Starting phenix.real_space_refine on Thu Jun 19 05:46:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cuk_45936/06_2025/9cuk_45936.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cuk_45936/06_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_45936/06_2025/9cuk_45936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cuk_45936/06_2025/9cuk_45936.map" model { file = "/net/cci-nas-00/data/ceres_data/9cuk_45936/06_2025/9cuk_45936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cuk_45936/06_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-5710/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: 13.38, per 1000 atoms: 0.59 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: 5.27 Conformation dependent library (CDL) restraints added in 2.5 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: 2.54 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: 6.37 Time building geometry restraints manager: 6.24 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: 1.550 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: 0.830 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 47.830 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.870 ------------------------------------------------------------------------------- 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= 0.589 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 Details of bonding type rmsd hydrogen bonds : bond 0.33124 ( 931) hydrogen bonds : angle 9.95960 ( 2709) covalent geometry : bond 0.01272 (22984) covalent geometry : angle 1.37402 (30958) *********************** 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 : 2.423 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: 0.4051 time to fit residues: 381.8413 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 : 3.384 ------------------------------------------------------------------------------- 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 = 28758.626| |-----------------------------------------------------------------------------| 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: 0.3127 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 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= 0.142 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 Details of bonding type rmsd hydrogen bonds : bond 0.04933 ( 931) hydrogen bonds : angle 4.61310 ( 2709) covalent geometry : bond 0.00319 (22984) covalent geometry : angle 0.68744 (30958) *********************** 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 : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8341 (ttmt) cc_final: 0.7597 (mmtp) REVERT: A 91 ASN cc_start: 0.6789 (m-40) cc_final: 0.6577 (m110) REVERT: A 174 ASN cc_start: 0.8429 (t0) cc_final: 0.8213 (t0) REVERT: A 211 PHE cc_start: 0.7941 (m-80) cc_final: 0.7474 (m-80) REVERT: A 216 TYR cc_start: 0.8640 (t80) cc_final: 0.8377 (t80) REVERT: A 303 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7892 (pt0) REVERT: A 306 GLN cc_start: 0.8465 (mt0) cc_final: 0.7969 (mm-40) REVERT: A 331 MET cc_start: 0.7775 (tpt) cc_final: 0.7422 (tpt) REVERT: A 435 MET cc_start: 0.7818 (mmt) cc_final: 0.7572 (mmt) REVERT: A 491 MET cc_start: 0.8624 (ttt) cc_final: 0.8374 (ttm) REVERT: A 616 SER cc_start: 0.8951 (m) cc_final: 0.8692 (p) REVERT: A 618 ILE cc_start: 0.8806 (mp) cc_final: 0.8557 (mm) REVERT: B 59 GLN cc_start: 0.8030 (tt0) cc_final: 0.7620 (mp10) REVERT: B 168 SER cc_start: 0.8284 (m) cc_final: 0.7859 (p) REVERT: B 230 GLN cc_start: 0.6366 (tp-100) cc_final: 0.5936 (mp-120) REVERT: B 371 LYS cc_start: 0.7472 (ptmt) cc_final: 0.7259 (ptpp) REVERT: B 381 LYS cc_start: 0.7911 (mttt) cc_final: 0.7418 (tttm) REVERT: B 448 SER cc_start: 0.8450 (p) cc_final: 0.8210 (t) REVERT: B 485 MET cc_start: 0.8083 (mmt) cc_final: 0.7781 (mmt) REVERT: B 532 SER cc_start: 0.8331 (m) cc_final: 0.8051 (m) REVERT: B 587 HIS cc_start: 0.7578 (OUTLIER) cc_final: 0.6985 (m90) REVERT: C 62 ASN cc_start: 0.7356 (m110) cc_final: 0.7029 (p0) REVERT: C 63 LYS cc_start: 0.8202 (mtpt) cc_final: 0.7834 (mtpt) REVERT: C 104 GLU cc_start: 0.8355 (mp0) cc_final: 0.7781 (mp0) REVERT: C 108 GLU cc_start: 0.8097 (pt0) cc_final: 0.7703 (pp20) REVERT: C 184 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8331 (mm-30) REVERT: C 300 LYS cc_start: 0.8678 (mptt) cc_final: 0.8461 (mmmt) REVERT: C 628 ARG cc_start: 0.8320 (ptp-170) cc_final: 0.7946 (mtm-85) REVERT: C 651 PHE cc_start: 0.8609 (m-80) cc_final: 0.8290 (m-80) REVERT: D 80 GLU cc_start: 0.8140 (pm20) cc_final: 0.7684 (pm20) REVERT: D 294 GLU cc_start: 0.8223 (mp0) cc_final: 0.7715 (mp0) REVERT: D 303 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7651 (mp0) REVERT: D 373 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6112 (tt) REVERT: D 519 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6759 (mm-30) REVERT: D 592 LEU cc_start: 0.8499 (mm) cc_final: 0.8229 (mp) REVERT: E 11 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7549 (tp30) REVERT: E 51 MET cc_start: 0.8406 (mtt) cc_final: 0.7810 (mmm) REVERT: E 76 MET cc_start: 0.6706 (tpp) cc_final: 0.6093 (ptm) REVERT: E 109 MET cc_start: 0.6967 (mmt) cc_final: 0.6717 (mmm) REVERT: E 119 GLU cc_start: 0.7271 (tp30) cc_final: 0.6824 (tp30) outliers start: 58 outliers final: 32 residues processed: 471 average time/residue: 0.3378 time to fit residues: 250.4989 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 : 2.546 ------------------------------------------------------------------------------- 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: 0.0870 chunk 232 optimal weight: 0.0770 chunk 94 optimal weight: 0.2980 chunk 28 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 254 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 197 optimal weight: 6.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN C 214 GLN C 426 HIS C 522 HIS C 582 HIS C 640 ASN C 694 ASN D 174 ASN D 267 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.169644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.132828 restraints weight = 28431.615| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.82 r_work: 0.3325 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22984 Z= 0.107 Angle : 0.604 8.869 30958 Z= 0.306 Chirality : 0.041 0.196 3424 Planarity : 0.005 0.093 3816 Dihedral : 14.811 163.163 4483 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.88 % Favored : 90.96 % Rotamer: Outliers : 3.19 % Allowed : 11.77 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.77 % 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: -2.31 (0.16), residues: 2623 helix: -0.61 (0.13), residues: 1567 sheet: -2.52 (0.53), residues: 84 loop : -2.94 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 613 HIS 0.006 0.001 HIS D 225 PHE 0.013 0.001 PHE B 553 TYR 0.017 0.001 TYR A 524 ARG 0.005 0.000 ARG C 643 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 931) hydrogen bonds : angle 4.04139 ( 2709) covalent geometry : bond 0.00223 (22984) covalent geometry : angle 0.60351 (30958) *********************** 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 468 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 395 time to evaluate : 2.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8513 (ttmt) cc_final: 0.7714 (mmtp) REVERT: A 91 ASN cc_start: 0.6795 (m-40) cc_final: 0.6533 (m110) REVERT: A 130 MET cc_start: 0.8090 (tpt) cc_final: 0.6789 (ptt) REVERT: A 174 ASN cc_start: 0.8474 (t0) cc_final: 0.8221 (t0) REVERT: A 211 PHE cc_start: 0.7989 (m-80) cc_final: 0.7700 (m-80) REVERT: A 345 MET cc_start: 0.8301 (mtm) cc_final: 0.8079 (mtt) REVERT: A 618 ILE cc_start: 0.9087 (mp) cc_final: 0.8840 (mm) REVERT: B 363 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7543 (pmt100) REVERT: B 381 LYS cc_start: 0.8021 (mttt) cc_final: 0.7806 (tttm) REVERT: B 421 LEU cc_start: 0.4354 (OUTLIER) cc_final: 0.4074 (tt) REVERT: B 528 MET cc_start: 0.7906 (tpp) cc_final: 0.7232 (tpp) REVERT: B 532 SER cc_start: 0.7877 (m) cc_final: 0.7647 (m) REVERT: B 587 HIS cc_start: 0.7691 (OUTLIER) cc_final: 0.7472 (m90) REVERT: C 61 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8205 (mm) REVERT: C 104 GLU cc_start: 0.8188 (mp0) cc_final: 0.7817 (pm20) REVERT: C 136 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8371 (mp) REVERT: C 184 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8347 (mm-30) REVERT: C 645 GLN cc_start: 0.7493 (mt0) cc_final: 0.7274 (mt0) REVERT: D 96 MET cc_start: 0.8656 (mmm) cc_final: 0.8443 (mmm) REVERT: D 294 GLU cc_start: 0.8502 (mp0) cc_final: 0.8295 (mp0) REVERT: D 373 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6729 (tt) REVERT: D 519 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7082 (mm-30) REVERT: E 51 MET cc_start: 0.8313 (mtt) cc_final: 0.7805 (mmm) REVERT: E 119 GLU cc_start: 0.7642 (tp30) cc_final: 0.7178 (tp30) outliers start: 73 outliers final: 34 residues processed: 446 average time/residue: 0.3473 time to fit residues: 242.6676 Evaluate side-chains 385 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 345 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 131 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 565 ILE 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 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 427 VAL 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 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 627 ASP Chi-restraints excluded: chain D residue 631 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 257 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 156 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** 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 118 GLN D 40 GLN D 174 ASN D 267 GLN D 522 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.165364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.129115 restraints weight = 28777.252| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.86 r_work: 0.3257 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3713 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= 0.135 Angle : 0.624 10.668 30958 Z= 0.312 Chirality : 0.042 0.196 3424 Planarity : 0.005 0.089 3816 Dihedral : 14.069 158.759 4481 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.26 % Favored : 90.58 % Rotamer: Outliers : 3.81 % Allowed : 13.13 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.83 % 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: -1.60 (0.16), residues: 2623 helix: 0.01 (0.13), residues: 1568 sheet: -2.42 (0.52), residues: 84 loop : -2.73 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 593 HIS 0.004 0.001 HIS D 587 PHE 0.017 0.001 PHE B 553 TYR 0.019 0.001 TYR A 524 ARG 0.008 0.000 ARG A 363 Details of bonding type rmsd hydrogen bonds : bond 0.03548 ( 931) hydrogen bonds : angle 4.01177 ( 2709) covalent geometry : bond 0.00317 (22984) covalent geometry : angle 0.62434 (30958) *********************** 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 447 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 360 time to evaluate : 2.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8587 (ttmt) cc_final: 0.7720 (mmtp) REVERT: A 91 ASN cc_start: 0.6828 (m-40) cc_final: 0.6521 (m110) REVERT: A 130 MET cc_start: 0.8102 (tpt) cc_final: 0.6792 (ptt) REVERT: A 174 ASN cc_start: 0.8645 (t0) cc_final: 0.8371 (t0) REVERT: A 211 PHE cc_start: 0.8024 (m-80) cc_final: 0.7709 (m-80) REVERT: A 331 MET cc_start: 0.8142 (tpt) cc_final: 0.7875 (tpt) REVERT: A 345 MET cc_start: 0.8433 (mtm) cc_final: 0.8202 (mtp) REVERT: A 592 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8256 (mt) REVERT: A 618 ILE cc_start: 0.9150 (mp) cc_final: 0.8818 (mm) REVERT: B 139 ARG cc_start: 0.8073 (mmt180) cc_final: 0.7526 (mtt180) REVERT: B 222 TYR cc_start: 0.7534 (OUTLIER) cc_final: 0.6777 (t80) REVERT: B 363 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7490 (pmt100) REVERT: B 381 LYS cc_start: 0.8071 (mttt) cc_final: 0.7816 (tttm) REVERT: B 528 MET cc_start: 0.7935 (tpp) cc_final: 0.7208 (tpp) REVERT: B 532 SER cc_start: 0.7933 (m) cc_final: 0.7705 (m) REVERT: B 587 HIS cc_start: 0.7653 (OUTLIER) cc_final: 0.7451 (m90) REVERT: C 136 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8306 (mp) REVERT: C 184 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8418 (mm-30) REVERT: C 215 MET cc_start: 0.9227 (mmm) cc_final: 0.8792 (tpt) REVERT: C 571 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8390 (mp) REVERT: C 645 GLN cc_start: 0.7509 (mt0) cc_final: 0.7307 (mt0) REVERT: D 373 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6815 (tt) REVERT: E 11 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7484 (mm-30) REVERT: E 51 MET cc_start: 0.8298 (mtt) cc_final: 0.7771 (mmm) REVERT: E 76 MET cc_start: 0.6481 (tpp) cc_final: 0.5921 (ptm) REVERT: E 119 GLU cc_start: 0.7658 (tp30) cc_final: 0.7288 (tp30) outliers start: 87 outliers final: 52 residues processed: 420 average time/residue: 0.3262 time to fit residues: 215.8318 Evaluate side-chains 389 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 330 time to evaluate : 2.468 ------------------------------------------------------------------------------- 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 502 LEU Chi-restraints excluded: chain A residue 592 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 143 VAL 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 387 VAL Chi-restraints excluded: chain B residue 404 VAL 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 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 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 410 MET Chi-restraints excluded: chain C residue 427 VAL 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 571 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 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 627 ASP Chi-restraints excluded: chain D residue 631 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 250 optimal weight: 3.9990 chunk 226 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 208 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 210 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 237 optimal weight: 0.5980 chunk 38 optimal weight: 0.0270 chunk 9 optimal weight: 6.9990 overall best weight: 2.7244 ------------------------------------------------------------------------------- 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** A 596 GLN ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.162564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.125994 restraints weight = 28909.772| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.88 r_work: 0.3191 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22984 Z= 0.172 Angle : 0.650 10.085 30958 Z= 0.324 Chirality : 0.043 0.210 3424 Planarity : 0.005 0.091 3816 Dihedral : 13.828 152.189 4481 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.57 % Favored : 90.28 % Rotamer: Outliers : 3.94 % Allowed : 13.52 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % 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: -1.21 (0.17), residues: 2623 helix: 0.39 (0.13), residues: 1560 sheet: -2.54 (0.50), residues: 84 loop : -2.65 (0.19), residues: 979 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 0.015 0.001 PHE B 553 TYR 0.020 0.001 TYR A 524 ARG 0.007 0.000 ARG A 190 Details of bonding type rmsd hydrogen bonds : bond 0.03819 ( 931) hydrogen bonds : angle 4.06974 ( 2709) covalent geometry : bond 0.00419 (22984) covalent geometry : angle 0.65029 (30958) *********************** 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 436 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 346 time to evaluate : 2.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 ASN cc_start: 0.6828 (m-40) cc_final: 0.6529 (m110) REVERT: A 130 MET cc_start: 0.8219 (tpt) cc_final: 0.6860 (ptt) REVERT: A 174 ASN cc_start: 0.8708 (t0) cc_final: 0.8454 (t0) REVERT: A 211 PHE cc_start: 0.8019 (m-80) cc_final: 0.7693 (m-80) REVERT: A 331 MET cc_start: 0.8178 (tpt) cc_final: 0.7866 (tpt) REVERT: A 592 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8334 (mt) REVERT: B 139 ARG cc_start: 0.8039 (mtt180) cc_final: 0.7607 (mtt-85) REVERT: B 222 TYR cc_start: 0.7607 (OUTLIER) cc_final: 0.6940 (t80) REVERT: B 363 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.7430 (pmt100) REVERT: B 381 LYS cc_start: 0.8076 (mttt) cc_final: 0.7771 (tttm) REVERT: B 421 LEU cc_start: 0.5019 (OUTLIER) cc_final: 0.4552 (tt) REVERT: B 532 SER cc_start: 0.7960 (m) cc_final: 0.7736 (m) REVERT: C 136 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8303 (mp) REVERT: C 184 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8423 (mm-30) REVERT: C 215 MET cc_start: 0.9259 (mmm) cc_final: 0.8827 (tpt) REVERT: C 297 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8466 (mm) REVERT: C 640 ASN cc_start: 0.6836 (t0) cc_final: 0.6623 (t0) REVERT: D 90 ASP cc_start: 0.8118 (t0) cc_final: 0.7608 (t0) REVERT: D 373 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.6884 (tt) REVERT: D 592 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8828 (mp) REVERT: D 603 MET cc_start: 0.8886 (ttp) cc_final: 0.8622 (ttp) REVERT: E 11 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7520 (mm-30) REVERT: E 51 MET cc_start: 0.8263 (mtt) cc_final: 0.7877 (mmm) REVERT: E 119 GLU cc_start: 0.7669 (tp30) cc_final: 0.7177 (tp30) REVERT: E 145 MET cc_start: 0.6061 (mmp) cc_final: 0.5856 (mmp) outliers start: 90 outliers final: 59 residues processed: 412 average time/residue: 0.3380 time to fit residues: 219.3681 Evaluate side-chains 398 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 331 time to evaluate : 2.436 ------------------------------------------------------------------------------- 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 502 LEU Chi-restraints excluded: chain A residue 592 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 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 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 410 MET 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 133 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 235 VAL 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 410 MET Chi-restraints excluded: chain C residue 420 ILE 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 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 367 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 592 LEU 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 48 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 112 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 185 optimal weight: 0.5980 chunk 241 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 116 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN C 522 HIS ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN D 464 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.163787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.126885 restraints weight = 28527.473| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.82 r_work: 0.3249 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22984 Z= 0.119 Angle : 0.598 9.407 30958 Z= 0.299 Chirality : 0.041 0.193 3424 Planarity : 0.005 0.090 3816 Dihedral : 13.190 141.835 4481 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.00 % Favored : 90.85 % Rotamer: Outliers : 3.63 % Allowed : 14.09 % Favored : 82.28 % 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: -0.78 (0.17), residues: 2623 helix: 0.82 (0.14), residues: 1546 sheet: -2.55 (0.49), residues: 84 loop : -2.56 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 593 HIS 0.004 0.000 HIS D 587 PHE 0.014 0.001 PHE B 553 TYR 0.021 0.001 TYR A 524 ARG 0.006 0.000 ARG D 140 Details of bonding type rmsd hydrogen bonds : bond 0.03222 ( 931) hydrogen bonds : angle 3.87420 ( 2709) covalent geometry : bond 0.00277 (22984) covalent geometry : angle 0.59798 (30958) *********************** 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 431 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 348 time to evaluate : 2.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ASN cc_start: 0.6760 (m-40) cc_final: 0.6469 (m110) REVERT: A 130 MET cc_start: 0.8115 (tpt) cc_final: 0.6956 (mtm) REVERT: A 174 ASN cc_start: 0.8701 (t0) cc_final: 0.8416 (t0) REVERT: A 188 ASP cc_start: 0.7432 (t0) cc_final: 0.7188 (t0) REVERT: A 211 PHE cc_start: 0.8021 (m-80) cc_final: 0.7727 (m-80) REVERT: A 331 MET cc_start: 0.8103 (tpt) cc_final: 0.7821 (tpt) REVERT: A 592 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8286 (mt) REVERT: B 98 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8480 (mm) REVERT: B 222 TYR cc_start: 0.7614 (OUTLIER) cc_final: 0.7092 (t80) REVERT: B 308 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9043 (mt) REVERT: B 381 LYS cc_start: 0.8081 (mttt) cc_final: 0.7792 (tttm) REVERT: B 421 LEU cc_start: 0.4712 (OUTLIER) cc_final: 0.4263 (tt) REVERT: B 528 MET cc_start: 0.7929 (tpp) cc_final: 0.7201 (tpp) REVERT: B 532 SER cc_start: 0.7900 (m) cc_final: 0.7669 (m) REVERT: C 136 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8304 (mp) REVERT: C 184 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8379 (mm-30) REVERT: C 215 MET cc_start: 0.9251 (mmm) cc_final: 0.8835 (tpt) REVERT: D 592 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8794 (mp) REVERT: E 51 MET cc_start: 0.8230 (mtt) cc_final: 0.7833 (mmm) REVERT: E 76 MET cc_start: 0.6398 (tpp) cc_final: 0.5827 (ptm) REVERT: E 119 GLU cc_start: 0.7709 (tp30) cc_final: 0.7226 (tp30) outliers start: 83 outliers final: 55 residues processed: 410 average time/residue: 0.3306 time to fit residues: 213.9871 Evaluate side-chains 393 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 331 time to evaluate : 2.206 ------------------------------------------------------------------------------- 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 502 LEU Chi-restraints excluded: chain A residue 592 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 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 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 474 MET 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 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 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 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 367 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain D residue 592 LEU 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 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: 9.9990 chunk 236 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 250 optimal weight: 5.9990 chunk 96 optimal weight: 0.0000 chunk 90 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 186 optimal weight: 9.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 HIS A 582 HIS ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 HIS C 640 ASN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.164720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.127901 restraints weight = 28535.928| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.82 r_work: 0.3267 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22984 Z= 0.110 Angle : 0.594 8.959 30958 Z= 0.296 Chirality : 0.041 0.189 3424 Planarity : 0.005 0.090 3816 Dihedral : 12.688 135.663 4481 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.34 % Favored : 90.51 % Rotamer: Outliers : 3.24 % Allowed : 15.62 % Favored : 81.14 % 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: -0.54 (0.17), residues: 2623 helix: 1.03 (0.14), residues: 1543 sheet: -2.45 (0.51), residues: 84 loop : -2.49 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 593 HIS 0.004 0.000 HIS D 587 PHE 0.017 0.001 PHE B 553 TYR 0.025 0.001 TYR A 524 ARG 0.005 0.000 ARG D 140 Details of bonding type rmsd hydrogen bonds : bond 0.03093 ( 931) hydrogen bonds : angle 3.82535 ( 2709) covalent geometry : bond 0.00254 (22984) covalent geometry : angle 0.59422 (30958) *********************** 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 429 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 355 time to evaluate : 2.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ASN cc_start: 0.6745 (m-40) cc_final: 0.6466 (m110) REVERT: A 130 MET cc_start: 0.7986 (tpt) cc_final: 0.6949 (mtm) REVERT: A 174 ASN cc_start: 0.8704 (t0) cc_final: 0.8406 (t0) REVERT: A 188 ASP cc_start: 0.7417 (t0) cc_final: 0.7198 (t0) REVERT: A 211 PHE cc_start: 0.8006 (m-80) cc_final: 0.7705 (m-80) REVERT: A 592 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8308 (mt) REVERT: B 98 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8442 (mm) REVERT: B 222 TYR cc_start: 0.7494 (OUTLIER) cc_final: 0.7193 (t80) REVERT: B 308 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9041 (mt) REVERT: B 381 LYS cc_start: 0.8022 (mttt) cc_final: 0.7772 (tttm) REVERT: B 421 LEU cc_start: 0.4864 (OUTLIER) cc_final: 0.4379 (tt) REVERT: B 528 MET cc_start: 0.7927 (tpp) cc_final: 0.7189 (tpp) REVERT: B 532 SER cc_start: 0.7913 (m) cc_final: 0.7692 (m) REVERT: C 136 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8260 (mp) REVERT: C 184 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8368 (mm-30) REVERT: C 215 MET cc_start: 0.9258 (mmm) cc_final: 0.8853 (tpt) REVERT: C 222 TYR cc_start: 0.7594 (OUTLIER) cc_final: 0.7282 (t80) REVERT: C 481 MET cc_start: 0.8596 (tpp) cc_final: 0.8199 (mmt) REVERT: D 308 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8458 (mp) REVERT: D 481 MET cc_start: 0.8745 (tpp) cc_final: 0.8355 (mmt) REVERT: D 592 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8780 (mp) REVERT: E 11 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7516 (mm-30) REVERT: E 51 MET cc_start: 0.8215 (mtt) cc_final: 0.7843 (mmm) outliers start: 74 outliers final: 54 residues processed: 407 average time/residue: 0.3273 time to fit residues: 210.5362 Evaluate side-chains 391 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 328 time to evaluate : 2.553 ------------------------------------------------------------------------------- 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 502 LEU Chi-restraints excluded: chain A residue 592 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 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 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 474 MET Chi-restraints excluded: chain B residue 546 ASN 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 210 THR 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 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 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 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 379 THR Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 592 LEU 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 Chi-restraints excluded: chain E residue 117 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 44 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 253 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 199 optimal weight: 7.9990 chunk 133 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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** C 217 ASN C 572 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 = 0.3804 r_free = 0.3804 target = 0.160463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.124761 restraints weight = 28887.645| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.92 r_work: 0.3169 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 22984 Z= 0.218 Angle : 0.689 9.726 30958 Z= 0.341 Chirality : 0.045 0.219 3424 Planarity : 0.005 0.095 3816 Dihedral : 13.347 146.568 4479 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.84 % Favored : 90.01 % Rotamer: Outliers : 3.59 % Allowed : 16.02 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.74 (0.17), residues: 2623 helix: 0.85 (0.14), residues: 1539 sheet: -2.59 (0.51), residues: 84 loop : -2.52 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 29 HIS 0.005 0.001 HIS D 587 PHE 0.020 0.002 PHE B 553 TYR 0.026 0.002 TYR A 524 ARG 0.005 0.001 ARG D 140 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 931) hydrogen bonds : angle 4.17670 ( 2709) covalent geometry : bond 0.00537 (22984) covalent geometry : angle 0.68877 (30958) *********************** 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 416 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 334 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.8674 (mtp) cc_final: 0.8447 (mtp) REVERT: A 130 MET cc_start: 0.8024 (tpt) cc_final: 0.6979 (mtm) REVERT: A 174 ASN cc_start: 0.8738 (t0) cc_final: 0.8459 (t0) REVERT: A 211 PHE cc_start: 0.8021 (m-80) cc_final: 0.7713 (m-80) REVERT: A 591 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7981 (mm-30) REVERT: B 80 GLU cc_start: 0.7999 (pm20) cc_final: 0.7789 (pm20) REVERT: B 98 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8342 (mm) REVERT: B 139 ARG cc_start: 0.8109 (mtt180) cc_final: 0.7613 (mpt-90) REVERT: B 308 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9049 (mt) REVERT: B 381 LYS cc_start: 0.8046 (mttt) cc_final: 0.7780 (tttm) REVERT: B 421 LEU cc_start: 0.4584 (OUTLIER) cc_final: 0.4168 (tt) REVERT: B 532 SER cc_start: 0.8013 (m) cc_final: 0.7798 (m) REVERT: C 136 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8230 (mp) REVERT: C 184 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8419 (mm-30) REVERT: C 215 MET cc_start: 0.9294 (mmm) cc_final: 0.8868 (tpt) REVERT: C 217 ASN cc_start: 0.8809 (OUTLIER) cc_final: 0.8567 (m-40) REVERT: D 308 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8491 (mp) REVERT: D 592 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8872 (mp) REVERT: D 603 MET cc_start: 0.9003 (ttp) cc_final: 0.8685 (ttp) REVERT: E 11 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7532 (mm-30) REVERT: E 51 MET cc_start: 0.8268 (mtt) cc_final: 0.7807 (mmm) outliers start: 82 outliers final: 57 residues processed: 394 average time/residue: 0.3339 time to fit residues: 207.0240 Evaluate side-chains 391 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 327 time to evaluate : 2.319 ------------------------------------------------------------------------------- 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 356 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 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 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 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 88 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 217 ASN 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 311 THR 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 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 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 379 THR Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 592 LEU 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 Chi-restraints excluded: chain E residue 117 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 109 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 78 optimal weight: 0.0970 chunk 180 optimal weight: 0.0040 chunk 174 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN C 267 GLN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN E 137 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.166837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.130457 restraints weight = 28610.345| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.84 r_work: 0.3273 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4578 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= 0.108 Angle : 0.613 9.829 30958 Z= 0.304 Chirality : 0.041 0.184 3424 Planarity : 0.005 0.091 3816 Dihedral : 12.526 131.460 4479 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.73 % Favored : 91.12 % Rotamer: Outliers : 2.71 % Allowed : 16.81 % Favored : 80.48 % 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: 1.11 (0.14), residues: 1542 sheet: -2.51 (0.51), residues: 86 loop : -2.39 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 593 HIS 0.006 0.000 HIS D 587 PHE 0.018 0.001 PHE B 553 TYR 0.028 0.001 TYR A 524 ARG 0.006 0.000 ARG D 140 Details of bonding type rmsd hydrogen bonds : bond 0.03106 ( 931) hydrogen bonds : angle 3.87978 ( 2709) covalent geometry : bond 0.00245 (22984) covalent geometry : angle 0.61255 (30958) *********************** 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 402 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 340 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7924 (tpt) cc_final: 0.6910 (mtm) REVERT: A 174 ASN cc_start: 0.8685 (t0) cc_final: 0.8373 (t0) REVERT: A 211 PHE cc_start: 0.7976 (m-80) cc_final: 0.7633 (m-80) REVERT: A 303 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7882 (mp0) REVERT: A 331 MET cc_start: 0.7942 (tpt) cc_final: 0.7637 (tpt) REVERT: B 80 GLU cc_start: 0.7876 (pm20) cc_final: 0.7222 (pm20) REVERT: B 98 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8329 (mm) REVERT: B 139 ARG cc_start: 0.8140 (mtt180) cc_final: 0.7680 (mpt-90) REVERT: B 222 TYR cc_start: 0.7410 (OUTLIER) cc_final: 0.7208 (t80) REVERT: B 308 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8966 (mt) REVERT: B 381 LYS cc_start: 0.7908 (mttt) cc_final: 0.7645 (tttm) REVERT: B 382 ASP cc_start: 0.7056 (p0) cc_final: 0.6533 (p0) REVERT: B 421 LEU cc_start: 0.4641 (OUTLIER) cc_final: 0.4150 (tt) REVERT: B 454 MET cc_start: 0.7751 (mtt) cc_final: 0.7475 (mtt) REVERT: B 532 SER cc_start: 0.8016 (m) cc_final: 0.7751 (m) REVERT: C 136 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8128 (mp) REVERT: C 184 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8339 (mm-30) REVERT: C 215 MET cc_start: 0.9344 (mmm) cc_final: 0.8935 (tpt) REVERT: C 217 ASN cc_start: 0.8770 (OUTLIER) cc_final: 0.8545 (m-40) REVERT: C 222 TYR cc_start: 0.7688 (OUTLIER) cc_final: 0.7282 (t80) REVERT: D 308 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8454 (mp) REVERT: D 403 GLU cc_start: 0.8131 (tp30) cc_final: 0.7790 (mm-30) REVERT: D 592 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8799 (mp) REVERT: E 11 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7526 (mm-30) REVERT: E 51 MET cc_start: 0.8101 (mtt) cc_final: 0.7756 (mmm) outliers start: 62 outliers final: 46 residues processed: 384 average time/residue: 0.3576 time to fit residues: 215.0629 Evaluate side-chains 388 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 333 time to evaluate : 2.457 ------------------------------------------------------------------------------- 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 356 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 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 222 TYR 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 546 ASN 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 217 ASN Chi-restraints excluded: chain C residue 222 TYR 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 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 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 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 379 THR Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 592 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 218 optimal weight: 2.9990 chunk 221 optimal weight: 7.9990 chunk 201 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 195 optimal weight: 10.0000 chunk 215 optimal weight: 8.9990 chunk 236 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 16 optimal weight: 0.0000 overall best weight: 0.7186 ------------------------------------------------------------------------------- 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** C 217 ASN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3866 r_free = 0.3866 target = 0.166334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.129898 restraints weight = 28589.604| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.82 r_work: 0.3274 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22984 Z= 0.103 Angle : 0.603 10.010 30958 Z= 0.299 Chirality : 0.041 0.195 3424 Planarity : 0.005 0.091 3816 Dihedral : 12.034 125.970 4479 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.00 % Favored : 90.85 % Rotamer: Outliers : 2.54 % Allowed : 17.24 % 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: -0.21 (0.17), residues: 2623 helix: 1.31 (0.14), residues: 1538 sheet: -2.51 (0.51), residues: 86 loop : -2.33 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 593 HIS 0.003 0.000 HIS C 587 PHE 0.022 0.001 PHE B 553 TYR 0.026 0.001 TYR A 524 ARG 0.005 0.000 ARG A 190 Details of bonding type rmsd hydrogen bonds : bond 0.02955 ( 931) hydrogen bonds : angle 3.84439 ( 2709) covalent geometry : bond 0.00229 (22984) covalent geometry : angle 0.60275 (30958) ********************** 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 400 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 342 time to evaluate : 3.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7948 (tpt) cc_final: 0.6904 (mtm) REVERT: A 174 ASN cc_start: 0.8686 (t0) cc_final: 0.8397 (t0) REVERT: A 188 ASP cc_start: 0.7353 (t0) cc_final: 0.7148 (t0) REVERT: A 211 PHE cc_start: 0.7986 (m-80) cc_final: 0.7660 (m-80) REVERT: A 303 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7931 (mp0) REVERT: A 373 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6357 (tt) REVERT: B 98 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8348 (mm) REVERT: B 139 ARG cc_start: 0.7980 (mtt180) cc_final: 0.7763 (mpt-90) REVERT: B 308 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8983 (mt) REVERT: B 382 ASP cc_start: 0.7062 (p0) cc_final: 0.6493 (p0) REVERT: B 421 LEU cc_start: 0.4130 (OUTLIER) cc_final: 0.3673 (tt) REVERT: B 454 MET cc_start: 0.7769 (mtt) cc_final: 0.7530 (mtt) REVERT: B 532 SER cc_start: 0.7973 (m) cc_final: 0.7744 (m) REVERT: C 136 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8151 (mp) REVERT: C 184 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8315 (mm-30) REVERT: C 217 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8414 (m-40) REVERT: C 222 TYR cc_start: 0.7533 (OUTLIER) cc_final: 0.7235 (t80) REVERT: D 134 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7876 (tpp-160) REVERT: D 308 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8415 (mp) REVERT: D 403 GLU cc_start: 0.8124 (tp30) cc_final: 0.7785 (mm-30) REVERT: D 481 MET cc_start: 0.8713 (tpp) cc_final: 0.8124 (mmt) REVERT: D 592 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8776 (mp) REVERT: E 11 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7619 (mm-30) REVERT: E 51 MET cc_start: 0.8019 (mtt) cc_final: 0.7765 (mmm) outliers start: 58 outliers final: 41 residues processed: 382 average time/residue: 0.4390 time to fit residues: 269.2460 Evaluate side-chains 381 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 330 time to evaluate : 3.834 ------------------------------------------------------------------------------- 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 356 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 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 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 546 ASN 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 217 ASN Chi-restraints excluded: chain C residue 222 TYR 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 373 LEU Chi-restraints excluded: chain C residue 420 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 379 THR Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 592 LEU 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 112 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: 9.9990 chunk 195 optimal weight: 8.9990 chunk 240 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 209 optimal weight: 5.9990 chunk 250 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN C 217 ASN C 267 GLN ** 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 = 0.3826 r_free = 0.3826 target = 0.162511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.124531 restraints weight = 28678.611| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.87 r_work: 0.3226 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22984 Z= 0.145 Angle : 0.640 10.168 30958 Z= 0.314 Chirality : 0.043 0.212 3424 Planarity : 0.005 0.091 3816 Dihedral : 12.207 124.583 4479 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.30 % Favored : 90.55 % Rotamer: Outliers : 2.63 % Allowed : 17.29 % 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: -0.27 (0.17), residues: 2623 helix: 1.25 (0.14), residues: 1541 sheet: -2.61 (0.51), residues: 86 loop : -2.34 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 593 HIS 0.005 0.001 HIS C 587 PHE 0.022 0.001 PHE B 553 TYR 0.026 0.001 TYR A 524 ARG 0.005 0.000 ARG A 190 Details of bonding type rmsd hydrogen bonds : bond 0.03326 ( 931) hydrogen bonds : angle 3.96724 ( 2709) covalent geometry : bond 0.00353 (22984) covalent geometry : angle 0.63951 (30958) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13983.00 seconds wall clock time: 244 minutes 2.28 seconds (14642.28 seconds total)