Starting phenix.real_space_refine on Fri Sep 27 12:53:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7md2_23763/09_2024/7md2_23763_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7md2_23763/09_2024/7md2_23763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7md2_23763/09_2024/7md2_23763.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7md2_23763/09_2024/7md2_23763.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7md2_23763/09_2024/7md2_23763_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7md2_23763/09_2024/7md2_23763_trim.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 22293 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians P 10 5.49 5 Mg 3 5.21 5 S 37 5.16 5 C 14870 2.51 5 N 4092 2.21 5 O 4462 1.98 5 H 23645 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 141 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 47119 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 7383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7383 Classifications: {'peptide': 485} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 464} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 6924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 6924 Classifications: {'peptide': 458} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 7423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7423 Classifications: {'peptide': 485} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 464} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 6996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 6996 Classifications: {'peptide': 469} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 445} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 11, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "E" Number of atoms: 7078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 7078 Classifications: {'peptide': 469} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 445} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "F" Number of atoms: 7041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 7041 Classifications: {'peptide': 469} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 445} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10} Unresolved non-hydrogen planarities: 44 Chain: "G" Number of atoms: 3493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3493 Classifications: {'peptide': 232} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 224} Chain breaks: 3 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 48 Chain: "H" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 599 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 81 Unusual residues: {'ZHD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.61, per 1000 atoms: 0.35 Number of scatterers: 47119 At special positions: 0 Unit cell: (130.81, 128.75, 145.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 37 16.00 P 10 15.00 Mg 3 11.99 O 4462 8.00 N 4092 7.00 C 14870 6.00 H 23645 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 9.10 Conformation dependent library (CDL) restraints added in 3.0 seconds 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5662 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 17 sheets defined 50.0% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.96 Creating SS restraints... Processing helix chain 'A' and resid 80 through 84 Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 176 through 188 removed outlier: 3.873A pdb=" N GLN A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 193 removed outlier: 3.951A pdb=" N ASN A 193 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 241 through 262 Proline residue: A 249 - end of helix removed outlier: 3.760A pdb=" N TRP A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 287 removed outlier: 3.702A pdb=" N GLN A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 297 through 298 No H-bonds generated for 'chain 'A' and resid 297 through 298' Processing helix chain 'A' and resid 299 through 309 removed outlier: 3.526A pdb=" N ARG A 306 " --> pdb=" O TYR A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 319 Processing helix chain 'A' and resid 332 through 335 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 376 through 380 Processing helix chain 'A' and resid 382 through 390 removed outlier: 3.673A pdb=" N VAL A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 403 removed outlier: 3.545A pdb=" N GLU A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.613A pdb=" N GLN A 407 " --> pdb=" O ALA A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 431 removed outlier: 4.261A pdb=" N THR A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A 424 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 452 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 453 through 458 removed outlier: 4.030A pdb=" N GLY A 457 " --> pdb=" O HIS A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 462 through 478 removed outlier: 3.865A pdb=" N SER A 472 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 489 removed outlier: 3.707A pdb=" N LEU A 482 " --> pdb=" O HIS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 510 removed outlier: 3.653A pdb=" N ALA A 497 " --> pdb=" O LYS A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 84 Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.626A pdb=" N LEU B 105 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 176 through 188 removed outlier: 3.771A pdb=" N ALA B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'B' and resid 211 through 225 Processing helix chain 'B' and resid 226 through 229 removed outlier: 3.644A pdb=" N LYS B 229 " --> pdb=" O ASP B 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 226 through 229' Processing helix chain 'B' and resid 241 through 262 Proline residue: B 249 - end of helix removed outlier: 3.784A pdb=" N TRP B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 removed outlier: 3.580A pdb=" N GLN B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 297 through 298 No H-bonds generated for 'chain 'B' and resid 297 through 298' Processing helix chain 'B' and resid 299 through 309 removed outlier: 3.641A pdb=" N ARG B 306 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 335 Processing helix chain 'B' and resid 338 through 348 Processing helix chain 'B' and resid 355 through 361 Processing helix chain 'B' and resid 376 through 380 removed outlier: 3.577A pdb=" N ALA B 379 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 390 removed outlier: 3.733A pdb=" N GLY B 390 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 431 Processing helix chain 'B' and resid 439 through 452 Proline residue: B 445 - end of helix removed outlier: 3.646A pdb=" N GLY B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.901A pdb=" N GLY B 457 " --> pdb=" O HIS B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 462 through 478 removed outlier: 3.726A pdb=" N SER B 468 " --> pdb=" O GLY B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 488 removed outlier: 3.706A pdb=" N LEU B 482 " --> pdb=" O HIS B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 510 removed outlier: 4.074A pdb=" N ALA B 508 " --> pdb=" O GLU B 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.747A pdb=" N LEU C 83 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.741A pdb=" N LEU C 105 " --> pdb=" O GLY C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 176 through 187 Processing helix chain 'C' and resid 188 through 193 removed outlier: 3.611A pdb=" N ASN C 193 " --> pdb=" O LYS C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 225 Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 241 through 262 Proline residue: C 249 - end of helix removed outlier: 3.527A pdb=" N TRP C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 287 removed outlier: 3.545A pdb=" N GLN C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 296 removed outlier: 3.665A pdb=" N ALA C 295 " --> pdb=" O GLY C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 309 removed outlier: 3.621A pdb=" N ARG C 306 " --> pdb=" O TYR C 302 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C 307 " --> pdb=" O LEU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 319 Processing helix chain 'C' and resid 332 through 335 Processing helix chain 'C' and resid 338 through 348 removed outlier: 3.624A pdb=" N SER C 346 " --> pdb=" O THR C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 361 removed outlier: 3.588A pdb=" N LYS C 361 " --> pdb=" O GLU C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 381 removed outlier: 3.661A pdb=" N ALA C 379 " --> pdb=" O VAL C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 403 removed outlier: 3.819A pdb=" N VAL C 388 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N SER C 391 " --> pdb=" O GLN C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 413 through 430 Processing helix chain 'C' and resid 439 through 452 Proline residue: C 445 - end of helix Processing helix chain 'C' and resid 453 through 458 removed outlier: 3.820A pdb=" N GLY C 457 " --> pdb=" O HIS C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 478 removed outlier: 3.637A pdb=" N SER C 468 " --> pdb=" O GLY C 464 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU C 471 " --> pdb=" O GLU C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 489 removed outlier: 3.932A pdb=" N LEU C 482 " --> pdb=" O HIS C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 508 removed outlier: 3.727A pdb=" N SER C 498 " --> pdb=" O GLU C 494 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE C 506 " --> pdb=" O ALA C 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 123 through 127 Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 158 through 161 removed outlier: 3.509A pdb=" N VAL D 161 " --> pdb=" O GLY D 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 158 through 161' Processing helix chain 'D' and resid 162 through 177 Processing helix chain 'D' and resid 190 through 204 Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 231 through 248 removed outlier: 3.759A pdb=" N ILE D 239 " --> pdb=" O THR D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 272 removed outlier: 3.764A pdb=" N THR D 262 " --> pdb=" O ILE D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 294 Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 319 through 327 removed outlier: 3.803A pdb=" N ALA D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 341 removed outlier: 3.780A pdb=" N SER D 340 " --> pdb=" O SER D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 364 through 391 removed outlier: 3.570A pdb=" N VAL D 370 " --> pdb=" O GLU D 366 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN D 379 " --> pdb=" O GLN D 375 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 414 Processing helix chain 'D' and resid 433 through 446 removed outlier: 3.557A pdb=" N SER D 440 " --> pdb=" O ASP D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 462 through 476 removed outlier: 4.205A pdb=" N ALA D 468 " --> pdb=" O GLU D 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 123 through 127 Processing helix chain 'E' and resid 138 through 145 Processing helix chain 'E' and resid 162 through 178 Processing helix chain 'E' and resid 190 through 205 Processing helix chain 'E' and resid 225 through 246 removed outlier: 4.060A pdb=" N ARG E 231 " --> pdb=" O GLY E 227 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 273 removed outlier: 3.539A pdb=" N PHE E 261 " --> pdb=" O ASN E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 294 removed outlier: 3.626A pdb=" N LEU E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 319 through 327 Processing helix chain 'E' and resid 336 through 342 Processing helix chain 'E' and resid 364 through 384 removed outlier: 3.936A pdb=" N VAL E 370 " --> pdb=" O GLU E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 392 Processing helix chain 'E' and resid 393 through 396 removed outlier: 3.515A pdb=" N LEU E 396 " --> pdb=" O MET E 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 393 through 396' Processing helix chain 'E' and resid 397 through 414 Processing helix chain 'E' and resid 421 through 426 Processing helix chain 'E' and resid 433 through 446 Processing helix chain 'E' and resid 453 through 458 Processing helix chain 'E' and resid 462 through 476 removed outlier: 3.734A pdb=" N ALA E 468 " --> pdb=" O GLU E 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 123 through 127 Processing helix chain 'F' and resid 138 through 145 Processing helix chain 'F' and resid 162 through 178 removed outlier: 4.553A pdb=" N LYS F 176 " --> pdb=" O ASN F 172 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA F 177 " --> pdb=" O ASN F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 204 removed outlier: 3.914A pdb=" N LEU F 197 " --> pdb=" O GLU F 193 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU F 200 " --> pdb=" O ASP F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 230 Processing helix chain 'F' and resid 231 through 246 removed outlier: 3.595A pdb=" N THR F 235 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 273 removed outlier: 3.937A pdb=" N THR F 262 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA F 270 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LEU F 271 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 294 removed outlier: 3.814A pdb=" N LEU F 292 " --> pdb=" O ASP F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 316 Processing helix chain 'F' and resid 319 through 326 Processing helix chain 'F' and resid 327 through 329 No H-bonds generated for 'chain 'F' and resid 327 through 329' Processing helix chain 'F' and resid 336 through 342 removed outlier: 3.584A pdb=" N SER F 340 " --> pdb=" O SER F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 364 Processing helix chain 'F' and resid 364 through 384 Processing helix chain 'F' and resid 384 through 391 Processing helix chain 'F' and resid 397 through 414 Processing helix chain 'F' and resid 421 through 426 Processing helix chain 'F' and resid 433 through 446 Processing helix chain 'F' and resid 453 through 457 Processing helix chain 'F' and resid 462 through 475 Processing helix chain 'G' and resid 2 through 30 removed outlier: 3.530A pdb=" N MET G 8 " --> pdb=" O LYS G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 55 removed outlier: 3.684A pdb=" N ALA G 34 " --> pdb=" O ARG G 30 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA G 47 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU G 48 " --> pdb=" O MET G 44 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TYR G 52 " --> pdb=" O GLU G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 99 Processing helix chain 'G' and resid 111 through 122 removed outlier: 3.689A pdb=" N THR G 121 " --> pdb=" O GLN G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 154 Processing helix chain 'G' and resid 155 through 159 Processing helix chain 'G' and resid 205 through 275 removed outlier: 3.800A pdb=" N ALA G 215 " --> pdb=" O GLU G 211 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET G 237 " --> pdb=" O ARG G 233 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE G 253 " --> pdb=" O ASN G 249 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN G 256 " --> pdb=" O SER G 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 24 removed outlier: 3.589A pdb=" N SER H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 37 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 68 removed outlier: 4.210A pdb=" N GLU A 53 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU A 54 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL A 76 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ALA A 65 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL E 16 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASP E 22 " --> pdb=" O THR E 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 100 Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 110 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 109 through 110 current: chain 'A' and resid 231 through 236 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 231 through 236 current: chain 'A' and resid 322 through 330 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 322 through 330 current: chain 'A' and resid 373 through 374 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 30 through 37 removed outlier: 6.620A pdb=" N ARG B 42 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL B 36 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 40 through 45 current: chain 'B' and resid 62 through 69 removed outlier: 5.589A pdb=" N ALA B 65 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL B 76 " --> pdb=" O ALA B 65 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 72 through 77 current: chain 'C' and resid 40 through 44 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 40 through 44 current: chain 'C' and resid 62 through 68 removed outlier: 5.653A pdb=" N ALA C 65 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL C 76 " --> pdb=" O ALA C 65 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 73 through 77 current: chain 'D' and resid 20 through 24 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 20 through 24 current: chain 'D' and resid 46 through 55 removed outlier: 6.580A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 58 through 63 current: chain 'F' and resid 20 through 25 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 20 through 25 current: chain 'F' and resid 46 through 55 removed outlier: 5.629A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR F 58 " --> pdb=" O LEU F 54 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 98 through 101 Processing sheet with id=AA6, first strand: chain 'B' and resid 109 through 110 removed outlier: 6.771A pdb=" N LEU B 168 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU B 354 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE B 170 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 98 through 101 Processing sheet with id=AA8, first strand: chain 'C' and resid 109 through 110 removed outlier: 6.535A pdb=" N CYS C 203 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N VAL C 234 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 84 through 87 removed outlier: 4.620A pdb=" N LEU D 113 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 95 through 96 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 95 through 96 current: chain 'D' and resid 216 through 221 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 216 through 221 current: chain 'D' and resid 302 through 309 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 133 through 134 removed outlier: 4.428A pdb=" N TYR D 147 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB4, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.270A pdb=" N ILE E 96 " --> pdb=" O PHE E 219 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLN E 221 " --> pdb=" O ILE E 96 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY E 188 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL E 183 " --> pdb=" O PHE E 254 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N ASP E 256 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR E 185 " --> pdb=" O ASP E 256 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL E 251 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL E 307 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU E 253 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ALA E 309 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE E 255 " --> pdb=" O ALA E 309 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE E 153 " --> pdb=" O GLN E 308 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LYS E 152 " --> pdb=" O ALA E 331 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N THR E 333 " --> pdb=" O LYS E 152 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLY E 154 " --> pdb=" O THR E 333 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AB6, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.479A pdb=" N ILE F 96 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N GLN F 221 " --> pdb=" O ILE F 96 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL F 251 " --> pdb=" O THR F 305 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N VAL F 307 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU F 253 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ALA F 309 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE F 255 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N TYR F 311 " --> pdb=" O ILE F 255 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS F 152 " --> pdb=" O ALA F 331 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N THR F 333 " --> pdb=" O LYS F 152 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLY F 154 " --> pdb=" O THR F 333 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU F 335 " --> pdb=" O GLY F 154 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N PHE F 156 " --> pdb=" O LEU F 335 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 132 through 134 removed outlier: 4.601A pdb=" N GLU F 132 " --> pdb=" O ARG F 149 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR F 147 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 174 through 182 removed outlier: 6.667A pdb=" N SER G 174 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL G 170 " --> pdb=" O SER G 174 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE G 162 " --> pdb=" O ILE G 182 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL G 75 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N ASN G 167 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N ILE G 77 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE G 74 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE G 110 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA G 76 " --> pdb=" O ILE G 110 " (cutoff:3.500A) 1088 hydrogen bonds defined for protein. 3045 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: 15.98 Time building geometry restraints manager: 11.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 23641 1.03 - 1.22: 5 1.22 - 1.42: 9422 1.42 - 1.61: 14340 1.61 - 1.81: 73 Bond restraints: 47481 Sorted by residual: bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.03e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.455 -0.067 1.00e-02 1.00e+04 4.52e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.455 -0.067 1.00e-02 1.00e+04 4.46e+01 bond pdb=" C61 ZHD G 301 " pdb=" C64 ZHD G 301 " ideal model delta sigma weight residual 1.451 1.585 -0.134 2.00e-02 2.50e+03 4.46e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.33e+01 ... (remaining 47476 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.42: 86043 4.42 - 8.85: 78 8.85 - 13.27: 4 13.27 - 17.69: 3 17.69 - 22.11: 3 Bond angle restraints: 86131 Sorted by residual: angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 117.76 22.11 1.00e+00 1.00e+00 4.89e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 118.06 21.81 1.00e+00 1.00e+00 4.76e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 120.15 19.72 1.00e+00 1.00e+00 3.89e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 119.64 17.19 1.00e+00 1.00e+00 2.96e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 120.68 16.15 1.00e+00 1.00e+00 2.61e+02 ... (remaining 86126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 20337 17.94 - 35.88: 1402 35.88 - 53.83: 418 53.83 - 71.77: 133 71.77 - 89.71: 34 Dihedral angle restraints: 22324 sinusoidal: 12488 harmonic: 9836 Sorted by residual: dihedral pdb=" CA PHE F 219 " pdb=" C PHE F 219 " pdb=" N GLY F 220 " pdb=" CA GLY F 220 " ideal model delta harmonic sigma weight residual 180.00 151.05 28.95 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA ALA E 278 " pdb=" C ALA E 278 " pdb=" N VAL E 279 " pdb=" CA VAL E 279 " ideal model delta harmonic sigma weight residual -180.00 -151.69 -28.31 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA ALA D 278 " pdb=" C ALA D 278 " pdb=" N VAL D 279 " pdb=" CA VAL D 279 " ideal model delta harmonic sigma weight residual -180.00 -152.18 -27.82 0 5.00e+00 4.00e-02 3.10e+01 ... (remaining 22321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3381 0.076 - 0.152: 451 0.152 - 0.228: 9 0.228 - 0.304: 0 0.304 - 0.379: 1 Chirality restraints: 3842 Sorted by residual: chirality pdb=" C25 ZHD G 301 " pdb=" C24 ZHD G 301 " pdb=" C26 ZHD G 301 " pdb=" C27 ZHD G 301 " both_signs ideal model delta sigma weight residual False 2.33 2.71 -0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" C55 ZHD G 301 " pdb=" C43 ZHD G 301 " pdb=" C56 ZHD G 301 " pdb=" C57 ZHD G 301 " both_signs ideal model delta sigma weight residual False 2.61 2.82 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA PRO D 346 " pdb=" N PRO D 346 " pdb=" C PRO D 346 " pdb=" CB PRO D 346 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.76e-01 ... (remaining 3839 not shown) Planarity restraints: 7137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 277 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" C SER E 277 " -0.039 2.00e-02 2.50e+03 pdb=" O SER E 277 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA E 278 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 277 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.37e+00 pdb=" C SER D 277 " 0.036 2.00e-02 2.50e+03 pdb=" O SER D 277 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA D 278 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 277 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" C SER F 277 " -0.036 2.00e-02 2.50e+03 pdb=" O SER F 277 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA F 278 " 0.012 2.00e-02 2.50e+03 ... (remaining 7134 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.11: 1203 2.11 - 2.73: 86357 2.73 - 3.35: 135709 3.35 - 3.98: 177566 3.98 - 4.60: 286881 Nonbonded interactions: 687716 Sorted by model distance: nonbonded pdb=" O ALA E 278 " pdb=" H GLY E 280 " model vdw 1.482 2.450 nonbonded pdb="HH22 ARG B 108 " pdb=" O GLY B 121 " model vdw 1.518 2.450 nonbonded pdb=" O GLY D 343 " pdb=" HH TYR D 458 " model vdw 1.527 2.450 nonbonded pdb=" OE1 GLN F 27 " pdb=" H GLU F 29 " model vdw 1.533 2.450 nonbonded pdb=" O ALA E 36 " pdb=" HG1 THR E 79 " model vdw 1.539 2.450 ... (remaining 687711 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 26 through 87 or (resid 88 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 89 through 177 or (resid \ 178 and (name N or name CA or name C or name O or name CB or name OG1 or name C \ G2 or name H or name HA or name HB or name HG21 or name HG22 or name HG23)) or r \ esid 179 through 194 or (resid 195 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 196 through 239 or (resid 240 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 2 \ 41 through 356 or (resid 357 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 358 through 393 or (resid 421 and (name N or \ name CA or name C or name O or name CB or name CG1 or name CG2 or name HA or na \ me HB or name HG11 or name HG12 or name HG13 or name HG21 or name HG22 or name H \ G23)) or resid 422 through 458 or (resid 459 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 460 through 474 or (resid 47 \ 5 through 477 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 478 through 479 or (resid 480 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 481 through 486 or (re \ sid 487 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 488 through 489 or (resid 490 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 491 or (resid 492 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 493 \ or (resid 494 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 495 through 497 or (resid 498 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 499 through 500 or (r \ esid 501 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 502 through 503 or (resid 504 through 505 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 506 through 508 \ or (resid 509 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 510 or resid 600 through 601)) selection = (chain 'B' and (resid 26 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 30 through 68 or (resid \ 69 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 70 through 87 or (resid 88 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 89 through 133 or (resid 134 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 135 through 171 or (resid 172 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 173 through 182 or (resid 183 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 184 th \ rough 356 or (resid 357 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 358 through 423 or (resid 424 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 425 through \ 499 or (resid 500 through 501 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 502 through 510 or resid 600 through 601)) selection = (chain 'C' and (resid 26 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 30 through 37 or (resid \ 38 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 39 through 68 or (resid 69 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 70 through 133 or (resid 134 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 135 through 171 or (resid 172 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 173 through 182 or (resid 183 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 184 th \ rough 194 or (resid 195 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 196 through 293 or (resid 294 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 295 through \ 393 or (resid 421 and (name N or name CA or name C or name O or name CB or name \ CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name HG13 or \ name HG21 or name HG22 or name HG23)) or resid 422 through 423 or (resid 424 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 425 through 458 or (resid 459 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 460 through 474 or (resid 475 through 4 \ 77 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 478 through 479 or (resid 480 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 481 through 486 or (resid 487 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 488 through 489 or (resid 490 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 491 or (resid 492 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 493 or (resid \ 494 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 495 through 497 or (resid 498 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 499 or (resid 500 through 501 an \ d (name N or name CA or name C or name O or name CB or name H or name HA )) or r \ esid 502 through 503 or (resid 504 through 505 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 506 through 510 or resid 6 \ 00 through 601)) } ncs_group { reference = (chain 'D' and (resid 8 through 25 or (resid 26 through 27 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 28 through 104 \ or (resid 105 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 106 through 358 or (resid 359 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 360 through 372 or (r \ esid 373 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 374 through 393 or (resid 394 through 395 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 396 through 397 \ or (resid 398 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 399 through 404 or (resid 405 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 406 through 463 or (r \ esid 464 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 465 through 470 or (resid 471 through 472 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 473 through 476 \ )) selection = (chain 'E' and (resid 8 through 25 or (resid 26 through 27 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 28 through 39 \ or (resid 40 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 41 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 44 through 67 or (resid 68 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 69 through 104 or (resid 105 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 106 through 111 or (resid 112 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 113 through 175 or (resid 176 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 177 through 188 or (resid 189 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 190 t \ hrough 202 or (resid 203 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 204 through 209 or (resid 210 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 211 or (res \ id 212 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 213 through 244 or (resid 245 through 247 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 248 through 336 o \ r (resid 337 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 338 through 372 or (resid 373 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 374 through 397 or (res \ id 398 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 399 through 445 or (resid 446 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 447 through 470 or (resid 471 \ through 472 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 473 through 476)) selection = (chain 'F' and (resid 8 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 28 through 55 or (resid 5 \ 6 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 57 through 67 or (resid 68 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 69 through 111 or (resid 112 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 1 \ 13 through 175 or (resid 176 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 177 through 188 or (resid 189 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 190 thr \ ough 209 or (resid 210 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 211 or (resid 212 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 213 through 244 or (resid \ 245 through 247 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 248 through 336 or (resid 337 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 338 through 358 or \ (resid 359 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 360 through 393 or (resid 394 through 395 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 396 through 4 \ 45 or (resid 446 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 447 through 463 or (resid 464 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 465 through 471 or \ (resid 472 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 473 through 476)) } 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 individual isotropic 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: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.310 Construct map_model_manager: 0.610 Extract box with map and model: 1.300 Check model and map are aligned: 0.270 Set scattering table: 0.330 Process input model: 75.410 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.110 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:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.134 23836 Z= 0.597 Angle : 0.798 22.114 32349 Z= 0.502 Chirality : 0.050 0.379 3842 Planarity : 0.004 0.046 4167 Dihedral : 14.285 89.709 8916 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.78 % Favored : 97.99 % Rotamer: Outliers : 0.25 % Allowed : 5.46 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.13), residues: 3089 helix: -1.55 (0.12), residues: 1244 sheet: -0.42 (0.22), residues: 479 loop : -1.05 (0.16), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 191 HIS 0.010 0.002 HIS C 478 PHE 0.024 0.002 PHE F 424 TYR 0.020 0.002 TYR E 198 ARG 0.009 0.001 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 134 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue SER 492 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue SER 505 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue SER 40 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Evaluate side-chains 798 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 792 time to evaluate : 2.721 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.6982 (tt0) cc_final: 0.6391 (mt-10) REVERT: A 53 GLU cc_start: 0.7980 (tt0) cc_final: 0.7346 (tt0) REVERT: A 66 LEU cc_start: 0.8249 (mt) cc_final: 0.8012 (mp) REVERT: A 129 SER cc_start: 0.7964 (m) cc_final: 0.7687 (t) REVERT: A 156 ASP cc_start: 0.7363 (m-30) cc_final: 0.7149 (m-30) REVERT: A 167 GLU cc_start: 0.7942 (tp30) cc_final: 0.7239 (tp30) REVERT: A 237 THR cc_start: 0.7180 (p) cc_final: 0.6951 (p) REVERT: A 342 THR cc_start: 0.8071 (m) cc_final: 0.7719 (p) REVERT: A 357 GLU cc_start: 0.7020 (tm-30) cc_final: 0.6383 (tm-30) REVERT: A 358 LEU cc_start: 0.8238 (mt) cc_final: 0.7899 (mt) REVERT: A 421 VAL cc_start: 0.7794 (t) cc_final: 0.7509 (p) REVERT: B 34 LEU cc_start: 0.8445 (mt) cc_final: 0.8145 (mt) REVERT: B 52 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6759 (mt-10) REVERT: B 67 ASN cc_start: 0.8068 (p0) cc_final: 0.7708 (p0) REVERT: B 118 ASP cc_start: 0.7808 (p0) cc_final: 0.7606 (p0) REVERT: B 123 ILE cc_start: 0.8302 (mm) cc_final: 0.7980 (mt) REVERT: B 159 VAL cc_start: 0.8423 (m) cc_final: 0.7848 (t) REVERT: B 183 ASP cc_start: 0.6253 (m-30) cc_final: 0.6051 (m-30) REVERT: B 199 LYS cc_start: 0.8205 (mttm) cc_final: 0.7898 (mtmm) REVERT: B 211 LYS cc_start: 0.8189 (mtpt) cc_final: 0.7713 (mtmt) REVERT: B 257 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6701 (mt-10) REVERT: B 261 ASP cc_start: 0.7312 (m-30) cc_final: 0.7025 (m-30) REVERT: B 331 THR cc_start: 0.8229 (p) cc_final: 0.7881 (p) REVERT: B 336 VAL cc_start: 0.8361 (m) cc_final: 0.8018 (t) REVERT: B 353 PHE cc_start: 0.7704 (t80) cc_final: 0.7385 (t80) REVERT: B 443 GLN cc_start: 0.7919 (mt0) cc_final: 0.7654 (mt0) REVERT: B 486 ARG cc_start: 0.8152 (ttp80) cc_final: 0.7878 (ttp80) REVERT: B 500 LYS cc_start: 0.6612 (ttmt) cc_final: 0.6089 (tppt) REVERT: C 32 ARG cc_start: 0.7335 (mmt180) cc_final: 0.7133 (mmt90) REVERT: C 52 GLU cc_start: 0.6927 (mt-10) cc_final: 0.6632 (mt-10) REVERT: C 81 ASP cc_start: 0.7458 (p0) cc_final: 0.7173 (p0) REVERT: C 93 THR cc_start: 0.8440 (m) cc_final: 0.8213 (p) REVERT: C 129 SER cc_start: 0.8448 (m) cc_final: 0.8053 (p) REVERT: C 142 ARG cc_start: 0.7619 (ttt90) cc_final: 0.7417 (ttt-90) REVERT: C 146 GLU cc_start: 0.8024 (pt0) cc_final: 0.7261 (pt0) REVERT: C 167 GLU cc_start: 0.7422 (tp30) cc_final: 0.6833 (mm-30) REVERT: C 228 MET cc_start: 0.7532 (mmm) cc_final: 0.7262 (mmt) REVERT: C 275 LYS cc_start: 0.7617 (mttp) cc_final: 0.7406 (mttp) REVERT: C 335 ASP cc_start: 0.6856 (t0) cc_final: 0.6234 (t0) REVERT: C 337 SER cc_start: 0.8278 (t) cc_final: 0.7770 (p) REVERT: C 386 LYS cc_start: 0.7892 (ttmt) cc_final: 0.7597 (ttmt) REVERT: C 393 LYS cc_start: 0.8230 (ttmt) cc_final: 0.7989 (ttmm) REVERT: C 424 GLU cc_start: 0.6838 (tp30) cc_final: 0.6331 (tp30) REVERT: C 431 LYS cc_start: 0.7507 (ptpt) cc_final: 0.7289 (mtpt) REVERT: C 480 GLU cc_start: 0.6913 (mm-30) cc_final: 0.6622 (mm-30) REVERT: D 64 MET cc_start: 0.8348 (mmm) cc_final: 0.7918 (mmt) REVERT: D 132 GLU cc_start: 0.7604 (tp30) cc_final: 0.7012 (tp30) REVERT: D 241 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6852 (mt-10) REVERT: D 288 ASP cc_start: 0.6986 (m-30) cc_final: 0.6443 (m-30) REVERT: D 294 GLU cc_start: 0.7011 (mm-30) cc_final: 0.6755 (mm-30) REVERT: D 373 LYS cc_start: 0.7487 (tttm) cc_final: 0.7251 (mtpp) REVERT: D 390 ILE cc_start: 0.8294 (mt) cc_final: 0.8083 (mt) REVERT: E 30 LEU cc_start: 0.8032 (mp) cc_final: 0.7784 (mt) REVERT: E 54 LEU cc_start: 0.8301 (mt) cc_final: 0.8066 (mp) REVERT: E 196 ASP cc_start: 0.6982 (m-30) cc_final: 0.6596 (m-30) REVERT: E 281 TYR cc_start: 0.8275 (m-80) cc_final: 0.8000 (m-80) REVERT: E 289 MET cc_start: 0.8262 (tpp) cc_final: 0.7939 (tpt) REVERT: E 300 LYS cc_start: 0.7950 (pttt) cc_final: 0.7695 (pttt) REVERT: E 301 LYS cc_start: 0.8090 (mmtt) cc_final: 0.7794 (mmtt) REVERT: E 317 LEU cc_start: 0.8415 (mt) cc_final: 0.8124 (mm) REVERT: E 356 ARG cc_start: 0.7144 (mtp180) cc_final: 0.6921 (mtp180) REVERT: E 448 LYS cc_start: 0.8449 (mtpt) cc_final: 0.8194 (mtpt) REVERT: F 12 LYS cc_start: 0.8272 (mttm) cc_final: 0.8006 (mttm) REVERT: F 64 MET cc_start: 0.8131 (mmp) cc_final: 0.7921 (mmt) REVERT: F 90 GLU cc_start: 0.6490 (mm-30) cc_final: 0.6226 (mm-30) REVERT: F 178 HIS cc_start: 0.7207 (t70) cc_final: 0.6558 (t-90) REVERT: F 214 LYS cc_start: 0.7948 (pttt) cc_final: 0.7709 (pttp) REVERT: F 219 PHE cc_start: 0.8452 (m-80) cc_final: 0.8099 (m-80) REVERT: F 245 ASP cc_start: 0.7223 (m-30) cc_final: 0.6900 (m-30) REVERT: F 268 VAL cc_start: 0.8214 (m) cc_final: 0.7994 (t) REVERT: F 277 SER cc_start: 0.8060 (p) cc_final: 0.7859 (m) REVERT: F 467 VAL cc_start: 0.8035 (t) cc_final: 0.7814 (m) REVERT: G 19 ILE cc_start: 0.8264 (mp) cc_final: 0.8057 (mt) REVERT: G 24 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7859 (ttpp) REVERT: G 43 LYS cc_start: 0.8082 (ttmm) cc_final: 0.7105 (ttpt) REVERT: G 109 THR cc_start: 0.8070 (p) cc_final: 0.7788 (p) REVERT: G 114 ILE cc_start: 0.8441 (tp) cc_final: 0.8179 (tt) REVERT: G 123 PRO cc_start: 0.8395 (Cg_endo) cc_final: 0.8191 (Cg_exo) REVERT: G 154 MET cc_start: 0.6383 (mmm) cc_final: 0.6163 (mmm) REVERT: G 217 GLN cc_start: 0.7583 (mm110) cc_final: 0.7356 (mm110) REVERT: G 252 SER cc_start: 0.7764 (m) cc_final: 0.7366 (t) outliers start: 6 outliers final: 3 residues processed: 794 average time/residue: 0.8985 time to fit residues: 1023.5165 Evaluate side-chains 667 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 663 time to evaluate : 2.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 24 LYS Chi-restraints excluded: chain G residue 80 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 1.9990 chunk 231 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 156 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 239 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 277 optimal weight: 0.8980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 434 GLN C 95 ASN C 265 HIS C 433 ASN C 452 ASN D 249 GLN D 375 GLN D 451 ASN F 57 ASN F 127 GLN F 168 GLN F 172 ASN F 293 GLN F 308 GLN F 411 GLN G 88 HIS G 167 ASN G 216 ASN H 15 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23836 Z= 0.278 Angle : 0.587 7.226 32349 Z= 0.314 Chirality : 0.044 0.169 3842 Planarity : 0.005 0.047 4167 Dihedral : 7.788 80.613 3602 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.65 % Favored : 98.15 % Rotamer: Outliers : 1.32 % Allowed : 11.84 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.14), residues: 3089 helix: -0.23 (0.14), residues: 1276 sheet: -0.49 (0.22), residues: 489 loop : -0.53 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 191 HIS 0.004 0.001 HIS D 367 PHE 0.019 0.001 PHE A 466 TYR 0.015 0.001 TYR C 230 ARG 0.008 0.001 ARG E 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 134 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue SER 492 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue SER 505 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue SER 40 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Evaluate side-chains 738 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 706 time to evaluate : 2.819 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.6879 (tt0) cc_final: 0.6459 (tt0) REVERT: A 91 LYS cc_start: 0.8101 (mttt) cc_final: 0.7839 (mtpp) REVERT: A 129 SER cc_start: 0.8036 (m) cc_final: 0.7731 (t) REVERT: A 132 GLN cc_start: 0.7429 (mm-40) cc_final: 0.6904 (mm-40) REVERT: A 156 ASP cc_start: 0.7522 (m-30) cc_final: 0.7296 (m-30) REVERT: A 167 GLU cc_start: 0.7938 (tp30) cc_final: 0.7277 (tp30) REVERT: A 289 ARG cc_start: 0.8626 (mtt180) cc_final: 0.8248 (mtt-85) REVERT: A 306 ARG cc_start: 0.7862 (ttp80) cc_final: 0.7179 (ttp80) REVERT: A 357 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6622 (tm-30) REVERT: A 358 LEU cc_start: 0.8316 (mt) cc_final: 0.7898 (mt) REVERT: A 421 VAL cc_start: 0.7823 (t) cc_final: 0.7597 (p) REVERT: A 475 LYS cc_start: 0.8285 (ttmm) cc_final: 0.7795 (mttp) REVERT: B 91 LYS cc_start: 0.8006 (mttt) cc_final: 0.7774 (mtmm) REVERT: B 118 ASP cc_start: 0.7976 (p0) cc_final: 0.7722 (p0) REVERT: B 123 ILE cc_start: 0.8335 (mm) cc_final: 0.8035 (mt) REVERT: B 159 VAL cc_start: 0.8311 (m) cc_final: 0.8025 (p) REVERT: B 199 LYS cc_start: 0.8248 (mttm) cc_final: 0.7906 (mtmm) REVERT: B 257 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6978 (mt-10) REVERT: B 261 ASP cc_start: 0.7383 (m-30) cc_final: 0.7106 (m-30) REVERT: B 336 VAL cc_start: 0.8389 (m) cc_final: 0.8112 (t) REVERT: B 353 PHE cc_start: 0.7733 (t80) cc_final: 0.7466 (t80) REVERT: B 443 GLN cc_start: 0.7904 (mt0) cc_final: 0.7679 (mt0) REVERT: C 52 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6621 (mt-10) REVERT: C 81 ASP cc_start: 0.7513 (p0) cc_final: 0.7273 (p0) REVERT: C 93 THR cc_start: 0.8457 (m) cc_final: 0.8246 (p) REVERT: C 128 ARG cc_start: 0.7994 (mtp180) cc_final: 0.7724 (mtp180) REVERT: C 129 SER cc_start: 0.8457 (m) cc_final: 0.8072 (p) REVERT: C 146 GLU cc_start: 0.7974 (pt0) cc_final: 0.7155 (pt0) REVERT: C 228 MET cc_start: 0.7743 (mmm) cc_final: 0.7495 (mmt) REVERT: C 246 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.8025 (t80) REVERT: C 271 ASP cc_start: 0.7297 (t0) cc_final: 0.7072 (t70) REVERT: C 335 ASP cc_start: 0.6826 (t0) cc_final: 0.6322 (t0) REVERT: C 337 SER cc_start: 0.8188 (t) cc_final: 0.7748 (p) REVERT: C 361 LYS cc_start: 0.8355 (mttt) cc_final: 0.8076 (mttp) REVERT: C 393 LYS cc_start: 0.8300 (ttmt) cc_final: 0.8055 (ttmm) REVERT: C 394 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8102 (mp) REVERT: C 424 GLU cc_start: 0.6968 (tp30) cc_final: 0.6598 (tp30) REVERT: C 442 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6691 (mt-10) REVERT: C 446 LEU cc_start: 0.7924 (mt) cc_final: 0.7687 (mt) REVERT: D 12 LYS cc_start: 0.7944 (mtpp) cc_final: 0.7646 (mttm) REVERT: D 126 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6564 (mt-10) REVERT: D 241 GLU cc_start: 0.7301 (mt-10) cc_final: 0.7004 (mt-10) REVERT: D 267 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6921 (mt-10) REVERT: D 288 ASP cc_start: 0.6982 (m-30) cc_final: 0.6464 (m-30) REVERT: D 365 GLN cc_start: 0.7539 (tp40) cc_final: 0.7199 (tp40) REVERT: D 435 LYS cc_start: 0.7919 (mptt) cc_final: 0.7698 (mmmt) REVERT: E 68 GLU cc_start: 0.6890 (mp0) cc_final: 0.6472 (mp0) REVERT: E 192 ARG cc_start: 0.8042 (ptm160) cc_final: 0.7492 (ptm-80) REVERT: E 196 ASP cc_start: 0.7105 (m-30) cc_final: 0.6623 (m-30) REVERT: E 199 ARG cc_start: 0.7503 (ptm-80) cc_final: 0.7289 (ttp-110) REVERT: E 241 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6620 (mt-10) REVERT: E 245 ASP cc_start: 0.7617 (m-30) cc_final: 0.7394 (m-30) REVERT: E 281 TYR cc_start: 0.8289 (m-80) cc_final: 0.7952 (m-80) REVERT: E 301 LYS cc_start: 0.7996 (mmtt) cc_final: 0.7706 (mmtt) REVERT: E 330 ASP cc_start: 0.7476 (m-30) cc_final: 0.7275 (m-30) REVERT: E 336 SER cc_start: 0.8102 (t) cc_final: 0.7807 (p) REVERT: E 379 GLN cc_start: 0.7606 (tp40) cc_final: 0.7347 (mm-40) REVERT: E 448 LYS cc_start: 0.8439 (mtpt) cc_final: 0.8174 (mtpt) REVERT: F 77 LEU cc_start: 0.8124 (mt) cc_final: 0.7881 (mm) REVERT: F 90 GLU cc_start: 0.6637 (mm-30) cc_final: 0.6392 (mm-30) REVERT: F 199 ARG cc_start: 0.7917 (ttp80) cc_final: 0.7462 (ttp-110) REVERT: F 214 LYS cc_start: 0.7935 (pttt) cc_final: 0.7692 (pttp) REVERT: F 245 ASP cc_start: 0.7263 (m-30) cc_final: 0.6905 (m-30) REVERT: F 277 SER cc_start: 0.8015 (p) cc_final: 0.7741 (m) REVERT: F 380 THR cc_start: 0.8151 (m) cc_final: 0.7949 (p) REVERT: G 24 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7922 (ttpp) REVERT: G 43 LYS cc_start: 0.8093 (ttmm) cc_final: 0.7076 (tttt) REVERT: G 109 THR cc_start: 0.8064 (p) cc_final: 0.7757 (p) REVERT: G 114 ILE cc_start: 0.8490 (tp) cc_final: 0.8181 (tt) REVERT: G 131 ASN cc_start: 0.7721 (p0) cc_final: 0.7427 (p0) REVERT: G 218 MET cc_start: 0.7079 (mtp) cc_final: 0.6874 (mtp) REVERT: G 249 ASN cc_start: 0.7971 (m-40) cc_final: 0.7685 (m110) REVERT: H 43 PHE cc_start: 0.7296 (m-80) cc_final: 0.6881 (m-80) outliers start: 32 outliers final: 19 residues processed: 715 average time/residue: 0.8993 time to fit residues: 938.1233 Evaluate side-chains 705 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 683 time to evaluate : 2.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 493 LYS Chi-restraints excluded: chain D residue 221 GLN Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 472 LYS Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 24 LYS Chi-restraints excluded: chain G residue 80 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 231 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 chunk 300 optimal weight: 1.9990 chunk 247 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 57 ASN F 293 GLN F 308 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 23836 Z= 0.369 Angle : 0.586 7.461 32349 Z= 0.311 Chirality : 0.045 0.180 3842 Planarity : 0.005 0.054 4167 Dihedral : 7.046 85.196 3600 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.33 % Favored : 97.47 % Rotamer: Outliers : 1.37 % Allowed : 13.82 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 3089 helix: 0.22 (0.14), residues: 1274 sheet: -0.64 (0.22), residues: 500 loop : -0.41 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 258 HIS 0.007 0.001 HIS D 367 PHE 0.016 0.002 PHE F 261 TYR 0.015 0.002 TYR C 230 ARG 0.006 0.001 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 134 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue SER 492 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue SER 505 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue SER 40 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Evaluate side-chains 737 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 704 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.6882 (tt0) cc_final: 0.6439 (tt0) REVERT: A 91 LYS cc_start: 0.8137 (mttt) cc_final: 0.7846 (mtpp) REVERT: A 129 SER cc_start: 0.8081 (m) cc_final: 0.7755 (t) REVERT: A 132 GLN cc_start: 0.7462 (mm-40) cc_final: 0.7208 (mm-40) REVERT: A 167 GLU cc_start: 0.7894 (tp30) cc_final: 0.7497 (tp30) REVERT: A 271 ASP cc_start: 0.6970 (t70) cc_final: 0.6535 (t0) REVERT: A 283 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7965 (mp) REVERT: A 289 ARG cc_start: 0.8628 (mtt180) cc_final: 0.8249 (mtt-85) REVERT: A 357 GLU cc_start: 0.7345 (tm-30) cc_final: 0.6747 (tm-30) REVERT: A 358 LEU cc_start: 0.8322 (mt) cc_final: 0.7721 (mt) REVERT: A 421 VAL cc_start: 0.7831 (t) cc_final: 0.7625 (p) REVERT: A 475 LYS cc_start: 0.8253 (ttmm) cc_final: 0.7737 (mttp) REVERT: B 118 ASP cc_start: 0.8032 (p0) cc_final: 0.7773 (p0) REVERT: B 123 ILE cc_start: 0.8344 (mm) cc_final: 0.8060 (mt) REVERT: B 159 VAL cc_start: 0.8375 (m) cc_final: 0.8063 (p) REVERT: B 199 LYS cc_start: 0.8247 (mttm) cc_final: 0.7932 (mtmm) REVERT: B 257 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6989 (mt-10) REVERT: B 261 ASP cc_start: 0.7431 (m-30) cc_final: 0.7162 (m-30) REVERT: B 336 VAL cc_start: 0.8329 (m) cc_final: 0.8046 (t) REVERT: B 353 PHE cc_start: 0.7749 (t80) cc_final: 0.7344 (t80) REVERT: C 52 GLU cc_start: 0.6904 (mt-10) cc_final: 0.6588 (mt-10) REVERT: C 81 ASP cc_start: 0.7533 (p0) cc_final: 0.7311 (p0) REVERT: C 118 ASP cc_start: 0.7912 (p0) cc_final: 0.7618 (p0) REVERT: C 128 ARG cc_start: 0.8003 (mtp180) cc_final: 0.7757 (mtp180) REVERT: C 129 SER cc_start: 0.8503 (m) cc_final: 0.8098 (p) REVERT: C 146 GLU cc_start: 0.7960 (pt0) cc_final: 0.7607 (pt0) REVERT: C 228 MET cc_start: 0.7894 (mmm) cc_final: 0.7680 (mmt) REVERT: C 246 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.8109 (t80) REVERT: C 257 GLU cc_start: 0.6411 (mt-10) cc_final: 0.6168 (mt-10) REVERT: C 271 ASP cc_start: 0.7376 (t0) cc_final: 0.7135 (t70) REVERT: C 275 LYS cc_start: 0.7965 (mttp) cc_final: 0.7727 (mttp) REVERT: C 335 ASP cc_start: 0.6909 (t0) cc_final: 0.6419 (t0) REVERT: C 337 SER cc_start: 0.8270 (t) cc_final: 0.7808 (p) REVERT: C 361 LYS cc_start: 0.8336 (mttt) cc_final: 0.8105 (mttp) REVERT: C 393 LYS cc_start: 0.8320 (ttmt) cc_final: 0.8063 (ttmm) REVERT: C 394 LEU cc_start: 0.8343 (tp) cc_final: 0.8102 (mp) REVERT: C 424 GLU cc_start: 0.7046 (tp30) cc_final: 0.6698 (tp30) REVERT: C 442 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6755 (mt-10) REVERT: C 446 LEU cc_start: 0.7980 (mt) cc_final: 0.7707 (mt) REVERT: D 12 LYS cc_start: 0.7920 (mtpp) cc_final: 0.7615 (mttm) REVERT: D 38 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6948 (mm-30) REVERT: D 126 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6798 (mp0) REVERT: D 267 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6855 (mt-10) REVERT: D 288 ASP cc_start: 0.7029 (m-30) cc_final: 0.6499 (m-30) REVERT: D 435 LYS cc_start: 0.7935 (mptt) cc_final: 0.7712 (mmmt) REVERT: E 90 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7144 (mm-30) REVERT: E 196 ASP cc_start: 0.7119 (m-30) cc_final: 0.6656 (m-30) REVERT: E 301 LYS cc_start: 0.7990 (mmtt) cc_final: 0.7692 (mmtt) REVERT: E 356 ARG cc_start: 0.7227 (mtp85) cc_final: 0.6988 (mtp180) REVERT: E 379 GLN cc_start: 0.7647 (tp40) cc_final: 0.7403 (mm-40) REVERT: E 448 LYS cc_start: 0.8433 (mtpt) cc_final: 0.8118 (mtpt) REVERT: F 77 LEU cc_start: 0.8143 (mt) cc_final: 0.7896 (mm) REVERT: F 90 GLU cc_start: 0.6640 (mm-30) cc_final: 0.6407 (mm-30) REVERT: F 199 ARG cc_start: 0.7916 (ttp80) cc_final: 0.7500 (ttp-110) REVERT: F 245 ASP cc_start: 0.7284 (m-30) cc_final: 0.6976 (m-30) REVERT: F 256 ASP cc_start: 0.6821 (t0) cc_final: 0.6543 (t0) REVERT: F 293 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7912 (tp40) REVERT: F 316 ASP cc_start: 0.7030 (t70) cc_final: 0.6813 (t0) REVERT: F 412 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7846 (tpp-160) REVERT: G 43 LYS cc_start: 0.8134 (ttmm) cc_final: 0.7142 (tttt) REVERT: G 109 THR cc_start: 0.8025 (p) cc_final: 0.7776 (p) REVERT: G 114 ILE cc_start: 0.8481 (tp) cc_final: 0.8173 (tt) REVERT: G 129 SER cc_start: 0.8096 (t) cc_final: 0.7764 (p) REVERT: G 131 ASN cc_start: 0.7819 (p0) cc_final: 0.7534 (p0) REVERT: G 249 ASN cc_start: 0.7952 (m-40) cc_final: 0.7634 (m-40) REVERT: H 43 PHE cc_start: 0.7353 (m-80) cc_final: 0.7024 (m-80) outliers start: 33 outliers final: 25 residues processed: 714 average time/residue: 0.8783 time to fit residues: 907.7736 Evaluate side-chains 698 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 669 time to evaluate : 2.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 493 LYS Chi-restraints excluded: chain D residue 221 GLN Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 293 GLN Chi-restraints excluded: chain F residue 412 ARG Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 80 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 0.6980 chunk 209 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 279 optimal weight: 0.5980 chunk 295 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 264 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 245 GLN F 57 ASN F 168 GLN G 265 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23836 Z= 0.229 Angle : 0.536 6.784 32349 Z= 0.283 Chirality : 0.043 0.156 3842 Planarity : 0.004 0.051 4167 Dihedral : 6.635 81.219 3596 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.94 % Favored : 97.86 % Rotamer: Outliers : 1.74 % Allowed : 14.49 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 3089 helix: 0.64 (0.15), residues: 1270 sheet: -0.65 (0.22), residues: 500 loop : -0.32 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 258 HIS 0.003 0.001 HIS F 53 PHE 0.014 0.001 PHE F 261 TYR 0.016 0.001 TYR G 159 ARG 0.006 0.000 ARG B 82 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 134 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue SER 492 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue SER 505 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue SER 40 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Evaluate side-chains 722 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 680 time to evaluate : 2.714 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.6917 (tt0) cc_final: 0.6451 (tt0) REVERT: A 91 LYS cc_start: 0.8131 (mttt) cc_final: 0.7816 (mtpp) REVERT: A 129 SER cc_start: 0.8092 (m) cc_final: 0.7750 (t) REVERT: A 132 GLN cc_start: 0.7514 (mm-40) cc_final: 0.7247 (mm-40) REVERT: A 167 GLU cc_start: 0.7900 (tp30) cc_final: 0.7521 (tp30) REVERT: A 271 ASP cc_start: 0.6957 (t70) cc_final: 0.6550 (t0) REVERT: A 283 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7987 (mp) REVERT: A 289 ARG cc_start: 0.8608 (mtt180) cc_final: 0.8248 (mtt-85) REVERT: A 330 GLU cc_start: 0.6986 (tt0) cc_final: 0.6775 (tt0) REVERT: A 357 GLU cc_start: 0.7359 (tm-30) cc_final: 0.6766 (tm-30) REVERT: A 358 LEU cc_start: 0.8291 (mt) cc_final: 0.7644 (mt) REVERT: A 475 LYS cc_start: 0.8251 (ttmm) cc_final: 0.7731 (mttp) REVERT: B 69 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6862 (mt-10) REVERT: B 118 ASP cc_start: 0.8033 (p0) cc_final: 0.7739 (p0) REVERT: B 123 ILE cc_start: 0.8350 (mm) cc_final: 0.8073 (mt) REVERT: B 159 VAL cc_start: 0.8381 (m) cc_final: 0.8041 (p) REVERT: B 199 LYS cc_start: 0.8237 (mttm) cc_final: 0.7963 (mtmm) REVERT: B 257 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6975 (mt-10) REVERT: B 261 ASP cc_start: 0.7396 (m-30) cc_final: 0.7116 (m-30) REVERT: B 336 VAL cc_start: 0.8365 (m) cc_final: 0.8063 (t) REVERT: B 353 PHE cc_start: 0.7802 (t80) cc_final: 0.7488 (t80) REVERT: C 52 GLU cc_start: 0.6868 (mt-10) cc_final: 0.6526 (mt-10) REVERT: C 118 ASP cc_start: 0.7880 (p0) cc_final: 0.7602 (p0) REVERT: C 128 ARG cc_start: 0.7975 (mtp180) cc_final: 0.7736 (mtp180) REVERT: C 129 SER cc_start: 0.8459 (m) cc_final: 0.8032 (p) REVERT: C 133 VAL cc_start: 0.8767 (m) cc_final: 0.8540 (p) REVERT: C 146 GLU cc_start: 0.7947 (pt0) cc_final: 0.7542 (pt0) REVERT: C 228 MET cc_start: 0.7894 (mmm) cc_final: 0.7673 (mmt) REVERT: C 246 TYR cc_start: 0.8542 (OUTLIER) cc_final: 0.8097 (t80) REVERT: C 257 GLU cc_start: 0.6355 (mt-10) cc_final: 0.6133 (mt-10) REVERT: C 271 ASP cc_start: 0.7339 (t0) cc_final: 0.7068 (t70) REVERT: C 275 LYS cc_start: 0.7856 (mttp) cc_final: 0.7559 (mttp) REVERT: C 335 ASP cc_start: 0.6927 (t0) cc_final: 0.6431 (t0) REVERT: C 337 SER cc_start: 0.8220 (t) cc_final: 0.7760 (p) REVERT: C 361 LYS cc_start: 0.8261 (mttt) cc_final: 0.8043 (mttp) REVERT: C 393 LYS cc_start: 0.8311 (ttmt) cc_final: 0.8033 (ttmm) REVERT: C 394 LEU cc_start: 0.8332 (tp) cc_final: 0.8094 (mp) REVERT: C 442 GLU cc_start: 0.6942 (mt-10) cc_final: 0.6725 (mt-10) REVERT: C 446 LEU cc_start: 0.7981 (mt) cc_final: 0.7711 (mt) REVERT: D 12 LYS cc_start: 0.7886 (mtpp) cc_final: 0.7647 (mttp) REVERT: D 74 GLU cc_start: 0.7512 (tt0) cc_final: 0.7288 (tt0) REVERT: D 126 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6718 (mt-10) REVERT: D 267 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6860 (mt-10) REVERT: D 288 ASP cc_start: 0.7016 (m-30) cc_final: 0.6474 (m-30) REVERT: D 435 LYS cc_start: 0.7954 (mptt) cc_final: 0.7710 (mmmt) REVERT: E 90 GLU cc_start: 0.7313 (mm-30) cc_final: 0.7032 (mm-30) REVERT: E 196 ASP cc_start: 0.7134 (m-30) cc_final: 0.6648 (m-30) REVERT: E 301 LYS cc_start: 0.7966 (mmtt) cc_final: 0.7679 (mmtt) REVERT: E 379 GLN cc_start: 0.7654 (tp40) cc_final: 0.7418 (mm-40) REVERT: E 448 LYS cc_start: 0.8400 (mtpt) cc_final: 0.8100 (mtpt) REVERT: F 90 GLU cc_start: 0.6630 (mm-30) cc_final: 0.6418 (mm-30) REVERT: F 196 ASP cc_start: 0.7179 (t70) cc_final: 0.6797 (t0) REVERT: F 199 ARG cc_start: 0.7912 (ttp80) cc_final: 0.7629 (ttp-110) REVERT: F 245 ASP cc_start: 0.7273 (m-30) cc_final: 0.6968 (m-30) REVERT: F 247 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7613 (mm-30) REVERT: F 256 ASP cc_start: 0.6810 (t0) cc_final: 0.6467 (t0) REVERT: F 281 TYR cc_start: 0.8239 (m-80) cc_final: 0.7927 (m-80) REVERT: F 301 LYS cc_start: 0.8187 (mtmm) cc_final: 0.7928 (mtmm) REVERT: F 412 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7826 (tpp-160) REVERT: G 23 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.6986 (mpt) REVERT: G 43 LYS cc_start: 0.8120 (ttmm) cc_final: 0.7122 (tttt) REVERT: G 109 THR cc_start: 0.8062 (p) cc_final: 0.7793 (p) REVERT: G 114 ILE cc_start: 0.8459 (tp) cc_final: 0.8126 (tt) REVERT: G 129 SER cc_start: 0.8067 (t) cc_final: 0.7753 (p) REVERT: G 131 ASN cc_start: 0.7816 (p0) cc_final: 0.7538 (p0) REVERT: G 154 MET cc_start: 0.6519 (mmm) cc_final: 0.6302 (mmm) REVERT: G 224 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7451 (mm-40) REVERT: G 249 ASN cc_start: 0.7913 (m-40) cc_final: 0.7556 (m-40) REVERT: H 19 GLN cc_start: 0.8299 (mm-40) cc_final: 0.7994 (tp40) REVERT: H 43 PHE cc_start: 0.7306 (m-80) cc_final: 0.6990 (m-80) outliers start: 42 outliers final: 25 residues processed: 692 average time/residue: 0.9201 time to fit residues: 929.6932 Evaluate side-chains 704 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 675 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 493 LYS Chi-restraints excluded: chain D residue 221 GLN Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 412 ARG Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain G residue 15 ASN Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 119 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 265 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 GLN ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 GLN B 95 ASN C 245 GLN ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN F 57 ASN F 168 GLN G 54 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 23836 Z= 0.416 Angle : 0.588 8.142 32349 Z= 0.310 Chirality : 0.046 0.182 3842 Planarity : 0.005 0.059 4167 Dihedral : 6.776 86.094 3596 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.75 % Favored : 97.05 % Rotamer: Outliers : 1.90 % Allowed : 15.15 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 3089 helix: 0.57 (0.14), residues: 1276 sheet: -0.73 (0.22), residues: 520 loop : -0.41 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 258 HIS 0.006 0.001 HIS D 367 PHE 0.019 0.002 PHE A 466 TYR 0.014 0.002 TYR B 246 ARG 0.006 0.001 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 134 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue SER 492 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue SER 505 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue SER 40 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Evaluate side-chains 755 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 709 time to evaluate : 2.670 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 52 GLU cc_start: 0.6917 (tt0) cc_final: 0.6475 (tt0) REVERT: A 91 LYS cc_start: 0.8142 (mttt) cc_final: 0.7810 (mtpp) REVERT: A 129 SER cc_start: 0.8071 (m) cc_final: 0.7715 (t) REVERT: A 132 GLN cc_start: 0.7491 (mm-40) cc_final: 0.6970 (mm-40) REVERT: A 167 GLU cc_start: 0.7867 (tp30) cc_final: 0.7498 (tp30) REVERT: A 271 ASP cc_start: 0.7074 (t70) cc_final: 0.6618 (t0) REVERT: A 283 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.8016 (mp) REVERT: A 357 GLU cc_start: 0.7406 (tm-30) cc_final: 0.6820 (tm-30) REVERT: A 358 LEU cc_start: 0.8389 (mt) cc_final: 0.7848 (mt) REVERT: A 475 LYS cc_start: 0.8264 (ttmm) cc_final: 0.7769 (mttp) REVERT: B 69 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6880 (mt-10) REVERT: B 118 ASP cc_start: 0.8045 (p0) cc_final: 0.7774 (p0) REVERT: B 123 ILE cc_start: 0.8369 (mm) cc_final: 0.8104 (mt) REVERT: B 159 VAL cc_start: 0.8388 (m) cc_final: 0.8038 (p) REVERT: B 172 ASP cc_start: 0.6622 (t0) cc_final: 0.6330 (m-30) REVERT: B 199 LYS cc_start: 0.8268 (mttm) cc_final: 0.7977 (mtmm) REVERT: B 257 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6970 (mt-10) REVERT: B 261 ASP cc_start: 0.7484 (m-30) cc_final: 0.7183 (m-30) REVERT: B 336 VAL cc_start: 0.8402 (m) cc_final: 0.8070 (t) REVERT: B 353 PHE cc_start: 0.7778 (t80) cc_final: 0.7522 (t80) REVERT: C 52 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6547 (mt-10) REVERT: C 118 ASP cc_start: 0.7847 (p0) cc_final: 0.7624 (p0) REVERT: C 128 ARG cc_start: 0.7994 (mtp180) cc_final: 0.7751 (mtp180) REVERT: C 129 SER cc_start: 0.8518 (m) cc_final: 0.8061 (p) REVERT: C 133 VAL cc_start: 0.8757 (m) cc_final: 0.8535 (p) REVERT: C 146 GLU cc_start: 0.7981 (pt0) cc_final: 0.7316 (mt-10) REVERT: C 228 MET cc_start: 0.7942 (mmm) cc_final: 0.7731 (mmt) REVERT: C 246 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.8182 (t80) REVERT: C 271 ASP cc_start: 0.7348 (t0) cc_final: 0.7093 (t70) REVERT: C 275 LYS cc_start: 0.7888 (mttp) cc_final: 0.7640 (mmtp) REVERT: C 361 LYS cc_start: 0.8300 (mttt) cc_final: 0.8025 (mttp) REVERT: C 393 LYS cc_start: 0.8311 (ttmt) cc_final: 0.8031 (ttmm) REVERT: C 442 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6756 (mt-10) REVERT: C 446 LEU cc_start: 0.8004 (mt) cc_final: 0.7754 (mt) REVERT: D 12 LYS cc_start: 0.7886 (mtpp) cc_final: 0.7588 (mttm) REVERT: D 38 GLU cc_start: 0.7289 (mt-10) cc_final: 0.7033 (mm-30) REVERT: D 126 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6716 (mt-10) REVERT: D 241 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7047 (mt-10) REVERT: D 267 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6849 (mt-10) REVERT: D 288 ASP cc_start: 0.7123 (m-30) cc_final: 0.6715 (m-30) REVERT: D 435 LYS cc_start: 0.7972 (mptt) cc_final: 0.7740 (mmmt) REVERT: E 90 GLU cc_start: 0.7288 (mm-30) cc_final: 0.7004 (mm-30) REVERT: E 196 ASP cc_start: 0.7202 (m-30) cc_final: 0.6661 (m-30) REVERT: E 274 ARG cc_start: 0.8229 (mtt180) cc_final: 0.8018 (mtt180) REVERT: E 301 LYS cc_start: 0.7972 (mmtt) cc_final: 0.7694 (mmtt) REVERT: E 431 LEU cc_start: 0.6918 (OUTLIER) cc_final: 0.6716 (mp) REVERT: E 448 LYS cc_start: 0.8468 (mtpt) cc_final: 0.8147 (mtpt) REVERT: F 196 ASP cc_start: 0.7199 (t70) cc_final: 0.6838 (t0) REVERT: F 199 ARG cc_start: 0.7930 (ttp80) cc_final: 0.7626 (ttp-110) REVERT: F 245 ASP cc_start: 0.7293 (m-30) cc_final: 0.6984 (m-30) REVERT: F 247 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7700 (mm-30) REVERT: F 256 ASP cc_start: 0.6810 (t0) cc_final: 0.6480 (t0) REVERT: F 412 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7917 (tpp-160) REVERT: G 43 LYS cc_start: 0.8202 (ttmm) cc_final: 0.7172 (tttt) REVERT: G 90 GLN cc_start: 0.8149 (mt0) cc_final: 0.7883 (mt0) REVERT: G 129 SER cc_start: 0.8132 (t) cc_final: 0.7728 (p) REVERT: G 131 ASN cc_start: 0.7868 (p0) cc_final: 0.7661 (p0) REVERT: G 249 ASN cc_start: 0.7968 (m-40) cc_final: 0.7595 (m110) REVERT: H 43 PHE cc_start: 0.7352 (m-80) cc_final: 0.7122 (m-80) outliers start: 46 outliers final: 30 residues processed: 724 average time/residue: 0.8674 time to fit residues: 905.4190 Evaluate side-chains 736 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 702 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 493 LYS Chi-restraints excluded: chain D residue 221 GLN Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 412 ARG Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain G residue 15 ASN Chi-restraints excluded: chain G residue 119 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 3.9990 chunk 266 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 296 optimal weight: 4.9990 chunk 245 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN F 57 ASN F 168 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 23836 Z= 0.353 Angle : 0.565 6.523 32349 Z= 0.299 Chirality : 0.045 0.173 3842 Planarity : 0.005 0.060 4167 Dihedral : 6.607 86.297 3591 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.49 % Favored : 97.31 % Rotamer: Outliers : 1.78 % Allowed : 15.52 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.15), residues: 3089 helix: 0.73 (0.14), residues: 1273 sheet: -0.74 (0.23), residues: 512 loop : -0.41 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 258 HIS 0.006 0.001 HIS D 367 PHE 0.015 0.002 PHE F 261 TYR 0.012 0.001 TYR C 230 ARG 0.009 0.001 ARG E 149 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 134 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue SER 492 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue SER 505 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue SER 40 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Evaluate side-chains 754 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 711 time to evaluate : 2.738 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: symmetry clash REVERT: A 52 GLU cc_start: 0.6905 (tt0) cc_final: 0.6442 (tt0) REVERT: A 91 LYS cc_start: 0.8142 (mttt) cc_final: 0.7809 (mtpp) REVERT: A 129 SER cc_start: 0.8046 (m) cc_final: 0.7680 (t) REVERT: A 132 GLN cc_start: 0.7476 (mm-40) cc_final: 0.7270 (mm-40) REVERT: A 167 GLU cc_start: 0.7839 (tp30) cc_final: 0.7414 (tp30) REVERT: A 271 ASP cc_start: 0.7058 (t70) cc_final: 0.6603 (t0) REVERT: A 283 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8070 (mp) REVERT: A 357 GLU cc_start: 0.7385 (tm-30) cc_final: 0.6926 (tm-30) REVERT: A 358 LEU cc_start: 0.8402 (mt) cc_final: 0.7818 (mt) REVERT: A 475 LYS cc_start: 0.8266 (ttmm) cc_final: 0.7778 (mttp) REVERT: B 69 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6884 (mt-10) REVERT: B 118 ASP cc_start: 0.8046 (p0) cc_final: 0.7775 (p0) REVERT: B 123 ILE cc_start: 0.8385 (mm) cc_final: 0.8144 (mt) REVERT: B 159 VAL cc_start: 0.8388 (m) cc_final: 0.8025 (p) REVERT: B 199 LYS cc_start: 0.8265 (mttm) cc_final: 0.7981 (mtmm) REVERT: B 257 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6994 (mt-10) REVERT: B 261 ASP cc_start: 0.7481 (m-30) cc_final: 0.7193 (m-30) REVERT: B 336 VAL cc_start: 0.8409 (m) cc_final: 0.8086 (t) REVERT: B 353 PHE cc_start: 0.7761 (t80) cc_final: 0.7531 (t80) REVERT: C 52 GLU cc_start: 0.6870 (mt-10) cc_final: 0.6517 (mt-10) REVERT: C 118 ASP cc_start: 0.7848 (p0) cc_final: 0.7641 (p0) REVERT: C 129 SER cc_start: 0.8501 (m) cc_final: 0.8012 (p) REVERT: C 146 GLU cc_start: 0.7979 (pt0) cc_final: 0.7550 (pt0) REVERT: C 167 GLU cc_start: 0.7429 (tp30) cc_final: 0.7206 (tp30) REVERT: C 228 MET cc_start: 0.7942 (mmm) cc_final: 0.7721 (mmt) REVERT: C 246 TYR cc_start: 0.8611 (OUTLIER) cc_final: 0.8191 (t80) REVERT: C 393 LYS cc_start: 0.8307 (ttmt) cc_final: 0.8032 (ttmm) REVERT: C 442 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6746 (mt-10) REVERT: C 446 LEU cc_start: 0.8003 (mt) cc_final: 0.7742 (mt) REVERT: D 12 LYS cc_start: 0.7893 (mtpp) cc_final: 0.7595 (mttm) REVERT: D 38 GLU cc_start: 0.7311 (mt-10) cc_final: 0.7032 (mm-30) REVERT: D 267 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6864 (mt-10) REVERT: D 288 ASP cc_start: 0.7135 (m-30) cc_final: 0.6603 (m-30) REVERT: D 435 LYS cc_start: 0.7975 (mptt) cc_final: 0.7757 (mmmt) REVERT: E 196 ASP cc_start: 0.7186 (m-30) cc_final: 0.6674 (m-30) REVERT: E 274 ARG cc_start: 0.8216 (mtt180) cc_final: 0.8012 (mtt180) REVERT: E 301 LYS cc_start: 0.7962 (mmtt) cc_final: 0.7678 (mmtt) REVERT: E 448 LYS cc_start: 0.8466 (mtpt) cc_final: 0.8120 (mtpt) REVERT: F 142 ASP cc_start: 0.7208 (m-30) cc_final: 0.6843 (m-30) REVERT: F 196 ASP cc_start: 0.7205 (t70) cc_final: 0.6895 (t0) REVERT: F 199 ARG cc_start: 0.7944 (ttp80) cc_final: 0.7667 (ttp-110) REVERT: F 245 ASP cc_start: 0.7278 (m-30) cc_final: 0.6982 (m-30) REVERT: F 247 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7714 (mm-30) REVERT: F 256 ASP cc_start: 0.6791 (t0) cc_final: 0.6477 (t0) REVERT: F 281 TYR cc_start: 0.8265 (m-80) cc_final: 0.7982 (m-80) REVERT: F 301 LYS cc_start: 0.8245 (mtmm) cc_final: 0.7994 (mtmm) REVERT: F 412 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7867 (tpp-160) REVERT: G 43 LYS cc_start: 0.8215 (ttmm) cc_final: 0.7165 (tttt) REVERT: G 90 GLN cc_start: 0.8168 (mt0) cc_final: 0.7894 (mt0) REVERT: G 114 ILE cc_start: 0.8376 (tp) cc_final: 0.8092 (tt) REVERT: G 129 SER cc_start: 0.8090 (t) cc_final: 0.7642 (p) REVERT: G 249 ASN cc_start: 0.7958 (m-40) cc_final: 0.7600 (m110) REVERT: H 43 PHE cc_start: 0.7326 (m-80) cc_final: 0.7066 (m-10) outliers start: 43 outliers final: 31 residues processed: 723 average time/residue: 0.8579 time to fit residues: 899.5980 Evaluate side-chains 732 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 698 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 493 LYS Chi-restraints excluded: chain D residue 221 GLN Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 459 MET Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 412 ARG Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain G residue 15 ASN Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain H residue 25 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 216 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 294 optimal weight: 0.7980 chunk 184 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN F 57 ASN G 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 23836 Z= 0.367 Angle : 0.567 6.422 32349 Z= 0.299 Chirality : 0.045 0.174 3842 Planarity : 0.005 0.067 4167 Dihedral : 6.565 87.224 3591 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.75 % Favored : 97.05 % Rotamer: Outliers : 1.86 % Allowed : 16.02 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 3089 helix: 0.78 (0.14), residues: 1273 sheet: -0.78 (0.23), residues: 511 loop : -0.40 (0.18), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 258 HIS 0.006 0.001 HIS D 367 PHE 0.018 0.002 PHE F 261 TYR 0.012 0.002 TYR C 230 ARG 0.011 0.001 ARG B 462 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 134 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue SER 492 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue SER 505 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue SER 40 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Evaluate side-chains 760 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 715 time to evaluate : 2.689 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: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.6891 (tt0) cc_final: 0.6452 (tt0) REVERT: A 91 LYS cc_start: 0.8144 (mttt) cc_final: 0.7845 (mttp) REVERT: A 129 SER cc_start: 0.8051 (m) cc_final: 0.7679 (t) REVERT: A 132 GLN cc_start: 0.7459 (mm-40) cc_final: 0.6919 (mm-40) REVERT: A 167 GLU cc_start: 0.7820 (tp30) cc_final: 0.7364 (tp30) REVERT: A 271 ASP cc_start: 0.6937 (t70) cc_final: 0.6489 (t0) REVERT: A 475 LYS cc_start: 0.8268 (ttmm) cc_final: 0.7771 (mttp) REVERT: B 69 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6892 (mt-10) REVERT: B 118 ASP cc_start: 0.8056 (p0) cc_final: 0.7784 (p0) REVERT: B 123 ILE cc_start: 0.8401 (mm) cc_final: 0.8168 (mt) REVERT: B 159 VAL cc_start: 0.8381 (m) cc_final: 0.8025 (p) REVERT: B 172 ASP cc_start: 0.6629 (t0) cc_final: 0.6399 (m-30) REVERT: B 199 LYS cc_start: 0.8256 (mttm) cc_final: 0.7909 (mtmm) REVERT: B 246 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.7804 (t80) REVERT: B 257 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6984 (mt-10) REVERT: B 261 ASP cc_start: 0.7462 (m-30) cc_final: 0.7181 (m-30) REVERT: B 336 VAL cc_start: 0.8396 (m) cc_final: 0.8061 (t) REVERT: B 353 PHE cc_start: 0.7757 (t80) cc_final: 0.7503 (t80) REVERT: C 52 GLU cc_start: 0.6868 (mt-10) cc_final: 0.6518 (mt-10) REVERT: C 129 SER cc_start: 0.8468 (m) cc_final: 0.7989 (p) REVERT: C 146 GLU cc_start: 0.7968 (pt0) cc_final: 0.7507 (pt0) REVERT: C 228 MET cc_start: 0.7967 (mmm) cc_final: 0.7751 (mmt) REVERT: C 246 TYR cc_start: 0.8633 (OUTLIER) cc_final: 0.8294 (t80) REVERT: C 271 ASP cc_start: 0.7347 (t0) cc_final: 0.7057 (t70) REVERT: C 393 LYS cc_start: 0.8304 (ttmt) cc_final: 0.8027 (ttmm) REVERT: C 442 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6744 (mt-10) REVERT: C 446 LEU cc_start: 0.8002 (mt) cc_final: 0.7750 (mt) REVERT: D 12 LYS cc_start: 0.7923 (mtpp) cc_final: 0.7628 (mttm) REVERT: D 126 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6810 (mp0) REVERT: D 241 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7078 (mt-10) REVERT: D 267 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6882 (mt-10) REVERT: D 288 ASP cc_start: 0.7190 (m-30) cc_final: 0.6840 (m-30) REVERT: D 435 LYS cc_start: 0.8034 (mptt) cc_final: 0.7810 (mmmt) REVERT: E 196 ASP cc_start: 0.7179 (m-30) cc_final: 0.6655 (m-30) REVERT: E 301 LYS cc_start: 0.7955 (mmtt) cc_final: 0.7666 (mmtt) REVERT: E 422 GLU cc_start: 0.6975 (tm-30) cc_final: 0.6662 (tm-30) REVERT: E 448 LYS cc_start: 0.8475 (mtpt) cc_final: 0.8132 (mtpt) REVERT: F 142 ASP cc_start: 0.7214 (m-30) cc_final: 0.6887 (m-30) REVERT: F 196 ASP cc_start: 0.7210 (t70) cc_final: 0.6522 (t0) REVERT: F 199 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7560 (ttp-110) REVERT: F 200 GLU cc_start: 0.6794 (mt-10) cc_final: 0.6558 (mt-10) REVERT: F 245 ASP cc_start: 0.7269 (m-30) cc_final: 0.6985 (m-30) REVERT: F 247 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7724 (mm-30) REVERT: F 301 LYS cc_start: 0.8253 (mtmm) cc_final: 0.8009 (mtmm) REVERT: F 412 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7859 (tpp-160) REVERT: G 43 LYS cc_start: 0.8226 (ttmm) cc_final: 0.7204 (ttpt) REVERT: G 90 GLN cc_start: 0.8146 (mt0) cc_final: 0.7860 (mt0) REVERT: G 114 ILE cc_start: 0.8389 (tp) cc_final: 0.8083 (tt) REVERT: G 129 SER cc_start: 0.8138 (t) cc_final: 0.7621 (p) REVERT: G 249 ASN cc_start: 0.7970 (m-40) cc_final: 0.7630 (m110) outliers start: 45 outliers final: 35 residues processed: 730 average time/residue: 0.8614 time to fit residues: 902.6311 Evaluate side-chains 749 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 711 time to evaluate : 2.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 493 LYS Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 221 GLN Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 459 MET Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 412 ARG Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain G residue 15 ASN Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain H residue 25 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 0.0970 chunk 117 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 187 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 231 optimal weight: 0.7980 chunk 268 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23836 Z= 0.285 Angle : 0.546 6.232 32349 Z= 0.287 Chirality : 0.043 0.164 3842 Planarity : 0.005 0.073 4167 Dihedral : 6.456 86.445 3591 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.49 % Favored : 97.31 % Rotamer: Outliers : 1.61 % Allowed : 16.72 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.15), residues: 3089 helix: 0.99 (0.15), residues: 1273 sheet: -0.75 (0.23), residues: 510 loop : -0.34 (0.18), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 258 HIS 0.005 0.001 HIS D 367 PHE 0.014 0.001 PHE F 261 TYR 0.012 0.001 TYR F 311 ARG 0.010 0.001 ARG F 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 134 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue SER 492 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue SER 505 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue SER 40 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Evaluate side-chains 756 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 717 time to evaluate : 2.750 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: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.6900 (tt0) cc_final: 0.6449 (tt0) REVERT: A 91 LYS cc_start: 0.8148 (mttt) cc_final: 0.7853 (mttp) REVERT: A 129 SER cc_start: 0.8042 (m) cc_final: 0.7665 (t) REVERT: A 132 GLN cc_start: 0.7459 (mm-40) cc_final: 0.6917 (mm-40) REVERT: A 167 GLU cc_start: 0.7813 (tp30) cc_final: 0.7343 (tp30) REVERT: A 271 ASP cc_start: 0.7077 (t70) cc_final: 0.6639 (t0) REVERT: A 475 LYS cc_start: 0.8263 (ttmm) cc_final: 0.7778 (mttp) REVERT: B 118 ASP cc_start: 0.8042 (p0) cc_final: 0.7754 (p0) REVERT: B 123 ILE cc_start: 0.8405 (mm) cc_final: 0.8172 (mt) REVERT: B 159 VAL cc_start: 0.8387 (m) cc_final: 0.8026 (p) REVERT: B 172 ASP cc_start: 0.6625 (t0) cc_final: 0.6368 (m-30) REVERT: B 183 ASP cc_start: 0.6959 (t0) cc_final: 0.6708 (t0) REVERT: B 199 LYS cc_start: 0.8247 (mttm) cc_final: 0.7942 (mtmm) REVERT: B 246 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.7872 (t80) REVERT: B 257 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6993 (mt-10) REVERT: B 261 ASP cc_start: 0.7461 (m-30) cc_final: 0.7177 (m-30) REVERT: B 336 VAL cc_start: 0.8393 (m) cc_final: 0.8064 (t) REVERT: B 353 PHE cc_start: 0.7749 (t80) cc_final: 0.7502 (t80) REVERT: C 52 GLU cc_start: 0.6771 (mt-10) cc_final: 0.6451 (mt-10) REVERT: C 118 ASP cc_start: 0.8028 (p0) cc_final: 0.7690 (p0) REVERT: C 129 SER cc_start: 0.8439 (m) cc_final: 0.7992 (p) REVERT: C 146 GLU cc_start: 0.7967 (pt0) cc_final: 0.7498 (pt0) REVERT: C 167 GLU cc_start: 0.7443 (tp30) cc_final: 0.7206 (tp30) REVERT: C 228 MET cc_start: 0.7958 (mmm) cc_final: 0.7750 (mmt) REVERT: C 246 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.8280 (t80) REVERT: C 271 ASP cc_start: 0.7328 (t0) cc_final: 0.7046 (t70) REVERT: C 393 LYS cc_start: 0.8301 (ttmt) cc_final: 0.8029 (ttmm) REVERT: C 442 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6738 (mt-10) REVERT: C 446 LEU cc_start: 0.7997 (mt) cc_final: 0.7738 (mt) REVERT: D 12 LYS cc_start: 0.7865 (mtpp) cc_final: 0.7570 (mttm) REVERT: D 126 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6786 (mp0) REVERT: D 241 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7081 (mt-10) REVERT: D 267 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6864 (mt-10) REVERT: D 288 ASP cc_start: 0.7134 (m-30) cc_final: 0.6593 (m-30) REVERT: D 353 SER cc_start: 0.8128 (m) cc_final: 0.7781 (p) REVERT: D 382 LYS cc_start: 0.8094 (tttt) cc_final: 0.7814 (ttmm) REVERT: D 435 LYS cc_start: 0.8037 (mptt) cc_final: 0.7804 (mmmt) REVERT: E 196 ASP cc_start: 0.7168 (m-30) cc_final: 0.6653 (m-30) REVERT: E 301 LYS cc_start: 0.7936 (mmtt) cc_final: 0.7652 (mmtt) REVERT: E 379 GLN cc_start: 0.7705 (tp40) cc_final: 0.7497 (mm-40) REVERT: E 422 GLU cc_start: 0.6978 (tm-30) cc_final: 0.6619 (tm-30) REVERT: E 448 LYS cc_start: 0.8466 (mtpt) cc_final: 0.8119 (mtpt) REVERT: F 142 ASP cc_start: 0.7216 (m-30) cc_final: 0.6882 (m-30) REVERT: F 195 ASN cc_start: 0.8374 (t0) cc_final: 0.8144 (t0) REVERT: F 196 ASP cc_start: 0.7198 (t70) cc_final: 0.6513 (t0) REVERT: F 199 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7558 (ttp-110) REVERT: F 200 GLU cc_start: 0.6794 (mt-10) cc_final: 0.6552 (mt-10) REVERT: F 245 ASP cc_start: 0.7269 (m-30) cc_final: 0.6975 (m-30) REVERT: F 247 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7699 (mm-30) REVERT: F 256 ASP cc_start: 0.6772 (t0) cc_final: 0.6493 (t0) REVERT: F 288 ASP cc_start: 0.7234 (m-30) cc_final: 0.6644 (m-30) REVERT: F 301 LYS cc_start: 0.8232 (mtmm) cc_final: 0.7998 (mtmm) REVERT: F 412 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7462 (ttm110) REVERT: G 43 LYS cc_start: 0.8217 (ttmm) cc_final: 0.7212 (ttpt) REVERT: G 90 GLN cc_start: 0.8158 (mt0) cc_final: 0.7870 (mt0) REVERT: G 114 ILE cc_start: 0.8354 (tp) cc_final: 0.8083 (tt) REVERT: G 129 SER cc_start: 0.8177 (t) cc_final: 0.7640 (p) outliers start: 39 outliers final: 32 residues processed: 728 average time/residue: 0.8943 time to fit residues: 948.1302 Evaluate side-chains 742 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 707 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 493 LYS Chi-restraints excluded: chain D residue 221 GLN Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 412 ARG Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain G residue 15 ASN Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain H residue 25 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 274 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 259 optimal weight: 1.9990 chunk 273 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN E 249 GLN F 57 ASN G 54 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 23836 Z= 0.375 Angle : 0.572 6.350 32349 Z= 0.301 Chirality : 0.045 0.179 3842 Planarity : 0.005 0.084 4167 Dihedral : 6.571 87.012 3591 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.08 % Favored : 96.73 % Rotamer: Outliers : 1.66 % Allowed : 16.89 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.15), residues: 3089 helix: 0.92 (0.15), residues: 1277 sheet: -0.74 (0.23), residues: 509 loop : -0.39 (0.18), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 258 HIS 0.007 0.001 HIS D 367 PHE 0.015 0.002 PHE F 261 TYR 0.014 0.002 TYR A 360 ARG 0.011 0.001 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 134 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue SER 492 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue SER 505 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue SER 40 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Evaluate side-chains 759 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 719 time to evaluate : 2.711 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 52 GLU cc_start: 0.6902 (tt0) cc_final: 0.6456 (tt0) REVERT: A 91 LYS cc_start: 0.8158 (mttt) cc_final: 0.7858 (mttp) REVERT: A 129 SER cc_start: 0.8045 (m) cc_final: 0.7670 (t) REVERT: A 132 GLN cc_start: 0.7452 (mm-40) cc_final: 0.6914 (mm-40) REVERT: A 167 GLU cc_start: 0.7862 (tp30) cc_final: 0.7233 (mm-30) REVERT: A 271 ASP cc_start: 0.7052 (t70) cc_final: 0.6598 (t0) REVERT: A 332 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7794 (mm110) REVERT: A 475 LYS cc_start: 0.8283 (ttmm) cc_final: 0.7789 (mttp) REVERT: B 26 ASN cc_start: 0.6367 (OUTLIER) cc_final: 0.6157 (p0) REVERT: B 118 ASP cc_start: 0.8030 (p0) cc_final: 0.7761 (p0) REVERT: B 123 ILE cc_start: 0.8411 (mm) cc_final: 0.8186 (mt) REVERT: B 172 ASP cc_start: 0.6687 (t0) cc_final: 0.6381 (m-30) REVERT: B 183 ASP cc_start: 0.6949 (t0) cc_final: 0.6695 (t0) REVERT: B 199 LYS cc_start: 0.8292 (mttm) cc_final: 0.7954 (mtmm) REVERT: B 246 TYR cc_start: 0.8465 (OUTLIER) cc_final: 0.7899 (t80) REVERT: B 257 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6985 (mt-10) REVERT: B 261 ASP cc_start: 0.7487 (m-30) cc_final: 0.7195 (m-30) REVERT: B 336 VAL cc_start: 0.8347 (m) cc_final: 0.8010 (t) REVERT: B 353 PHE cc_start: 0.7753 (t80) cc_final: 0.7535 (t80) REVERT: C 52 GLU cc_start: 0.6767 (mt-10) cc_final: 0.6482 (mt-10) REVERT: C 129 SER cc_start: 0.8471 (m) cc_final: 0.8012 (p) REVERT: C 146 GLU cc_start: 0.7958 (pt0) cc_final: 0.7495 (pt0) REVERT: C 167 GLU cc_start: 0.7451 (tp30) cc_final: 0.7210 (tp30) REVERT: C 228 MET cc_start: 0.7979 (mmm) cc_final: 0.7767 (mmt) REVERT: C 246 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.8373 (t80) REVERT: C 271 ASP cc_start: 0.7343 (t0) cc_final: 0.7064 (t70) REVERT: C 361 LYS cc_start: 0.8260 (mttt) cc_final: 0.7897 (mttp) REVERT: C 375 ARG cc_start: 0.7594 (mtp85) cc_final: 0.7067 (mtp85) REVERT: C 393 LYS cc_start: 0.8305 (ttmt) cc_final: 0.8025 (ttmm) REVERT: C 442 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6744 (mt-10) REVERT: C 446 LEU cc_start: 0.8005 (mt) cc_final: 0.7757 (mt) REVERT: D 12 LYS cc_start: 0.7923 (mtpp) cc_final: 0.7630 (mttm) REVERT: D 126 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6791 (mp0) REVERT: D 241 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7089 (mt-10) REVERT: D 267 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6907 (mt-10) REVERT: D 288 ASP cc_start: 0.7156 (m-30) cc_final: 0.6821 (m-30) REVERT: D 345 TYR cc_start: 0.7355 (m-80) cc_final: 0.7125 (m-80) REVERT: D 354 LYS cc_start: 0.8092 (ptpp) cc_final: 0.7531 (mtmm) REVERT: D 435 LYS cc_start: 0.8041 (mptt) cc_final: 0.7807 (mmmt) REVERT: E 192 ARG cc_start: 0.8133 (ptm160) cc_final: 0.7547 (ptm-80) REVERT: E 196 ASP cc_start: 0.7179 (m-30) cc_final: 0.6652 (m-30) REVERT: E 281 TYR cc_start: 0.8313 (m-80) cc_final: 0.8045 (m-80) REVERT: E 301 LYS cc_start: 0.7998 (mmtt) cc_final: 0.7713 (mmtt) REVERT: E 422 GLU cc_start: 0.6989 (tm-30) cc_final: 0.6647 (tm-30) REVERT: F 142 ASP cc_start: 0.7225 (m-30) cc_final: 0.6891 (m-30) REVERT: F 196 ASP cc_start: 0.7203 (t70) cc_final: 0.6500 (t0) REVERT: F 199 ARG cc_start: 0.7960 (ttp80) cc_final: 0.7568 (ttp-110) REVERT: F 200 GLU cc_start: 0.6805 (mt-10) cc_final: 0.6567 (mt-10) REVERT: F 245 ASP cc_start: 0.7270 (m-30) cc_final: 0.6985 (m-30) REVERT: F 247 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7723 (mm-30) REVERT: F 256 ASP cc_start: 0.6827 (t0) cc_final: 0.6451 (t0) REVERT: F 288 ASP cc_start: 0.7239 (m-30) cc_final: 0.6684 (m-30) REVERT: F 301 LYS cc_start: 0.8247 (mtmm) cc_final: 0.8010 (mtmm) REVERT: F 412 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7842 (tpp-160) REVERT: G 43 LYS cc_start: 0.8246 (ttmm) cc_final: 0.7205 (ttpt) REVERT: G 107 ILE cc_start: 0.8278 (mm) cc_final: 0.7721 (tt) REVERT: G 114 ILE cc_start: 0.8375 (tp) cc_final: 0.8089 (tt) REVERT: G 129 SER cc_start: 0.8140 (t) cc_final: 0.7653 (p) outliers start: 40 outliers final: 33 residues processed: 732 average time/residue: 0.9196 time to fit residues: 980.6916 Evaluate side-chains 751 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 714 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 493 LYS Chi-restraints excluded: chain D residue 221 GLN Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 459 MET Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 412 ARG Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain G residue 15 ASN Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain H residue 25 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 202 optimal weight: 2.9990 chunk 304 optimal weight: 2.9990 chunk 280 optimal weight: 0.6980 chunk 242 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 148 optimal weight: 0.7980 chunk 192 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN E 249 GLN F 52 GLN G 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 23836 Z= 0.346 Angle : 0.709 59.200 32349 Z= 0.396 Chirality : 0.044 0.480 3842 Planarity : 0.005 0.083 4167 Dihedral : 6.564 87.171 3591 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.08 % Favored : 96.73 % Rotamer: Outliers : 1.61 % Allowed : 17.22 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.15), residues: 3089 helix: 0.93 (0.15), residues: 1277 sheet: -0.74 (0.23), residues: 509 loop : -0.39 (0.18), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 258 HIS 0.006 0.001 HIS D 367 PHE 0.015 0.001 PHE F 261 TYR 0.014 0.001 TYR F 311 ARG 0.010 0.001 ARG A 142 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6178 Ramachandran restraints generated. 3089 Oldfield, 0 Emsley, 3089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 134 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Residue SER 476 is missing expected H atoms. Skipping. Residue SER 492 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue SER 501 is missing expected H atoms. Skipping. Residue SER 505 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue THR 178 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue THR 509 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue LYS 472 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue SER 40 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Evaluate side-chains 749 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 710 time to evaluate : 2.701 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 52 GLU cc_start: 0.6894 (tt0) cc_final: 0.6449 (tt0) REVERT: A 91 LYS cc_start: 0.8157 (mttt) cc_final: 0.7854 (mttp) REVERT: A 129 SER cc_start: 0.8040 (m) cc_final: 0.7666 (t) REVERT: A 132 GLN cc_start: 0.7449 (mm-40) cc_final: 0.6913 (mm-40) REVERT: A 167 GLU cc_start: 0.7863 (tp30) cc_final: 0.7222 (mm-30) REVERT: A 271 ASP cc_start: 0.7050 (t70) cc_final: 0.6593 (t0) REVERT: A 332 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7790 (mm110) REVERT: A 475 LYS cc_start: 0.8286 (ttmm) cc_final: 0.7786 (mttp) REVERT: B 118 ASP cc_start: 0.8030 (p0) cc_final: 0.7746 (p0) REVERT: B 123 ILE cc_start: 0.8408 (mm) cc_final: 0.8184 (mt) REVERT: B 172 ASP cc_start: 0.6658 (t0) cc_final: 0.6376 (m-30) REVERT: B 183 ASP cc_start: 0.6942 (t0) cc_final: 0.6683 (t0) REVERT: B 199 LYS cc_start: 0.8291 (mttm) cc_final: 0.7951 (mtmm) REVERT: B 246 TYR cc_start: 0.8461 (OUTLIER) cc_final: 0.7894 (t80) REVERT: B 257 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6978 (mt-10) REVERT: B 261 ASP cc_start: 0.7480 (m-30) cc_final: 0.7191 (m-30) REVERT: B 336 VAL cc_start: 0.8344 (m) cc_final: 0.8006 (t) REVERT: B 353 PHE cc_start: 0.7752 (t80) cc_final: 0.7535 (t80) REVERT: C 52 GLU cc_start: 0.6761 (mt-10) cc_final: 0.6460 (mt-10) REVERT: C 129 SER cc_start: 0.8472 (m) cc_final: 0.7990 (p) REVERT: C 146 GLU cc_start: 0.7957 (pt0) cc_final: 0.7492 (pt0) REVERT: C 167 GLU cc_start: 0.7448 (tp30) cc_final: 0.7200 (tp30) REVERT: C 228 MET cc_start: 0.7978 (mmm) cc_final: 0.7762 (mmt) REVERT: C 246 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.8373 (t80) REVERT: C 361 LYS cc_start: 0.8258 (mttt) cc_final: 0.7892 (mttp) REVERT: C 393 LYS cc_start: 0.8302 (ttmt) cc_final: 0.8022 (ttmm) REVERT: C 442 GLU cc_start: 0.6962 (mt-10) cc_final: 0.6738 (mt-10) REVERT: C 446 LEU cc_start: 0.8003 (mt) cc_final: 0.7755 (mt) REVERT: D 12 LYS cc_start: 0.7920 (mtpp) cc_final: 0.7628 (mttm) REVERT: D 126 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6788 (mp0) REVERT: D 241 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7085 (mt-10) REVERT: D 267 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6901 (mt-10) REVERT: D 288 ASP cc_start: 0.7165 (m-30) cc_final: 0.6822 (m-30) REVERT: D 345 TYR cc_start: 0.7352 (m-80) cc_final: 0.7120 (m-80) REVERT: D 354 LYS cc_start: 0.8070 (ptpp) cc_final: 0.7527 (mtmm) REVERT: D 435 LYS cc_start: 0.8033 (mptt) cc_final: 0.7803 (mmmt) REVERT: E 163 LYS cc_start: 0.7690 (ttpt) cc_final: 0.7431 (ttpp) REVERT: E 176 LYS cc_start: 0.8041 (mttm) cc_final: 0.7825 (mtpp) REVERT: E 196 ASP cc_start: 0.7175 (m-30) cc_final: 0.6652 (m-30) REVERT: E 281 TYR cc_start: 0.8310 (m-80) cc_final: 0.8018 (m-80) REVERT: E 301 LYS cc_start: 0.7995 (mmtt) cc_final: 0.7714 (mmtt) REVERT: E 382 LYS cc_start: 0.8156 (tttp) cc_final: 0.7944 (ttmm) REVERT: E 422 GLU cc_start: 0.6986 (tm-30) cc_final: 0.6639 (tm-30) REVERT: E 448 LYS cc_start: 0.8468 (mtpt) cc_final: 0.8092 (mtpp) REVERT: F 142 ASP cc_start: 0.7222 (m-30) cc_final: 0.6883 (m-30) REVERT: F 196 ASP cc_start: 0.7199 (t70) cc_final: 0.6486 (t0) REVERT: F 199 ARG cc_start: 0.7957 (ttp80) cc_final: 0.7571 (ttp-110) REVERT: F 200 GLU cc_start: 0.6799 (mt-10) cc_final: 0.6563 (mt-10) REVERT: F 245 ASP cc_start: 0.7265 (m-30) cc_final: 0.6979 (m-30) REVERT: F 247 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7723 (mm-30) REVERT: F 256 ASP cc_start: 0.6818 (t0) cc_final: 0.6450 (t0) REVERT: F 288 ASP cc_start: 0.7237 (m-30) cc_final: 0.6676 (m-30) REVERT: F 301 LYS cc_start: 0.8245 (mtmm) cc_final: 0.8008 (mtmm) REVERT: F 412 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7839 (tpp-160) REVERT: G 43 LYS cc_start: 0.8243 (ttmm) cc_final: 0.7202 (ttpt) REVERT: G 107 ILE cc_start: 0.8276 (mm) cc_final: 0.7722 (tt) REVERT: G 114 ILE cc_start: 0.8376 (tp) cc_final: 0.8090 (tt) REVERT: G 129 SER cc_start: 0.8158 (t) cc_final: 0.7628 (p) outliers start: 39 outliers final: 35 residues processed: 722 average time/residue: 0.8868 time to fit residues: 930.9418 Evaluate side-chains 746 residues out of total 2527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 708 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 493 LYS Chi-restraints excluded: chain D residue 221 GLN Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 451 ASN Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 459 MET Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 412 ARG Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain G residue 15 ASN Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain H residue 25 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 243 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 213 optimal weight: 0.6980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.101294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.092228 restraints weight = 102176.049| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.85 r_work: 0.3064 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 23836 Z= 0.346 Angle : 0.709 59.200 32349 Z= 0.396 Chirality : 0.044 0.480 3842 Planarity : 0.005 0.083 4167 Dihedral : 6.564 87.171 3591 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.08 % Favored : 96.73 % Rotamer: Outliers : 1.57 % Allowed : 17.43 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.15), residues: 3089 helix: 0.93 (0.15), residues: 1277 sheet: -0.74 (0.23), residues: 509 loop : -0.39 (0.18), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 258 HIS 0.006 0.001 HIS D 367 PHE 0.015 0.001 PHE F 261 TYR 0.014 0.001 TYR F 311 ARG 0.010 0.001 ARG A 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14014.92 seconds wall clock time: 237 minutes 40.10 seconds (14260.10 seconds total)