Starting phenix.real_space_refine on Fri Jan 24 17:04:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cuk_45936/01_2025/9cuk_45936.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cuk_45936/01_2025/9cuk_45936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cuk_45936/01_2025/9cuk_45936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cuk_45936/01_2025/9cuk_45936.map" model { file = "/net/cci-nas-00/data/ceres_data/9cuk_45936/01_2025/9cuk_45936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cuk_45936/01_2025/9cuk_45936.cif" } resolution = 3.26 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= 0.003 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 7 9.91 5 P 12 5.49 5 S 169 5.16 5 C 14827 2.51 5 N 3599 2.21 5 O 3917 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 22531 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4912 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "B" Number of atoms: 4976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4976 Classifications: {'peptide': 619} Link IDs: {'PTRANS': 26, 'TRANS': 592} Chain: "C" Number of atoms: 5182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5182 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 26, 'TRANS': 617} Chain breaks: 1 Chain: "D" Number of atoms: 4912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4912 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "E" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1165 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 2, 'TRANS': 145} Chain: "A" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 347 Unusual residues: {' CA': 1, 'CLR': 1, 'PCW': 11, 'Y01': 2} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 346 Unresolved non-hydrogen angles: 418 Unresolved non-hydrogen dihedrals: 314 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PCW:plan-1': 8, 'PCW:plan-2': 2, 'PCW:plan-3': 8, 'PCW:plan-4': 8} Unresolved non-hydrogen planarities: 91 Chain: "B" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 348 Unusual residues: {' CA': 2, 'CLR': 1, 'PCW': 11, 'Y01': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 346 Unresolved non-hydrogen angles: 418 Unresolved non-hydrogen dihedrals: 314 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PCW:plan-1': 8, 'PCW:plan-2': 2, 'PCW:plan-3': 8, 'PCW:plan-4': 8} Unresolved non-hydrogen planarities: 91 Chain: "C" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 373 Unusual residues: {'CLR': 1, 'PCW': 10, 'Y01': 3} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 300 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 272 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PCW:plan-1': 7, 'PCW:plan-2': 1, 'PCW:plan-3': 7, 'PCW:plan-4': 7} Unresolved non-hydrogen planarities: 78 Chain: "D" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 311 Unusual residues: {'CLR': 1, 'PCW': 11, 'Y01': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 346 Unresolved non-hydrogen angles: 418 Unresolved non-hydrogen dihedrals: 314 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PCW:plan-1': 8, 'PCW:plan-2': 2, 'PCW:plan-3': 8, 'PCW:plan-4': 8} Unresolved non-hydrogen planarities: 91 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 13.00, per 1000 atoms: 0.58 Number of scatterers: 22531 At special positions: 0 Unit cell: (130.31, 130.31, 126.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 7 19.99 S 169 16.00 P 12 15.00 O 3917 8.00 N 3599 7.00 C 14827 6.00 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: 6.11 Conformation dependent library (CDL) restraints added in 2.4 seconds 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4974 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 8 sheets defined 61.1% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'A' and resid 27 through 46 removed outlier: 3.593A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.506A pdb=" N ALA A 52 " --> pdb=" O PRO A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 removed outlier: 3.933A pdb=" N ASN A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.677A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 106 removed outlier: 3.681A pdb=" N VAL A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.682A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 139 removed outlier: 3.524A pdb=" N ARG A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.533A pdb=" N CYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.506A pdb=" N ILE A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 222 removed outlier: 3.572A pdb=" N LEU A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 291 through 299 removed outlier: 3.529A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 310 removed outlier: 3.806A pdb=" N GLN A 306 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 removed outlier: 3.729A pdb=" N ARG A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 349 removed outlier: 3.887A pdb=" N TYR A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 334 " --> pdb=" O CYS A 330 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 337 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 403 removed outlier: 3.619A pdb=" N ASP A 383 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG A 385 " --> pdb=" O LYS A 381 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 399 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 424 through 445 removed outlier: 3.525A pdb=" N ILE A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 463 removed outlier: 4.020A pdb=" N VAL A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 470 removed outlier: 3.616A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 removed outlier: 3.609A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 499 removed outlier: 3.686A pdb=" N ALA A 498 " --> pdb=" O CYS A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 504 Processing helix chain 'A' and resid 504 through 512 removed outlier: 3.822A pdb=" N ILE A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 515 No H-bonds generated for 'chain 'A' and resid 513 through 515' Processing helix chain 'A' and resid 525 through 539 removed outlier: 3.592A pdb=" N GLU A 535 " --> pdb=" O PHE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 568 removed outlier: 3.831A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 583 removed outlier: 4.045A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 608 removed outlier: 3.794A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 46 Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.506A pdb=" N ALA B 52 " --> pdb=" O PRO B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 65 removed outlier: 3.932A pdb=" N ASN B 62 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.676A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 106 removed outlier: 3.681A pdb=" N VAL B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.682A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 139 removed outlier: 3.524A pdb=" N ARG B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 removed outlier: 3.533A pdb=" N CYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.506A pdb=" N ILE B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 222 removed outlier: 3.572A pdb=" N LEU B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 251 Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.529A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 310 removed outlier: 3.806A pdb=" N GLN B 306 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 324 removed outlier: 3.729A pdb=" N ARG B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 349 removed outlier: 3.887A pdb=" N TYR B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 334 " --> pdb=" O CYS B 330 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 337 " --> pdb=" O GLY B 333 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 403 removed outlier: 3.619A pdb=" N ASP B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG B 385 " --> pdb=" O LYS B 381 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 399 " --> pdb=" O GLY B 395 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 400 " --> pdb=" O ALA B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 Processing helix chain 'B' and resid 424 through 445 removed outlier: 3.524A pdb=" N ILE B 429 " --> pdb=" O PHE B 425 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 463 removed outlier: 4.019A pdb=" N VAL B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N CYS B 463 " --> pdb=" O VAL B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 470 removed outlier: 3.615A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 487 removed outlier: 3.610A pdb=" N ILE B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET B 481 " --> pdb=" O PRO B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 499 removed outlier: 3.686A pdb=" N ALA B 498 " --> pdb=" O CYS B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 504 Processing helix chain 'B' and resid 504 through 512 removed outlier: 3.822A pdb=" N ILE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 511 " --> pdb=" O ALA B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 515 No H-bonds generated for 'chain 'B' and resid 513 through 515' Processing helix chain 'B' and resid 525 through 539 removed outlier: 3.593A pdb=" N GLU B 535 " --> pdb=" O PHE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 568 removed outlier: 3.831A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 565 " --> pdb=" O ALA B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 583 removed outlier: 4.045A pdb=" N TRP B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 608 removed outlier: 3.794A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 46 Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.507A pdb=" N ALA C 52 " --> pdb=" O PRO C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 65 removed outlier: 3.932A pdb=" N ASN C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.676A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 106 removed outlier: 3.681A pdb=" N VAL C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 106' Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.682A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 139 removed outlier: 3.525A pdb=" N ARG C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 173 removed outlier: 3.533A pdb=" N CYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.507A pdb=" N ILE C 202 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 222 removed outlier: 3.572A pdb=" N LEU C 218 " --> pdb=" O GLN C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 251 Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 291 through 299 removed outlier: 3.529A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 310 removed outlier: 3.806A pdb=" N GLN C 306 " --> pdb=" O GLU C 303 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 324 removed outlier: 3.729A pdb=" N ARG C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.887A pdb=" N TYR C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 334 " --> pdb=" O CYS C 330 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 403 removed outlier: 3.619A pdb=" N ASP C 383 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE C 384 " --> pdb=" O PRO C 380 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG C 385 " --> pdb=" O LYS C 381 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C 399 " --> pdb=" O GLY C 395 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C 400 " --> pdb=" O ALA C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 424 through 445 removed outlier: 3.525A pdb=" N ILE C 429 " --> pdb=" O PHE C 425 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 463 removed outlier: 4.019A pdb=" N VAL C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS C 463 " --> pdb=" O VAL C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 470 removed outlier: 3.615A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 487 removed outlier: 3.610A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET C 481 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 499 removed outlier: 3.686A pdb=" N ALA C 498 " --> pdb=" O CYS C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 504 Processing helix chain 'C' and resid 504 through 512 removed outlier: 3.823A pdb=" N ILE C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C 511 " --> pdb=" O ALA C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 515 No H-bonds generated for 'chain 'C' and resid 513 through 515' Processing helix chain 'C' and resid 525 through 539 removed outlier: 3.593A pdb=" N GLU C 535 " --> pdb=" O PHE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 568 removed outlier: 3.831A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 583 removed outlier: 4.045A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 608 removed outlier: 3.794A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 650 removed outlier: 3.671A pdb=" N ARG C 646 " --> pdb=" O GLN C 642 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA C 650 " --> pdb=" O ARG C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 703 removed outlier: 3.589A pdb=" N GLU C 696 " --> pdb=" O SER C 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 46 Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.506A pdb=" N ALA D 52 " --> pdb=" O PRO D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 65 removed outlier: 3.933A pdb=" N ASN D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.676A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 106 removed outlier: 3.681A pdb=" N VAL D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 106' Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.682A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 139 removed outlier: 3.524A pdb=" N ARG D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 173 removed outlier: 3.533A pdb=" N CYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.507A pdb=" N ILE D 202 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 222 removed outlier: 3.572A pdb=" N LEU D 218 " --> pdb=" O GLN D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 251 Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 291 through 299 removed outlier: 3.529A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 310 removed outlier: 3.806A pdb=" N GLN D 306 " --> pdb=" O GLU D 303 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 removed outlier: 3.729A pdb=" N ARG D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 349 removed outlier: 3.887A pdb=" N TYR D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA D 334 " --> pdb=" O CYS D 330 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU D 337 " --> pdb=" O GLY D 333 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 403 removed outlier: 3.619A pdb=" N ASP D 383 " --> pdb=" O THR D 379 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE D 384 " --> pdb=" O PRO D 380 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG D 385 " --> pdb=" O LYS D 381 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE D 399 " --> pdb=" O GLY D 395 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 408 Processing helix chain 'D' and resid 424 through 445 removed outlier: 3.525A pdb=" N ILE D 429 " --> pdb=" O PHE D 425 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 463 removed outlier: 4.020A pdb=" N VAL D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N CYS D 463 " --> pdb=" O VAL D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 470 removed outlier: 3.615A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 487 removed outlier: 3.610A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET D 481 " --> pdb=" O PRO D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 499 removed outlier: 3.687A pdb=" N ALA D 498 " --> pdb=" O CYS D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 504 Processing helix chain 'D' and resid 504 through 512 removed outlier: 3.822A pdb=" N ILE D 510 " --> pdb=" O SER D 506 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D 511 " --> pdb=" O ALA D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 515 No H-bonds generated for 'chain 'D' and resid 513 through 515' Processing helix chain 'D' and resid 525 through 539 removed outlier: 3.593A pdb=" N GLU D 535 " --> pdb=" O PHE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 568 removed outlier: 3.832A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE D 565 " --> pdb=" O ALA D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 583 removed outlier: 4.045A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 608 removed outlier: 3.795A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 18 removed outlier: 3.871A pdb=" N GLU E 14 " --> pdb=" O ALA E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 39 Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.816A pdb=" N ILE E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL E 55 " --> pdb=" O MET E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 75 Processing helix chain 'E' and resid 82 through 93 removed outlier: 3.591A pdb=" N VAL E 91 " --> pdb=" O GLU E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 112 removed outlier: 3.756A pdb=" N VAL E 108 " --> pdb=" O GLU E 104 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU E 112 " --> pdb=" O VAL E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 129 removed outlier: 4.058A pdb=" N GLU E 127 " --> pdb=" O GLU E 123 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA E 128 " --> pdb=" O MET E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 144 Processing sheet with id=AA1, first strand: chain 'A' and resid 266 through 269 removed outlier: 6.829A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 266 through 269 removed outlier: 6.830A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 266 through 269 removed outlier: 6.830A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 266 through 269 removed outlier: 6.829A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 931 hydrogen bonds defined for protein. 2709 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: 8.10 Time building geometry restraints manager: 6.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3474 1.31 - 1.43: 5897 1.43 - 1.56: 13212 1.56 - 1.69: 111 1.69 - 1.82: 290 Bond restraints: 22984 Sorted by residual: bond pdb=" C19 PCW D 805 " pdb=" C20 PCW D 805 " ideal model delta sigma weight residual 1.333 1.549 -0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C19 PCW B 803 " pdb=" C20 PCW B 803 " ideal model delta sigma weight residual 1.333 1.548 -0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C19 PCW A 804 " pdb=" C20 PCW A 804 " ideal model delta sigma weight residual 1.333 1.547 -0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C19 PCW C 803 " pdb=" C20 PCW C 803 " ideal model delta sigma weight residual 1.333 1.547 -0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C19 PCW B 807 " pdb=" C20 PCW B 807 " ideal model delta sigma weight residual 1.333 1.547 -0.214 2.00e-02 2.50e+03 1.15e+02 ... (remaining 22979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 30151 3.45 - 6.89: 608 6.89 - 10.34: 137 10.34 - 13.79: 47 13.79 - 17.24: 15 Bond angle restraints: 30958 Sorted by residual: angle pdb=" N HIS C 652 " pdb=" CA HIS C 652 " pdb=" C HIS C 652 " ideal model delta sigma weight residual 110.24 118.51 -8.27 1.30e+00 5.92e-01 4.05e+01 angle pdb=" N LEU A 421 " pdb=" CA LEU A 421 " pdb=" C LEU A 421 " ideal model delta sigma weight residual 114.16 104.79 9.37 1.48e+00 4.57e-01 4.01e+01 angle pdb=" N LEU B 421 " pdb=" CA LEU B 421 " pdb=" C LEU B 421 " ideal model delta sigma weight residual 114.16 104.82 9.34 1.48e+00 4.57e-01 3.98e+01 angle pdb=" N LEU C 421 " pdb=" CA LEU C 421 " pdb=" C LEU C 421 " ideal model delta sigma weight residual 114.16 104.82 9.34 1.48e+00 4.57e-01 3.98e+01 angle pdb=" N LEU D 421 " pdb=" CA LEU D 421 " pdb=" C LEU D 421 " ideal model delta sigma weight residual 114.16 104.88 9.28 1.48e+00 4.57e-01 3.93e+01 ... (remaining 30953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.88: 13956 32.88 - 65.77: 523 65.77 - 98.65: 54 98.65 - 131.53: 13 131.53 - 164.41: 6 Dihedral angle restraints: 14552 sinusoidal: 6854 harmonic: 7698 Sorted by residual: dihedral pdb=" CA ASP C 638 " pdb=" C ASP C 638 " pdb=" N LEU C 639 " pdb=" CA LEU C 639 " ideal model delta harmonic sigma weight residual 180.00 127.94 52.06 0 5.00e+00 4.00e-02 1.08e+02 dihedral pdb=" CA GLY A 422 " pdb=" C GLY A 422 " pdb=" N GLY A 423 " pdb=" CA GLY A 423 " ideal model delta harmonic sigma weight residual 180.00 140.57 39.43 0 5.00e+00 4.00e-02 6.22e+01 dihedral pdb=" CA GLY D 422 " pdb=" C GLY D 422 " pdb=" N GLY D 423 " pdb=" CA GLY D 423 " ideal model delta harmonic sigma weight residual 180.00 140.58 39.42 0 5.00e+00 4.00e-02 6.21e+01 ... (remaining 14549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2784 0.067 - 0.134: 564 0.134 - 0.201: 43 0.201 - 0.268: 25 0.268 - 0.335: 8 Chirality restraints: 3424 Sorted by residual: chirality pdb=" CG LEU B 367 " pdb=" CB LEU B 367 " pdb=" CD1 LEU B 367 " pdb=" CD2 LEU B 367 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CG LEU C 367 " pdb=" CB LEU C 367 " pdb=" CD1 LEU C 367 " pdb=" CD2 LEU C 367 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CG LEU A 367 " pdb=" CB LEU A 367 " pdb=" CD1 LEU A 367 " pdb=" CD2 LEU A 367 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 3421 not shown) Planarity restraints: 3816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C18 PCW B 803 " 0.275 2.00e-02 2.50e+03 2.93e-01 8.58e+02 pdb=" C19 PCW B 803 " -0.482 2.00e-02 2.50e+03 pdb=" C20 PCW B 803 " 0.187 2.00e-02 2.50e+03 pdb=" C21 PCW B 803 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 PCW D 809 " -0.273 2.00e-02 2.50e+03 2.85e-01 8.11e+02 pdb=" C19 PCW D 809 " 0.471 2.00e-02 2.50e+03 pdb=" C20 PCW D 809 " -0.165 2.00e-02 2.50e+03 pdb=" C21 PCW D 809 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 PCW B 811 " 0.290 2.00e-02 2.50e+03 2.75e-01 7.56e+02 pdb=" C19 PCW B 811 " -0.452 2.00e-02 2.50e+03 pdb=" C20 PCW B 811 " 0.064 2.00e-02 2.50e+03 pdb=" C21 PCW B 811 " 0.098 2.00e-02 2.50e+03 ... (remaining 3813 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5836 2.80 - 3.32: 19050 3.32 - 3.85: 34319 3.85 - 4.37: 42610 4.37 - 4.90: 72305 Nonbonded interactions: 174120 Sorted by model distance: nonbonded pdb=" OG SER D 291 " pdb=" OE1 GLU D 294 " model vdw 2.269 3.040 nonbonded pdb=" OG SER A 291 " pdb=" OE1 GLU A 294 " model vdw 2.270 3.040 nonbonded pdb=" OG SER B 291 " pdb=" OE1 GLU B 294 " model vdw 2.270 3.040 nonbonded pdb=" OG SER C 291 " pdb=" OE1 GLU C 294 " model vdw 2.270 3.040 nonbonded pdb=" OG SER B 506 " pdb=" OH TYR B 526 " model vdw 2.307 3.040 ... (remaining 174115 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 27 through 638 or (resid 808 and (name C12 or name C13 or \ name C14 or name C15 or name C16 or name C17 or name C18 or name C19)) or (resid \ 809 and (name C15 or name C16 or name C17 or name C18 or name C19)) or (resid 8 \ 10 and (name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or \ name C18 or name C19 or name C20 or name C21 or name C22)) or (resid 813 and (na \ me C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 o \ r name C22 or name C23 or name C24 or name C25 or name C26)))) selection = (chain 'B' and (resid 27 through 638 or resid 809 or (resid 810 and (name C15 or \ name C16 or name C17 or name C18 or name C19)) or (resid 811 and (name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22)) or (resid 814 and (name C15 or name C16 or \ name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C2 \ 3 or name C24 or name C25 or name C26)))) selection = (chain 'C' and (resid 27 through 638 or (resid 807 and (name C12 or name C13 or \ name C14 or name C15 or name C16 or name C17 or name C18 or name C19)) or (resid \ 808 and (name C15 or name C16 or name C17 or name C18 or name C19)) or resid 80 \ 9 or (resid 812 and (name C15 or name C16 or name C17 or name C18 or name C19 or \ name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name C2 \ 6)))) selection = (chain 'D' and (resid 27 through 638 or (resid 808 and (name C12 or name C13 or \ name C14 or name C15 or name C16 or name C17 or name C18 or name C19)) or (resid \ 809 and (name C15 or name C16 or name C17 or name C18 or name C19)) or resid 81 \ 0 or (resid 813 and (name C15 or name C16 or name C17 or name C18 or name C19 or \ name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name C2 \ 6)))) } 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.180 Set scattering table: 0.200 Process input model: 47.280 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.120 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 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 : 0.013 0.216 22984 Z= 0.773 Angle : 1.374 17.235 30958 Z= 0.693 Chirality : 0.057 0.335 3424 Planarity : 0.014 0.293 3816 Dihedral : 16.398 164.413 9578 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.03 % Favored : 89.67 % Rotamer: Outliers : 0.44 % Allowed : 4.46 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.77 % Twisted General : 0.67 % 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: -6.36 (0.10), residues: 2623 helix: -4.41 (0.06), residues: 1524 sheet: -3.52 (0.42), residues: 88 loop : -3.68 (0.15), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 613 HIS 0.011 0.002 HIS B 522 PHE 0.034 0.003 PHE C 508 TYR 0.026 0.002 TYR A 547 ARG 0.009 0.001 ARG B 641 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 615 time to evaluate : 2.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8238 (ttmt) cc_final: 0.7565 (mmtp) REVERT: A 130 MET cc_start: 0.7768 (tpt) cc_final: 0.7205 (ptt) REVERT: A 174 ASN cc_start: 0.8330 (t160) cc_final: 0.7771 (t0) REVERT: A 233 ASP cc_start: 0.8458 (p0) cc_final: 0.8039 (p0) REVERT: A 306 GLN cc_start: 0.8237 (mt0) cc_final: 0.7941 (mm-40) REVERT: A 340 ILE cc_start: 0.8761 (tp) cc_final: 0.8493 (tp) REVERT: A 379 THR cc_start: 0.8217 (t) cc_final: 0.7931 (m) REVERT: A 435 MET cc_start: 0.7795 (mmt) cc_final: 0.7491 (mmt) REVERT: A 481 MET cc_start: 0.8397 (mmm) cc_final: 0.7658 (mmt) REVERT: A 591 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7116 (mm-30) REVERT: A 618 ILE cc_start: 0.8886 (mp) cc_final: 0.8621 (mm) REVERT: B 59 GLN cc_start: 0.7803 (tt0) cc_final: 0.7512 (mp10) REVERT: B 168 SER cc_start: 0.8528 (m) cc_final: 0.7958 (t) REVERT: B 230 GLN cc_start: 0.6206 (tp40) cc_final: 0.5709 (mm-40) REVERT: B 371 LYS cc_start: 0.7552 (ptmt) cc_final: 0.7333 (ptpp) REVERT: B 381 LYS cc_start: 0.8109 (mttt) cc_final: 0.7907 (tttm) REVERT: B 474 MET cc_start: 0.8281 (ttm) cc_final: 0.8062 (ttm) REVERT: C 379 THR cc_start: 0.7181 (t) cc_final: 0.6871 (t) REVERT: D 80 GLU cc_start: 0.7790 (pm20) cc_final: 0.7428 (pm20) REVERT: D 90 ASP cc_start: 0.8611 (t70) cc_final: 0.8220 (t70) REVERT: D 177 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7786 (mm-30) REVERT: E 145 MET cc_start: 0.6709 (mmt) cc_final: 0.6177 (mmp) outliers start: 10 outliers final: 5 residues processed: 624 average time/residue: 0.3711 time to fit residues: 348.4862 Evaluate side-chains 385 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 380 time to evaluate : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 367 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 220 optimal weight: 8.9990 chunk 197 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 chunk 204 optimal weight: 0.0370 chunk 79 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 237 optimal weight: 4.9990 overall best weight: 1.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 118 GLN A 129 ASN A 174 ASN A 214 GLN A 228 HIS A 230 GLN A 267 GLN A 572 ASN B 84 HIS B 118 GLN B 129 ASN ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 HIS B 230 GLN B 572 ASN B 640 ASN C 129 ASN C 158 ASN C 174 ASN C 228 HIS C 267 GLN C 464 ASN C 652 HIS C 694 ASN D 84 HIS D 91 ASN D 118 GLN D 129 ASN D 174 ASN D 206 GLN D 228 HIS D 230 GLN D 252 ASN D 258 HIS D 267 GLN D 572 ASN E 111 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.164621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.126942 restraints weight = 28758.690| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.11 r_work: 0.3268 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22984 Z= 0.203 Angle : 0.687 9.721 30958 Z= 0.350 Chirality : 0.043 0.211 3424 Planarity : 0.006 0.091 3816 Dihedral : 16.671 178.526 4483 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.65 % Favored : 91.19 % Rotamer: Outliers : 2.54 % Allowed : 9.98 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.77 % Twisted General : 0.32 % 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: -3.81 (0.14), residues: 2623 helix: -2.00 (0.11), residues: 1571 sheet: -2.76 (0.49), residues: 84 loop : -3.23 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 695 HIS 0.006 0.001 HIS D 587 PHE 0.013 0.001 PHE C 508 TYR 0.021 0.001 TYR A 524 ARG 0.005 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 433 time to evaluate : 2.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8348 (ttmt) cc_final: 0.7601 (mmtp) REVERT: A 91 ASN cc_start: 0.6791 (m-40) cc_final: 0.6579 (m110) REVERT: A 174 ASN cc_start: 0.8431 (t0) cc_final: 0.8215 (t0) REVERT: A 211 PHE cc_start: 0.7940 (m-80) cc_final: 0.7475 (m-80) REVERT: A 216 TYR cc_start: 0.8645 (t80) cc_final: 0.8383 (t80) REVERT: A 303 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7878 (pt0) REVERT: A 306 GLN cc_start: 0.8461 (mt0) cc_final: 0.7965 (mm-40) REVERT: A 331 MET cc_start: 0.7772 (tpt) cc_final: 0.7419 (tpt) REVERT: A 435 MET cc_start: 0.7815 (mmt) cc_final: 0.7568 (mmt) REVERT: A 491 MET cc_start: 0.8625 (ttt) cc_final: 0.8375 (ttm) REVERT: A 616 SER cc_start: 0.8952 (m) cc_final: 0.8693 (p) REVERT: A 618 ILE cc_start: 0.8804 (mp) cc_final: 0.8555 (mm) REVERT: B 59 GLN cc_start: 0.8027 (tt0) cc_final: 0.7622 (mp10) REVERT: B 168 SER cc_start: 0.8288 (m) cc_final: 0.7865 (p) REVERT: B 230 GLN cc_start: 0.6367 (tp-100) cc_final: 0.5937 (mp-120) REVERT: B 371 LYS cc_start: 0.7476 (ptmt) cc_final: 0.7264 (ptpp) REVERT: B 381 LYS cc_start: 0.7911 (mttt) cc_final: 0.7417 (tttm) REVERT: B 448 SER cc_start: 0.8448 (p) cc_final: 0.8208 (t) REVERT: B 485 MET cc_start: 0.8081 (mmt) cc_final: 0.7778 (mmt) REVERT: B 532 SER cc_start: 0.8332 (m) cc_final: 0.8052 (m) REVERT: B 587 HIS cc_start: 0.7569 (OUTLIER) cc_final: 0.6983 (m90) REVERT: C 62 ASN cc_start: 0.7356 (m110) cc_final: 0.7031 (p0) REVERT: C 63 LYS cc_start: 0.8206 (mtpt) cc_final: 0.7835 (mtpt) REVERT: C 104 GLU cc_start: 0.8352 (mp0) cc_final: 0.7777 (mp0) REVERT: C 108 GLU cc_start: 0.8093 (pt0) cc_final: 0.7702 (pp20) REVERT: C 184 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8330 (mm-30) REVERT: C 300 LYS cc_start: 0.8676 (mptt) cc_final: 0.8458 (mmmt) REVERT: C 628 ARG cc_start: 0.8313 (ptp-170) cc_final: 0.7940 (mtm-85) REVERT: C 651 PHE cc_start: 0.8608 (m-80) cc_final: 0.8288 (m-80) REVERT: D 80 GLU cc_start: 0.8147 (pm20) cc_final: 0.7694 (pm20) REVERT: D 294 GLU cc_start: 0.8224 (mp0) cc_final: 0.7716 (mp0) REVERT: D 303 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7651 (mp0) REVERT: D 373 LEU cc_start: 0.6611 (OUTLIER) cc_final: 0.6112 (tt) REVERT: D 519 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6756 (mm-30) REVERT: D 592 LEU cc_start: 0.8493 (mm) cc_final: 0.8224 (mp) REVERT: E 11 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7553 (tp30) REVERT: E 51 MET cc_start: 0.8407 (mtt) cc_final: 0.7811 (mmm) REVERT: E 76 MET cc_start: 0.6704 (tpp) cc_final: 0.6093 (ptm) REVERT: E 109 MET cc_start: 0.6969 (mmt) cc_final: 0.6720 (mmm) REVERT: E 119 GLU cc_start: 0.7279 (tp30) cc_final: 0.6831 (tp30) outliers start: 58 outliers final: 32 residues processed: 471 average time/residue: 0.3433 time to fit residues: 253.0422 Evaluate side-chains 391 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 357 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 55 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 234 optimal weight: 0.5980 chunk 204 optimal weight: 20.0000 chunk 24 optimal weight: 0.0970 chunk 232 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 254 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 197 optimal weight: 9.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 HIS C 73 HIS C 174 ASN C 214 GLN C 426 HIS C 522 HIS C 582 HIS C 640 ASN D 174 ASN D 522 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.163376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.122312 restraints weight = 28545.480| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.55 r_work: 0.3214 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22984 Z= 0.226 Angle : 0.644 8.600 30958 Z= 0.326 Chirality : 0.043 0.211 3424 Planarity : 0.005 0.094 3816 Dihedral : 14.963 163.502 4483 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.49 % Favored : 90.35 % Rotamer: Outliers : 4.25 % Allowed : 11.33 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.77 % Twisted General : 0.20 % 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: -2.31 (0.16), residues: 2623 helix: -0.63 (0.13), residues: 1573 sheet: -2.52 (0.52), residues: 84 loop : -2.92 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 613 HIS 0.006 0.001 HIS D 225 PHE 0.014 0.001 PHE B 553 TYR 0.021 0.001 TYR C 216 ARG 0.006 0.000 ARG C 643 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 378 time to evaluate : 2.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8317 (ttmt) cc_final: 0.7517 (mmtp) REVERT: A 91 ASN cc_start: 0.6634 (m-40) cc_final: 0.6425 (m110) REVERT: A 130 MET cc_start: 0.8075 (tpt) cc_final: 0.6515 (ptt) REVERT: A 174 ASN cc_start: 0.8568 (t0) cc_final: 0.8261 (t0) REVERT: A 181 LEU cc_start: 0.7466 (tp) cc_final: 0.7015 (tp) REVERT: A 211 PHE cc_start: 0.7861 (m-80) cc_final: 0.7445 (m-80) REVERT: A 216 TYR cc_start: 0.8535 (t80) cc_final: 0.8329 (t80) REVERT: A 255 MET cc_start: 0.8854 (mmm) cc_final: 0.8571 (mmm) REVERT: A 306 GLN cc_start: 0.8409 (mt0) cc_final: 0.7826 (mm-40) REVERT: A 421 LEU cc_start: 0.6418 (OUTLIER) cc_final: 0.6108 (tt) REVERT: A 435 MET cc_start: 0.7671 (mmt) cc_final: 0.7418 (mmt) REVERT: A 491 MET cc_start: 0.8453 (ttt) cc_final: 0.8228 (ttt) REVERT: A 528 MET cc_start: 0.8135 (tpp) cc_final: 0.7827 (tpp) REVERT: A 571 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8148 (mp) REVERT: A 592 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7753 (mt) REVERT: A 618 ILE cc_start: 0.8663 (mp) cc_final: 0.8312 (mm) REVERT: B 59 GLN cc_start: 0.8113 (tt0) cc_final: 0.7648 (mp10) REVERT: B 129 ASN cc_start: 0.7888 (t0) cc_final: 0.7314 (t0) REVERT: B 168 SER cc_start: 0.8275 (m) cc_final: 0.7852 (p) REVERT: B 230 GLN cc_start: 0.6166 (OUTLIER) cc_final: 0.5916 (mp-120) REVERT: B 290 GLN cc_start: 0.7519 (tp-100) cc_final: 0.7239 (tp40) REVERT: B 363 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7681 (pmt100) REVERT: B 381 LYS cc_start: 0.7827 (mttt) cc_final: 0.7297 (tttm) REVERT: B 405 PRO cc_start: 0.7806 (Cg_exo) cc_final: 0.7537 (Cg_endo) REVERT: B 421 LEU cc_start: 0.4522 (OUTLIER) cc_final: 0.4107 (tt) REVERT: B 528 MET cc_start: 0.7830 (tpp) cc_final: 0.6969 (tpp) REVERT: B 532 SER cc_start: 0.8170 (m) cc_final: 0.7821 (m) REVERT: B 587 HIS cc_start: 0.7630 (OUTLIER) cc_final: 0.6960 (m90) REVERT: C 61 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7900 (mm) REVERT: C 104 GLU cc_start: 0.8331 (mp0) cc_final: 0.7713 (pm20) REVERT: C 108 GLU cc_start: 0.8108 (pt0) cc_final: 0.7710 (pp20) REVERT: C 136 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7794 (mp) REVERT: C 184 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8379 (mm-30) REVERT: C 300 LYS cc_start: 0.8681 (mptt) cc_final: 0.8430 (mmmt) REVERT: C 571 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8560 (mp) REVERT: C 628 ARG cc_start: 0.8376 (ptp-170) cc_final: 0.7875 (mtm-85) REVERT: C 651 PHE cc_start: 0.8709 (m-80) cc_final: 0.8086 (m-80) REVERT: D 80 GLU cc_start: 0.8072 (pm20) cc_final: 0.7478 (pm20) REVERT: D 90 ASP cc_start: 0.7821 (t0) cc_final: 0.7488 (t0) REVERT: D 139 ARG cc_start: 0.7777 (mmt180) cc_final: 0.7509 (tpp80) REVERT: D 294 GLU cc_start: 0.8379 (mp0) cc_final: 0.7855 (mp0) REVERT: D 303 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7604 (mp0) REVERT: D 373 LEU cc_start: 0.6643 (OUTLIER) cc_final: 0.6117 (tt) REVERT: D 389 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7741 (mt-10) REVERT: D 519 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6984 (mm-30) REVERT: E 51 MET cc_start: 0.8276 (mtt) cc_final: 0.7702 (mmm) REVERT: E 119 GLU cc_start: 0.7269 (tp30) cc_final: 0.6721 (tp30) outliers start: 97 outliers final: 47 residues processed: 449 average time/residue: 0.3497 time to fit residues: 243.4838 Evaluate side-chains 401 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 343 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 55 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 257 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 156 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN A 267 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN C 217 ASN C 522 HIS C 694 ASN D 174 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.163277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.127155 restraints weight = 28904.321| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.84 r_work: 0.3208 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22984 Z= 0.237 Angle : 0.630 8.422 30958 Z= 0.317 Chirality : 0.043 0.202 3424 Planarity : 0.005 0.092 3816 Dihedral : 14.285 154.182 4481 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.96 % Favored : 90.89 % Rotamer: Outliers : 3.89 % Allowed : 12.78 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.16 % 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: -1.59 (0.16), residues: 2623 helix: 0.06 (0.13), residues: 1558 sheet: -2.56 (0.51), residues: 84 loop : -2.78 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 613 HIS 0.005 0.001 HIS D 587 PHE 0.013 0.001 PHE B 553 TYR 0.020 0.001 TYR A 524 ARG 0.006 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 359 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8656 (ttmt) cc_final: 0.7734 (mmtp) REVERT: A 91 ASN cc_start: 0.6855 (m-40) cc_final: 0.6579 (m110) REVERT: A 130 MET cc_start: 0.8185 (tpt) cc_final: 0.6880 (ptt) REVERT: A 174 ASN cc_start: 0.8688 (t0) cc_final: 0.8425 (t0) REVERT: A 181 LEU cc_start: 0.8066 (tp) cc_final: 0.7733 (tp) REVERT: A 211 PHE cc_start: 0.8056 (m-80) cc_final: 0.7720 (m-80) REVERT: A 306 GLN cc_start: 0.8477 (mt0) cc_final: 0.8245 (mm-40) REVERT: A 331 MET cc_start: 0.8200 (tpt) cc_final: 0.7859 (tpt) REVERT: B 139 ARG cc_start: 0.8140 (mmt180) cc_final: 0.7627 (mtt180) REVERT: B 222 TYR cc_start: 0.7634 (OUTLIER) cc_final: 0.6887 (t80) REVERT: B 363 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7520 (pmt100) REVERT: B 381 LYS cc_start: 0.8124 (mttt) cc_final: 0.7772 (tttm) REVERT: B 421 LEU cc_start: 0.4667 (OUTLIER) cc_final: 0.4145 (tt) REVERT: B 528 MET cc_start: 0.7928 (tpp) cc_final: 0.7194 (tpp) REVERT: B 532 SER cc_start: 0.7923 (m) cc_final: 0.7685 (m) REVERT: B 587 HIS cc_start: 0.7715 (OUTLIER) cc_final: 0.7505 (m90) REVERT: C 104 GLU cc_start: 0.8268 (mp0) cc_final: 0.7808 (pm20) REVERT: C 136 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8287 (mp) REVERT: C 184 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8417 (mm-30) REVERT: D 80 GLU cc_start: 0.8105 (pm20) cc_final: 0.7882 (pm20) REVERT: D 90 ASP cc_start: 0.8079 (t0) cc_final: 0.7581 (t0) REVERT: D 255 MET cc_start: 0.9149 (mmm) cc_final: 0.8941 (mmp) REVERT: D 294 GLU cc_start: 0.8549 (mp0) cc_final: 0.8341 (mp0) REVERT: D 373 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.6889 (tt) REVERT: D 603 MET cc_start: 0.8909 (ttp) cc_final: 0.8650 (ttp) REVERT: E 11 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7485 (mm-30) REVERT: E 51 MET cc_start: 0.8271 (mtt) cc_final: 0.7762 (mmm) REVERT: E 76 MET cc_start: 0.6520 (tpp) cc_final: 0.5962 (ptm) REVERT: E 119 GLU cc_start: 0.7640 (tp30) cc_final: 0.7171 (tp30) outliers start: 89 outliers final: 58 residues processed: 423 average time/residue: 0.3403 time to fit residues: 226.4584 Evaluate side-chains 402 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 338 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 546 ASN Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 363 ARG Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 112 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 250 optimal weight: 7.9990 chunk 226 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 208 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 210 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 237 optimal weight: 0.1980 chunk 38 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 HIS ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.164616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.128430 restraints weight = 28696.195| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.82 r_work: 0.3265 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22984 Z= 0.158 Angle : 0.586 8.302 30958 Z= 0.295 Chirality : 0.041 0.193 3424 Planarity : 0.005 0.091 3816 Dihedral : 13.416 144.303 4481 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.34 % Favored : 90.51 % Rotamer: Outliers : 3.06 % Allowed : 13.92 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.16 % 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: -0.97 (0.17), residues: 2623 helix: 0.59 (0.14), residues: 1554 sheet: -2.48 (0.50), residues: 84 loop : -2.55 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 593 HIS 0.004 0.000 HIS D 587 PHE 0.012 0.001 PHE B 553 TYR 0.021 0.001 TYR A 524 ARG 0.005 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 373 time to evaluate : 2.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ASN cc_start: 0.6798 (m-40) cc_final: 0.6518 (m110) REVERT: A 130 MET cc_start: 0.8107 (tpt) cc_final: 0.6891 (mtm) REVERT: A 174 ASN cc_start: 0.8682 (t0) cc_final: 0.8419 (t0) REVERT: A 181 LEU cc_start: 0.8014 (tp) cc_final: 0.7709 (tp) REVERT: A 188 ASP cc_start: 0.7426 (t0) cc_final: 0.7205 (t0) REVERT: A 211 PHE cc_start: 0.8022 (m-80) cc_final: 0.7737 (m-80) REVERT: A 306 GLN cc_start: 0.8371 (mt0) cc_final: 0.8160 (mm-40) REVERT: A 421 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6395 (tt) REVERT: A 592 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8295 (mt) REVERT: B 139 ARG cc_start: 0.8041 (mtt180) cc_final: 0.7585 (mmt90) REVERT: B 222 TYR cc_start: 0.7518 (OUTLIER) cc_final: 0.6923 (t80) REVERT: B 257 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7818 (tp-100) REVERT: B 381 LYS cc_start: 0.8062 (mttt) cc_final: 0.7774 (tttm) REVERT: B 421 LEU cc_start: 0.5038 (OUTLIER) cc_final: 0.4450 (tt) REVERT: B 528 MET cc_start: 0.7860 (tpp) cc_final: 0.7158 (tpp) REVERT: B 532 SER cc_start: 0.7899 (m) cc_final: 0.7669 (m) REVERT: B 587 HIS cc_start: 0.7692 (OUTLIER) cc_final: 0.7469 (m90) REVERT: C 136 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8300 (mp) REVERT: C 184 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8346 (mm-30) REVERT: C 215 MET cc_start: 0.9268 (mmm) cc_final: 0.8882 (tpt) REVERT: D 294 GLU cc_start: 0.8501 (mp0) cc_final: 0.8279 (mp0) REVERT: D 373 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.6904 (tt) REVERT: E 11 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7477 (mm-30) REVERT: E 51 MET cc_start: 0.8182 (mtt) cc_final: 0.7846 (mmm) outliers start: 70 outliers final: 42 residues processed: 421 average time/residue: 0.3455 time to fit residues: 227.3691 Evaluate side-chains 397 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 348 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 546 ASN Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 363 ARG Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 117 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 185 optimal weight: 3.9990 chunk 241 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 120 optimal weight: 20.0000 chunk 78 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN C 640 ASN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.159662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.124044 restraints weight = 28838.214| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.83 r_work: 0.3161 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 22984 Z= 0.362 Angle : 0.694 7.942 30958 Z= 0.346 Chirality : 0.045 0.214 3424 Planarity : 0.005 0.095 3816 Dihedral : 14.052 158.173 4481 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.84 % Favored : 90.01 % Rotamer: Outliers : 3.85 % Allowed : 14.97 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.24 % 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: -1.05 (0.17), residues: 2623 helix: 0.54 (0.13), residues: 1545 sheet: -2.56 (0.51), residues: 84 loop : -2.58 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 29 HIS 0.005 0.001 HIS D 587 PHE 0.016 0.002 PHE B 553 TYR 0.021 0.002 TYR C 524 ARG 0.009 0.001 ARG E 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 345 time to evaluate : 2.286 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.8177 (tpt) cc_final: 0.6908 (ptt) REVERT: A 174 ASN cc_start: 0.8761 (t0) cc_final: 0.8505 (t0) REVERT: A 181 LEU cc_start: 0.8240 (tp) cc_final: 0.7935 (tp) REVERT: A 211 PHE cc_start: 0.8067 (m-80) cc_final: 0.7742 (m-80) REVERT: A 306 GLN cc_start: 0.8565 (mt0) cc_final: 0.8304 (mm-40) REVERT: A 421 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6625 (tt) REVERT: A 591 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8075 (mm-30) REVERT: B 98 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8620 (mm) REVERT: B 308 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9066 (mt) REVERT: B 381 LYS cc_start: 0.8142 (mttt) cc_final: 0.7811 (tttm) REVERT: B 421 LEU cc_start: 0.4863 (OUTLIER) cc_final: 0.4445 (tt) REVERT: B 532 SER cc_start: 0.7920 (m) cc_final: 0.7703 (m) REVERT: C 118 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8550 (tt0) REVERT: C 136 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8271 (mp) REVERT: C 215 MET cc_start: 0.9283 (mmm) cc_final: 0.8841 (tpt) REVERT: C 297 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8541 (mm) REVERT: D 90 ASP cc_start: 0.8265 (t0) cc_final: 0.7889 (t0) REVERT: D 308 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8475 (mp) REVERT: D 373 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7101 (tt) REVERT: D 603 MET cc_start: 0.9015 (ttp) cc_final: 0.8753 (ttp) REVERT: E 51 MET cc_start: 0.8296 (mtt) cc_final: 0.7831 (mmm) REVERT: E 76 MET cc_start: 0.6492 (tpp) cc_final: 0.5892 (ptm) outliers start: 88 outliers final: 56 residues processed: 410 average time/residue: 0.3463 time to fit residues: 223.6247 Evaluate side-chains 394 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 329 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 546 ASN Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 118 GLN Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 222 TYR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 117 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 70 optimal weight: 7.9990 chunk 236 optimal weight: 0.9990 chunk 193 optimal weight: 0.9990 chunk 250 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 186 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN A 258 HIS A 267 GLN ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN C 217 ASN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.164495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.127631 restraints weight = 28617.444| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.82 r_work: 0.3249 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22984 Z= 0.184 Angle : 0.603 7.498 30958 Z= 0.303 Chirality : 0.041 0.197 3424 Planarity : 0.005 0.089 3816 Dihedral : 13.281 144.205 4481 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.07 % Favored : 90.77 % Rotamer: Outliers : 3.63 % Allowed : 15.71 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.16 % 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: -0.70 (0.17), residues: 2623 helix: 0.86 (0.14), residues: 1547 sheet: -2.51 (0.51), residues: 84 loop : -2.48 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 593 HIS 0.005 0.001 HIS C 587 PHE 0.019 0.001 PHE D 434 TYR 0.028 0.001 TYR A 524 ARG 0.009 0.000 ARG E 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 351 time to evaluate : 2.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.8041 (tpt) cc_final: 0.6885 (mtm) REVERT: A 174 ASN cc_start: 0.8697 (t0) cc_final: 0.8454 (t0) REVERT: A 181 LEU cc_start: 0.7964 (tp) cc_final: 0.7672 (tp) REVERT: A 211 PHE cc_start: 0.7991 (m-80) cc_final: 0.7643 (m-80) REVERT: A 306 GLN cc_start: 0.8439 (mt0) cc_final: 0.8119 (mm-40) REVERT: A 331 MET cc_start: 0.8029 (tpt) cc_final: 0.7714 (tpt) REVERT: A 421 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6399 (tt) REVERT: A 592 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8291 (mt) REVERT: B 98 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8421 (mm) REVERT: B 139 ARG cc_start: 0.8213 (mtt180) cc_final: 0.7886 (mtt180) REVERT: B 308 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9007 (mt) REVERT: B 381 LYS cc_start: 0.8061 (mttt) cc_final: 0.7636 (tttm) REVERT: B 421 LEU cc_start: 0.4866 (OUTLIER) cc_final: 0.4322 (tt) REVERT: B 528 MET cc_start: 0.7947 (tpp) cc_final: 0.7289 (tpp) REVERT: B 532 SER cc_start: 0.7997 (m) cc_final: 0.7701 (m) REVERT: C 136 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8172 (mp) REVERT: C 215 MET cc_start: 0.9294 (mmm) cc_final: 0.8869 (tpt) REVERT: D 134 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7750 (tpp-160) REVERT: D 308 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8440 (mp) REVERT: D 373 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6835 (tt) REVERT: E 11 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7387 (tp30) REVERT: E 51 MET cc_start: 0.8144 (mtt) cc_final: 0.7741 (mmm) REVERT: E 119 GLU cc_start: 0.7451 (mp0) cc_final: 0.7239 (tt0) outliers start: 83 outliers final: 57 residues processed: 406 average time/residue: 0.3526 time to fit residues: 224.6844 Evaluate side-chains 400 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 334 time to evaluate : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 607 LYS Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 546 ASN Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 222 TYR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 363 ARG Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 112 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 44 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 253 optimal weight: 6.9990 chunk 141 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 199 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 179 optimal weight: 0.6980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.161822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.125402 restraints weight = 28653.859| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.80 r_work: 0.3225 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22984 Z= 0.206 Angle : 0.612 7.853 30958 Z= 0.305 Chirality : 0.042 0.197 3424 Planarity : 0.005 0.091 3816 Dihedral : 12.968 141.472 4481 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.76 % Favored : 90.09 % Rotamer: Outliers : 3.33 % Allowed : 16.50 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.16 % 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: -0.55 (0.17), residues: 2623 helix: 0.98 (0.14), residues: 1547 sheet: -2.60 (0.50), residues: 84 loop : -2.42 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 593 HIS 0.003 0.001 HIS C 587 PHE 0.016 0.001 PHE B 553 TYR 0.027 0.001 TYR A 524 ARG 0.007 0.000 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 342 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.8076 (tpt) cc_final: 0.6909 (ptt) REVERT: A 174 ASN cc_start: 0.8729 (t0) cc_final: 0.8477 (t0) REVERT: A 181 LEU cc_start: 0.8043 (tp) cc_final: 0.7770 (tp) REVERT: A 188 ASP cc_start: 0.7521 (t0) cc_final: 0.7306 (t0) REVERT: A 211 PHE cc_start: 0.8022 (m-80) cc_final: 0.7694 (m-80) REVERT: A 306 GLN cc_start: 0.8429 (mt0) cc_final: 0.8179 (mm-40) REVERT: A 421 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6560 (tt) REVERT: A 591 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8000 (mm-30) REVERT: A 592 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8332 (mt) REVERT: A 607 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8464 (mmtt) REVERT: B 98 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8327 (mm) REVERT: B 139 ARG cc_start: 0.8110 (mtt180) cc_final: 0.7834 (mpt-90) REVERT: B 222 TYR cc_start: 0.7550 (OUTLIER) cc_final: 0.7258 (t80) REVERT: B 308 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9048 (mt) REVERT: B 381 LYS cc_start: 0.8078 (mttt) cc_final: 0.7752 (tttm) REVERT: B 421 LEU cc_start: 0.4456 (OUTLIER) cc_final: 0.3935 (tt) REVERT: B 528 MET cc_start: 0.7986 (tpp) cc_final: 0.7328 (tpp) REVERT: B 532 SER cc_start: 0.7961 (m) cc_final: 0.7691 (m) REVERT: C 136 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8212 (mp) REVERT: C 215 MET cc_start: 0.9275 (mmm) cc_final: 0.8871 (tpt) REVERT: D 134 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7818 (tpp-160) REVERT: D 308 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8435 (mp) REVERT: D 373 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.6965 (tt) REVERT: D 603 MET cc_start: 0.8956 (ttp) cc_final: 0.8592 (ttp) REVERT: E 51 MET cc_start: 0.8061 (mtt) cc_final: 0.7763 (mmm) outliers start: 76 outliers final: 54 residues processed: 394 average time/residue: 0.3488 time to fit residues: 214.5485 Evaluate side-chains 392 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 327 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 607 LYS Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 546 ASN Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 222 TYR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 363 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 112 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 109 optimal weight: 1.9990 chunk 203 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 24 optimal weight: 0.0870 chunk 75 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 180 optimal weight: 4.9990 chunk 174 optimal weight: 0.3980 chunk 64 optimal weight: 10.0000 overall best weight: 1.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 267 GLN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.165567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.128606 restraints weight = 28643.526| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.79 r_work: 0.3266 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22984 Z= 0.178 Angle : 0.602 10.870 30958 Z= 0.300 Chirality : 0.041 0.196 3424 Planarity : 0.005 0.090 3816 Dihedral : 12.564 134.126 4479 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.19 % Favored : 90.66 % Rotamer: Outliers : 3.02 % Allowed : 16.89 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.42 (0.17), residues: 2623 helix: 1.09 (0.14), residues: 1550 sheet: -2.62 (0.51), residues: 86 loop : -2.36 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 593 HIS 0.005 0.000 HIS C 587 PHE 0.019 0.001 PHE D 434 TYR 0.027 0.001 TYR A 524 ARG 0.003 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 337 time to evaluate : 2.371 Fit side-chains revert: symmetry clash REVERT: A 106 VAL cc_start: 0.7312 (t) cc_final: 0.7091 (p) REVERT: A 130 MET cc_start: 0.7998 (tpt) cc_final: 0.6866 (ptt) REVERT: A 174 ASN cc_start: 0.8714 (t0) cc_final: 0.8451 (t0) REVERT: A 181 LEU cc_start: 0.7929 (tp) cc_final: 0.7667 (tp) REVERT: A 211 PHE cc_start: 0.7963 (m-80) cc_final: 0.7613 (m-80) REVERT: A 303 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7867 (mp0) REVERT: A 306 GLN cc_start: 0.8412 (mt0) cc_final: 0.8124 (mm-40) REVERT: A 373 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6376 (tt) REVERT: A 421 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6547 (tt) REVERT: B 98 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8374 (mm) REVERT: B 203 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8753 (mm) REVERT: B 308 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8982 (mt) REVERT: B 381 LYS cc_start: 0.7970 (mttt) cc_final: 0.7646 (tttm) REVERT: B 421 LEU cc_start: 0.4520 (OUTLIER) cc_final: 0.3996 (tt) REVERT: B 528 MET cc_start: 0.7957 (tpp) cc_final: 0.7330 (tpp) REVERT: B 532 SER cc_start: 0.8032 (m) cc_final: 0.7762 (m) REVERT: C 78 MET cc_start: 0.7828 (mmp) cc_final: 0.7465 (mmp) REVERT: C 136 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8089 (mp) REVERT: C 215 MET cc_start: 0.9303 (mmm) cc_final: 0.8886 (tpt) REVERT: C 300 LYS cc_start: 0.8823 (mmmt) cc_final: 0.8355 (mttt) REVERT: D 134 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7799 (tpp-160) REVERT: D 308 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8430 (mp) REVERT: D 373 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6826 (tt) REVERT: E 11 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7427 (mm-30) REVERT: E 51 MET cc_start: 0.8006 (mtt) cc_final: 0.7710 (mmm) REVERT: E 119 GLU cc_start: 0.7572 (tt0) cc_final: 0.7144 (tp30) REVERT: E 126 ARG cc_start: 0.7801 (ttp-110) cc_final: 0.7315 (mtm-85) outliers start: 69 outliers final: 47 residues processed: 381 average time/residue: 0.3497 time to fit residues: 207.3853 Evaluate side-chains 378 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 321 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 546 ASN Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 363 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 48 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 218 optimal weight: 2.9990 chunk 221 optimal weight: 0.0570 chunk 201 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 140 optimal weight: 30.0000 chunk 195 optimal weight: 0.6980 chunk 215 optimal weight: 8.9990 chunk 236 optimal weight: 2.9990 chunk 244 optimal weight: 0.0040 chunk 120 optimal weight: 0.0370 chunk 16 optimal weight: 0.3980 overall best weight: 0.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN B 206 GLN ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN E 137 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.169102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.132982 restraints weight = 28586.281| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.86 r_work: 0.3320 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 22984 Z= 0.132 Angle : 0.590 10.186 30958 Z= 0.295 Chirality : 0.040 0.202 3424 Planarity : 0.005 0.091 3816 Dihedral : 11.794 120.767 4479 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.88 % Favored : 90.96 % Rotamer: Outliers : 2.23 % Allowed : 17.55 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.16 (0.18), residues: 2623 helix: 1.34 (0.14), residues: 1542 sheet: -2.54 (0.51), residues: 86 loop : -2.30 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 593 HIS 0.003 0.000 HIS C 587 PHE 0.019 0.001 PHE B 553 TYR 0.026 0.001 TYR A 524 ARG 0.007 0.000 ARG E 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 364 time to evaluate : 2.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 VAL cc_start: 0.7142 (t) cc_final: 0.6899 (p) REVERT: A 130 MET cc_start: 0.8002 (tpt) cc_final: 0.6826 (mtm) REVERT: A 153 ARG cc_start: 0.7991 (mtt180) cc_final: 0.7584 (mtt-85) REVERT: A 174 ASN cc_start: 0.8669 (t0) cc_final: 0.8429 (t0) REVERT: A 181 LEU cc_start: 0.7613 (tp) cc_final: 0.7382 (tp) REVERT: A 211 PHE cc_start: 0.7911 (m-80) cc_final: 0.7472 (m-80) REVERT: A 303 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7798 (mp0) REVERT: A 306 GLN cc_start: 0.8292 (mt0) cc_final: 0.7946 (mm-40) REVERT: A 373 LEU cc_start: 0.6622 (OUTLIER) cc_final: 0.6021 (tt) REVERT: A 421 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6601 (tt) REVERT: B 98 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8152 (mm) REVERT: B 308 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8839 (mt) REVERT: B 381 LYS cc_start: 0.7828 (mttt) cc_final: 0.7525 (tttm) REVERT: B 421 LEU cc_start: 0.3925 (OUTLIER) cc_final: 0.3482 (tt) REVERT: B 454 MET cc_start: 0.7589 (mtt) cc_final: 0.7288 (mtt) REVERT: B 528 MET cc_start: 0.7812 (tpp) cc_final: 0.7244 (tpp) REVERT: B 532 SER cc_start: 0.8100 (m) cc_final: 0.7832 (m) REVERT: C 215 MET cc_start: 0.9300 (mmm) cc_final: 0.8872 (tpt) REVERT: C 300 LYS cc_start: 0.8715 (mmmt) cc_final: 0.8230 (mttt) REVERT: C 481 MET cc_start: 0.8799 (mmt) cc_final: 0.8295 (mmt) REVERT: C 651 PHE cc_start: 0.8647 (m-80) cc_final: 0.7695 (m-80) REVERT: D 80 GLU cc_start: 0.7752 (pm20) cc_final: 0.7534 (pm20) REVERT: D 134 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7776 (tpp-160) REVERT: D 195 LEU cc_start: 0.9131 (mp) cc_final: 0.8838 (mp) REVERT: E 11 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7453 (mm-30) REVERT: E 26 THR cc_start: 0.8199 (p) cc_final: 0.7993 (t) REVERT: E 51 MET cc_start: 0.7930 (mtt) cc_final: 0.7693 (mmm) REVERT: E 76 MET cc_start: 0.6388 (tpp) cc_final: 0.5760 (ptm) REVERT: E 99 TYR cc_start: 0.8092 (m-80) cc_final: 0.7743 (m-80) REVERT: E 119 GLU cc_start: 0.7478 (tt0) cc_final: 0.7008 (tp30) REVERT: E 126 ARG cc_start: 0.7616 (ttp-110) cc_final: 0.7134 (mtm-85) outliers start: 51 outliers final: 31 residues processed: 400 average time/residue: 0.3455 time to fit residues: 214.8443 Evaluate side-chains 377 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 340 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 363 ARG Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 48 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 138 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 195 optimal weight: 0.6980 chunk 240 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 91 optimal weight: 0.0470 chunk 111 optimal weight: 4.9990 chunk 209 optimal weight: 1.9990 chunk 250 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 overall best weight: 1.0482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 640 ASN D 40 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN D 582 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.166086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.129241 restraints weight = 28429.549| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.93 r_work: 0.3284 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22984 Z= 0.160 Angle : 0.608 9.630 30958 Z= 0.303 Chirality : 0.041 0.196 3424 Planarity : 0.005 0.092 3816 Dihedral : 11.685 116.990 4479 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.96 % Favored : 90.89 % Rotamer: Outliers : 2.10 % Allowed : 18.29 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 (0.18), residues: 2623 helix: 1.44 (0.14), residues: 1538 sheet: -2.59 (0.51), residues: 86 loop : -2.30 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 593 HIS 0.003 0.000 HIS C 587 PHE 0.021 0.001 PHE B 553 TYR 0.026 0.001 TYR A 524 ARG 0.004 0.000 ARG A 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12669.70 seconds wall clock time: 226 minutes 4.61 seconds (13564.61 seconds total)