" N ARG E1421 " --> pdb=" O THR E1417 " (cutoff:3.500A) Processing helix chain 'E' and resid 1435 through 1441 Processing helix chain 'E' and resid 1448 through 1459 removed outlier: 3.780A pdb=" N GLN E1459 " --> pdb=" O LEU E1455 " (cutoff:3.500A) Processing helix chain 'E' and resid 1460 through 1467 removed outlier: 3.572A pdb=" N VAL E1464 " --> pdb=" O LEU E1460 " (cutoff:3.500A) Processing helix chain 'E' and resid 1485 through 1499 removed outlier: 4.029A pdb=" N LEU E1489 " --> pdb=" O GLY E1485 " (cutoff:3.500A) Processing helix chain 'E' and resid 1512 through 1530 removed outlier: 3.906A pdb=" N ASN E1518 " --> pdb=" O MET E1514 " (cutoff:3.500A) Processing helix chain 'E' and resid 1539 through 1545 removed outlier: 4.146A pdb=" N ILE E1543 " --> pdb=" O ARG E1539 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER E1545 " --> pdb=" O HIS E1541 " (cutoff:3.500A) Processing helix chain 'E' and resid 1562 through 1566 removed outlier: 3.974A pdb=" N THR E1565 " --> pdb=" O LYS E1562 " (cutoff:3.500A) Processing helix chain 'E' and resid 1572 through 1578 Processing helix chain 'B' and resid 55 through 65 removed outlier: 3.795A pdb=" N VAL B 59 " --> pdb=" O PHE B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 97 Processing helix chain 'B' and resid 116 through 129 Processing helix chain 'B' and resid 142 through 177 removed outlier: 4.132A pdb=" N ARG B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B 177 " --> pdb=" O GLN B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 276 removed outlier: 3.964A pdb=" N HIS B 276 " --> pdb=" O SER B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 333 Processing helix chain 'B' and resid 345 through 356 Processing helix chain 'C' and resid 56 through 65 removed outlier: 3.813A pdb=" N PHE C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 97 removed outlier: 3.790A pdb=" N HIS C 97 " --> pdb=" O ILE C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 129 Processing helix chain 'C' and resid 142 through 176 removed outlier: 3.741A pdb=" N ILE C 146 " --> pdb=" O CYS C 142 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS C 175 " --> pdb=" O THR C 171 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARG C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 270 removed outlier: 3.658A pdb=" N TYR C 268 " --> pdb=" O SER C 265 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP C 269 " --> pdb=" O PRO C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 276 removed outlier: 3.881A pdb=" N HIS C 276 " --> pdb=" O SER C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 356 Processing helix chain 'D' and resid 55 through 65 removed outlier: 3.876A pdb=" N VAL D 59 " --> pdb=" O PHE D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 97 Processing helix chain 'D' and resid 116 through 129 Processing helix chain 'D' and resid 142 through 174 removed outlier: 3.503A pdb=" N ILE D 146 " --> pdb=" O CYS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 265 through 270 removed outlier: 4.257A pdb=" N ASP D 269 " --> pdb=" O PRO D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 333 No H-bonds generated for 'chain 'D' and resid 331 through 333' Processing helix chain 'D' and resid 345 through 356 Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 183 removed outlier: 3.671A pdb=" N VAL A 202 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 259 through 260 removed outlier: 6.202A pdb=" N ALA A 187 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 234 through 238 removed outlier: 4.297A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N SER A 212 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N VAL A 290 " --> pdb=" O SER A 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 248 through 249 removed outlier: 3.714A pdb=" N ALA A 213 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N SER A 212 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N VAL A 290 " --> pdb=" O SER A 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 313 through 315 Processing sheet with id=AA6, first strand: chain 'A' and resid 319 through 321 Processing sheet with id=AA7, first strand: chain 'E' and resid 339 through 340 removed outlier: 3.547A pdb=" N VAL E 343 " --> pdb=" O PHE E 340 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 679 through 681 Processing sheet with id=AA9, first strand: chain 'E' and resid 685 through 687 removed outlier: 6.832A pdb=" N PHE E 685 " --> pdb=" O VAL E 733 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 708 through 709 removed outlier: 6.760A pdb=" N THR E 709 " --> pdb=" O LEU E 886 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL E 887 " --> pdb=" O LEU E 853 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ALA E 771 " --> pdb=" O PHE E 852 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ASP E 854 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 1345 through 1347 Processing sheet with id=AB3, first strand: chain 'E' and resid 1351 through 1352 removed outlier: 4.003A pdb=" N LYS E1363 " --> pdb=" O VAL E1352 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 1535 through 1536 removed outlier: 6.367A pdb=" N ILE E1375 " --> pdb=" O THR E1535 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 1552 through 1553 Processing sheet with id=AB6, first strand: chain 'B' and resid 45 through 47 removed outlier: 6.808A pdb=" N ALA B 45 " --> pdb=" O VAL C 328 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 182 through 183 Processing sheet with id=AB8, first strand: chain 'B' and resid 182 through 183 removed outlier: 6.511A pdb=" N ALA B 187 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 230 through 238 removed outlier: 4.066A pdb=" N LEU B 233 " --> pdb=" O ARG B 221 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ARG B 221 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN B 235 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL B 219 " --> pdb=" O GLN B 235 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ASP B 237 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N MET B 217 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N SER B 212 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N VAL B 290 " --> pdb=" O SER B 212 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE B 296 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 230 through 238 removed outlier: 4.066A pdb=" N LEU B 233 " --> pdb=" O ARG B 221 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ARG B 221 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN B 235 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL B 219 " --> pdb=" O GLN B 235 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ASP B 237 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N MET B 217 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N SER B 212 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N VAL B 290 " --> pdb=" O SER B 212 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 313 through 315 Processing sheet with id=AC3, first strand: chain 'B' and resid 319 through 320 Processing sheet with id=AC4, first strand: chain 'C' and resid 44 through 47 removed outlier: 6.899A pdb=" N ALA C 45 " --> pdb=" O VAL D 328 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AC6, first strand: chain 'C' and resid 181 through 183 removed outlier: 6.949A pdb=" N ALA C 187 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 230 through 238 removed outlier: 4.733A pdb=" N LEU C 233 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ARG C 221 " --> pdb=" O LEU C 233 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN C 235 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL C 219 " --> pdb=" O GLN C 235 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASP C 237 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N MET C 217 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA C 213 " --> pdb=" O ILE C 249 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 230 through 238 removed outlier: 4.733A pdb=" N LEU C 233 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ARG C 221 " --> pdb=" O LEU C 233 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN C 235 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL C 219 " --> pdb=" O GLN C 235 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASP C 237 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N MET C 217 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N SER C 212 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N VAL C 290 " --> pdb=" O SER C 212 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR C 214 " --> pdb=" O GLU C 288 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 313 through 315 Processing sheet with id=AD1, first strand: chain 'D' and resid 182 through 183 Processing sheet with id=AD2, first strand: chain 'D' and resid 188 through 192 Processing sheet with id=AD3, first strand: chain 'D' and resid 210 through 211 Processing sheet with id=AD4, first strand: chain 'D' and resid 230 through 238 removed outlier: 4.624A pdb=" N LEU D 233 " --> pdb=" O ARG D 221 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ARG D 221 " --> pdb=" O LEU D 233 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN D 235 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL D 219 " --> pdb=" O GLN D 235 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ASP D 237 " --> pdb=" O MET D 217 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N MET D 217 " --> pdb=" O ASP D 237 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 313 through 315 1195 hydrogen bonds defined for protein. 3444 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: 4.98 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3170 1.32 - 1.44: 5196 1.44 - 1.57: 11369 1.57 - 1.69: 33 1.69 - 1.81: 116 Bond restraints: 19884 Sorted by residual: bond pdb=" C VAL C 252 " pdb=" N ALA C 253 " ideal model delta sigma weight residual 1.333 1.260 0.073 2.74e-02 1.33e+03 7.06e+00 bond pdb=" C LEU E 894 " pdb=" N PRO E 895 " ideal model delta sigma weight residual 1.331 1.346 -0.014 7.90e-03 1.60e+04 3.15e+00 bond pdb=" C GLY B 289 " pdb=" N VAL B 290 " ideal model delta sigma weight residual 1.334 1.312 0.022 1.29e-02 6.01e+03 2.80e+00 bond pdb=" CA GLY E 818 " pdb=" C GLY E 818 " ideal model delta sigma weight residual 1.530 1.514 0.017 1.04e-02 9.25e+03 2.58e+00 bond pdb=" CB TRP A 91 " pdb=" CG TRP A 91 " ideal model delta sigma weight residual 1.498 1.449 0.049 3.10e-02 1.04e+03 2.46e+00 ... (remaining 19879 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 26561 1.74 - 3.48: 578 3.48 - 5.22: 79 5.22 - 6.96: 13 6.96 - 8.70: 3 Bond angle restraints: 27234 Sorted by residual: angle pdb=" N GLY E 818 " pdb=" CA GLY E 818 " pdb=" C GLY E 818 " ideal model delta sigma weight residual 111.67 115.31 -3.64 9.20e-01 1.18e+00 1.56e+01 angle pdb=" N ILE E1475 " pdb=" CA ILE E1475 " pdb=" C ILE E1475 " ideal model delta sigma weight residual 106.21 110.10 -3.89 1.07e+00 8.73e-01 1.32e+01 angle pdb=" C ILE E 550 " pdb=" CA ILE E 550 " pdb=" CB ILE E 550 " ideal model delta sigma weight residual 114.35 110.94 3.41 1.06e+00 8.90e-01 1.04e+01 angle pdb=" N VAL B 244 " pdb=" CA VAL B 244 " pdb=" C VAL B 244 " ideal model delta sigma weight residual 112.98 108.96 4.02 1.25e+00 6.40e-01 1.03e+01 angle pdb=" C LEU E 174 " pdb=" N LEU E 175 " pdb=" CA LEU E 175 " ideal model delta sigma weight residual 121.58 115.73 5.85 1.95e+00 2.63e-01 9.01e+00 ... (remaining 27229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.17: 11070 24.17 - 48.33: 382 48.33 - 72.50: 41 72.50 - 96.66: 7 96.66 - 120.83: 4 Dihedral angle restraints: 11504 sinusoidal: 3522 harmonic: 7982 Sorted by residual: dihedral pdb=" C3 PTY E1602 " pdb=" O11 PTY E1602 " pdb=" P1 PTY E1602 " pdb=" O12 PTY E1602 " ideal model delta sinusoidal sigma weight residual -59.77 61.06 -120.83 1 3.00e+01 1.11e-03 1.61e+01 dihedral pdb=" CA GLY E 706 " pdb=" C GLY E 706 " pdb=" N GLN E 707 " pdb=" CA GLN E 707 " ideal model delta harmonic sigma weight residual 180.00 -160.49 -19.51 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" C31 P5S E1604 " pdb=" C32 P5S E1604 " pdb=" C33 P5S E1604 " pdb=" C34 P5S E1604 " ideal model delta sinusoidal sigma weight residual 179.95 65.56 114.39 1 3.00e+01 1.11e-03 1.51e+01 ... (remaining 11501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2236 0.039 - 0.078: 788 0.078 - 0.116: 270 0.116 - 0.155: 45 0.155 - 0.194: 3 Chirality restraints: 3342 Sorted by residual: chirality pdb=" CG LEU E1227 " pdb=" CB LEU E1227 " pdb=" CD1 LEU E1227 " pdb=" CD2 LEU E1227 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.42e-01 chirality pdb=" CA VAL A 339 " pdb=" N VAL A 339 " pdb=" C VAL A 339 " pdb=" CB VAL A 339 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.23e-01 chirality pdb=" CB VAL A 339 " pdb=" CA VAL A 339 " pdb=" CG1 VAL A 339 " pdb=" CG2 VAL A 339 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.20e-01 ... (remaining 3339 not shown) Planarity restraints: 3400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE E 44 " -0.047 5.00e-02 4.00e+02 7.21e-02 8.31e+00 pdb=" N PRO E 45 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO E 45 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 45 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 339 " 0.045 5.00e-02 4.00e+02 6.78e-02 7.35e+00 pdb=" N PRO A 340 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 340 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 340 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 316 " -0.042 5.00e-02 4.00e+02 6.45e-02 6.65e+00 pdb=" N PRO E 317 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO E 317 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 317 " -0.036 5.00e-02 4.00e+02 ... (remaining 3397 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 255 2.67 - 3.23: 19645 3.23 - 3.79: 29692 3.79 - 4.34: 34883 4.34 - 4.90: 59216 Nonbonded interactions: 143691 Sorted by model distance: nonbonded pdb=" O SER C 116 " pdb=" OG SER C 119 " model vdw 2.118 3.040 nonbonded pdb=" OG SER E1423 " pdb=" O ILE E1502 " model vdw 2.174 3.040 nonbonded pdb=" O SER A 116 " pdb=" OG SER A 119 " model vdw 2.180 3.040 nonbonded pdb=" OD1 ASP A 329 " pdb=" OG SER A 331 " model vdw 2.210 3.040 nonbonded pdb=" OG SER E 774 " pdb=" O LYS E 776 " model vdw 2.226 3.040 ... (remaining 143686 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 31 through 35 or (resid 36 through 39 and (name N or name \ CA or name C or name O or name CB )) or resid 40 or (resid 41 and (name N or nam \ e CA or name C or name O or name CB )) or resid 42 or (resid 43 through 45 and ( \ name N or name CA or name C or name O or name CB )) or resid 46 through 48 or (r \ esid 49 and (name N or name CA or name C or name O or name CB )) or resid 50 thr \ ough 53 or (resid 54 through 59 and (name N or name CA or name C or name O or na \ me CB )) or resid 60 through 63 or (resid 64 through 67 and (name N or name CA o \ r name C or name O or name CB )) or resid 68 through 72 or (resid 73 through 74 \ and (name N or name CA or name C or name O or name CB )) or resid 75 through 80 \ or (resid 81 through 82 and (name N or name CA or name C or name O or name CB )) \ or resid 83 through 91 or (resid 92 through 94 and (name N or name CA or name C \ or name O or name CB )) or resid 95 through 117 or (resid 118 and (name N or na \ me CA or name C or name O or name CB )) or resid 119 through 147 or (resid 148 a \ nd (name N or name CA or name C or name O or name CB )) or resid 149 through 151 \ or (resid 152 and (name N or name CA or name C or name O or name CB )) or resid \ 153 through 179 or (resid 180 and (name N or name CA or name C or name O or nam \ e CB )) or resid 181 through 187 or (resid 188 through 189 and (name N or name C \ A or name C or name O or name CB )) or resid 190 through 192 or (resid 193 and ( \ name N or name CA or name C or name O or name CB )) or resid 194 or (resid 195 a \ nd (name N or name CA or name C or name O or name CB )) or resid 196 through 204 \ or (resid 205 through 207 and (name N or name CA or name C or name O or name CB \ )) or resid 208 through 209 or (resid 210 through 211 and (name N or name CA or \ name C or name O or name CB )) or resid 212 through 221 or (resid 222 and (name \ N or name CA or name C or name O or name CB )) or resid 223 through 237 or (res \ id 238 and (name N or name CA or name C or name O or name CB )) or resid 239 thr \ ough 254 or (resid 255 and (name N or name CA or name C or name O or name CB )) \ or resid 256 through 272 or (resid 273 through 276 and (name N or name CA or nam \ e C or name O or name CB )) or resid 277 or (resid 278 through 282 and (name N o \ r name CA or name C or name O or name CB )) or resid 283 through 309 or (resid 3 \ 10 and (name N or name CA or name C or name O or name CB )) or resid 311 through \ 317 or (resid 318 and (name N or name CA or name C or name O or name CB )) or r \ esid 319 through 326 or (resid 327 through 330 and (name N or name CA or name C \ or name O or name CB )) or resid 331 through 344 or (resid 345 through 356 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and ((resid 31 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 35 or (resid 36 through 39 and (name N or name \ CA or name C or name O or name CB )) or resid 40 through 43 or (resid 44 throug \ h 45 and (name N or name CA or name C or name O or name CB )) or resid 46 throug \ h 47 or (resid 48 through 49 and (name N or name CA or name C or name O or name \ CB )) or resid 50 through 54 or (resid 55 through 59 and (name N or name CA or n \ ame C or name O or name CB )) or resid 60 through 63 or (resid 64 through 67 and \ (name N or name CA or name C or name O or name CB )) or resid 68 through 70 or \ (resid 71 and (name N or name CA or name C or name O or name CB )) or resid 72 t \ hrough 76 or (resid 77 and (name N or name CA or name C or name O or name CB )) \ or resid 78 through 80 or (resid 81 through 82 and (name N or name CA or name C \ or name O or name CB )) or resid 83 through 91 or (resid 92 through 94 and (name \ N or name CA or name C or name O or name CB )) or resid 95 through 99 or (resid \ 100 through 101 and (name N or name CA or name C or name O or name CB )) or res \ id 102 through 147 or (resid 148 and (name N or name CA or name C or name O or n \ ame CB )) or resid 149 through 153 or (resid 154 and (name N or name CA or name \ C or name O or name CB )) or resid 155 through 168 or (resid 169 and (name N or \ name CA or name C or name O or name CB )) or resid 170 through 187 or (resid 188 \ through 189 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 90 through 191 or (resid 192 through 193 and (name N or name CA or name C or nam \ e O or name CB )) or resid 194 or (resid 195 and (name N or name CA or name C or \ name O or name CB )) or resid 196 through 205 or (resid 206 through 207 and (na \ me N or name CA or name C or name O or name CB )) or resid 208 through 209 or (r \ esid 210 through 211 and (name N or name CA or name C or name O or name CB )) or \ resid 212 through 220 or (resid 221 through 222 and (name N or name CA or name \ C or name O or name CB )) or resid 223 through 250 or (resid 251 and (name N or \ name CA or name C or name O or name CB )) or resid 252 through 258 or (resid 259 \ and (name N or name CA or name C or name O or name CB )) or resid 260 through 2 \ 64 or (resid 265 and (name N or name CA or name C or name O or name CB )) or res \ id 266 or (resid 267 and (name N or name CA or name C or name O or name CB )) or \ resid 268 or (resid 269 through 271 and (name N or name CA or name C or name O \ or name CB )) or resid 272 through 277 or (resid 278 through 282 and (name N or \ name CA or name C or name O or name CB )) or resid 283 through 292 or (resid 293 \ and (name N or name CA or name C or name O or name CB )) or resid 294 through 3 \ 17 or (resid 318 and (name N or name CA or name C or name O or name CB )) or res \ id 319 through 327 or (resid 328 through 330 and (name N or name CA or name C or \ name O or name CB )) or resid 331 through 337 or (resid 338 and (name N or name \ CA or name C or name O or name CB )) or resid 339 through 340 or (resid 341 and \ (name N or name CA or name C or name O or name CB )) or resid 342 or (resid 343 \ through 356 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 31 through 35 or (resid 36 through 39 and (name N or name \ CA or name C or name O or name CB )) or resid 40 or (resid 41 and (name N or nam \ e CA or name C or name O or name CB )) or resid 42 through 43 or (resid 44 throu \ gh 45 and (name N or name CA or name C or name O or name CB )) or resid 46 throu \ gh 47 or (resid 48 through 49 and (name N or name CA or name C or name O or name \ CB )) or resid 50 through 63 or (resid 64 through 67 and (name N or name CA or \ name C or name O or name CB )) or resid 68 through 70 or (resid 71 and (name N o \ r name CA or name C or name O or name CB )) or resid 72 or (resid 73 through 74 \ and (name N or name CA or name C or name O or name CB )) or resid 75 through 76 \ or (resid 77 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 8 through 80 or (resid 81 through 82 and (name N or name CA or name C or name O \ or name CB )) or resid 83 through 99 or (resid 100 through 101 and (name N or na \ me CA or name C or name O or name CB )) or resid 102 through 153 or (resid 154 a \ nd (name N or name CA or name C or name O or name CB )) or resid 155 through 188 \ or (resid 189 and (name N or name CA or name C or name O or name CB )) or resid \ 190 through 191 or (resid 192 through 193 and (name N or name CA or name C or n \ ame O or name CB )) or resid 194 or (resid 195 and (name N or name CA or name C \ or name O or name CB )) or resid 196 through 205 or (resid 206 through 207 and ( \ name N or name CA or name C or name O or name CB )) or resid 208 through 209 or \ (resid 210 through 211 and (name N or name CA or name C or name O or name CB )) \ or resid 212 through 220 or (resid 221 through 222 and (name N or name CA or nam \ e C or name O or name CB )) or resid 223 through 237 or (resid 238 and (name N o \ r name CA or name C or name O or name CB )) or resid 239 through 250 or (resid 2 \ 51 and (name N or name CA or name C or name O or name CB )) or resid 252 through \ 254 or (resid 255 and (name N or name CA or name C or name O or name CB )) or r \ esid 256 through 262 or (resid 263 and (name N or name CA or name C or name O or \ name CB )) or resid 264 or (resid 265 and (name N or name CA or name C or name \ O or name CB )) or resid 266 or (resid 267 and (name N or name CA or name C or n \ ame O or name CB )) or resid 268 through 272 or (resid 273 through 276 and (name \ N or name CA or name C or name O or name CB )) or resid 277 or (resid 278 throu \ gh 282 and (name N or name CA or name C or name O or name CB )) or resid 283 thr \ ough 292 or (resid 293 and (name N or name CA or name C or name O or name CB )) \ or resid 294 through 317 or (resid 318 and (name N or name CA or name C or name \ O or name CB )) or resid 319 through 327 or (resid 328 through 330 and (name N o \ r name CA or name C or name O or name CB )) or resid 331 through 337 or (resid 3 \ 38 and (name N or name CA or name C or name O or name CB )) or resid 339 through \ 340 or (resid 341 and (name N or name CA or name C or name O or name CB )) or r \ esid 342 through 343 or (resid 344 through 356 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'D' and (resid 31 through 36 or (resid 37 through 39 and (name N or name \ CA or name C or name O or name CB )) or resid 40 or (resid 41 and (name N or nam \ e CA or name C or name O or name CB )) or resid 42 or (resid 43 through 45 and ( \ name N or name CA or name C or name O or name CB )) or resid 46 through 55 or (r \ esid 56 through 59 and (name N or name CA or name C or name O or name CB )) or r \ esid 60 through 76 or (resid 77 and (name N or name CA or name C or name O or na \ me CB )) or resid 78 through 81 or (resid 82 and (name N or name CA or name C or \ name O or name CB )) or resid 83 through 91 or (resid 92 through 94 and (name N \ or name CA or name C or name O or name CB )) or resid 95 through 99 or (resid 1 \ 00 through 101 and (name N or name CA or name C or name O or name CB )) or resid \ 102 through 139 or (resid 140 through 141 and (name N or name CA or name C or n \ ame O or name CB )) or resid 142 through 147 or (resid 148 and (name N or name C \ A or name C or name O or name CB )) or resid 149 through 151 or (resid 152 and ( \ name N or name CA or name C or name O or name CB )) or resid 153 or (resid 154 a \ nd (name N or name CA or name C or name O or name CB )) or resid 155 through 179 \ or (resid 180 and (name N or name CA or name C or name O or name CB )) or resid \ 181 or (resid 182 and (name N or name CA or name C or name O or name CB )) or r \ esid 183 through 188 or (resid 189 and (name N or name CA or name C or name O or \ name CB )) or resid 190 through 192 or (resid 193 and (name N or name CA or nam \ e C or name O or name CB )) or resid 194 through 198 or (resid 199 through 200 a \ nd (name N or name CA or name C or name O or name CB )) or resid 201 through 204 \ or (resid 205 through 207 and (name N or name CA or name C or name O or name CB \ )) or resid 208 through 210 or (resid 211 and (name N or name CA or name C or n \ ame O or name CB )) or resid 212 through 220 or (resid 221 through 222 and (name \ N or name CA or name C or name O or name CB )) or resid 223 through 237 or (res \ id 238 and (name N or name CA or name C or name O or name CB )) or resid 239 thr \ ough 250 or (resid 251 and (name N or name CA or name C or name O or name CB )) \ or resid 252 through 254 or (resid 255 and (name N or name CA or name C or name \ O or name CB )) or resid 256 through 258 or (resid 259 and (name N or name CA or \ name C or name O or name CB )) or resid 260 through 264 or (resid 265 and (name \ N or name CA or name C or name O or name CB )) or resid 266 or (resid 267 and ( \ name N or name CA or name C or name O or name CB )) or resid 268 through 269 or \ (resid 270 through 271 and (name N or name CA or name C or name O or name CB )) \ or resid 272 or (resid 273 through 276 and (name N or name CA or name C or name \ O or name CB )) or resid 277 through 280 or (resid 281 through 282 and (name N o \ r name CA or name C or name O or name CB )) or resid 283 through 287 or (resid 2 \ 88 and (name N or name CA or name C or name O or name CB )) or resid 289 through \ 292 or (resid 293 and (name N or name CA or name C or name O or name CB )) or r \ esid 294 through 295 or (resid 296 and (name N or name CA or name C or name O or \ name CB )) or resid 297 through 324 or (resid 325 and (name N or name CA or nam \ e C or name O or name CB )) or resid 326 or (resid 327 through 330 and (name N o \ r name CA or name C or name O or name CB )) or resid 331 or (resid 332 and (name \ N or name CA or name C or name O or name CB )) or resid 333 through 337 or (res \ id 338 and (name N or name CA or name C or name O or name CB )) or resid 339 thr \ ough 340 or (resid 341 and (name N or name CA or name C or name O or name CB )) \ or resid 342 or (resid 343 through 356 and (name N or name CA or name C or name \ O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 21.050 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 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 : 0.005 0.073 19889 Z= 0.237 Angle : 0.645 8.701 27244 Z= 0.359 Chirality : 0.044 0.194 3342 Planarity : 0.005 0.072 3400 Dihedral : 12.643 120.826 6301 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.81 % Allowed : 9.64 % Favored : 89.54 % 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: -0.17 (0.16), residues: 2729 helix: 1.48 (0.14), residues: 1317 sheet: -1.51 (0.31), residues: 263 loop : -1.71 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 74 TYR 0.019 0.002 TYR E1254 PHE 0.018 0.002 PHE E1164 TRP 0.020 0.002 TRP B 91 HIS 0.006 0.001 HIS C 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.24 (19884) covalent geometry : angle 0.64509 / 0.36 (27234) SS BOND : bond 0.00142 / 0.07 ( 5) SS BOND : angle 0.92575 / 0.54 ( 10) hydrogen bonds : bond 0.13268 / 9.59 ( 1171) hydrogen bonds : angle 5.50271 / 3.95 ( 3444) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 933 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 TRP cc_start: 0.9145 (m-10) cc_final: 0.8636 (m-10) REVERT: A 90 TRP cc_start: 0.9003 (m100) cc_final: 0.6381 (m100) REVERT: A 91 TRP cc_start: 0.9176 (t60) cc_final: 0.8848 (t60) REVERT: A 210 ILE cc_start: 0.8977 (mt) cc_final: 0.8770 (mt) REVERT: A 260 VAL cc_start: 0.8901 (t) cc_final: 0.8423 (p) REVERT: A 299 GLN cc_start: 0.9058 (mt0) cc_final: 0.8837 (tt0) REVERT: A 301 ARG cc_start: 0.8665 (mtm-85) cc_final: 0.8154 (mtm-85) REVERT: A 305 LEU cc_start: 0.9112 (mp) cc_final: 0.8907 (mp) REVERT: E 6 CYS cc_start: 0.4872 (m) cc_final: 0.4315 (m) REVERT: E 12 SER cc_start: 0.8966 (m) cc_final: 0.8445 (p) REVERT: E 16 ARG cc_start: 0.8351 (mmt180) cc_final: 0.7918 (mtp85) REVERT: E 71 HIS cc_start: 0.8194 (t70) cc_final: 0.7343 (t70) REVERT: E 126 ASN cc_start: 0.8987 (t0) cc_final: 0.8643 (t0) REVERT: E 135 LEU cc_start: 0.9205 (tp) cc_final: 0.8981 (tp) REVERT: E 193 ARG cc_start: 0.8434 (mtp85) cc_final: 0.8059 (mtt180) REVERT: E 216 ARG cc_start: 0.7286 (mpt90) cc_final: 0.6825 (mmt-90) REVERT: E 260 LEU cc_start: 0.8950 (tp) cc_final: 0.8388 (tp) REVERT: E 263 TYR cc_start: 0.9296 (t80) cc_final: 0.8650 (t80) REVERT: E 377 TYR cc_start: 0.8712 (m-10) cc_final: 0.8487 (m-80) REVERT: E 396 TYR cc_start: 0.8880 (t80) cc_final: 0.8654 (t80) REVERT: E 397 ASN cc_start: 0.8514 (t0) cc_final: 0.8006 (t0) REVERT: E 498 GLN cc_start: 0.7965 (tt0) cc_final: 0.7399 (mt0) REVERT: E 512 TYR cc_start: 0.7445 (m-80) cc_final: 0.7140 (m-80) REVERT: E 577 PHE cc_start: 0.8564 (m-80) cc_final: 0.8357 (m-80) REVERT: E 797 GLN cc_start: 0.8635 (pt0) cc_final: 0.8086 (pm20) REVERT: E 799 TYR cc_start: 0.8813 (t80) cc_final: 0.8414 (t80) REVERT: E 911 GLU cc_start: 0.6558 (pt0) cc_final: 0.4390 (tm-30) REVERT: E 1025 MET cc_start: 0.7427 (mmm) cc_final: 0.7179 (mmp) REVERT: E 1088 TRP cc_start: 0.8023 (t-100) cc_final: 0.7785 (t60) REVERT: E 1149 LEU cc_start: 0.8892 (mp) cc_final: 0.8596 (tp) REVERT: E 1200 LEU cc_start: 0.9236 (tt) cc_final: 0.9036 (tt) REVERT: E 1225 GLN cc_start: 0.9106 (mm-40) cc_final: 0.8262 (tm-30) REVERT: E 1277 SER cc_start: 0.9007 (m) cc_final: 0.8662 (t) REVERT: E 1298 MET cc_start: 0.8705 (ttp) cc_final: 0.8385 (ttp) REVERT: E 1406 ASP cc_start: 0.6570 (m-30) cc_final: 0.6317 (m-30) REVERT: B 60 PHE cc_start: 0.9350 (t80) cc_final: 0.8944 (t80) REVERT: B 83 TRP cc_start: 0.9070 (m-10) cc_final: 0.8680 (m-10) REVERT: B 97 HIS cc_start: 0.8959 (t70) cc_final: 0.8730 (t-90) REVERT: B 123 PHE cc_start: 0.9023 (t80) cc_final: 0.8775 (t80) REVERT: B 129 VAL cc_start: 0.9580 (t) cc_final: 0.9336 (t) REVERT: B 250 PHE cc_start: 0.8977 (t80) cc_final: 0.8724 (t80) REVERT: B 254 PRO cc_start: 0.9512 (Cg_exo) cc_final: 0.9296 (Cg_endo) REVERT: B 277 HIS cc_start: 0.8162 (t70) cc_final: 0.7688 (t-170) REVERT: B 299 GLN cc_start: 0.8796 (mt0) cc_final: 0.8581 (mt0) REVERT: B 313 GLN cc_start: 0.7905 (mt0) cc_final: 0.7445 (tt0) REVERT: B 338 LYS cc_start: 0.8993 (tttm) cc_final: 0.8751 (ttmt) REVERT: C 68 TRP cc_start: 0.8279 (m100) cc_final: 0.7950 (m100) REVERT: C 125 ILE cc_start: 0.9339 (mm) cc_final: 0.8875 (tp) REVERT: C 128 GLN cc_start: 0.8987 (tt0) cc_final: 0.8709 (tt0) REVERT: C 168 PHE cc_start: 0.6905 (t80) cc_final: 0.6582 (t80) REVERT: C 211 ILE cc_start: 0.9546 (mt) cc_final: 0.9296 (mt) REVERT: C 258 TYR cc_start: 0.8580 (p90) cc_final: 0.7939 (p90) REVERT: C 273 SER cc_start: 0.9471 (m) cc_final: 0.9215 (t) REVERT: C 313 GLN cc_start: 0.8704 (mt0) cc_final: 0.8329 (mt0) REVERT: C 318 ILE cc_start: 0.8555 (mm) cc_final: 0.8351 (mm) REVERT: C 333 PHE cc_start: 0.8916 (t80) cc_final: 0.8712 (t80) REVERT: D 37 SER cc_start: 0.8686 (t) cc_final: 0.8434 (p) REVERT: D 97 HIS cc_start: 0.9471 (t-90) cc_final: 0.9192 (t-90) REVERT: D 157 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8097 (tt) REVERT: D 233 LEU cc_start: 0.8581 (mt) cc_final: 0.8180 (mt) REVERT: D 273 SER cc_start: 0.9607 (m) cc_final: 0.9050 (t) REVERT: D 274 ASP cc_start: 0.8527 (t70) cc_final: 0.8001 (t0) REVERT: D 299 GLN cc_start: 0.8822 (mt0) cc_final: 0.8520 (mt0) outliers start: 13 outliers final: 7 residues processed: 938 average time/residue: 0.1281 time to fit residues: 190.6003 Evaluate side-chains 842 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 834 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.0050 chunk 111 optimal weight: 20.0000 overall best weight: 2.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 HIS A 216 HIS A 235 GLN ** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS E 131 ASN E1179 GLN B 235 GLN B 259 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.188782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.153432 restraints weight = 28878.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.157565 restraints weight = 14806.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.160316 restraints weight = 9226.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.162129 restraints weight = 6638.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.163343 restraints weight = 5295.143| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19889 Z= 0.141 Angle : 0.549 9.985 27244 Z= 0.290 Chirality : 0.043 0.236 3342 Planarity : 0.005 0.063 3400 Dihedral : 10.031 116.966 3166 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.16), residues: 2729 helix: 1.91 (0.14), residues: 1342 sheet: -1.38 (0.31), residues: 263 loop : -1.36 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 527 TYR 0.026 0.002 TYR A 258 PHE 0.040 0.002 PHE C 168 TRP 0.022 0.001 TRP E 739 HIS 0.009 0.001 HIS E 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (19884) covalent geometry : angle 0.54817 / 0.29 (27234) SS BOND : bond 0.00908 / 0.70 ( 5) SS BOND : angle 1.19223 / 0.69 ( 10) hydrogen bonds : bond 0.04605 / 3.25 ( 1171) hydrogen bonds : angle 4.24786 / 3.01 ( 3444) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 915 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 TRP cc_start: 0.9261 (m-10) cc_final: 0.8810 (m-10) REVERT: A 90 TRP cc_start: 0.8923 (m100) cc_final: 0.6226 (m100) REVERT: A 91 TRP cc_start: 0.9115 (t60) cc_final: 0.7915 (t60) REVERT: A 92 LEU cc_start: 0.9435 (tt) cc_final: 0.9196 (tt) REVERT: A 121 PHE cc_start: 0.9562 (t80) cc_final: 0.9154 (t80) REVERT: A 152 GLN cc_start: 0.8888 (tt0) cc_final: 0.8558 (tt0) REVERT: A 210 ILE cc_start: 0.8992 (mt) cc_final: 0.8768 (mt) REVERT: A 211 ILE cc_start: 0.9370 (mt) cc_final: 0.8974 (mt) REVERT: A 260 VAL cc_start: 0.8634 (t) cc_final: 0.8243 (p) REVERT: A 301 ARG cc_start: 0.8611 (mtm-85) cc_final: 0.8210 (mtm-85) REVERT: E 16 ARG cc_start: 0.8346 (mmt180) cc_final: 0.7928 (mtp85) REVERT: E 71 HIS cc_start: 0.7860 (t70) cc_final: 0.7094 (t70) REVERT: E 104 LEU cc_start: 0.9057 (tp) cc_final: 0.8853 (tp) REVERT: E 150 LYS cc_start: 0.8726 (tptp) cc_final: 0.8518 (mmmt) REVERT: E 263 TYR cc_start: 0.9310 (t80) cc_final: 0.8616 (t80) REVERT: E 396 TYR cc_start: 0.8885 (t80) cc_final: 0.8637 (t80) REVERT: E 397 ASN cc_start: 0.7875 (t0) cc_final: 0.7398 (t0) REVERT: E 398 LYS cc_start: 0.8958 (tptt) cc_final: 0.8758 (tptt) REVERT: E 498 GLN cc_start: 0.7931 (tt0) cc_final: 0.7343 (mt0) REVERT: E 512 TYR cc_start: 0.7525 (m-80) cc_final: 0.6941 (m-80) REVERT: E 577 PHE cc_start: 0.8478 (m-80) cc_final: 0.8185 (m-80) REVERT: E 595 SER cc_start: 0.8950 (p) cc_final: 0.8571 (t) REVERT: E 685 PHE cc_start: 0.6191 (m-10) cc_final: 0.5876 (m-80) REVERT: E 772 TYR cc_start: 0.8746 (t80) cc_final: 0.8366 (t80) REVERT: E 797 GLN cc_start: 0.8555 (pt0) cc_final: 0.8072 (pm20) REVERT: E 799 TYR cc_start: 0.8772 (t80) cc_final: 0.8412 (t80) REVERT: E 848 THR cc_start: 0.7973 (p) cc_final: 0.7758 (p) REVERT: E 911 GLU cc_start: 0.6884 (pt0) cc_final: 0.4813 (tm-30) REVERT: E 1025 MET cc_start: 0.7270 (mmm) cc_final: 0.6934 (mmp) REVERT: E 1080 LEU cc_start: 0.9197 (tp) cc_final: 0.8886 (tp) REVERT: E 1088 TRP cc_start: 0.8025 (t-100) cc_final: 0.7783 (t60) REVERT: E 1123 ASN cc_start: 0.8376 (t0) cc_final: 0.8120 (t0) REVERT: E 1201 VAL cc_start: 0.8529 (m) cc_final: 0.8195 (t) REVERT: E 1225 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8267 (tm-30) REVERT: E 1298 MET cc_start: 0.8714 (ttp) cc_final: 0.8270 (ttp) REVERT: E 1308 GLN cc_start: 0.8751 (mt0) cc_final: 0.8347 (tt0) REVERT: B 60 PHE cc_start: 0.9349 (t80) cc_final: 0.8799 (t80) REVERT: B 71 THR cc_start: 0.9265 (m) cc_final: 0.9051 (m) REVERT: B 83 TRP cc_start: 0.9288 (m-10) cc_final: 0.8884 (m-10) REVERT: B 97 HIS cc_start: 0.8858 (t70) cc_final: 0.8600 (t-90) REVERT: B 114 ILE cc_start: 0.8842 (mm) cc_final: 0.8469 (tp) REVERT: B 116 SER cc_start: 0.9444 (p) cc_final: 0.9156 (t) REVERT: B 123 PHE cc_start: 0.9008 (t80) cc_final: 0.8741 (t80) REVERT: B 149 LEU cc_start: 0.8414 (tt) cc_final: 0.8069 (tt) REVERT: B 212 SER cc_start: 0.9375 (t) cc_final: 0.9113 (t) REVERT: B 250 PHE cc_start: 0.9101 (t80) cc_final: 0.8796 (t80) REVERT: B 252 VAL cc_start: 0.9319 (t) cc_final: 0.9115 (t) REVERT: B 254 PRO cc_start: 0.9465 (Cg_exo) cc_final: 0.9088 (Cg_endo) REVERT: B 277 HIS cc_start: 0.8101 (t70) cc_final: 0.7548 (t-170) REVERT: B 299 GLN cc_start: 0.8865 (mt0) cc_final: 0.8638 (mt0) REVERT: B 313 GLN cc_start: 0.7847 (mt0) cc_final: 0.7515 (tt0) REVERT: B 338 LYS cc_start: 0.9058 (tttm) cc_final: 0.8827 (ttmt) REVERT: C 68 TRP cc_start: 0.8166 (m100) cc_final: 0.7854 (m100) REVERT: C 128 GLN cc_start: 0.8841 (tt0) cc_final: 0.8459 (tt0) REVERT: C 211 ILE cc_start: 0.9662 (mt) cc_final: 0.9403 (mt) REVERT: C 215 ILE cc_start: 0.9291 (mm) cc_final: 0.8927 (mm) REVERT: C 258 TYR cc_start: 0.8426 (p90) cc_final: 0.7935 (p90) REVERT: C 287 LEU cc_start: 0.9368 (tp) cc_final: 0.9153 (tp) REVERT: C 318 ILE cc_start: 0.8441 (mm) cc_final: 0.8240 (mm) REVERT: D 112 THR cc_start: 0.9390 (p) cc_final: 0.9148 (t) REVERT: D 211 ILE cc_start: 0.9353 (mt) cc_final: 0.8948 (mt) REVERT: D 273 SER cc_start: 0.9617 (m) cc_final: 0.9055 (t) REVERT: D 274 ASP cc_start: 0.8531 (t70) cc_final: 0.7975 (t0) REVERT: D 299 GLN cc_start: 0.8744 (mt0) cc_final: 0.8318 (mt0) outliers start: 0 outliers final: 0 residues processed: 915 average time/residue: 0.1228 time to fit residues: 178.1193 Evaluate side-chains 845 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 845 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 25 optimal weight: 20.0000 chunk 162 optimal weight: 50.0000 chunk 166 optimal weight: 30.0000 chunk 7 optimal weight: 4.9990 chunk 243 optimal weight: 10.0000 chunk 200 optimal weight: 30.0000 chunk 145 optimal weight: 7.9990 chunk 125 optimal weight: 30.0000 chunk 242 optimal weight: 0.4980 chunk 80 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 overall best weight: 5.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 HIS A 235 GLN A 247 ASN ** E 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1179 GLN E1197 GLN B 216 HIS B 247 ASN D 43 ASN ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.185145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.148699 restraints weight = 29222.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.152709 restraints weight = 15280.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.155325 restraints weight = 9661.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.157163 restraints weight = 7059.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.158282 restraints weight = 5695.514| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 19889 Z= 0.223 Angle : 0.606 10.717 27244 Z= 0.321 Chirality : 0.045 0.212 3342 Planarity : 0.004 0.053 3400 Dihedral : 9.990 115.660 3166 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.13 % Allowed : 3.26 % Favored : 96.62 % 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: 0.43 (0.16), residues: 2729 helix: 1.87 (0.14), residues: 1341 sheet: -1.26 (0.32), residues: 256 loop : -1.32 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 527 TYR 0.021 0.002 TYR E 142 PHE 0.036 0.002 PHE E 44 TRP 0.024 0.002 TRP E 143 HIS 0.009 0.001 HIS E 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.22 (19884) covalent geometry : angle 0.60579 / 0.32 (27234) SS BOND : bond 0.00981 / 0.50 ( 5) SS BOND : angle 0.99799 / 0.50 ( 10) hydrogen bonds : bond 0.04640 / 3.32 ( 1171) hydrogen bonds : angle 4.28362 / 3.05 ( 3444) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 897 time to evaluate : 0.767 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 83 TRP cc_start: 0.9102 (m-10) cc_final: 0.8901 (m-10) REVERT: A 90 TRP cc_start: 0.9015 (m100) cc_final: 0.6279 (m100) REVERT: A 91 TRP cc_start: 0.9167 (t60) cc_final: 0.8397 (t60) REVERT: A 92 LEU cc_start: 0.9467 (tt) cc_final: 0.9224 (tt) REVERT: A 148 ILE cc_start: 0.9315 (tt) cc_final: 0.9022 (tt) REVERT: A 152 GLN cc_start: 0.9106 (tt0) cc_final: 0.8763 (tt0) REVERT: A 210 ILE cc_start: 0.9031 (mt) cc_final: 0.8823 (mt) REVERT: A 260 VAL cc_start: 0.8579 (t) cc_final: 0.8317 (p) REVERT: A 301 ARG cc_start: 0.8646 (mtm-85) cc_final: 0.8253 (mtm-85) REVERT: E 16 ARG cc_start: 0.8386 (mmt180) cc_final: 0.8064 (mtp85) REVERT: E 71 HIS cc_start: 0.8256 (t70) cc_final: 0.7296 (t-170) REVERT: E 104 LEU cc_start: 0.9024 (tp) cc_final: 0.8798 (tp) REVERT: E 112 MET cc_start: 0.8948 (mmt) cc_final: 0.8461 (mmt) REVERT: E 145 LEU cc_start: 0.9313 (tp) cc_final: 0.9057 (tp) REVERT: E 263 TYR cc_start: 0.9270 (t80) cc_final: 0.8720 (t80) REVERT: E 397 ASN cc_start: 0.8186 (t0) cc_final: 0.7767 (t0) REVERT: E 398 LYS cc_start: 0.8947 (tptt) cc_final: 0.8716 (tptt) REVERT: E 498 GLN cc_start: 0.7996 (tt0) cc_final: 0.7493 (mt0) REVERT: E 512 TYR cc_start: 0.7357 (m-80) cc_final: 0.6903 (m-80) REVERT: E 577 PHE cc_start: 0.8518 (m-80) cc_final: 0.8253 (m-80) REVERT: E 595 SER cc_start: 0.8985 (p) cc_final: 0.8711 (t) REVERT: E 772 TYR cc_start: 0.8764 (t80) cc_final: 0.8405 (t80) REVERT: E 781 ASN cc_start: 0.8337 (p0) cc_final: 0.7893 (p0) REVERT: E 797 GLN cc_start: 0.8641 (pt0) cc_final: 0.8096 (pm20) REVERT: E 799 TYR cc_start: 0.8817 (t80) cc_final: 0.8496 (t80) REVERT: E 911 GLU cc_start: 0.6958 (pt0) cc_final: 0.4956 (tm-30) REVERT: E 1025 MET cc_start: 0.7306 (mmm) cc_final: 0.7008 (mmp) REVERT: E 1080 LEU cc_start: 0.9208 (tp) cc_final: 0.8885 (tp) REVERT: E 1088 TRP cc_start: 0.8066 (t-100) cc_final: 0.7775 (t60) REVERT: E 1225 GLN cc_start: 0.9146 (mm-40) cc_final: 0.8384 (tm-30) REVERT: E 1269 SER cc_start: 0.8980 (t) cc_final: 0.8752 (p) REVERT: E 1277 SER cc_start: 0.8542 (m) cc_final: 0.7894 (t) REVERT: E 1419 ARG cc_start: 0.6615 (ttm110) cc_final: 0.5609 (ttm170) REVERT: B 34 ARG cc_start: 0.8450 (mtp180) cc_final: 0.8217 (mtp180) REVERT: B 60 PHE cc_start: 0.9364 (t80) cc_final: 0.8871 (t80) REVERT: B 83 TRP cc_start: 0.9152 (m-10) cc_final: 0.8850 (m-10) REVERT: B 97 HIS cc_start: 0.8974 (t70) cc_final: 0.8640 (t-90) REVERT: B 123 PHE cc_start: 0.8994 (t80) cc_final: 0.8686 (t80) REVERT: B 129 VAL cc_start: 0.9571 (t) cc_final: 0.9345 (t) REVERT: B 212 SER cc_start: 0.9563 (t) cc_final: 0.9281 (t) REVERT: B 216 HIS cc_start: 0.7602 (m-70) cc_final: 0.7277 (m-70) REVERT: B 250 PHE cc_start: 0.9097 (t80) cc_final: 0.8697 (t80) REVERT: B 252 VAL cc_start: 0.9349 (t) cc_final: 0.9096 (t) REVERT: B 254 PRO cc_start: 0.9481 (Cg_exo) cc_final: 0.9169 (Cg_endo) REVERT: B 277 HIS cc_start: 0.8183 (t70) cc_final: 0.7591 (t-170) REVERT: B 299 GLN cc_start: 0.8976 (mt0) cc_final: 0.8666 (mt0) REVERT: B 313 GLN cc_start: 0.7808 (mt0) cc_final: 0.7585 (tt0) REVERT: B 338 LYS cc_start: 0.9115 (tttm) cc_final: 0.8818 (ttmt) REVERT: C 128 GLN cc_start: 0.8951 (tt0) cc_final: 0.8550 (tt0) REVERT: C 146 ILE cc_start: 0.9560 (mt) cc_final: 0.9344 (mt) REVERT: C 147 LEU cc_start: 0.8993 (tp) cc_final: 0.8783 (tp) REVERT: C 206 ARG cc_start: 0.7284 (mtm110) cc_final: 0.7070 (mmp80) REVERT: C 211 ILE cc_start: 0.9664 (mt) cc_final: 0.9431 (mt) REVERT: C 215 ILE cc_start: 0.9330 (mm) cc_final: 0.8949 (mm) REVERT: C 258 TYR cc_start: 0.8410 (p90) cc_final: 0.7843 (p90) REVERT: D 37 SER cc_start: 0.8846 (t) cc_final: 0.8459 (p) REVERT: D 191 LEU cc_start: 0.8328 (mt) cc_final: 0.8127 (mt) REVERT: D 233 LEU cc_start: 0.8676 (mt) cc_final: 0.8382 (mt) REVERT: D 240 MET cc_start: 0.8440 (tmm) cc_final: 0.7904 (tmm) REVERT: D 273 SER cc_start: 0.9615 (m) cc_final: 0.9029 (t) REVERT: D 274 ASP cc_start: 0.8590 (t70) cc_final: 0.7973 (t0) outliers start: 2 outliers final: 0 residues processed: 897 average time/residue: 0.1274 time to fit residues: 181.2410 Evaluate side-chains 845 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 845 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 201 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 172 optimal weight: 50.0000 chunk 150 optimal weight: 10.0000 chunk 140 optimal weight: 0.9990 chunk 247 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 184 optimal weight: 6.9990 chunk 23 optimal weight: 0.0370 chunk 148 optimal weight: 1.9990 overall best weight: 1.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 HIS A 235 GLN A 277 HIS E 24 ASN E 32 ASN ** E 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN D 43 ASN D 216 HIS D 259 HIS ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.176692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.145170 restraints weight = 28543.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.147377 restraints weight = 17358.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.148260 restraints weight = 10780.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.149179 restraints weight = 10421.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.149265 restraints weight = 8561.595| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19889 Z= 0.114 Angle : 0.524 10.107 27244 Z= 0.272 Chirality : 0.043 0.257 3342 Planarity : 0.004 0.047 3400 Dihedral : 9.712 111.012 3166 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.06 % Allowed : 2.38 % Favored : 97.56 % 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: 0.72 (0.16), residues: 2729 helix: 2.08 (0.14), residues: 1348 sheet: -1.17 (0.32), residues: 265 loop : -1.14 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 201 TYR 0.019 0.001 TYR E 378 PHE 0.036 0.002 PHE E 44 TRP 0.011 0.001 TRP E 65 HIS 0.008 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (19884) covalent geometry : angle 0.52365 / 0.27 (27234) SS BOND : bond 0.00632 / 0.34 ( 5) SS BOND : angle 1.07083 / 0.52 ( 10) hydrogen bonds : bond 0.04141 / 2.95 ( 1171) hydrogen bonds : angle 3.88486 / 2.76 ( 3444) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 885 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 TRP cc_start: 0.9163 (m-10) cc_final: 0.8916 (m-10) REVERT: A 90 TRP cc_start: 0.9003 (m100) cc_final: 0.6763 (m100) REVERT: A 92 LEU cc_start: 0.9242 (tt) cc_final: 0.8989 (tt) REVERT: A 201 ARG cc_start: 0.8420 (ttt90) cc_final: 0.8024 (ttt180) REVERT: A 248 SER cc_start: 0.8363 (p) cc_final: 0.8029 (p) REVERT: A 301 ARG cc_start: 0.8554 (mtm-85) cc_final: 0.8235 (mtm-85) REVERT: E 16 ARG cc_start: 0.8231 (mmt180) cc_final: 0.7870 (mtp85) REVERT: E 71 HIS cc_start: 0.7875 (t70) cc_final: 0.7145 (t-90) REVERT: E 112 MET cc_start: 0.8859 (mmt) cc_final: 0.8295 (mmt) REVERT: E 145 LEU cc_start: 0.9348 (tp) cc_final: 0.9123 (tp) REVERT: E 168 ARG cc_start: 0.8325 (ttp-110) cc_final: 0.8007 (ttp-110) REVERT: E 216 ARG cc_start: 0.7549 (mpt90) cc_final: 0.7272 (mmm-85) REVERT: E 245 ILE cc_start: 0.9151 (mm) cc_final: 0.8785 (mm) REVERT: E 397 ASN cc_start: 0.8221 (t0) cc_final: 0.7509 (t0) REVERT: E 398 LYS cc_start: 0.9037 (tptt) cc_final: 0.8755 (tptt) REVERT: E 479 THR cc_start: 0.8153 (m) cc_final: 0.7847 (m) REVERT: E 498 GLN cc_start: 0.8096 (tt0) cc_final: 0.7641 (mt0) REVERT: E 512 TYR cc_start: 0.7309 (m-80) cc_final: 0.6811 (m-80) REVERT: E 577 PHE cc_start: 0.8494 (m-80) cc_final: 0.8201 (m-80) REVERT: E 595 SER cc_start: 0.8852 (p) cc_final: 0.8354 (t) REVERT: E 772 TYR cc_start: 0.8791 (t80) cc_final: 0.8550 (t80) REVERT: E 781 ASN cc_start: 0.8115 (p0) cc_final: 0.7658 (p0) REVERT: E 797 GLN cc_start: 0.8452 (pt0) cc_final: 0.7998 (pm20) REVERT: E 799 TYR cc_start: 0.8846 (t80) cc_final: 0.8623 (t80) REVERT: E 845 TYR cc_start: 0.7124 (t80) cc_final: 0.6778 (t80) REVERT: E 911 GLU cc_start: 0.6998 (pt0) cc_final: 0.5224 (tm-30) REVERT: E 1080 LEU cc_start: 0.9307 (tp) cc_final: 0.9053 (tp) REVERT: E 1088 TRP cc_start: 0.7999 (t-100) cc_final: 0.7791 (t60) REVERT: E 1149 LEU cc_start: 0.8788 (mp) cc_final: 0.8465 (mp) REVERT: E 1225 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8653 (tm-30) REVERT: B 60 PHE cc_start: 0.9231 (t80) cc_final: 0.8823 (t80) REVERT: B 83 TRP cc_start: 0.9242 (m-10) cc_final: 0.8920 (m-10) REVERT: B 97 HIS cc_start: 0.8778 (t70) cc_final: 0.8473 (t-90) REVERT: B 114 ILE cc_start: 0.8756 (mm) cc_final: 0.8440 (tp) REVERT: B 116 SER cc_start: 0.9371 (p) cc_final: 0.8964 (t) REVERT: B 123 PHE cc_start: 0.8990 (t80) cc_final: 0.8679 (t80) REVERT: B 129 VAL cc_start: 0.9411 (t) cc_final: 0.9187 (t) REVERT: B 212 SER cc_start: 0.9463 (t) cc_final: 0.9226 (t) REVERT: B 216 HIS cc_start: 0.7486 (m-70) cc_final: 0.7201 (m-70) REVERT: B 250 PHE cc_start: 0.8975 (t80) cc_final: 0.8402 (t80) REVERT: B 252 VAL cc_start: 0.9338 (t) cc_final: 0.8946 (t) REVERT: B 254 PRO cc_start: 0.9417 (Cg_exo) cc_final: 0.9057 (Cg_endo) REVERT: B 277 HIS cc_start: 0.8328 (t70) cc_final: 0.7922 (t-170) REVERT: B 299 GLN cc_start: 0.8869 (mt0) cc_final: 0.8521 (mt0) REVERT: C 60 PHE cc_start: 0.8799 (t80) cc_final: 0.8576 (t80) REVERT: C 128 GLN cc_start: 0.8776 (tt0) cc_final: 0.8318 (tt0) REVERT: C 146 ILE cc_start: 0.9503 (mt) cc_final: 0.9231 (mt) REVERT: C 147 LEU cc_start: 0.8861 (tp) cc_final: 0.8642 (tp) REVERT: C 206 ARG cc_start: 0.7226 (mtm110) cc_final: 0.6974 (mmp80) REVERT: C 211 ILE cc_start: 0.9626 (mt) cc_final: 0.9334 (mt) REVERT: C 215 ILE cc_start: 0.9432 (mm) cc_final: 0.9098 (mm) REVERT: C 258 TYR cc_start: 0.8412 (p90) cc_final: 0.7890 (p90) REVERT: D 181 LEU cc_start: 0.9183 (mm) cc_final: 0.8953 (mm) REVERT: D 233 LEU cc_start: 0.8553 (mt) cc_final: 0.8225 (mt) REVERT: D 273 SER cc_start: 0.9576 (m) cc_final: 0.8950 (t) REVERT: D 274 ASP cc_start: 0.8457 (t70) cc_final: 0.7940 (t0) outliers start: 1 outliers final: 0 residues processed: 885 average time/residue: 0.1290 time to fit residues: 181.3722 Evaluate side-chains 831 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 831 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 187 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 62 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 195 optimal weight: 20.0000 chunk 117 optimal weight: 30.0000 chunk 4 optimal weight: 30.0000 chunk 150 optimal weight: 8.9990 chunk 96 optimal weight: 50.0000 chunk 199 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 HIS A 235 GLN A 299 GLN E 32 ASN E1197 GLN E1203 HIS E1296 ASN B 46 HIS B 48 ASN C 299 GLN D 43 ASN D 128 GLN D 277 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.171664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.139878 restraints weight = 28490.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.141907 restraints weight = 16799.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.143163 restraints weight = 11738.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.144200 restraints weight = 9328.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.144474 restraints weight = 8106.145| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 19889 Z= 0.196 Angle : 0.572 9.812 27244 Z= 0.300 Chirality : 0.044 0.190 3342 Planarity : 0.004 0.048 3400 Dihedral : 9.760 108.412 3166 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.06 % Allowed : 2.57 % Favored : 97.37 % 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: 0.68 (0.16), residues: 2729 helix: 2.08 (0.14), residues: 1340 sheet: -1.23 (0.32), residues: 265 loop : -1.17 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 314 TYR 0.033 0.002 TYR D 268 PHE 0.034 0.002 PHE E 44 TRP 0.010 0.001 TRP C 90 HIS 0.007 0.001 HIS A 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 (19884) covalent geometry : angle 0.57196 / 0.30 (27234) SS BOND : bond 0.00310 / 0.16 ( 5) SS BOND : angle 0.88727 / 0.43 ( 10) hydrogen bonds : bond 0.04272 / 3.06 ( 1171) hydrogen bonds : angle 4.02554 / 2.88 ( 3444) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 882 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 TRP cc_start: 0.8979 (m100) cc_final: 0.6383 (m100) REVERT: A 91 TRP cc_start: 0.9200 (t60) cc_final: 0.8429 (t60) REVERT: A 92 LEU cc_start: 0.9359 (tt) cc_final: 0.9095 (tt) REVERT: A 111 VAL cc_start: 0.8711 (t) cc_final: 0.8407 (t) REVERT: A 148 ILE cc_start: 0.9170 (tt) cc_final: 0.8920 (tt) REVERT: A 201 ARG cc_start: 0.8416 (ttt90) cc_final: 0.8049 (ttt180) REVERT: A 299 GLN cc_start: 0.8930 (tt0) cc_final: 0.8721 (tt0) REVERT: A 318 ILE cc_start: 0.9208 (mm) cc_final: 0.9003 (mm) REVERT: A 328 VAL cc_start: 0.8587 (t) cc_final: 0.8366 (t) REVERT: E 39 LEU cc_start: 0.9330 (tt) cc_final: 0.9117 (tt) REVERT: E 71 HIS cc_start: 0.8188 (t70) cc_final: 0.7347 (t-170) REVERT: E 104 LEU cc_start: 0.8912 (tp) cc_final: 0.8660 (tp) REVERT: E 112 MET cc_start: 0.9001 (mmt) cc_final: 0.8310 (mmt) REVERT: E 123 TYR cc_start: 0.9073 (t80) cc_final: 0.8663 (t80) REVERT: E 145 LEU cc_start: 0.9439 (tp) cc_final: 0.9190 (tp) REVERT: E 164 PHE cc_start: 0.8664 (m-80) cc_final: 0.8334 (m-80) REVERT: E 179 TYR cc_start: 0.8837 (m-10) cc_final: 0.8492 (m-10) REVERT: E 215 VAL cc_start: 0.7741 (p) cc_final: 0.7202 (m) REVERT: E 479 THR cc_start: 0.8396 (m) cc_final: 0.7864 (m) REVERT: E 498 GLN cc_start: 0.8140 (tt0) cc_final: 0.7676 (mt0) REVERT: E 512 TYR cc_start: 0.7346 (m-80) cc_final: 0.6780 (m-80) REVERT: E 524 VAL cc_start: 0.8471 (t) cc_final: 0.7576 (t) REVERT: E 527 ARG cc_start: 0.9003 (ttm110) cc_final: 0.8087 (mtm110) REVERT: E 577 PHE cc_start: 0.8537 (m-80) cc_final: 0.8273 (m-80) REVERT: E 595 SER cc_start: 0.8926 (p) cc_final: 0.8520 (t) REVERT: E 772 TYR cc_start: 0.8658 (t80) cc_final: 0.8383 (t80) REVERT: E 781 ASN cc_start: 0.8219 (p0) cc_final: 0.7786 (p0) REVERT: E 797 GLN cc_start: 0.8452 (pt0) cc_final: 0.7987 (pm20) REVERT: E 799 TYR cc_start: 0.8824 (t80) cc_final: 0.8498 (t80) REVERT: E 845 TYR cc_start: 0.7168 (t80) cc_final: 0.6767 (t80) REVERT: E 911 GLU cc_start: 0.7019 (pt0) cc_final: 0.5223 (tm-30) REVERT: E 1080 LEU cc_start: 0.9243 (tp) cc_final: 0.8955 (tp) REVERT: E 1088 TRP cc_start: 0.8053 (t-100) cc_final: 0.7795 (t60) REVERT: E 1138 SER cc_start: 0.8943 (t) cc_final: 0.8433 (t) REVERT: E 1149 LEU cc_start: 0.8876 (mp) cc_final: 0.8504 (mp) REVERT: E 1225 GLN cc_start: 0.9100 (mm-40) cc_final: 0.8576 (tm-30) REVERT: B 78 SER cc_start: 0.9285 (p) cc_final: 0.8944 (p) REVERT: B 83 TRP cc_start: 0.9221 (m-10) cc_final: 0.8959 (m-10) REVERT: B 97 HIS cc_start: 0.8913 (t70) cc_final: 0.8692 (t-90) REVERT: B 114 ILE cc_start: 0.8829 (mm) cc_final: 0.8436 (tp) REVERT: B 123 PHE cc_start: 0.8984 (t80) cc_final: 0.8661 (t80) REVERT: B 129 VAL cc_start: 0.9476 (t) cc_final: 0.9246 (t) REVERT: B 212 SER cc_start: 0.9576 (t) cc_final: 0.9327 (t) REVERT: B 216 HIS cc_start: 0.7723 (m-70) cc_final: 0.7445 (m-70) REVERT: B 254 PRO cc_start: 0.9435 (Cg_exo) cc_final: 0.9114 (Cg_endo) REVERT: B 277 HIS cc_start: 0.8341 (t70) cc_final: 0.7949 (t-170) REVERT: B 313 GLN cc_start: 0.7598 (tt0) cc_final: 0.7280 (tt0) REVERT: C 128 GLN cc_start: 0.8878 (tt0) cc_final: 0.8469 (tt0) REVERT: C 147 LEU cc_start: 0.8908 (tp) cc_final: 0.8703 (tp) REVERT: C 206 ARG cc_start: 0.7544 (mtm110) cc_final: 0.7204 (mmp80) REVERT: C 215 ILE cc_start: 0.9429 (mm) cc_final: 0.9131 (mm) REVERT: C 258 TYR cc_start: 0.8526 (p90) cc_final: 0.7971 (p90) REVERT: C 336 THR cc_start: 0.8441 (p) cc_final: 0.8015 (p) REVERT: D 233 LEU cc_start: 0.8585 (mt) cc_final: 0.8262 (mt) REVERT: D 273 SER cc_start: 0.9595 (m) cc_final: 0.8956 (t) REVERT: D 274 ASP cc_start: 0.8488 (t70) cc_final: 0.7889 (t0) outliers start: 1 outliers final: 0 residues processed: 882 average time/residue: 0.1281 time to fit residues: 180.9875 Evaluate side-chains 839 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 839 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 120 optimal weight: 0.6980 chunk 266 optimal weight: 10.0000 chunk 99 optimal weight: 40.0000 chunk 104 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 112 optimal weight: 30.0000 chunk 70 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 226 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 HIS A 235 GLN A 247 ASN E 131 ASN D 259 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.172010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.139641 restraints weight = 28386.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.142130 restraints weight = 16494.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.143795 restraints weight = 10845.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.144690 restraints weight = 8609.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.144888 restraints weight = 7524.546| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19889 Z= 0.171 Angle : 0.560 12.874 27244 Z= 0.292 Chirality : 0.044 0.305 3342 Planarity : 0.004 0.048 3400 Dihedral : 9.755 104.998 3166 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.13 % Allowed : 1.38 % Favored : 98.50 % 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: 0.68 (0.16), residues: 2729 helix: 2.13 (0.14), residues: 1342 sheet: -1.33 (0.30), residues: 280 loop : -1.21 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 34 TYR 0.034 0.002 TYR A 258 PHE 0.033 0.002 PHE C 168 TRP 0.011 0.001 TRP C 90 HIS 0.007 0.001 HIS D 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (19884) covalent geometry : angle 0.55995 / 0.29 (27234) SS BOND : bond 0.00304 / 0.16 ( 5) SS BOND : angle 0.86479 / 0.41 ( 10) hydrogen bonds : bond 0.04198 / 3.01 ( 1171) hydrogen bonds : angle 3.97014 / 2.84 ( 3444) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 877 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 TRP cc_start: 0.9132 (m-10) cc_final: 0.8587 (m-90) REVERT: A 90 TRP cc_start: 0.8971 (m100) cc_final: 0.6640 (m100) REVERT: A 92 LEU cc_start: 0.9381 (tt) cc_final: 0.9168 (tt) REVERT: A 111 VAL cc_start: 0.8779 (t) cc_final: 0.8358 (t) REVERT: A 148 ILE cc_start: 0.9183 (tt) cc_final: 0.8915 (tt) REVERT: A 185 LYS cc_start: 0.9407 (mttt) cc_final: 0.9177 (mttm) REVERT: E 71 HIS cc_start: 0.8143 (t70) cc_final: 0.7585 (t-90) REVERT: E 104 LEU cc_start: 0.8886 (tp) cc_final: 0.8646 (tp) REVERT: E 112 MET cc_start: 0.9097 (mmt) cc_final: 0.8461 (mmt) REVERT: E 123 TYR cc_start: 0.9050 (t80) cc_final: 0.8666 (t80) REVERT: E 145 LEU cc_start: 0.9436 (tp) cc_final: 0.9179 (tp) REVERT: E 150 LYS cc_start: 0.9036 (mmmt) cc_final: 0.8647 (mmmt) REVERT: E 164 PHE cc_start: 0.8663 (m-80) cc_final: 0.8291 (m-80) REVERT: E 179 TYR cc_start: 0.8847 (m-10) cc_final: 0.8441 (m-10) REVERT: E 215 VAL cc_start: 0.7803 (p) cc_final: 0.7046 (m) REVERT: E 216 ARG cc_start: 0.7828 (mmt90) cc_final: 0.7343 (tpp80) REVERT: E 417 ILE cc_start: 0.9361 (tt) cc_final: 0.9141 (tt) REVERT: E 418 CYS cc_start: 0.9012 (t) cc_final: 0.8734 (t) REVERT: E 479 THR cc_start: 0.8314 (m) cc_final: 0.7838 (m) REVERT: E 498 GLN cc_start: 0.8144 (tt0) cc_final: 0.7697 (mt0) REVERT: E 512 TYR cc_start: 0.7366 (m-80) cc_final: 0.6779 (m-80) REVERT: E 524 VAL cc_start: 0.8452 (t) cc_final: 0.7356 (t) REVERT: E 527 ARG cc_start: 0.9010 (ttm110) cc_final: 0.8026 (mtm110) REVERT: E 577 PHE cc_start: 0.8523 (m-80) cc_final: 0.8255 (m-80) REVERT: E 595 SER cc_start: 0.8930 (p) cc_final: 0.8468 (t) REVERT: E 772 TYR cc_start: 0.8687 (t80) cc_final: 0.8411 (t80) REVERT: E 781 ASN cc_start: 0.8222 (p0) cc_final: 0.7769 (p0) REVERT: E 797 GLN cc_start: 0.8379 (pt0) cc_final: 0.8002 (pm20) REVERT: E 845 TYR cc_start: 0.6922 (t80) cc_final: 0.6554 (t80) REVERT: E 911 GLU cc_start: 0.6632 (pt0) cc_final: 0.4869 (tm-30) REVERT: E 1080 LEU cc_start: 0.9305 (tp) cc_final: 0.9048 (tp) REVERT: E 1088 TRP cc_start: 0.8053 (t-100) cc_final: 0.7783 (t60) REVERT: E 1138 SER cc_start: 0.8900 (t) cc_final: 0.8505 (t) REVERT: E 1147 THR cc_start: 0.8913 (t) cc_final: 0.8163 (t) REVERT: E 1201 VAL cc_start: 0.8943 (m) cc_final: 0.8326 (t) REVERT: E 1225 GLN cc_start: 0.9128 (mm-40) cc_final: 0.8494 (tm-30) REVERT: E 1298 MET cc_start: 0.8444 (ttp) cc_final: 0.7460 (ttp) REVERT: B 78 SER cc_start: 0.9247 (p) cc_final: 0.8928 (p) REVERT: B 83 TRP cc_start: 0.9193 (m-10) cc_final: 0.8919 (m-10) REVERT: B 97 HIS cc_start: 0.8870 (t70) cc_final: 0.8641 (t-90) REVERT: B 123 PHE cc_start: 0.8979 (t80) cc_final: 0.8700 (t80) REVERT: B 131 ILE cc_start: 0.9339 (mt) cc_final: 0.9092 (mt) REVERT: B 212 SER cc_start: 0.9533 (t) cc_final: 0.9312 (t) REVERT: B 254 PRO cc_start: 0.9423 (Cg_exo) cc_final: 0.9072 (Cg_endo) REVERT: B 277 HIS cc_start: 0.8420 (t70) cc_final: 0.7958 (t-170) REVERT: B 313 GLN cc_start: 0.7655 (tt0) cc_final: 0.7112 (tt0) REVERT: C 60 PHE cc_start: 0.8879 (t80) cc_final: 0.8664 (t80) REVERT: C 128 GLN cc_start: 0.8838 (tt0) cc_final: 0.8458 (tt0) REVERT: C 215 ILE cc_start: 0.9345 (mm) cc_final: 0.9045 (mm) REVERT: C 242 ASN cc_start: 0.8582 (m-40) cc_final: 0.8351 (m-40) REVERT: C 258 TYR cc_start: 0.8579 (p90) cc_final: 0.8081 (p90) REVERT: C 315 PHE cc_start: 0.8491 (m-10) cc_final: 0.8172 (m-10) REVERT: D 77 MET cc_start: 0.8501 (mmm) cc_final: 0.8053 (mtp) REVERT: D 234 HIS cc_start: 0.8235 (t70) cc_final: 0.7494 (t70) REVERT: D 273 SER cc_start: 0.9592 (m) cc_final: 0.8956 (t) REVERT: D 274 ASP cc_start: 0.8469 (t70) cc_final: 0.7885 (t0) outliers start: 2 outliers final: 1 residues processed: 878 average time/residue: 0.1262 time to fit residues: 177.1154 Evaluate side-chains 831 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 830 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 28 optimal weight: 9.9990 chunk 73 optimal weight: 20.0000 chunk 238 optimal weight: 10.0000 chunk 66 optimal weight: 0.0060 chunk 247 optimal weight: 0.3980 chunk 171 optimal weight: 30.0000 chunk 108 optimal weight: 40.0000 chunk 141 optimal weight: 10.0000 chunk 172 optimal weight: 50.0000 chunk 57 optimal weight: 10.0000 chunk 259 optimal weight: 20.0000 overall best weight: 6.0806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 HIS A 235 GLN A 247 ASN A 299 GLN E 32 ASN E1135 HIS E1203 HIS B 216 HIS B 247 ASN B 299 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.169278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.136655 restraints weight = 28751.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.139198 restraints weight = 16990.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.140570 restraints weight = 11214.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.141586 restraints weight = 8983.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.141777 restraints weight = 7806.904| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 19889 Z= 0.224 Angle : 0.615 12.273 27244 Z= 0.321 Chirality : 0.045 0.188 3342 Planarity : 0.004 0.049 3400 Dihedral : 9.846 102.936 3166 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.06 % Allowed : 1.94 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.16), residues: 2729 helix: 2.05 (0.14), residues: 1342 sheet: -1.39 (0.30), residues: 280 loop : -1.23 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 301 TYR 0.018 0.002 TYR A 258 PHE 0.035 0.002 PHE D 168 TRP 0.015 0.002 TRP C 90 HIS 0.006 0.001 HIS A 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.22 (19884) covalent geometry : angle 0.61452 / 0.32 (27234) SS BOND : bond 0.00559 / 0.28 ( 5) SS BOND : angle 0.89930 / 0.47 ( 10) hydrogen bonds : bond 0.04369 / 3.14 ( 1171) hydrogen bonds : angle 4.15691 / 2.98 ( 3444) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 883 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 TRP cc_start: 0.9101 (m-10) cc_final: 0.8710 (m-90) REVERT: A 90 TRP cc_start: 0.8940 (m100) cc_final: 0.6021 (m100) REVERT: A 91 TRP cc_start: 0.9190 (t60) cc_final: 0.8411 (t60) REVERT: A 92 LEU cc_start: 0.9434 (tt) cc_final: 0.9205 (tt) REVERT: A 111 VAL cc_start: 0.8714 (t) cc_final: 0.8185 (t) REVERT: A 158 MET cc_start: 0.7296 (ttt) cc_final: 0.7092 (ttp) REVERT: E 71 HIS cc_start: 0.8165 (t70) cc_final: 0.7623 (t-90) REVERT: E 104 LEU cc_start: 0.8894 (tp) cc_final: 0.8630 (tp) REVERT: E 112 MET cc_start: 0.9053 (mmt) cc_final: 0.8450 (mmt) REVERT: E 123 TYR cc_start: 0.9085 (t80) cc_final: 0.8690 (t80) REVERT: E 131 ASN cc_start: 0.9215 (t0) cc_final: 0.8963 (t0) REVERT: E 145 LEU cc_start: 0.9438 (tp) cc_final: 0.9181 (tp) REVERT: E 150 LYS cc_start: 0.9033 (mmmt) cc_final: 0.8756 (mmmt) REVERT: E 179 TYR cc_start: 0.8879 (m-10) cc_final: 0.8514 (m-10) REVERT: E 216 ARG cc_start: 0.7945 (mmt90) cc_final: 0.7542 (tpp80) REVERT: E 398 LYS cc_start: 0.9079 (tptt) cc_final: 0.8742 (tptm) REVERT: E 479 THR cc_start: 0.8380 (m) cc_final: 0.7955 (m) REVERT: E 498 GLN cc_start: 0.8153 (tt0) cc_final: 0.7695 (mt0) REVERT: E 512 TYR cc_start: 0.7385 (m-80) cc_final: 0.6806 (m-80) REVERT: E 524 VAL cc_start: 0.8468 (t) cc_final: 0.7275 (t) REVERT: E 527 ARG cc_start: 0.9028 (ttm110) cc_final: 0.7997 (mtm110) REVERT: E 577 PHE cc_start: 0.8547 (m-80) cc_final: 0.8279 (m-80) REVERT: E 595 SER cc_start: 0.8950 (p) cc_final: 0.8567 (t) REVERT: E 614 LEU cc_start: 0.7717 (tp) cc_final: 0.7430 (tp) REVERT: E 772 TYR cc_start: 0.8710 (t80) cc_final: 0.8455 (t80) REVERT: E 781 ASN cc_start: 0.8346 (p0) cc_final: 0.7905 (p0) REVERT: E 797 GLN cc_start: 0.8346 (pt0) cc_final: 0.7943 (pm20) REVERT: E 911 GLU cc_start: 0.6618 (pt0) cc_final: 0.4825 (tm-30) REVERT: E 1080 LEU cc_start: 0.9235 (tp) cc_final: 0.8937 (tp) REVERT: E 1088 TRP cc_start: 0.8100 (t-100) cc_final: 0.7802 (t60) REVERT: E 1138 SER cc_start: 0.9016 (t) cc_final: 0.8522 (t) REVERT: E 1147 THR cc_start: 0.8985 (t) cc_final: 0.8232 (t) REVERT: E 1149 LEU cc_start: 0.8909 (mp) cc_final: 0.8585 (mp) REVERT: E 1212 THR cc_start: 0.9182 (p) cc_final: 0.8702 (p) REVERT: E 1215 ARG cc_start: 0.8638 (mtm110) cc_final: 0.7727 (mtm110) REVERT: E 1225 GLN cc_start: 0.9167 (mm-40) cc_final: 0.8489 (tm-30) REVERT: E 1298 MET cc_start: 0.8477 (ttp) cc_final: 0.7510 (ttp) REVERT: B 78 SER cc_start: 0.9254 (p) cc_final: 0.8930 (p) REVERT: B 97 HIS cc_start: 0.8936 (t70) cc_final: 0.8722 (t-90) REVERT: B 116 SER cc_start: 0.9329 (p) cc_final: 0.8744 (m) REVERT: B 277 HIS cc_start: 0.8448 (t70) cc_final: 0.7964 (t-170) REVERT: B 313 GLN cc_start: 0.7606 (tt0) cc_final: 0.7112 (tt0) REVERT: C 60 PHE cc_start: 0.8915 (t80) cc_final: 0.8694 (t80) REVERT: C 128 GLN cc_start: 0.8852 (tt0) cc_final: 0.8453 (tt0) REVERT: C 215 ILE cc_start: 0.9387 (mm) cc_final: 0.9027 (mm) REVERT: C 258 TYR cc_start: 0.8638 (p90) cc_final: 0.8126 (p90) REVERT: D 157 LEU cc_start: 0.8312 (tt) cc_final: 0.8110 (tt) REVERT: D 234 HIS cc_start: 0.8247 (t70) cc_final: 0.7662 (t70) REVERT: D 273 SER cc_start: 0.9599 (m) cc_final: 0.8944 (t) REVERT: D 274 ASP cc_start: 0.8489 (t70) cc_final: 0.7941 (t0) outliers start: 1 outliers final: 0 residues processed: 883 average time/residue: 0.1286 time to fit residues: 180.5478 Evaluate side-chains 835 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 835 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 259 optimal weight: 20.0000 chunk 248 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 201 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 153 optimal weight: 9.9990 chunk 235 optimal weight: 10.0000 chunk 122 optimal weight: 30.0000 chunk 64 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 HIS A 235 GLN E 32 ASN E 262 ASN E1203 HIS ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.170193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.138884 restraints weight = 28491.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.141021 restraints weight = 19234.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.143345 restraints weight = 12736.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.143993 restraints weight = 10315.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.144079 restraints weight = 8031.045| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 19889 Z= 0.185 Angle : 0.592 12.799 27244 Z= 0.307 Chirality : 0.044 0.280 3342 Planarity : 0.004 0.049 3400 Dihedral : 9.795 102.694 3166 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.06 % Allowed : 1.50 % Favored : 98.43 % 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: 0.76 (0.16), residues: 2729 helix: 2.21 (0.14), residues: 1313 sheet: -1.19 (0.32), residues: 262 loop : -1.15 (0.18), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E1419 TYR 0.028 0.002 TYR D 268 PHE 0.036 0.002 PHE C 168 TRP 0.019 0.001 TRP B 83 HIS 0.005 0.001 HIS D 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (19884) covalent geometry : angle 0.59140 / 0.31 (27234) SS BOND : bond 0.00232 / 0.13 ( 5) SS BOND : angle 1.14404 / 0.62 ( 10) hydrogen bonds : bond 0.04265 / 3.06 ( 1171) hydrogen bonds : angle 4.08727 / 2.93 ( 3444) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 876 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.6669 (m-80) cc_final: 0.6391 (m-80) REVERT: A 83 TRP cc_start: 0.9098 (m-10) cc_final: 0.8671 (m-90) REVERT: A 90 TRP cc_start: 0.8929 (m100) cc_final: 0.6448 (m100) REVERT: A 92 LEU cc_start: 0.9403 (tt) cc_final: 0.9178 (tt) REVERT: A 111 VAL cc_start: 0.8665 (t) cc_final: 0.8189 (t) REVERT: A 130 THR cc_start: 0.9022 (p) cc_final: 0.8781 (p) REVERT: A 299 GLN cc_start: 0.8972 (tt0) cc_final: 0.8497 (tt0) REVERT: E 32 ASN cc_start: 0.9245 (t0) cc_final: 0.9031 (t0) REVERT: E 71 HIS cc_start: 0.8106 (t70) cc_final: 0.7608 (t-90) REVERT: E 104 LEU cc_start: 0.8854 (tp) cc_final: 0.8625 (tp) REVERT: E 123 TYR cc_start: 0.9069 (t80) cc_final: 0.8615 (t80) REVERT: E 131 ASN cc_start: 0.9137 (t0) cc_final: 0.8858 (t0) REVERT: E 145 LEU cc_start: 0.9429 (tp) cc_final: 0.9167 (tp) REVERT: E 150 LYS cc_start: 0.9041 (mmmt) cc_final: 0.8644 (mmmt) REVERT: E 179 TYR cc_start: 0.8832 (m-10) cc_final: 0.8485 (m-10) REVERT: E 386 ASN cc_start: 0.9309 (m-40) cc_final: 0.8918 (m-40) REVERT: E 398 LYS cc_start: 0.9106 (tptt) cc_final: 0.8879 (tptt) REVERT: E 418 CYS cc_start: 0.8998 (t) cc_final: 0.8770 (t) REVERT: E 479 THR cc_start: 0.8450 (m) cc_final: 0.7980 (m) REVERT: E 498 GLN cc_start: 0.8197 (tt0) cc_final: 0.7722 (mt0) REVERT: E 527 ARG cc_start: 0.9021 (ttm110) cc_final: 0.8180 (mtm110) REVERT: E 577 PHE cc_start: 0.8516 (m-80) cc_final: 0.8245 (m-80) REVERT: E 595 SER cc_start: 0.8960 (p) cc_final: 0.8516 (t) REVERT: E 614 LEU cc_start: 0.7664 (tp) cc_final: 0.7407 (tp) REVERT: E 772 TYR cc_start: 0.8695 (t80) cc_final: 0.8476 (t80) REVERT: E 781 ASN cc_start: 0.8276 (p0) cc_final: 0.7810 (p0) REVERT: E 797 GLN cc_start: 0.8207 (pt0) cc_final: 0.7751 (pm20) REVERT: E 845 TYR cc_start: 0.7118 (t80) cc_final: 0.6721 (t80) REVERT: E 911 GLU cc_start: 0.6413 (pt0) cc_final: 0.4497 (tm-30) REVERT: E 1080 LEU cc_start: 0.9307 (tp) cc_final: 0.9050 (tp) REVERT: E 1088 TRP cc_start: 0.8075 (t-100) cc_final: 0.7798 (t60) REVERT: E 1138 SER cc_start: 0.8977 (t) cc_final: 0.8519 (t) REVERT: E 1147 THR cc_start: 0.8764 (t) cc_final: 0.7877 (t) REVERT: E 1201 VAL cc_start: 0.8970 (m) cc_final: 0.8727 (t) REVERT: E 1212 THR cc_start: 0.9206 (p) cc_final: 0.8720 (p) REVERT: E 1215 ARG cc_start: 0.8488 (mtm110) cc_final: 0.7423 (mtm110) REVERT: E 1225 GLN cc_start: 0.9152 (mm-40) cc_final: 0.8532 (tm-30) REVERT: E 1298 MET cc_start: 0.8465 (ttp) cc_final: 0.7432 (ttp) REVERT: B 97 HIS cc_start: 0.8889 (t70) cc_final: 0.8478 (t-90) REVERT: B 116 SER cc_start: 0.9238 (p) cc_final: 0.8569 (t) REVERT: B 123 PHE cc_start: 0.8927 (t80) cc_final: 0.8689 (t80) REVERT: B 131 ILE cc_start: 0.9410 (mt) cc_final: 0.9048 (mt) REVERT: B 216 HIS cc_start: 0.8017 (m170) cc_final: 0.7792 (m170) REVERT: B 277 HIS cc_start: 0.8400 (t70) cc_final: 0.8017 (t-170) REVERT: C 60 PHE cc_start: 0.8879 (t80) cc_final: 0.8643 (t80) REVERT: C 128 GLN cc_start: 0.8822 (tt0) cc_final: 0.8456 (tt0) REVERT: C 212 SER cc_start: 0.9594 (m) cc_final: 0.9159 (p) REVERT: C 215 ILE cc_start: 0.9368 (mm) cc_final: 0.9075 (mm) REVERT: C 258 TYR cc_start: 0.8640 (p90) cc_final: 0.8102 (p90) REVERT: C 313 GLN cc_start: 0.8436 (mt0) cc_final: 0.8001 (mt0) REVERT: C 315 PHE cc_start: 0.8659 (m-10) cc_final: 0.8445 (m-10) REVERT: D 77 MET cc_start: 0.8467 (mmm) cc_final: 0.7943 (mtp) REVERT: D 234 HIS cc_start: 0.8193 (t70) cc_final: 0.7626 (t70) REVERT: D 270 LEU cc_start: 0.8487 (mt) cc_final: 0.8268 (mt) REVERT: D 273 SER cc_start: 0.9579 (m) cc_final: 0.8902 (t) REVERT: D 274 ASP cc_start: 0.8415 (t70) cc_final: 0.7864 (t0) outliers start: 1 outliers final: 1 residues processed: 876 average time/residue: 0.1313 time to fit residues: 183.5955 Evaluate side-chains 833 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 832 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 158 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 268 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 193 optimal weight: 30.0000 chunk 252 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 2 optimal weight: 20.0000 chunk 210 optimal weight: 20.0000 chunk 171 optimal weight: 40.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 HIS A 152 GLN A 235 GLN E 103 HIS E1203 HIS B 216 HIS B 247 ASN B 259 HIS ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 HIS D 335 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.171445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.139542 restraints weight = 28392.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.141995 restraints weight = 16352.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.143121 restraints weight = 10990.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.144326 restraints weight = 8885.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.144464 restraints weight = 7650.418| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 19889 Z= 0.175 Angle : 0.582 13.034 27244 Z= 0.302 Chirality : 0.044 0.164 3342 Planarity : 0.004 0.048 3400 Dihedral : 9.733 102.137 3166 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.06 % Allowed : 1.13 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.16), residues: 2729 helix: 2.17 (0.14), residues: 1320 sheet: -1.05 (0.33), residues: 255 loop : -1.13 (0.18), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 486 TYR 0.016 0.001 TYR A 258 PHE 0.032 0.002 PHE E 44 TRP 0.062 0.002 TRP B 83 HIS 0.007 0.001 HIS D 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (19884) covalent geometry : angle 0.58209 / 0.30 (27234) SS BOND : bond 0.00308 / 0.17 ( 5) SS BOND : angle 0.79592 / 0.44 ( 10) hydrogen bonds : bond 0.04234 / 3.04 ( 1171) hydrogen bonds : angle 4.04702 / 2.91 ( 3444) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 882 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.6632 (m-80) cc_final: 0.6383 (m-80) REVERT: A 83 TRP cc_start: 0.9083 (m-10) cc_final: 0.8580 (m-90) REVERT: A 90 TRP cc_start: 0.8799 (m100) cc_final: 0.6638 (m100) REVERT: A 92 LEU cc_start: 0.9396 (tt) cc_final: 0.9180 (tt) REVERT: A 111 VAL cc_start: 0.8635 (t) cc_final: 0.8259 (t) REVERT: A 299 GLN cc_start: 0.9117 (tt0) cc_final: 0.8615 (tt0) REVERT: E 71 HIS cc_start: 0.8093 (t70) cc_final: 0.7605 (t-90) REVERT: E 104 LEU cc_start: 0.8847 (tp) cc_final: 0.8620 (tp) REVERT: E 123 TYR cc_start: 0.9069 (t80) cc_final: 0.8616 (t80) REVERT: E 131 ASN cc_start: 0.9182 (t0) cc_final: 0.8775 (t0) REVERT: E 145 LEU cc_start: 0.9427 (tp) cc_final: 0.9144 (tp) REVERT: E 179 TYR cc_start: 0.8820 (m-10) cc_final: 0.8494 (m-10) REVERT: E 382 GLU cc_start: 0.8397 (tm-30) cc_final: 0.7837 (tm-30) REVERT: E 398 LYS cc_start: 0.9057 (tptt) cc_final: 0.8825 (tptt) REVERT: E 479 THR cc_start: 0.8424 (m) cc_final: 0.7948 (m) REVERT: E 498 GLN cc_start: 0.8191 (tt0) cc_final: 0.7735 (mt0) REVERT: E 527 ARG cc_start: 0.8989 (ttm110) cc_final: 0.8162 (mtm110) REVERT: E 577 PHE cc_start: 0.8517 (m-80) cc_final: 0.8282 (m-80) REVERT: E 595 SER cc_start: 0.8931 (p) cc_final: 0.8530 (t) REVERT: E 614 LEU cc_start: 0.7703 (tp) cc_final: 0.7413 (tp) REVERT: E 772 TYR cc_start: 0.8689 (t80) cc_final: 0.8475 (t80) REVERT: E 781 ASN cc_start: 0.8259 (p0) cc_final: 0.7803 (p0) REVERT: E 797 GLN cc_start: 0.8276 (pt0) cc_final: 0.7796 (pm20) REVERT: E 911 GLU cc_start: 0.6762 (pt0) cc_final: 0.4683 (tm-30) REVERT: E 1080 LEU cc_start: 0.9310 (tp) cc_final: 0.9047 (tp) REVERT: E 1088 TRP cc_start: 0.8069 (t-100) cc_final: 0.7788 (t60) REVERT: E 1138 SER cc_start: 0.8993 (t) cc_final: 0.8522 (t) REVERT: E 1147 THR cc_start: 0.8833 (t) cc_final: 0.7926 (t) REVERT: E 1212 THR cc_start: 0.9179 (p) cc_final: 0.8668 (p) REVERT: E 1215 ARG cc_start: 0.8454 (mtm110) cc_final: 0.7422 (mtm110) REVERT: E 1225 GLN cc_start: 0.9132 (mm-40) cc_final: 0.8489 (tm-30) REVERT: E 1298 MET cc_start: 0.8517 (ttp) cc_final: 0.7431 (ttp) REVERT: E 1395 MET cc_start: 0.7749 (ptt) cc_final: 0.7493 (ptt) REVERT: B 97 HIS cc_start: 0.8926 (t70) cc_final: 0.8663 (t-90) REVERT: B 116 SER cc_start: 0.9222 (p) cc_final: 0.8543 (t) REVERT: B 123 PHE cc_start: 0.8970 (t80) cc_final: 0.8154 (t80) REVERT: B 131 ILE cc_start: 0.9309 (mt) cc_final: 0.9084 (mt) REVERT: B 216 HIS cc_start: 0.8161 (m-70) cc_final: 0.7924 (m-70) REVERT: B 259 HIS cc_start: 0.8131 (OUTLIER) cc_final: 0.7336 (t-90) REVERT: B 277 HIS cc_start: 0.8463 (t70) cc_final: 0.8077 (t-170) REVERT: B 313 GLN cc_start: 0.7275 (tt0) cc_final: 0.6779 (tt0) REVERT: C 60 PHE cc_start: 0.8862 (t80) cc_final: 0.8639 (t80) REVERT: C 128 GLN cc_start: 0.8770 (tt0) cc_final: 0.8427 (tt0) REVERT: C 171 THR cc_start: 0.7251 (t) cc_final: 0.7034 (m) REVERT: C 212 SER cc_start: 0.9585 (m) cc_final: 0.9175 (p) REVERT: C 258 TYR cc_start: 0.8663 (p90) cc_final: 0.8113 (p90) REVERT: C 309 ILE cc_start: 0.9317 (mm) cc_final: 0.9014 (mm) REVERT: C 315 PHE cc_start: 0.8585 (m-10) cc_final: 0.8374 (m-10) REVERT: D 77 MET cc_start: 0.8491 (mmm) cc_final: 0.7930 (mtp) REVERT: D 234 HIS cc_start: 0.8221 (t70) cc_final: 0.7652 (t70) REVERT: D 259 HIS cc_start: 0.7654 (t-170) cc_final: 0.7406 (t-170) REVERT: D 273 SER cc_start: 0.9600 (m) cc_final: 0.8924 (t) REVERT: D 274 ASP cc_start: 0.8451 (t70) cc_final: 0.7904 (t0) outliers start: 1 outliers final: 0 residues processed: 883 average time/residue: 0.1282 time to fit residues: 180.9529 Evaluate side-chains 841 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 840 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 145 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 252 optimal weight: 6.9990 chunk 229 optimal weight: 9.9990 chunk 198 optimal weight: 0.8980 chunk 120 optimal weight: 0.0060 chunk 268 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 21 optimal weight: 30.0000 chunk 176 optimal weight: 10.0000 chunk 219 optimal weight: 4.9990 overall best weight: 2.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 HIS A 152 GLN A 235 GLN E 32 ASN ** E 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 HIS B 259 HIS D 43 ASN ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.173390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.141863 restraints weight = 28608.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.143802 restraints weight = 17293.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.144232 restraints weight = 12308.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.145300 restraints weight = 10508.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.145493 restraints weight = 9044.398| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19889 Z= 0.136 Angle : 0.570 13.400 27244 Z= 0.294 Chirality : 0.043 0.191 3342 Planarity : 0.005 0.208 3400 Dihedral : 9.594 101.063 3166 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.06 % Allowed : 0.19 % Favored : 99.75 % 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: 0.86 (0.16), residues: 2729 helix: 2.22 (0.14), residues: 1323 sheet: -0.94 (0.33), residues: 255 loop : -1.07 (0.18), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E1419 TYR 0.023 0.002 TYR D 268 PHE 0.030 0.002 PHE D 168 TRP 0.052 0.001 TRP B 83 HIS 0.007 0.001 HIS D 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (19884) covalent geometry : angle 0.57007 / 0.29 (27234) SS BOND : bond 0.00307 / 0.19 ( 5) SS BOND : angle 1.21135 / 0.70 ( 10) hydrogen bonds : bond 0.04162 / 2.98 ( 1171) hydrogen bonds : angle 3.94449 / 2.83 ( 3444) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5458 Ramachandran restraints generated. 2729 Oldfield, 0 Emsley, 2729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 877 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.6696 (m-80) cc_final: 0.6282 (m-80) REVERT: A 83 TRP cc_start: 0.9025 (m-10) cc_final: 0.8535 (m-90) REVERT: A 90 TRP cc_start: 0.8872 (m100) cc_final: 0.6709 (m100) REVERT: A 92 LEU cc_start: 0.9374 (tt) cc_final: 0.9152 (tt) REVERT: A 111 VAL cc_start: 0.8568 (t) cc_final: 0.8223 (t) REVERT: E 71 HIS cc_start: 0.8072 (t70) cc_final: 0.7865 (t-170) REVERT: E 123 TYR cc_start: 0.9024 (t80) cc_final: 0.8599 (t80) REVERT: E 131 ASN cc_start: 0.9077 (t0) cc_final: 0.8783 (t0) REVERT: E 145 LEU cc_start: 0.9375 (tp) cc_final: 0.9143 (tp) REVERT: E 150 LYS cc_start: 0.8928 (mmmt) cc_final: 0.8624 (mmmt) REVERT: E 265 ARG cc_start: 0.8571 (mtp180) cc_final: 0.8341 (mmm-85) REVERT: E 382 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7798 (tm-30) REVERT: E 396 TYR cc_start: 0.8705 (t80) cc_final: 0.8477 (t80) REVERT: E 398 LYS cc_start: 0.9106 (tptt) cc_final: 0.8701 (tptt) REVERT: E 418 CYS cc_start: 0.8995 (t) cc_final: 0.8786 (t) REVERT: E 479 THR cc_start: 0.8624 (m) cc_final: 0.8207 (m) REVERT: E 498 GLN cc_start: 0.8142 (tt0) cc_final: 0.7727 (mt0) REVERT: E 524 VAL cc_start: 0.8111 (t) cc_final: 0.6878 (t) REVERT: E 527 ARG cc_start: 0.8970 (ttm110) cc_final: 0.7933 (mtm110) REVERT: E 595 SER cc_start: 0.8878 (p) cc_final: 0.8450 (t) REVERT: E 614 LEU cc_start: 0.7669 (tp) cc_final: 0.7322 (tp) REVERT: E 772 TYR cc_start: 0.8641 (t80) cc_final: 0.8430 (t80) REVERT: E 781 ASN cc_start: 0.8174 (p0) cc_final: 0.7725 (p0) REVERT: E 797 GLN cc_start: 0.8302 (pt0) cc_final: 0.7790 (pm20) REVERT: E 911 GLU cc_start: 0.6732 (pt0) cc_final: 0.4659 (tm-30) REVERT: E 1080 LEU cc_start: 0.9300 (tp) cc_final: 0.9036 (tp) REVERT: E 1088 TRP cc_start: 0.8062 (t-100) cc_final: 0.7766 (t60) REVERT: E 1138 SER cc_start: 0.8928 (t) cc_final: 0.8490 (t) REVERT: E 1147 THR cc_start: 0.8807 (t) cc_final: 0.7774 (t) REVERT: E 1201 VAL cc_start: 0.8934 (m) cc_final: 0.8434 (t) REVERT: E 1212 THR cc_start: 0.9169 (p) cc_final: 0.8669 (p) REVERT: E 1215 ARG cc_start: 0.8472 (mtm110) cc_final: 0.7459 (mtm110) REVERT: E 1225 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8498 (tm-30) REVERT: E 1298 MET cc_start: 0.8468 (ttp) cc_final: 0.7362 (ttp) REVERT: B 97 HIS cc_start: 0.8861 (t70) cc_final: 0.8565 (t-90) REVERT: B 116 SER cc_start: 0.9199 (p) cc_final: 0.8487 (t) REVERT: B 123 PHE cc_start: 0.8962 (t80) cc_final: 0.8751 (t80) REVERT: B 131 ILE cc_start: 0.9335 (mt) cc_final: 0.9095 (mt) REVERT: B 277 HIS cc_start: 0.8436 (t70) cc_final: 0.8078 (t-170) REVERT: B 313 GLN cc_start: 0.7374 (tt0) cc_final: 0.6776 (tt0) REVERT: C 60 PHE cc_start: 0.8827 (t80) cc_final: 0.8624 (t80) REVERT: C 128 GLN cc_start: 0.8764 (tt0) cc_final: 0.8389 (tt0) REVERT: C 146 ILE cc_start: 0.9495 (mt) cc_final: 0.9292 (mt) REVERT: C 212 SER cc_start: 0.9583 (m) cc_final: 0.9182 (p) REVERT: C 258 TYR cc_start: 0.8667 (p90) cc_final: 0.8082 (p90) REVERT: C 309 ILE cc_start: 0.9367 (mm) cc_final: 0.9107 (mm) REVERT: D 77 MET cc_start: 0.8470 (mmm) cc_final: 0.7931 (ttp) REVERT: D 136 ARG cc_start: 0.8483 (mtm-85) cc_final: 0.8272 (ptp-110) REVERT: D 234 HIS cc_start: 0.8208 (t70) cc_final: 0.7629 (t70) REVERT: D 273 SER cc_start: 0.9603 (m) cc_final: 0.8908 (t) REVERT: D 274 ASP cc_start: 0.8456 (t70) cc_final: 0.7916 (t0) outliers start: 1 outliers final: 1 residues processed: 877 average time/residue: 0.1272 time to fit residues: 178.1868 Evaluate side-chains 832 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 831 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 36 optimal weight: 4.9990 chunk 207 optimal weight: 0.0050 chunk 61 optimal weight: 40.0000 chunk 106 optimal weight: 5.9990 chunk 253 optimal weight: 5.9990 chunk 200 optimal weight: 40.0000 chunk 39 optimal weight: 20.0000 chunk 238 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 204 optimal weight: 5.9990 overall best weight: 2.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 GLN E 397 ASN ** E 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1203 HIS D 259 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.173992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.142414 restraints weight = 28500.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.144614 restraints weight = 19524.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.146492 restraints weight = 12595.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.147233 restraints weight = 10298.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.147381 restraints weight = 8615.219| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19889 Z= 0.125 Angle : 0.551 13.266 27244 Z= 0.285 Chirality : 0.043 0.158 3342 Planarity : 0.004 0.064 3400 Dihedral : 9.438 101.029 3166 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: 0.97 (0.16), residues: 2729 helix: 2.31 (0.14), residues: 1322 sheet: -0.87 (0.33), residues: 255 loop : -1.02 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 34 TYR 0.018 0.001 TYR E 475 PHE 0.052 0.002 PHE C 168 TRP 0.066 0.001 TRP B 83 HIS 0.006 0.001 HIS D 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (19884) covalent geometry : angle 0.55086 / 0.29 (27234) SS BOND : bond 0.00374 / 0.21 ( 5) SS BOND : angle 0.97551 / 0.52 ( 10) hydrogen bonds : bond 0.04028 / 2.88 ( 1171) hydrogen bonds : angle 3.86017 / 2.78 ( 3444) =============================================================================== Job complete usr+sys time: 3986.54 seconds wall clock time: 69 minutes 20.61 seconds (4160.61 seconds total)