Starting phenix.real_space_refine on Thu Sep 18 21:54:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u2x_26321/09_2025/7u2x_26321.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u2x_26321/09_2025/7u2x_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 { model { file = "/net/cci-nas-00/data/ceres_data/7u2x_26321/09_2025/7u2x_26321.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u2x_26321/09_2025/7u2x_26321.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u2x_26321/09_2025/7u2x_26321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u2x_26321/09_2025/7u2x_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-2.0-5805/lib/python3.9/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: 73 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: 4.81, 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: 1.99 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.79 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: 4.30 Time building geometry restraints manager: 2.56 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: 26550 1.74 - 3.48: 587 3.48 - 5.22: 80 5.22 - 6.96: 14 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 - 35.21: 11427 35.21 - 70.41: 206 70.41 - 105.62: 14 105.62 - 140.83: 7 140.83 - 176.04: 3 Dihedral angle restraints: 11657 sinusoidal: 3675 harmonic: 7982 Sorted by residual: dihedral pdb=" C27 P5S E1604 " pdb=" C28 P5S E1604 " pdb=" C29 P5S E1604 " pdb=" C30 P5S E1604 " ideal model delta sinusoidal sigma weight residual 298.90 122.86 176.04 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C21 P5S E1604 " pdb=" C22 P5S E1604 " pdb=" C23 P5S E1604 " pdb=" C24 P5S E1604 " ideal model delta sinusoidal sigma weight residual -64.63 106.33 -170.96 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C17 P5S E1604 " pdb=" C20 P5S E1604 " pdb=" C21 P5S E1604 " pdb=" C22 P5S E1604 " ideal model delta sinusoidal sigma weight residual 71.45 -76.55 148.00 1 3.00e+01 1.11e-03 1.97e+01 ... (remaining 11654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2852 0.063 - 0.126: 466 0.126 - 0.188: 22 0.188 - 0.251: 1 0.251 - 0.314: 1 Chirality restraints: 3342 Sorted by residual: chirality pdb=" C2 P5S E1604 " pdb=" C1 P5S E1604 " pdb=" C3 P5S E1604 " pdb=" O37 P5S E1604 " both_signs ideal model delta sigma weight residual False 2.59 2.28 0.31 2.00e-01 2.50e+01 2.46e+00 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 ... (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: 0.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 19.840 Find NCS groups from input model: 0.260 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 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= 0.239 Angle : 0.650 8.701 27244 Z= 0.360 Chirality : 0.045 0.314 3342 Planarity : 0.005 0.072 3400 Dihedral : 14.394 176.037 6454 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 aren 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 covalent geometry : bond 0.00500 (19884) covalent geometry : angle 0.64940 (27234) SS BOND : bond 0.00142 ( 5) SS BOND : angle 0.92575 ( 10) hydrogen bonds : bond 0.13268 ( 1171) hydrogen bonds : angle 5.50271 ( 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 : 0.541 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: 0.8635 (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: 0.9111 (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: 0.8891 (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: 0.8976 (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: 0.8521 (mt0) outliers start: 13 outliers final: 7 residues processed: 938 average time/residue: 0.1239 time to fit residues: 183.2148 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 : 0.696 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.188812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.153493 restraints weight = 28861.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.157585 restraints weight = 14779.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.160333 restraints weight = 9250.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.162072 restraints weight = 6649.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.163387 restraints weight = 5320.966| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 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 0.049 19889 Z= 0.146 Angle : 0.552 10.043 27244 Z= 0.293 Chirality : 0.043 0.234 3342 Planarity : 0.005 0.063 3400 Dihedral : 12.956 173.667 3319 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % 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 aren not related in a simple way. whole: 0.41 (0.16), residues: 2729 helix: 1.90 (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 0.011 0.001 ARG B 314 TYR 0.025 0.002 TYR A 258 PHE 0.038 0.002 PHE C 168 TRP 0.021 0.001 TRP E 739 HIS 0.009 0.001 HIS E 326 Details of bonding type rmsd covalent geometry : bond 0.00305 (19884) covalent geometry : angle 0.55211 (27234) SS BOND : bond 0.00516 ( 5) SS BOND : angle 1.08583 ( 10) hydrogen bonds : bond 0.04647 ( 1171) hydrogen bonds : angle 4.25867 ( 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 : 0.557 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: 0.9262 (m-10) cc_final: 0.8807 (m-10) REVERT: A 90 TRP cc_start: 0.8923 (m100) cc_final: 0.6219 (m100) REVERT: A 91 TRP cc_start: 0.9115 (t60) cc_final: 0.7912 (t60) REVERT: A 92 LEU cc_start: 0.9438 (tt) cc_final: 0.9199 (tt) REVERT: A 121 PHE cc_start: 0.9566 (t80) cc_final: 0.9156 (t80) REVERT: A 152 GLN cc_start: 0.8887 (tt0) cc_final: 0.8551 (tt0) REVERT: A 210 ILE cc_start: 0.8995 (mt) cc_final: 0.8775 (mt) REVERT: A 211 ILE cc_start: 0.9373 (mt) cc_final: 0.8981 (mt) REVERT: A 260 VAL cc_start: 0.8642 (t) cc_final: 0.8246 (p) REVERT: A 301 ARG cc_start: 0.8610 (mtm-85) cc_final: 0.8203 (mtm-85) REVERT: E 16 ARG cc_start: 0.8351 (mmt180) cc_final: 0.7928 (mtp85) REVERT: E 71 HIS cc_start: 0.7957 (t70) cc_final: 0.7154 (t70) REVERT: E 104 LEU cc_start: 0.9065 (tp) cc_final: 0.8858 (tp) REVERT: E 150 LYS cc_start: 0.8714 (tptp) cc_final: 0.8506 (mmmt) REVERT: E 263 TYR cc_start: 0.9315 (t80) cc_final: 0.8550 (t80) REVERT: E 372 PHE cc_start: 0.9087 (m-10) cc_final: 0.8746 (m-80) REVERT: E 396 TYR cc_start: 0.8891 (t80) cc_final: 0.8642 (t80) REVERT: E 397 ASN cc_start: 0.7866 (t0) cc_final: 0.7403 (t0) REVERT: E 398 LYS cc_start: 0.8947 (tptt) cc_final: 0.8744 (tptt) REVERT: E 498 GLN cc_start: 0.7931 (tt0) cc_final: 0.7340 (mt0) REVERT: E 512 TYR cc_start: 0.7527 (m-80) cc_final: 0.6942 (m-80) REVERT: E 577 PHE cc_start: 0.8476 (m-80) cc_final: 0.8188 (m-80) REVERT: E 595 SER cc_start: 0.8947 (p) cc_final: 0.8576 (t) REVERT: E 685 PHE cc_start: 0.6196 (m-10) cc_final: 0.5973 (m-10) REVERT: E 772 TYR cc_start: 0.8741 (t80) cc_final: 0.8356 (t80) REVERT: E 797 GLN cc_start: 0.8560 (pt0) cc_final: 0.8072 (pm20) REVERT: E 799 TYR cc_start: 0.8771 (t80) cc_final: 0.8410 (t80) REVERT: E 848 THR cc_start: 0.7963 (p) cc_final: 0.7747 (p) REVERT: E 911 GLU cc_start: 0.6888 (pt0) cc_final: 0.4812 (tm-30) REVERT: E 1025 MET cc_start: 0.7274 (mmm) cc_final: 0.6936 (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: 0.7785 (t60) REVERT: E 1123 ASN cc_start: 0.8373 (t0) cc_final: 0.8118 (t0) REVERT: E 1201 VAL cc_start: 0.8512 (m) cc_final: 0.8185 (t) REVERT: E 1225 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8262 (tm-30) REVERT: E 1298 MET cc_start: 0.8715 (ttp) cc_final: 0.8275 (ttp) REVERT: E 1308 GLN cc_start: 0.8756 (mt0) cc_final: 0.8346 (tt0) REVERT: B 60 PHE cc_start: 0.9350 (t80) cc_final: 0.8815 (t80) REVERT: B 71 THR cc_start: 0.9267 (m) cc_final: 0.9058 (m) REVERT: B 83 TRP cc_start: 0.9289 (m-10) cc_final: 0.8884 (m-10) REVERT: B 97 HIS cc_start: 0.8864 (t70) cc_final: 0.8604 (t-90) REVERT: B 114 ILE cc_start: 0.8841 (mm) cc_final: 0.8471 (tp) REVERT: B 116 SER cc_start: 0.9442 (p) cc_final: 0.9161 (t) REVERT: B 123 PHE cc_start: 0.9005 (t80) cc_final: 0.8740 (t80) REVERT: B 149 LEU cc_start: 0.8411 (tt) cc_final: 0.8079 (tt) REVERT: B 212 SER cc_start: 0.9370 (t) cc_final: 0.9109 (t) REVERT: B 250 PHE cc_start: 0.9101 (t80) cc_final: 0.8808 (t80) REVERT: B 252 VAL cc_start: 0.9318 (t) cc_final: 0.9091 (t) REVERT: B 254 PRO cc_start: 0.9466 (Cg_exo) cc_final: 0.9088 (Cg_endo) REVERT: B 277 HIS cc_start: 0.8109 (t70) cc_final: 0.7559 (t-170) REVERT: B 299 GLN cc_start: 0.8867 (mt0) cc_final: 0.8641 (mt0) REVERT: B 313 GLN cc_start: 0.7849 (mt0) cc_final: 0.7525 (tt0) REVERT: B 338 LYS cc_start: 0.9058 (tttm) cc_final: 0.8825 (ttmt) REVERT: C 68 TRP cc_start: 0.8169 (m100) cc_final: 0.7854 (m100) REVERT: C 128 GLN cc_start: 0.8846 (tt0) cc_final: 0.8447 (tt0) REVERT: C 211 ILE cc_start: 0.9664 (mt) cc_final: 0.9405 (mt) REVERT: C 215 ILE cc_start: 0.9285 (mm) cc_final: 0.8921 (mm) REVERT: C 258 TYR cc_start: 0.8429 (p90) cc_final: 0.7942 (p90) REVERT: C 287 LEU cc_start: 0.9369 (tp) cc_final: 0.9147 (tp) REVERT: C 318 ILE cc_start: 0.8443 (mm) cc_final: 0.8240 (mm) REVERT: D 112 THR cc_start: 0.9386 (p) cc_final: 0.9145 (t) REVERT: D 211 ILE cc_start: 0.9355 (mt) cc_final: 0.8949 (mt) REVERT: D 273 SER cc_start: 0.9619 (m) cc_final: 0.9061 (t) REVERT: D 274 ASP cc_start: 0.8537 (t70) cc_final: 0.7978 (t0) REVERT: D 299 GLN cc_start: 0.8750 (mt0) cc_final: 0.8327 (mt0) outliers start: 0 outliers final: 0 residues processed: 915 average time/residue: 0.1186 time to fit residues: 171.7011 Evaluate side-chains 847 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 847 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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: 8.9990 chunk 7 optimal weight: 5.9990 chunk 243 optimal weight: 9.9990 chunk 200 optimal weight: 0.0020 chunk 145 optimal weight: 6.9990 chunk 125 optimal weight: 30.0000 chunk 242 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 overall best weight: 4.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 235 GLN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.186481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.150010 restraints weight = 29108.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.154082 restraints weight = 15168.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.156773 restraints weight = 9590.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.158487 restraints weight = 6976.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.159749 restraints weight = 5642.048| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 19889 Z= 0.193 Angle : 0.582 10.353 27244 Z= 0.307 Chirality : 0.044 0.220 3342 Planarity : 0.004 0.053 3400 Dihedral : 12.101 148.749 3319 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.13 % Allowed : 2.82 % Favored : 97.06 % 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 aren not related in a simple way. whole: 0.49 (0.16), residues: 2729 helix: 1.91 (0.14), residues: 1346 sheet: -1.26 (0.32), residues: 258 loop : -1.27 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 527 TYR 0.020 0.002 TYR E 142 PHE 0.034 0.002 PHE E 44 TRP 0.025 0.002 TRP E 143 HIS 0.009 0.001 HIS E 326 Details of bonding type rmsd covalent geometry : bond 0.00422 (19884) covalent geometry : angle 0.58146 (27234) SS BOND : bond 0.01202 ( 5) SS BOND : angle 0.98428 ( 10) hydrogen bonds : bond 0.04573 ( 1171) hydrogen bonds : angle 4.20042 ( 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 891 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 889 time to evaluate : 0.565 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 90 TRP cc_start: 0.9002 (m100) cc_final: 0.6280 (m100) REVERT: A 91 TRP cc_start: 0.9155 (t60) cc_final: 0.8371 (t60) REVERT: A 92 LEU cc_start: 0.9449 (tt) cc_final: 0.9198 (tt) REVERT: A 148 ILE cc_start: 0.9310 (tt) cc_final: 0.9020 (tt) REVERT: A 152 GLN cc_start: 0.9068 (tt0) cc_final: 0.8726 (tt0) REVERT: A 210 ILE cc_start: 0.9022 (mt) cc_final: 0.8808 (mt) REVERT: A 255 LEU cc_start: 0.8819 (mt) cc_final: 0.8601 (mt) REVERT: A 260 VAL cc_start: 0.8649 (t) cc_final: 0.8267 (p) REVERT: A 301 ARG cc_start: 0.8638 (mtm-85) cc_final: 0.8240 (mtm-85) REVERT: E 16 ARG cc_start: 0.8375 (mmt180) cc_final: 0.8060 (mtp85) REVERT: E 71 HIS cc_start: 0.8145 (t70) cc_final: 0.7272 (t-170) REVERT: E 145 LEU cc_start: 0.9294 (tp) cc_final: 0.9031 (tp) REVERT: E 179 TYR cc_start: 0.8859 (m-10) cc_final: 0.8642 (m-10) REVERT: E 263 TYR cc_start: 0.9265 (t80) cc_final: 0.8691 (t80) REVERT: E 397 ASN cc_start: 0.8167 (t0) cc_final: 0.7704 (t0) REVERT: E 398 LYS cc_start: 0.8931 (tptt) cc_final: 0.8687 (tptt) REVERT: E 498 GLN cc_start: 0.7986 (tt0) cc_final: 0.7486 (mt0) REVERT: E 512 TYR cc_start: 0.7296 (m-80) cc_final: 0.6744 (m-80) REVERT: E 577 PHE cc_start: 0.8502 (m-80) cc_final: 0.8242 (m-80) REVERT: E 595 SER cc_start: 0.8972 (p) cc_final: 0.8695 (t) REVERT: E 772 TYR cc_start: 0.8740 (t80) cc_final: 0.8379 (t80) REVERT: E 781 ASN cc_start: 0.8346 (p0) cc_final: 0.7943 (p0) REVERT: E 797 GLN cc_start: 0.8621 (pt0) cc_final: 0.8070 (pm20) REVERT: E 799 TYR cc_start: 0.8805 (t80) cc_final: 0.8482 (t80) REVERT: E 845 TYR cc_start: 0.7314 (t80) cc_final: 0.6944 (t80) REVERT: E 911 GLU cc_start: 0.6951 (pt0) cc_final: 0.4959 (tm-30) REVERT: E 1025 MET cc_start: 0.7293 (mmm) cc_final: 0.6997 (mmp) REVERT: E 1080 LEU cc_start: 0.9212 (tp) cc_final: 0.8889 (tp) REVERT: E 1088 TRP cc_start: 0.8057 (t-100) cc_final: 0.7787 (t60) REVERT: E 1225 GLN cc_start: 0.9136 (mm-40) cc_final: 0.8383 (tm-30) REVERT: E 1269 SER cc_start: 0.8978 (t) cc_final: 0.8747 (p) REVERT: E 1308 GLN cc_start: 0.8809 (mt0) cc_final: 0.8591 (tt0) REVERT: B 60 PHE cc_start: 0.9364 (t80) cc_final: 0.8882 (t80) REVERT: B 83 TRP cc_start: 0.9125 (m-10) cc_final: 0.8878 (m-10) REVERT: B 97 HIS cc_start: 0.8956 (t70) cc_final: 0.8672 (t-90) REVERT: B 114 ILE cc_start: 0.8916 (mm) cc_final: 0.8506 (tp) REVERT: B 116 SER cc_start: 0.9480 (p) cc_final: 0.9073 (t) REVERT: B 129 VAL cc_start: 0.9566 (t) cc_final: 0.9349 (t) REVERT: B 212 SER cc_start: 0.9533 (t) cc_final: 0.9238 (t) REVERT: B 216 HIS cc_start: 0.7560 (m-70) cc_final: 0.7182 (m-70) REVERT: B 240 MET cc_start: 0.8256 (tmm) cc_final: 0.7949 (tmm) REVERT: B 250 PHE cc_start: 0.9092 (t80) cc_final: 0.8677 (t80) REVERT: B 252 VAL cc_start: 0.9341 (t) cc_final: 0.9117 (t) REVERT: B 254 PRO cc_start: 0.9481 (Cg_exo) cc_final: 0.9165 (Cg_endo) REVERT: B 277 HIS cc_start: 0.8170 (t70) cc_final: 0.7597 (t-170) REVERT: B 299 GLN cc_start: 0.8968 (mt0) cc_final: 0.8646 (mt0) REVERT: B 313 GLN cc_start: 0.7779 (mt0) cc_final: 0.7555 (tt0) REVERT: B 338 LYS cc_start: 0.9112 (tttm) cc_final: 0.8843 (ttmt) REVERT: C 128 GLN cc_start: 0.8915 (tt0) cc_final: 0.8589 (tt0) REVERT: C 147 LEU cc_start: 0.8984 (tp) cc_final: 0.8776 (tp) REVERT: C 211 ILE cc_start: 0.9658 (mt) cc_final: 0.9413 (mt) REVERT: C 215 ILE cc_start: 0.9328 (mm) cc_final: 0.8947 (mm) REVERT: C 258 TYR cc_start: 0.8403 (p90) cc_final: 0.7835 (p90) REVERT: C 318 ILE cc_start: 0.8622 (mm) cc_final: 0.8416 (mm) REVERT: D 37 SER cc_start: 0.8833 (t) cc_final: 0.8447 (p) REVERT: D 180 THR cc_start: 0.8792 (p) cc_final: 0.8589 (p) REVERT: D 181 LEU cc_start: 0.9271 (mm) cc_final: 0.9064 (mm) REVERT: D 201 ARG cc_start: 0.8363 (mtt-85) cc_final: 0.7903 (mtt-85) REVERT: D 233 LEU cc_start: 0.8678 (mt) cc_final: 0.8380 (mt) REVERT: D 240 MET cc_start: 0.8417 (tmm) cc_final: 0.7920 (tmm) REVERT: D 273 SER cc_start: 0.9617 (m) cc_final: 0.9042 (t) REVERT: D 274 ASP cc_start: 0.8597 (t70) cc_final: 0.8027 (t0) outliers start: 2 outliers final: 0 residues processed: 889 average time/residue: 0.1195 time to fit residues: 167.4893 Evaluate side-chains 840 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 840 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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: 7.9990 chunk 9 optimal weight: 7.9990 chunk 172 optimal weight: 50.0000 chunk 150 optimal weight: 6.9990 chunk 140 optimal weight: 8.9990 chunk 247 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 235 GLN A 277 HIS E 24 ASN E 32 ASN ** E 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1296 ASN B 218 GLN 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 = 0.3822 r_free = 0.3822 target = 0.172008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.140736 restraints weight = 28662.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.142893 restraints weight = 17886.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.144122 restraints weight = 11436.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.144838 restraints weight = 10720.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.144891 restraints weight = 8669.540| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 19889 Z= 0.172 Angle : 0.559 9.638 27244 Z= 0.293 Chirality : 0.044 0.259 3342 Planarity : 0.004 0.048 3400 Dihedral : 11.709 137.272 3319 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.06 % Allowed : 3.01 % 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 aren not related in a simple way. whole: 0.60 (0.16), residues: 2729 helix: 2.01 (0.14), residues: 1347 sheet: -1.30 (0.31), residues: 264 loop : -1.22 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 136 TYR 0.020 0.002 TYR E 142 PHE 0.032 0.002 PHE C 168 TRP 0.014 0.001 TRP A 83 HIS 0.007 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00382 (19884) covalent geometry : angle 0.55893 (27234) SS BOND : bond 0.00104 ( 5) SS BOND : angle 0.93902 ( 10) hydrogen bonds : bond 0.04295 ( 1171) hydrogen bonds : angle 4.06380 ( 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 887 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 886 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 TRP cc_start: 0.9009 (m100) cc_final: 0.6384 (m100) REVERT: A 91 TRP cc_start: 0.9143 (t60) cc_final: 0.8432 (t60) REVERT: A 92 LEU cc_start: 0.9373 (tt) cc_final: 0.9106 (tt) REVERT: A 148 ILE cc_start: 0.9249 (tt) cc_final: 0.8980 (tt) REVERT: A 152 GLN cc_start: 0.9120 (tt0) cc_final: 0.8816 (tt0) REVERT: A 301 ARG cc_start: 0.8648 (mtm-85) cc_final: 0.8251 (mtm-85) REVERT: E 71 HIS cc_start: 0.8139 (t70) cc_final: 0.7452 (t-90) REVERT: E 123 TYR cc_start: 0.9093 (t80) cc_final: 0.8672 (t80) REVERT: E 131 ASN cc_start: 0.9295 (t0) cc_final: 0.8976 (t0) REVERT: E 145 LEU cc_start: 0.9410 (tp) cc_final: 0.9197 (tp) REVERT: E 179 TYR cc_start: 0.8810 (m-10) cc_final: 0.8542 (m-10) REVERT: E 215 VAL cc_start: 0.8117 (p) cc_final: 0.7719 (m) REVERT: E 397 ASN cc_start: 0.8298 (t0) cc_final: 0.7617 (t0) REVERT: E 398 LYS cc_start: 0.9129 (tptt) cc_final: 0.8907 (tptt) REVERT: E 479 THR cc_start: 0.8235 (m) cc_final: 0.7791 (m) REVERT: E 498 GLN cc_start: 0.8156 (tt0) cc_final: 0.7708 (mt0) REVERT: E 512 TYR cc_start: 0.7318 (m-80) cc_final: 0.6781 (m-80) REVERT: E 524 VAL cc_start: 0.8531 (t) cc_final: 0.7626 (t) REVERT: E 527 ARG cc_start: 0.9005 (ttm110) cc_final: 0.8165 (mtm110) REVERT: E 577 PHE cc_start: 0.8529 (m-80) cc_final: 0.8250 (m-80) REVERT: E 595 SER cc_start: 0.8899 (p) cc_final: 0.8436 (t) REVERT: E 772 TYR cc_start: 0.8815 (t80) cc_final: 0.8559 (t80) REVERT: E 781 ASN cc_start: 0.8257 (p0) cc_final: 0.7791 (p0) REVERT: E 797 GLN cc_start: 0.8425 (pt0) cc_final: 0.7984 (pm20) REVERT: E 799 TYR cc_start: 0.8841 (t80) cc_final: 0.8527 (t80) REVERT: E 845 TYR cc_start: 0.6971 (t80) cc_final: 0.6613 (t80) REVERT: E 911 GLU cc_start: 0.7014 (pt0) cc_final: 0.5224 (tm-30) REVERT: E 1025 MET cc_start: 0.7124 (mmm) cc_final: 0.6899 (mmp) REVERT: E 1080 LEU cc_start: 0.9232 (tp) cc_final: 0.8939 (tp) REVERT: E 1088 TRP cc_start: 0.8026 (t-100) cc_final: 0.7800 (t60) REVERT: E 1149 LEU cc_start: 0.8862 (mp) cc_final: 0.8549 (mp) REVERT: E 1201 VAL cc_start: 0.8909 (m) cc_final: 0.8476 (m) REVERT: E 1225 GLN cc_start: 0.9102 (mm-40) cc_final: 0.8629 (tm-30) REVERT: E 1308 GLN cc_start: 0.8519 (mt0) cc_final: 0.8263 (tt0) REVERT: B 83 TRP cc_start: 0.9241 (m-10) cc_final: 0.9004 (m-10) REVERT: B 97 HIS cc_start: 0.8881 (t70) cc_final: 0.8586 (t-90) REVERT: B 212 SER cc_start: 0.9565 (t) cc_final: 0.9313 (t) REVERT: B 216 HIS cc_start: 0.7617 (m-70) cc_final: 0.7349 (m-70) REVERT: B 254 PRO cc_start: 0.9413 (Cg_exo) cc_final: 0.9082 (Cg_endo) REVERT: B 277 HIS cc_start: 0.8363 (t70) cc_final: 0.7934 (t-170) REVERT: B 338 LYS cc_start: 0.9229 (tttm) cc_final: 0.8928 (ttmt) REVERT: C 90 TRP cc_start: 0.9042 (m100) cc_final: 0.8828 (m100) REVERT: C 128 GLN cc_start: 0.8867 (tt0) cc_final: 0.8429 (tt0) REVERT: C 215 ILE cc_start: 0.9437 (mm) cc_final: 0.9142 (mm) REVERT: C 258 TYR cc_start: 0.8437 (p90) cc_final: 0.7876 (p90) REVERT: D 37 SER cc_start: 0.8791 (t) cc_final: 0.8442 (p) REVERT: D 201 ARG cc_start: 0.8560 (mtt-85) cc_final: 0.8239 (mtt-85) REVERT: D 233 LEU cc_start: 0.8569 (mt) cc_final: 0.8292 (mt) REVERT: D 273 SER cc_start: 0.9588 (m) cc_final: 0.8968 (t) REVERT: D 274 ASP cc_start: 0.8463 (t70) cc_final: 0.7877 (t0) outliers start: 1 outliers final: 0 residues processed: 886 average time/residue: 0.1180 time to fit residues: 166.4741 Evaluate side-chains 844 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 844 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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: 2.9990 chunk 208 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 195 optimal weight: 20.0000 chunk 117 optimal weight: 40.0000 chunk 4 optimal weight: 30.0000 chunk 150 optimal weight: 6.9990 chunk 96 optimal weight: 50.0000 chunk 199 optimal weight: 20.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 235 GLN E 32 ASN B 299 GLN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN D 259 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.173717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.141715 restraints weight = 28461.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.144137 restraints weight = 17468.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.146021 restraints weight = 11486.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.147128 restraints weight = 9241.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.146904 restraints weight = 7575.228| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2561 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= 0.145 Angle : 0.546 10.295 27244 Z= 0.285 Chirality : 0.043 0.203 3342 Planarity : 0.004 0.048 3400 Dihedral : 11.439 140.495 3319 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.13 % Allowed : 2.32 % 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 aren not related in a simple way. whole: 0.67 (0.16), residues: 2729 helix: 2.14 (0.14), residues: 1341 sheet: -1.34 (0.30), residues: 283 loop : -1.23 (0.19), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 301 TYR 0.016 0.001 TYR A 258 PHE 0.035 0.002 PHE E 44 TRP 0.011 0.001 TRP A 83 HIS 0.006 0.001 HIS E 103 Details of bonding type rmsd covalent geometry : bond 0.00320 (19884) covalent geometry : angle 0.54616 (27234) SS BOND : bond 0.00471 ( 5) SS BOND : angle 0.97279 ( 10) hydrogen bonds : bond 0.04178 ( 1171) hydrogen bonds : angle 3.95858 ( 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 884 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 882 time to evaluate : 0.513 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: 0.8957 (m100) cc_final: 0.6432 (m100) REVERT: A 91 TRP cc_start: 0.9154 (t60) cc_final: 0.8370 (t60) REVERT: A 92 LEU cc_start: 0.9320 (tt) cc_final: 0.9059 (tt) REVERT: A 111 VAL cc_start: 0.8777 (t) cc_final: 0.8407 (t) REVERT: A 148 ILE cc_start: 0.9227 (tt) cc_final: 0.8935 (tt) REVERT: A 152 GLN cc_start: 0.9155 (tt0) cc_final: 0.8781 (tt0) REVERT: A 299 GLN cc_start: 0.8959 (tt0) cc_final: 0.8727 (tt0) REVERT: A 301 ARG cc_start: 0.8522 (mtm-85) cc_final: 0.8267 (mtm-85) REVERT: E 39 LEU cc_start: 0.9285 (tt) cc_final: 0.9083 (tt) REVERT: E 71 HIS cc_start: 0.7984 (t70) cc_final: 0.7782 (t-170) REVERT: E 112 MET cc_start: 0.8888 (mmt) cc_final: 0.8508 (mmt) REVERT: E 123 TYR cc_start: 0.9051 (t80) cc_final: 0.8672 (t80) REVERT: E 131 ASN cc_start: 0.9290 (t0) cc_final: 0.8871 (t0) REVERT: E 145 LEU cc_start: 0.9397 (tp) cc_final: 0.9098 (tp) REVERT: E 179 TYR cc_start: 0.8847 (m-10) cc_final: 0.8413 (m-10) REVERT: E 215 VAL cc_start: 0.7867 (p) cc_final: 0.7332 (m) REVERT: E 216 ARG cc_start: 0.7989 (mpt180) cc_final: 0.7554 (mpt180) REVERT: E 417 ILE cc_start: 0.9310 (tt) cc_final: 0.9054 (tt) REVERT: E 498 GLN cc_start: 0.8138 (tt0) cc_final: 0.7672 (mt0) REVERT: E 512 TYR cc_start: 0.7329 (m-80) cc_final: 0.6777 (m-80) REVERT: E 524 VAL cc_start: 0.8476 (t) cc_final: 0.7286 (t) REVERT: E 527 ARG cc_start: 0.9028 (ttm110) cc_final: 0.8057 (mtm110) REVERT: E 577 PHE cc_start: 0.8520 (m-80) cc_final: 0.8254 (m-80) REVERT: E 595 SER cc_start: 0.8860 (p) cc_final: 0.8422 (t) REVERT: E 685 PHE cc_start: 0.6318 (m-10) cc_final: 0.6098 (m-80) REVERT: E 772 TYR cc_start: 0.8664 (t80) cc_final: 0.8359 (t80) REVERT: E 781 ASN cc_start: 0.8127 (p0) cc_final: 0.7690 (p0) REVERT: E 797 GLN cc_start: 0.8417 (pt0) cc_final: 0.7972 (pm20) REVERT: E 799 TYR cc_start: 0.8801 (t80) cc_final: 0.8516 (t80) REVERT: E 845 TYR cc_start: 0.6947 (t80) cc_final: 0.6552 (t80) REVERT: E 911 GLU cc_start: 0.7001 (pt0) cc_final: 0.5238 (tm-30) REVERT: E 1025 MET cc_start: 0.7068 (mmm) cc_final: 0.6862 (mmp) REVERT: E 1080 LEU cc_start: 0.9307 (tp) cc_final: 0.9056 (tp) REVERT: E 1088 TRP cc_start: 0.8045 (t-100) cc_final: 0.7784 (t60) REVERT: E 1138 SER cc_start: 0.8884 (t) cc_final: 0.8414 (t) REVERT: E 1149 LEU cc_start: 0.8851 (mp) cc_final: 0.8511 (mp) REVERT: E 1207 THR cc_start: 0.8566 (m) cc_final: 0.8313 (m) REVERT: E 1225 GLN cc_start: 0.9083 (mm-40) cc_final: 0.8618 (tm-30) REVERT: E 1308 GLN cc_start: 0.8424 (mt0) cc_final: 0.8205 (tt0) REVERT: B 50 ARG cc_start: 0.7800 (mpp80) cc_final: 0.7432 (mmm160) REVERT: B 78 SER cc_start: 0.9291 (p) cc_final: 0.8978 (p) REVERT: B 83 TRP cc_start: 0.9185 (m-10) cc_final: 0.8917 (m-10) REVERT: B 97 HIS cc_start: 0.8906 (t70) cc_final: 0.8702 (t-90) REVERT: B 116 SER cc_start: 0.9346 (p) cc_final: 0.9019 (t) REVERT: B 123 PHE cc_start: 0.8963 (t80) cc_final: 0.8736 (t80) REVERT: B 131 ILE cc_start: 0.9331 (mt) cc_final: 0.9060 (mt) REVERT: B 158 MET cc_start: 0.8673 (mmp) cc_final: 0.8432 (mmp) REVERT: B 212 SER cc_start: 0.9607 (t) cc_final: 0.9325 (t) REVERT: B 216 HIS cc_start: 0.7644 (m-70) cc_final: 0.7355 (m-70) REVERT: B 277 HIS cc_start: 0.8309 (t70) cc_final: 0.7936 (t-170) REVERT: C 60 PHE cc_start: 0.8874 (t80) cc_final: 0.8670 (t80) REVERT: C 128 GLN cc_start: 0.8814 (tt0) cc_final: 0.8430 (tt0) REVERT: C 146 ILE cc_start: 0.9522 (mt) cc_final: 0.9314 (mt) REVERT: C 215 ILE cc_start: 0.9426 (mm) cc_final: 0.9162 (mm) REVERT: C 258 TYR cc_start: 0.8508 (p90) cc_final: 0.7912 (p90) REVERT: C 318 ILE cc_start: 0.8418 (mm) cc_final: 0.8168 (mm) REVERT: D 37 SER cc_start: 0.8769 (t) cc_final: 0.8454 (p) REVERT: D 77 MET cc_start: 0.8487 (mmm) cc_final: 0.8034 (mtp) REVERT: D 201 ARG cc_start: 0.8556 (mtt-85) cc_final: 0.8098 (mtt-85) REVERT: D 233 LEU cc_start: 0.8636 (mt) cc_final: 0.8292 (mt) REVERT: D 268 TYR cc_start: 0.8639 (t80) cc_final: 0.8148 (t80) REVERT: D 273 SER cc_start: 0.9583 (m) cc_final: 0.8950 (t) REVERT: D 274 ASP cc_start: 0.8482 (t70) cc_final: 0.7894 (t0) outliers start: 2 outliers final: 1 residues processed: 882 average time/residue: 0.1134 time to fit residues: 159.8619 Evaluate side-chains 843 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 842 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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: 10.0000 chunk 266 optimal weight: 0.0570 chunk 99 optimal weight: 50.0000 chunk 104 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 191 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 226 optimal weight: 9.9990 chunk 178 optimal weight: 1.9990 overall best weight: 3.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 247 ASN E 32 ASN E 103 HIS B 299 GLN B 313 GLN D 277 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.172912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.141546 restraints weight = 28384.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.143649 restraints weight = 17718.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.145671 restraints weight = 11455.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.146399 restraints weight = 9894.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.146411 restraints weight = 7837.834| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19889 Z= 0.152 Angle : 0.548 12.682 27244 Z= 0.285 Chirality : 0.043 0.299 3342 Planarity : 0.004 0.048 3400 Dihedral : 11.214 138.678 3319 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.13 % Allowed : 2.00 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.16), residues: 2729 helix: 2.19 (0.14), residues: 1344 sheet: -1.25 (0.31), residues: 282 loop : -1.18 (0.19), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 486 TYR 0.029 0.002 TYR D 268 PHE 0.037 0.002 PHE C 168 TRP 0.010 0.001 TRP E 232 HIS 0.005 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00339 (19884) covalent geometry : angle 0.54782 (27234) SS BOND : bond 0.00111 ( 5) SS BOND : angle 0.74332 ( 10) hydrogen bonds : bond 0.04125 ( 1171) hydrogen bonds : angle 3.92230 ( 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 883 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 881 time to evaluate : 0.487 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 90 TRP cc_start: 0.8964 (m100) cc_final: 0.6483 (m100) REVERT: A 92 LEU cc_start: 0.9347 (tt) cc_final: 0.9118 (tt) REVERT: A 111 VAL cc_start: 0.8747 (t) cc_final: 0.8355 (t) REVERT: A 130 THR cc_start: 0.9002 (p) cc_final: 0.8764 (p) REVERT: A 148 ILE cc_start: 0.9196 (tt) cc_final: 0.8954 (tt) REVERT: A 152 GLN cc_start: 0.9138 (tt0) cc_final: 0.8775 (tt0) REVERT: A 185 LYS cc_start: 0.9407 (mttt) cc_final: 0.9182 (mttm) REVERT: A 201 ARG cc_start: 0.8384 (ttt90) cc_final: 0.8016 (ttt180) REVERT: A 299 GLN cc_start: 0.8915 (tt0) cc_final: 0.8596 (tt0) REVERT: A 301 ARG cc_start: 0.8567 (mtm-85) cc_final: 0.8268 (mtm-85) REVERT: E 71 HIS cc_start: 0.8049 (t70) cc_final: 0.7292 (t-170) REVERT: E 112 MET cc_start: 0.9021 (mmt) cc_final: 0.8404 (mmt) REVERT: E 123 TYR cc_start: 0.9027 (t80) cc_final: 0.8660 (t80) REVERT: E 131 ASN cc_start: 0.9279 (t0) cc_final: 0.8902 (t0) REVERT: E 145 LEU cc_start: 0.9398 (tp) cc_final: 0.9165 (tp) REVERT: E 215 VAL cc_start: 0.7882 (p) cc_final: 0.7317 (m) REVERT: E 216 ARG cc_start: 0.7984 (mpt180) cc_final: 0.7502 (mpt180) REVERT: E 498 GLN cc_start: 0.8140 (tt0) cc_final: 0.7668 (mt0) REVERT: E 512 TYR cc_start: 0.7353 (m-80) cc_final: 0.6770 (m-80) REVERT: E 527 ARG cc_start: 0.9024 (ttm110) cc_final: 0.8213 (mtm110) REVERT: E 577 PHE cc_start: 0.8531 (m-80) cc_final: 0.8250 (m-80) REVERT: E 595 SER cc_start: 0.8875 (p) cc_final: 0.8462 (t) REVERT: E 598 ARG cc_start: 0.8520 (tpp80) cc_final: 0.8243 (mmt-90) REVERT: E 685 PHE cc_start: 0.6278 (m-10) cc_final: 0.6053 (m-80) REVERT: E 772 TYR cc_start: 0.8670 (t80) cc_final: 0.8394 (t80) REVERT: E 781 ASN cc_start: 0.8141 (p0) cc_final: 0.7684 (p0) REVERT: E 797 GLN cc_start: 0.8355 (pt0) cc_final: 0.7982 (pm20) REVERT: E 799 TYR cc_start: 0.8806 (t80) cc_final: 0.8507 (t80) REVERT: E 845 TYR cc_start: 0.6919 (t80) cc_final: 0.6419 (t80) REVERT: E 911 GLU cc_start: 0.6263 (pt0) cc_final: 0.4530 (tm-30) REVERT: E 1080 LEU cc_start: 0.9307 (tp) cc_final: 0.9051 (tp) REVERT: E 1088 TRP cc_start: 0.8043 (t-100) cc_final: 0.7787 (t60) REVERT: E 1138 SER cc_start: 0.8982 (t) cc_final: 0.8546 (t) REVERT: E 1212 THR cc_start: 0.9163 (p) cc_final: 0.8726 (p) REVERT: E 1215 ARG cc_start: 0.8720 (mtm110) cc_final: 0.8324 (mtm110) REVERT: E 1225 GLN cc_start: 0.9124 (mm-40) cc_final: 0.8487 (tm-30) REVERT: E 1308 GLN cc_start: 0.8484 (mt0) cc_final: 0.8260 (tt0) REVERT: B 46 HIS cc_start: 0.8566 (m90) cc_final: 0.8205 (m-70) REVERT: B 78 SER cc_start: 0.9255 (p) cc_final: 0.8905 (p) REVERT: B 83 TRP cc_start: 0.9177 (m-10) cc_final: 0.8923 (m-10) REVERT: B 116 SER cc_start: 0.9326 (p) cc_final: 0.8971 (t) REVERT: B 123 PHE cc_start: 0.8918 (t80) cc_final: 0.8653 (t80) REVERT: B 131 ILE cc_start: 0.9382 (mt) cc_final: 0.9026 (mt) REVERT: B 212 SER cc_start: 0.9613 (t) cc_final: 0.9346 (t) REVERT: B 216 HIS cc_start: 0.7699 (m-70) cc_final: 0.7441 (m-70) REVERT: B 277 HIS cc_start: 0.8387 (t70) cc_final: 0.7959 (t-170) REVERT: C 60 PHE cc_start: 0.8872 (t80) cc_final: 0.8594 (t80) REVERT: C 128 GLN cc_start: 0.8845 (tt0) cc_final: 0.8416 (tt0) REVERT: C 146 ILE cc_start: 0.9523 (mt) cc_final: 0.9264 (mt) REVERT: C 147 LEU cc_start: 0.8939 (tp) cc_final: 0.8709 (tp) REVERT: C 171 THR cc_start: 0.7741 (t) cc_final: 0.7499 (m) REVERT: C 215 ILE cc_start: 0.9345 (mm) cc_final: 0.9069 (mm) REVERT: C 242 ASN cc_start: 0.8572 (m-40) cc_final: 0.8274 (m-40) REVERT: C 258 TYR cc_start: 0.8520 (p90) cc_final: 0.7932 (p90) REVERT: C 330 TYR cc_start: 0.8309 (m-10) cc_final: 0.8102 (m-10) REVERT: D 37 SER cc_start: 0.8746 (t) cc_final: 0.8436 (p) REVERT: D 77 MET cc_start: 0.8513 (mmm) cc_final: 0.8012 (mtp) REVERT: D 224 THR cc_start: 0.8546 (p) cc_final: 0.8346 (p) REVERT: D 234 HIS cc_start: 0.8297 (t70) cc_final: 0.7537 (t70) REVERT: D 273 SER cc_start: 0.9591 (m) cc_final: 0.8947 (t) REVERT: D 274 ASP cc_start: 0.8474 (t70) cc_final: 0.7900 (t0) outliers start: 2 outliers final: 0 residues processed: 881 average time/residue: 0.1167 time to fit residues: 163.5129 Evaluate side-chains 834 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 834 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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: 20.0000 chunk 73 optimal weight: 20.0000 chunk 238 optimal weight: 0.0980 chunk 66 optimal weight: 9.9990 chunk 247 optimal weight: 0.6980 chunk 171 optimal weight: 40.0000 chunk 108 optimal weight: 50.0000 chunk 141 optimal weight: 10.0000 chunk 172 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 259 optimal weight: 30.0000 overall best weight: 4.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS E 103 HIS E1203 HIS E1296 ASN B 259 HIS B 299 GLN D 259 HIS ** D 299 GLN ** 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 = 0.3827 r_free = 0.3827 target = 0.172460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.140705 restraints weight = 28574.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.142868 restraints weight = 17857.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.145705 restraints weight = 11322.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.146114 restraints weight = 9352.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.146031 restraints weight = 7451.090| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 19889 Z= 0.190 Angle : 0.585 12.080 27244 Z= 0.305 Chirality : 0.044 0.209 3342 Planarity : 0.004 0.048 3400 Dihedral : 11.119 137.507 3319 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.13 % Allowed : 1.57 % Favored : 98.31 % 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 aren not related in a simple way. whole: 0.71 (0.16), residues: 2729 helix: 2.14 (0.14), residues: 1344 sheet: -1.29 (0.30), residues: 282 loop : -1.19 (0.18), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 314 TYR 0.017 0.002 TYR A 258 PHE 0.035 0.002 PHE D 168 TRP 0.022 0.001 TRP B 311 HIS 0.008 0.001 HIS D 259 Details of bonding type rmsd covalent geometry : bond 0.00423 (19884) covalent geometry : angle 0.58461 (27234) SS BOND : bond 0.00233 ( 5) SS BOND : angle 0.80202 ( 10) hydrogen bonds : bond 0.04227 ( 1171) hydrogen bonds : angle 4.04993 ( 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 881 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 879 time to evaluate : 0.659 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: 0.8993 (m100) cc_final: 0.6471 (m100) REVERT: A 91 TRP cc_start: 0.9185 (t60) cc_final: 0.8403 (t60) REVERT: A 92 LEU cc_start: 0.9372 (tt) cc_final: 0.9151 (tt) REVERT: A 111 VAL cc_start: 0.8747 (t) cc_final: 0.8296 (t) REVERT: A 148 ILE cc_start: 0.9184 (tt) cc_final: 0.8876 (tt) REVERT: A 152 GLN cc_start: 0.9293 (tt0) cc_final: 0.8973 (tt0) REVERT: A 301 ARG cc_start: 0.8611 (mtm-85) cc_final: 0.8250 (mtm-85) REVERT: E 71 HIS cc_start: 0.8192 (t70) cc_final: 0.7430 (t-170) REVERT: E 104 LEU cc_start: 0.8927 (tp) cc_final: 0.8666 (tp) REVERT: E 112 MET cc_start: 0.9090 (mmt) cc_final: 0.8585 (mmt) REVERT: E 123 TYR cc_start: 0.9053 (t80) cc_final: 0.8690 (t80) REVERT: E 131 ASN cc_start: 0.9283 (t0) cc_final: 0.8923 (t0) REVERT: E 145 LEU cc_start: 0.9433 (tp) cc_final: 0.9198 (tp) REVERT: E 164 PHE cc_start: 0.8640 (m-80) cc_final: 0.8293 (m-80) REVERT: E 216 ARG cc_start: 0.7971 (mpt180) cc_final: 0.7688 (mpt180) REVERT: E 417 ILE cc_start: 0.9415 (tt) cc_final: 0.9214 (tt) REVERT: E 479 THR cc_start: 0.8341 (m) cc_final: 0.7860 (m) REVERT: E 498 GLN cc_start: 0.8172 (tt0) cc_final: 0.7715 (mt0) REVERT: E 512 TYR cc_start: 0.7363 (m-80) cc_final: 0.6763 (m-80) REVERT: E 524 VAL cc_start: 0.8461 (t) cc_final: 0.7126 (t) REVERT: E 527 ARG cc_start: 0.8933 (ttm110) cc_final: 0.7844 (mtm110) REVERT: E 577 PHE cc_start: 0.8543 (m-80) cc_final: 0.8261 (m-80) REVERT: E 595 SER cc_start: 0.8885 (p) cc_final: 0.8473 (t) REVERT: E 614 LEU cc_start: 0.7685 (tp) cc_final: 0.7427 (tp) REVERT: E 685 PHE cc_start: 0.6336 (m-10) cc_final: 0.6045 (m-80) REVERT: E 772 TYR cc_start: 0.8711 (t80) cc_final: 0.8457 (t80) REVERT: E 781 ASN cc_start: 0.8212 (p0) cc_final: 0.7771 (p0) REVERT: E 797 GLN cc_start: 0.8272 (pt0) cc_final: 0.7915 (pm20) REVERT: E 911 GLU cc_start: 0.6192 (pt0) cc_final: 0.4456 (tm-30) REVERT: E 1080 LEU cc_start: 0.9308 (tp) cc_final: 0.9054 (tp) REVERT: E 1088 TRP cc_start: 0.8066 (t-100) cc_final: 0.7799 (t60) REVERT: E 1138 SER cc_start: 0.9055 (t) cc_final: 0.8577 (t) REVERT: E 1147 THR cc_start: 0.8923 (t) cc_final: 0.8137 (t) REVERT: E 1149 LEU cc_start: 0.8909 (mp) cc_final: 0.8544 (mp) REVERT: E 1212 THR cc_start: 0.9202 (p) cc_final: 0.8742 (p) REVERT: E 1215 ARG cc_start: 0.8717 (mtm110) cc_final: 0.8354 (mtm110) REVERT: E 1225 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8505 (tm-30) REVERT: E 1298 MET cc_start: 0.8360 (ttp) cc_final: 0.7425 (ttp) REVERT: B 46 HIS cc_start: 0.8586 (m90) cc_final: 0.8197 (m-70) REVERT: B 68 TRP cc_start: 0.8963 (t-100) cc_final: 0.8695 (t-100) REVERT: B 78 SER cc_start: 0.9239 (p) cc_final: 0.8915 (p) REVERT: B 83 TRP cc_start: 0.9148 (m-10) cc_final: 0.8930 (m-10) REVERT: B 116 SER cc_start: 0.9257 (p) cc_final: 0.8563 (t) REVERT: B 131 ILE cc_start: 0.9296 (mt) cc_final: 0.9018 (mt) REVERT: B 212 SER cc_start: 0.9607 (t) cc_final: 0.9370 (t) REVERT: B 216 HIS cc_start: 0.7880 (m-70) cc_final: 0.7584 (m-70) REVERT: B 259 HIS cc_start: 0.8136 (OUTLIER) cc_final: 0.7413 (t-90) REVERT: B 277 HIS cc_start: 0.8396 (t70) cc_final: 0.7964 (t-170) REVERT: C 60 PHE cc_start: 0.8875 (t80) cc_final: 0.8643 (t80) REVERT: C 128 GLN cc_start: 0.8882 (tt0) cc_final: 0.8489 (tt0) REVERT: C 215 ILE cc_start: 0.9383 (mm) cc_final: 0.9028 (mm) REVERT: C 258 TYR cc_start: 0.8591 (p90) cc_final: 0.7964 (p90) REVERT: C 318 ILE cc_start: 0.8537 (mm) cc_final: 0.8323 (mm) REVERT: D 37 SER cc_start: 0.8750 (t) cc_final: 0.8473 (p) REVERT: D 77 MET cc_start: 0.8480 (mmm) cc_final: 0.7964 (mtp) REVERT: D 234 HIS cc_start: 0.8350 (t70) cc_final: 0.7631 (t70) REVERT: D 273 SER cc_start: 0.9579 (m) cc_final: 0.8913 (t) REVERT: D 274 ASP cc_start: 0.8430 (t70) cc_final: 0.7898 (t0) outliers start: 2 outliers final: 1 residues processed: 880 average time/residue: 0.1157 time to fit residues: 161.6831 Evaluate side-chains 833 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 831 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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: 10.0000 chunk 77 optimal weight: 10.0000 chunk 201 optimal weight: 9.9990 chunk 144 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 chunk 235 optimal weight: 9.9990 chunk 122 optimal weight: 30.0000 chunk 64 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 235 GLN A 247 ASN E 103 HIS E 262 ASN E1135 HIS E1203 HIS B 46 HIS B 259 HIS B 299 GLN D 43 ASN D 277 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.168799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.136962 restraints weight = 28632.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.138652 restraints weight = 17558.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.140655 restraints weight = 11727.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.141405 restraints weight = 9207.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.141643 restraints weight = 7634.127| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 19889 Z= 0.238 Angle : 0.641 13.193 27244 Z= 0.335 Chirality : 0.045 0.283 3342 Planarity : 0.004 0.048 3400 Dihedral : 11.190 135.049 3319 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % 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 aren not related in a simple way. whole: 0.68 (0.16), residues: 2729 helix: 2.09 (0.14), residues: 1318 sheet: -1.19 (0.32), residues: 262 loop : -1.14 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E1419 TYR 0.021 0.002 TYR E 263 PHE 0.042 0.002 PHE C 168 TRP 0.026 0.002 TRP B 311 HIS 0.006 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00524 (19884) covalent geometry : angle 0.64066 (27234) SS BOND : bond 0.00258 ( 5) SS BOND : angle 1.25694 ( 10) hydrogen bonds : bond 0.04410 ( 1171) hydrogen bonds : angle 4.23958 ( 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 879 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 877 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.6643 (m-80) cc_final: 0.6412 (m-80) REVERT: A 90 TRP cc_start: 0.8963 (m100) cc_final: 0.6641 (m100) REVERT: A 91 TRP cc_start: 0.9203 (t60) cc_final: 0.8761 (t60) REVERT: A 92 LEU cc_start: 0.9420 (tt) cc_final: 0.9190 (tt) REVERT: A 111 VAL cc_start: 0.8667 (t) cc_final: 0.8255 (t) REVERT: A 130 THR cc_start: 0.9145 (p) cc_final: 0.8863 (p) REVERT: A 148 ILE cc_start: 0.9206 (tt) cc_final: 0.8976 (tt) REVERT: A 152 GLN cc_start: 0.9257 (tt0) cc_final: 0.9007 (tt0) REVERT: A 183 PHE cc_start: 0.8947 (m-80) cc_final: 0.8616 (m-10) REVERT: A 299 GLN cc_start: 0.9169 (tt0) cc_final: 0.8719 (tt0) REVERT: E 104 LEU cc_start: 0.8937 (tp) cc_final: 0.8680 (tp) REVERT: E 123 TYR cc_start: 0.9110 (t80) cc_final: 0.8689 (t80) REVERT: E 131 ASN cc_start: 0.9262 (t0) cc_final: 0.8759 (t0) REVERT: E 145 LEU cc_start: 0.9445 (tp) cc_final: 0.9217 (tp) REVERT: E 216 ARG cc_start: 0.7974 (mpt180) cc_final: 0.7751 (mpt180) REVERT: E 261 THR cc_start: 0.9416 (p) cc_final: 0.8827 (p) REVERT: E 377 TYR cc_start: 0.8816 (m-10) cc_final: 0.8568 (m-80) REVERT: E 386 ASN cc_start: 0.9339 (m-40) cc_final: 0.9005 (m-40) REVERT: E 398 LYS cc_start: 0.9025 (tptt) cc_final: 0.8704 (tptm) REVERT: E 479 THR cc_start: 0.8351 (m) cc_final: 0.7795 (m) REVERT: E 498 GLN cc_start: 0.8213 (tt0) cc_final: 0.7760 (mt0) REVERT: E 512 TYR cc_start: 0.7213 (m-80) cc_final: 0.6739 (m-80) REVERT: E 524 VAL cc_start: 0.8453 (t) cc_final: 0.7097 (t) REVERT: E 527 ARG cc_start: 0.8917 (ttm110) cc_final: 0.7741 (mtm110) REVERT: E 577 PHE cc_start: 0.8558 (m-80) cc_final: 0.8298 (m-80) REVERT: E 595 SER cc_start: 0.8941 (p) cc_final: 0.8640 (t) REVERT: E 614 LEU cc_start: 0.7689 (tp) cc_final: 0.7393 (tp) REVERT: E 685 PHE cc_start: 0.5940 (m-10) cc_final: 0.5631 (m-80) REVERT: E 772 TYR cc_start: 0.8864 (t80) cc_final: 0.8623 (t80) REVERT: E 781 ASN cc_start: 0.8415 (p0) cc_final: 0.7948 (p0) REVERT: E 797 GLN cc_start: 0.8330 (pt0) cc_final: 0.7813 (pm20) REVERT: E 845 TYR cc_start: 0.7188 (t80) cc_final: 0.6801 (t80) REVERT: E 911 GLU cc_start: 0.6898 (pt0) cc_final: 0.4867 (tm-30) REVERT: E 1080 LEU cc_start: 0.9240 (tp) cc_final: 0.8940 (tp) REVERT: E 1088 TRP cc_start: 0.8094 (t-100) cc_final: 0.7801 (t60) REVERT: E 1138 SER cc_start: 0.9085 (t) cc_final: 0.8595 (t) REVERT: E 1149 LEU cc_start: 0.8898 (mp) cc_final: 0.8635 (mp) REVERT: E 1212 THR cc_start: 0.9174 (p) cc_final: 0.8699 (p) REVERT: E 1215 ARG cc_start: 0.8621 (mtm110) cc_final: 0.7689 (mtm110) REVERT: E 1225 GLN cc_start: 0.9166 (mm-40) cc_final: 0.8541 (tm-30) REVERT: B 68 TRP cc_start: 0.9002 (t-100) cc_final: 0.8739 (t-100) REVERT: B 78 SER cc_start: 0.9241 (p) cc_final: 0.8937 (p) REVERT: B 83 TRP cc_start: 0.9209 (m-10) cc_final: 0.8908 (m-10) REVERT: B 116 SER cc_start: 0.9255 (p) cc_final: 0.8543 (m) REVERT: B 212 SER cc_start: 0.9592 (t) cc_final: 0.9379 (t) REVERT: B 277 HIS cc_start: 0.8496 (t70) cc_final: 0.8090 (t-170) REVERT: C 60 PHE cc_start: 0.8915 (t80) cc_final: 0.8691 (t80) REVERT: C 128 GLN cc_start: 0.8818 (tt0) cc_final: 0.8496 (tt0) REVERT: C 212 SER cc_start: 0.9594 (m) cc_final: 0.9166 (p) REVERT: C 215 ILE cc_start: 0.9379 (mm) cc_final: 0.9060 (mm) REVERT: C 258 TYR cc_start: 0.8652 (p90) cc_final: 0.8015 (p90) REVERT: C 318 ILE cc_start: 0.8581 (mm) cc_final: 0.8364 (mm) REVERT: D 234 HIS cc_start: 0.8249 (t70) cc_final: 0.7644 (t70) REVERT: D 273 SER cc_start: 0.9584 (m) cc_final: 0.8924 (t) REVERT: D 274 ASP cc_start: 0.8471 (t70) cc_final: 0.7921 (t0) outliers start: 2 outliers final: 1 residues processed: 877 average time/residue: 0.1178 time to fit residues: 164.4434 Evaluate side-chains 836 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 835 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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: 30.0000 chunk 86 optimal weight: 7.9990 chunk 268 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 193 optimal weight: 30.0000 chunk 252 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 208 optimal weight: 0.8980 chunk 2 optimal weight: 20.0000 chunk 210 optimal weight: 9.9990 chunk 171 optimal weight: 30.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 235 GLN ** E 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 HIS E1203 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.171313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.140711 restraints weight = 28482.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.142199 restraints weight = 18238.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.143520 restraints weight = 12001.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.144067 restraints weight = 11192.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.144284 restraints weight = 9361.590| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 19889 Z= 0.161 Angle : 0.589 12.978 27244 Z= 0.305 Chirality : 0.044 0.230 3342 Planarity : 0.004 0.049 3400 Dihedral : 11.024 136.432 3319 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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 aren not related in a simple way. whole: 0.80 (0.16), residues: 2729 helix: 2.18 (0.14), residues: 1319 sheet: -1.06 (0.33), residues: 257 loop : -1.09 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 34 TYR 0.032 0.002 TYR D 268 PHE 0.034 0.002 PHE E 44 TRP 0.018 0.001 TRP B 311 HIS 0.009 0.001 HIS D 259 Details of bonding type rmsd covalent geometry : bond 0.00361 (19884) covalent geometry : angle 0.58872 (27234) SS BOND : bond 0.00409 ( 5) SS BOND : angle 1.37633 ( 10) hydrogen bonds : bond 0.04250 ( 1171) hydrogen bonds : angle 4.07093 ( 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 870 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 870 time to evaluate : 0.509 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: 0.6617 (m-80) cc_final: 0.6396 (m-80) REVERT: A 90 TRP cc_start: 0.8997 (m100) cc_final: 0.6516 (m100) REVERT: A 92 LEU cc_start: 0.9379 (tt) cc_final: 0.9165 (tt) REVERT: A 111 VAL cc_start: 0.8623 (t) cc_final: 0.8219 (t) REVERT: A 152 GLN cc_start: 0.9217 (tt0) cc_final: 0.8852 (tt0) REVERT: A 301 ARG cc_start: 0.8588 (mtm-85) cc_final: 0.8232 (mtm-85) REVERT: E 71 HIS cc_start: 0.8261 (t-90) cc_final: 0.7425 (t-170) REVERT: E 104 LEU cc_start: 0.8954 (tp) cc_final: 0.8699 (tp) REVERT: E 112 MET cc_start: 0.9019 (mmt) cc_final: 0.8546 (mmt) REVERT: E 123 TYR cc_start: 0.9035 (t80) cc_final: 0.8629 (t80) REVERT: E 131 ASN cc_start: 0.9289 (t0) cc_final: 0.8758 (t0) REVERT: E 145 LEU cc_start: 0.9419 (tp) cc_final: 0.9176 (tp) REVERT: E 216 ARG cc_start: 0.7961 (mpt180) cc_final: 0.7717 (mpt180) REVERT: E 261 THR cc_start: 0.9446 (p) cc_final: 0.9080 (p) REVERT: E 263 TYR cc_start: 0.9110 (t80) cc_final: 0.8643 (t80) REVERT: E 377 TYR cc_start: 0.8805 (m-10) cc_final: 0.8539 (m-80) REVERT: E 398 LYS cc_start: 0.9027 (tptt) cc_final: 0.8640 (tptm) REVERT: E 479 THR cc_start: 0.8363 (m) cc_final: 0.7940 (m) REVERT: E 498 GLN cc_start: 0.8224 (tt0) cc_final: 0.7789 (mt0) REVERT: E 524 VAL cc_start: 0.8429 (t) cc_final: 0.7047 (t) REVERT: E 527 ARG cc_start: 0.8967 (ttm110) cc_final: 0.7865 (mtm110) REVERT: E 577 PHE cc_start: 0.8507 (m-80) cc_final: 0.8246 (m-80) REVERT: E 595 SER cc_start: 0.8922 (p) cc_final: 0.8482 (t) REVERT: E 614 LEU cc_start: 0.7656 (tp) cc_final: 0.7351 (tp) REVERT: E 772 TYR cc_start: 0.8682 (t80) cc_final: 0.8458 (t80) REVERT: E 781 ASN cc_start: 0.8239 (p0) cc_final: 0.7789 (p0) REVERT: E 797 GLN cc_start: 0.8237 (pt0) cc_final: 0.7786 (pm20) REVERT: E 911 GLU cc_start: 0.6722 (pt0) cc_final: 0.4661 (tm-30) REVERT: E 1080 LEU cc_start: 0.9303 (tp) cc_final: 0.9047 (tp) REVERT: E 1088 TRP cc_start: 0.8061 (t-100) cc_final: 0.7796 (t60) REVERT: E 1138 SER cc_start: 0.9021 (t) cc_final: 0.8582 (t) REVERT: E 1212 THR cc_start: 0.9199 (p) cc_final: 0.8707 (p) REVERT: E 1215 ARG cc_start: 0.8505 (mtm110) cc_final: 0.7472 (mtm110) REVERT: E 1225 GLN cc_start: 0.9075 (mm-40) cc_final: 0.8510 (tm-30) REVERT: B 68 TRP cc_start: 0.8939 (t-100) cc_final: 0.8693 (t-100) REVERT: B 116 SER cc_start: 0.9236 (p) cc_final: 0.8574 (t) REVERT: B 123 PHE cc_start: 0.8920 (t80) cc_final: 0.8659 (t80) REVERT: B 212 SER cc_start: 0.9523 (t) cc_final: 0.9305 (t) REVERT: B 277 HIS cc_start: 0.8439 (t70) cc_final: 0.8092 (t-170) REVERT: C 60 PHE cc_start: 0.8880 (t80) cc_final: 0.8630 (t80) REVERT: C 90 TRP cc_start: 0.9156 (m100) cc_final: 0.8074 (m100) REVERT: C 128 GLN cc_start: 0.8812 (tt0) cc_final: 0.8422 (tt0) REVERT: C 212 SER cc_start: 0.9571 (m) cc_final: 0.9137 (p) REVERT: C 215 ILE cc_start: 0.9349 (mm) cc_final: 0.8992 (mm) REVERT: C 258 TYR cc_start: 0.8661 (p90) cc_final: 0.7987 (p90) REVERT: C 309 ILE cc_start: 0.9414 (mm) cc_final: 0.9182 (mm) REVERT: C 318 ILE cc_start: 0.8572 (mm) cc_final: 0.8351 (mm) REVERT: D 77 MET cc_start: 0.8480 (mmm) cc_final: 0.7933 (mtp) REVERT: D 234 HIS cc_start: 0.8195 (t70) cc_final: 0.7642 (t70) REVERT: D 273 SER cc_start: 0.9583 (m) cc_final: 0.8911 (t) REVERT: D 274 ASP cc_start: 0.8438 (t70) cc_final: 0.7888 (t0) outliers start: 0 outliers final: 0 residues processed: 870 average time/residue: 0.1148 time to fit residues: 159.1503 Evaluate side-chains 825 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 825 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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: 10.0000 chunk 136 optimal weight: 6.9990 chunk 252 optimal weight: 6.9990 chunk 229 optimal weight: 9.9990 chunk 198 optimal weight: 8.9990 chunk 120 optimal weight: 8.9990 chunk 268 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 21 optimal weight: 30.0000 chunk 176 optimal weight: 10.0000 chunk 219 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 235 GLN A 299 GLN E 32 ASN E 71 HIS E 103 HIS E 262 ASN ** E 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN D 43 ASN ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.170569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.140022 restraints weight = 28786.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.141814 restraints weight = 17542.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.142982 restraints weight = 11702.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.143813 restraints weight = 9992.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.143821 restraints weight = 9186.113| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 19889 Z= 0.207 Angle : 0.628 14.641 27244 Z= 0.328 Chirality : 0.045 0.254 3342 Planarity : 0.004 0.047 3400 Dihedral : 10.997 128.493 3319 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.13 % Allowed : 0.19 % Favored : 99.69 % 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 aren not related in a simple way. whole: 0.73 (0.16), residues: 2729 helix: 2.15 (0.14), residues: 1307 sheet: -1.10 (0.33), residues: 257 loop : -1.13 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 202 TYR 0.020 0.002 TYR E 263 PHE 0.038 0.002 PHE C 168 TRP 0.025 0.002 TRP B 83 HIS 0.008 0.001 HIS D 259 Details of bonding type rmsd covalent geometry : bond 0.00463 (19884) covalent geometry : angle 0.62809 (27234) SS BOND : bond 0.00178 ( 5) SS BOND : angle 1.15173 ( 10) hydrogen bonds : bond 0.04389 ( 1171) hydrogen bonds : angle 4.17581 ( 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 873 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 871 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.6634 (m-80) cc_final: 0.6361 (m-80) REVERT: A 90 TRP cc_start: 0.8985 (m100) cc_final: 0.6580 (m100) REVERT: A 91 TRP cc_start: 0.9185 (t60) cc_final: 0.8398 (t60) REVERT: A 92 LEU cc_start: 0.9380 (tt) cc_final: 0.9157 (tt) REVERT: A 111 VAL cc_start: 0.8624 (t) cc_final: 0.8248 (t) REVERT: A 130 THR cc_start: 0.9031 (p) cc_final: 0.8744 (p) REVERT: A 183 PHE cc_start: 0.8989 (m-80) cc_final: 0.8530 (m-80) REVERT: E 104 LEU cc_start: 0.8967 (tp) cc_final: 0.8700 (tp) REVERT: E 112 MET cc_start: 0.9015 (mmt) cc_final: 0.8544 (mmt) REVERT: E 123 TYR cc_start: 0.9057 (t80) cc_final: 0.8695 (t80) REVERT: E 131 ASN cc_start: 0.9284 (t0) cc_final: 0.8766 (t0) REVERT: E 145 LEU cc_start: 0.9452 (tp) cc_final: 0.9238 (tp) REVERT: E 216 ARG cc_start: 0.7836 (mpt180) cc_final: 0.7575 (mpt180) REVERT: E 398 LYS cc_start: 0.9032 (tptt) cc_final: 0.8632 (tptm) REVERT: E 479 THR cc_start: 0.8477 (m) cc_final: 0.7889 (m) REVERT: E 498 GLN cc_start: 0.8219 (tt0) cc_final: 0.7794 (mt0) REVERT: E 524 VAL cc_start: 0.8345 (t) cc_final: 0.6863 (t) REVERT: E 527 ARG cc_start: 0.8964 (ttm110) cc_final: 0.7828 (mtm110) REVERT: E 577 PHE cc_start: 0.8526 (m-80) cc_final: 0.8276 (m-80) REVERT: E 595 SER cc_start: 0.8943 (p) cc_final: 0.8494 (t) REVERT: E 614 LEU cc_start: 0.7666 (tp) cc_final: 0.7353 (tp) REVERT: E 772 TYR cc_start: 0.8712 (t80) cc_final: 0.8500 (t80) REVERT: E 781 ASN cc_start: 0.8332 (p0) cc_final: 0.7876 (p0) REVERT: E 797 GLN cc_start: 0.8271 (pt0) cc_final: 0.7803 (pm20) REVERT: E 911 GLU cc_start: 0.7025 (pt0) cc_final: 0.4999 (tp30) REVERT: E 1080 LEU cc_start: 0.9235 (tp) cc_final: 0.8935 (tp) REVERT: E 1088 TRP cc_start: 0.8074 (t-100) cc_final: 0.7790 (t60) REVERT: E 1138 SER cc_start: 0.9066 (t) cc_final: 0.8618 (t) REVERT: E 1147 THR cc_start: 0.8755 (t) cc_final: 0.7843 (t) REVERT: E 1215 ARG cc_start: 0.8619 (mtm110) cc_final: 0.7489 (tpm170) REVERT: E 1225 GLN cc_start: 0.9129 (mm-40) cc_final: 0.8531 (tm-30) REVERT: E 1298 MET cc_start: 0.8427 (ttp) cc_final: 0.7402 (ttp) REVERT: B 116 SER cc_start: 0.9224 (p) cc_final: 0.8536 (m) REVERT: B 277 HIS cc_start: 0.8439 (t70) cc_final: 0.8107 (t-170) REVERT: C 60 PHE cc_start: 0.8867 (t80) cc_final: 0.8651 (t80) REVERT: C 128 GLN cc_start: 0.8849 (tt0) cc_final: 0.8464 (tt0) REVERT: C 212 SER cc_start: 0.9590 (m) cc_final: 0.9183 (p) REVERT: C 215 ILE cc_start: 0.9319 (mm) cc_final: 0.9027 (mm) REVERT: C 258 TYR cc_start: 0.8639 (p90) cc_final: 0.7976 (p90) REVERT: C 309 ILE cc_start: 0.9468 (mm) cc_final: 0.9233 (mm) REVERT: C 318 ILE cc_start: 0.8609 (mm) cc_final: 0.8407 (mm) REVERT: D 77 MET cc_start: 0.8462 (mmm) cc_final: 0.7955 (mtp) REVERT: D 234 HIS cc_start: 0.8287 (t70) cc_final: 0.7657 (t70) REVERT: D 273 SER cc_start: 0.9593 (m) cc_final: 0.8927 (t) REVERT: D 274 ASP cc_start: 0.8439 (t70) cc_final: 0.7869 (t0) outliers start: 2 outliers final: 1 residues processed: 871 average time/residue: 0.1202 time to fit residues: 166.4650 Evaluate side-chains 830 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 829 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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: 10.0000 chunk 207 optimal weight: 1.9990 chunk 61 optimal weight: 30.0000 chunk 106 optimal weight: 3.9990 chunk 253 optimal weight: 8.9990 chunk 200 optimal weight: 30.0000 chunk 39 optimal weight: 6.9990 chunk 238 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 30.0000 chunk 204 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 235 GLN A 299 GLN E 406 ASN ** E 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1203 HIS ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.170991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.139890 restraints weight = 28687.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.142050 restraints weight = 17931.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.143623 restraints weight = 11965.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.144538 restraints weight = 10100.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.144680 restraints weight = 7722.765| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 19889 Z= 0.188 Angle : 0.603 13.288 27244 Z= 0.317 Chirality : 0.045 0.194 3342 Planarity : 0.004 0.082 3400 Dihedral : 10.957 127.580 3319 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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 aren not related in a simple way. whole: 0.70 (0.16), residues: 2729 helix: 2.14 (0.14), residues: 1319 sheet: -1.06 (0.29), residues: 302 loop : -1.19 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 34 TYR 0.018 0.002 TYR E 475 PHE 0.031 0.002 PHE D 168 TRP 0.064 0.002 TRP B 83 HIS 0.008 0.001 HIS D 259 Details of bonding type rmsd covalent geometry : bond 0.00423 (19884) covalent geometry : angle 0.60304 (27234) SS BOND : bond 0.00481 ( 5) SS BOND : angle 1.34181 ( 10) hydrogen bonds : bond 0.04302 ( 1171) hydrogen bonds : angle 4.15596 ( 3444) =============================================================================== Job complete usr+sys time: 3542.36 seconds wall clock time: 61 minutes 31.46 seconds (3691.46 seconds total)