Starting phenix.real_space_refine on Sat Jul 4 16:39:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cuk_45936/07_2026/9cuk_45936.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cuk_45936/07_2026/9cuk_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_45936/07_2026/9cuk_45936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cuk_45936/07_2026/9cuk_45936.map" model { file = "/net/cci-nas-00/data/ceres_data/9cuk_45936/07_2026/9cuk_45936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cuk_45936/07_2026/9cuk_45936.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 346 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'CLR': 1, 'PCW': 11, 'Y01': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain breaks: 1 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-3': 8, 'PCW:plan-4': 8, 'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 91 Chain: "B" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 346 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'CLR': 1, 'PCW': 11, 'Y01': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain breaks: 2 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-3': 8, 'PCW:plan-4': 8, 'PCW:plan-2': 2} 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-3': 7, 'PCW:plan-4': 7, 'PCW:plan-2': 1} 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-3': 8, 'PCW:plan-4': 8, 'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 91 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' CA': 4} Chain breaks: 4 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.96, per 1000 atoms: 0.22 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: 1.76 Conformation dependent library (CDL) restraints added in 1.1 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: 0.71 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: 3.50 Time building geometry restraints manager: 2.37 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.280 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.009 0.001 ARG B 641 TYR 0.026 0.002 TYR A 547 PHE 0.034 0.003 PHE C 508 TRP 0.021 0.003 TRP B 613 HIS 0.011 0.002 HIS B 522 Details of bonding type rmsd/Z covalent geometry : bond 0.01272 / 0.59 (22984) covalent geometry : angle 1.37402 / 0.69 (30958) hydrogen bonds : bond 0.33124 / 21.32 ( 931) hydrogen bonds : angle 9.95960 / 6.97 ( 2709) *********************** 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 : 0.705 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: 0.6176 (mmp) outliers start: 10 outliers final: 5 residues processed: 624 average time/residue: 0.1572 time to fit residues: 148.9238 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 : 0.865 ------------------------------------------------------------------------------- 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 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 0.6980 chunk 258 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 53 ASN E 111 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.164614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.126718 restraints weight = 28895.138| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.09 r_work: 0.3269 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22984 Z= 0.144 Angle : 0.688 9.678 30958 Z= 0.351 Chirality : 0.043 0.210 3424 Planarity : 0.006 0.091 3816 Dihedral : 16.684 178.962 4483 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.69 % Favored : 91.16 % Rotamer: Outliers : 2.54 % Allowed : 10.11 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.77 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.84 (0.14), residues: 2623 helix: -2.03 (0.11), residues: 1571 sheet: -2.78 (0.49), residues: 84 loop : -3.23 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 470 TYR 0.021 0.001 TYR A 524 PHE 0.014 0.001 PHE C 508 TRP 0.011 0.001 TRP C 695 HIS 0.006 0.001 HIS D 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (22984) covalent geometry : angle 0.68846 / 0.35 (30958) hydrogen bonds : bond 0.04971 / 3.22 ( 931) hydrogen bonds : angle 4.62686 / 3.25 ( 2709) *********************** 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 490 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 432 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8346 (ttmt) cc_final: 0.7600 (mmtp) REVERT: A 91 ASN cc_start: 0.6784 (m-40) cc_final: 0.6572 (m110) REVERT: A 174 ASN cc_start: 0.8452 (t0) cc_final: 0.8228 (t0) REVERT: A 211 PHE cc_start: 0.7939 (m-80) cc_final: 0.7454 (m-80) REVERT: A 216 TYR cc_start: 0.8639 (t80) cc_final: 0.8384 (t80) REVERT: A 303 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7903 (pt0) REVERT: A 306 GLN cc_start: 0.8468 (mt0) cc_final: 0.7974 (mm-40) REVERT: A 331 MET cc_start: 0.7783 (tpt) cc_final: 0.7396 (tpt) REVERT: A 435 MET cc_start: 0.7815 (mmt) cc_final: 0.7568 (mmt) REVERT: A 491 MET cc_start: 0.8641 (ttt) cc_final: 0.8391 (ttm) REVERT: A 616 SER cc_start: 0.8956 (m) cc_final: 0.8699 (p) REVERT: A 618 ILE cc_start: 0.8805 (mp) cc_final: 0.8558 (mm) REVERT: B 59 GLN cc_start: 0.8014 (tt0) cc_final: 0.7618 (mp10) REVERT: B 168 SER cc_start: 0.8288 (m) cc_final: 0.7864 (p) REVERT: B 230 GLN cc_start: 0.6386 (tp-100) cc_final: 0.5946 (mp-120) REVERT: B 371 LYS cc_start: 0.7477 (ptmt) cc_final: 0.7262 (ptpp) REVERT: B 381 LYS cc_start: 0.7914 (mttt) cc_final: 0.7423 (tttm) REVERT: B 485 MET cc_start: 0.8085 (mmt) cc_final: 0.7789 (mmt) REVERT: B 532 SER cc_start: 0.8331 (m) cc_final: 0.8054 (m) REVERT: B 587 HIS cc_start: 0.7577 (OUTLIER) cc_final: 0.6990 (m90) REVERT: C 62 ASN cc_start: 0.7362 (m110) cc_final: 0.7012 (p0) REVERT: C 63 LYS cc_start: 0.8208 (mtpt) cc_final: 0.7816 (mtpt) REVERT: C 104 GLU cc_start: 0.8356 (mp0) cc_final: 0.7787 (mp0) REVERT: C 108 GLU cc_start: 0.8093 (pt0) cc_final: 0.7700 (pp20) REVERT: C 184 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8326 (mm-30) REVERT: C 300 LYS cc_start: 0.8675 (mptt) cc_final: 0.8461 (mmmt) REVERT: C 628 ARG cc_start: 0.8305 (ptp-170) cc_final: 0.7935 (mtm-85) REVERT: D 80 GLU cc_start: 0.8138 (pm20) cc_final: 0.7686 (pm20) REVERT: D 294 GLU cc_start: 0.8230 (mp0) cc_final: 0.7722 (mp0) REVERT: D 303 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7651 (mp0) REVERT: D 373 LEU cc_start: 0.6596 (OUTLIER) cc_final: 0.6097 (tt) REVERT: D 519 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6756 (mm-30) REVERT: D 592 LEU cc_start: 0.8499 (mm) cc_final: 0.8231 (mp) REVERT: E 11 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7661 (tp30) REVERT: E 28 THR cc_start: 0.7809 (OUTLIER) cc_final: 0.7605 (p) REVERT: E 51 MET cc_start: 0.8400 (mtt) cc_final: 0.7810 (mmm) REVERT: E 76 MET cc_start: 0.6677 (tpp) cc_final: 0.6062 (ptm) REVERT: E 109 MET cc_start: 0.6964 (mmt) cc_final: 0.6725 (mmm) REVERT: E 119 GLU cc_start: 0.7255 (tp30) cc_final: 0.6821 (tp30) outliers start: 58 outliers final: 31 residues processed: 470 average time/residue: 0.1338 time to fit residues: 99.1035 Evaluate side-chains 393 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 359 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 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 28 THR 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 111 optimal weight: 0.6980 chunk 169 optimal weight: 0.6980 chunk 231 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 160 optimal weight: 20.0000 chunk 202 optimal weight: 0.6980 chunk 157 optimal weight: 7.9990 chunk 69 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 GLN A 258 HIS A 267 GLN B 206 GLN ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN C 214 GLN C 522 HIS C 640 ASN C 694 ASN D 174 ASN D 522 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.166117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.125601 restraints weight = 28955.171| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.43 r_work: 0.3265 rms_B_bonded: 3.03 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: 0.8268 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22984 Z= 0.113 Angle : 0.610 8.286 30958 Z= 0.309 Chirality : 0.041 0.199 3424 Planarity : 0.005 0.092 3816 Dihedral : 14.957 163.781 4483 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.07 % Favored : 90.77 % Rotamer: Outliers : 3.37 % Allowed : 11.90 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.77 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.16), residues: 2623 helix: -0.60 (0.13), residues: 1563 sheet: -2.52 (0.53), residues: 84 loop : -2.94 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 643 TYR 0.018 0.001 TYR C 216 PHE 0.014 0.001 PHE B 553 TRP 0.008 0.001 TRP C 613 HIS 0.005 0.001 HIS D 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (22984) covalent geometry : angle 0.61037 / 0.31 (30958) hydrogen bonds : bond 0.03699 / 2.41 ( 931) hydrogen bonds : angle 4.07141 / 2.88 ( 2709) *********************** 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 469 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 392 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8275 (ttmt) cc_final: 0.7508 (mmtp) REVERT: A 91 ASN cc_start: 0.6647 (m-40) cc_final: 0.6416 (m110) REVERT: A 130 MET cc_start: 0.8026 (tpt) cc_final: 0.6578 (ptt) REVERT: A 174 ASN cc_start: 0.8480 (t0) cc_final: 0.8194 (t0) REVERT: A 211 PHE cc_start: 0.7880 (m-80) cc_final: 0.7445 (m-80) REVERT: A 216 TYR cc_start: 0.8547 (t80) cc_final: 0.8344 (t80) REVERT: A 255 MET cc_start: 0.8845 (mmm) cc_final: 0.8612 (mmm) REVERT: A 306 GLN cc_start: 0.8388 (mt0) cc_final: 0.7805 (mm-40) REVERT: A 345 MET cc_start: 0.8315 (mtm) cc_final: 0.8067 (mtp) REVERT: A 421 LEU cc_start: 0.6311 (OUTLIER) cc_final: 0.6084 (tt) REVERT: A 435 MET cc_start: 0.7698 (mmt) cc_final: 0.7469 (mmt) REVERT: A 618 ILE cc_start: 0.8693 (mp) cc_final: 0.8383 (mm) REVERT: A 628 ARG cc_start: 0.8152 (mtp85) cc_final: 0.7851 (mtp85) REVERT: B 59 GLN cc_start: 0.8078 (tt0) cc_final: 0.7612 (mp10) REVERT: B 129 ASN cc_start: 0.7975 (t0) cc_final: 0.7371 (t0) REVERT: B 139 ARG cc_start: 0.7911 (mmt180) cc_final: 0.7634 (mtt180) REVERT: B 168 SER cc_start: 0.8283 (m) cc_final: 0.7862 (p) REVERT: B 230 GLN cc_start: 0.6072 (OUTLIER) cc_final: 0.5841 (mp-120) REVERT: B 363 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7668 (pmt100) REVERT: B 381 LYS cc_start: 0.7805 (mttt) cc_final: 0.7345 (tttm) REVERT: B 405 PRO cc_start: 0.7855 (Cg_exo) cc_final: 0.7607 (Cg_endo) REVERT: B 421 LEU cc_start: 0.4307 (OUTLIER) cc_final: 0.3964 (tt) REVERT: B 448 SER cc_start: 0.8384 (p) cc_final: 0.8175 (t) REVERT: B 528 MET cc_start: 0.7794 (tpp) cc_final: 0.6974 (tpp) REVERT: B 532 SER cc_start: 0.8237 (m) cc_final: 0.7884 (m) REVERT: B 587 HIS cc_start: 0.7561 (OUTLIER) cc_final: 0.6916 (m90) REVERT: C 61 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7845 (mm) REVERT: C 104 GLU cc_start: 0.8288 (mp0) cc_final: 0.7720 (pm20) REVERT: C 108 GLU cc_start: 0.8157 (pt0) cc_final: 0.7950 (pp20) REVERT: C 136 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7826 (mp) REVERT: C 184 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8372 (mm-30) REVERT: C 300 LYS cc_start: 0.8643 (mptt) cc_final: 0.8400 (mmmt) REVERT: C 628 ARG cc_start: 0.8292 (ptp-170) cc_final: 0.7886 (mtm-85) REVERT: D 80 GLU cc_start: 0.8115 (pm20) cc_final: 0.7567 (pm20) REVERT: D 90 ASP cc_start: 0.7784 (t0) cc_final: 0.7448 (t0) REVERT: D 96 MET cc_start: 0.8563 (mmm) cc_final: 0.8259 (mmm) REVERT: D 139 ARG cc_start: 0.7681 (mmt180) cc_final: 0.7428 (tpp80) REVERT: D 294 GLU cc_start: 0.8362 (mp0) cc_final: 0.7823 (mp0) REVERT: D 303 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7574 (mp0) REVERT: D 368 LEU cc_start: 0.8095 (pt) cc_final: 0.7804 (tt) REVERT: D 373 LEU cc_start: 0.6582 (OUTLIER) cc_final: 0.6021 (tt) REVERT: D 519 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6783 (mm-30) REVERT: D 592 LEU cc_start: 0.8339 (mm) cc_final: 0.8086 (mp) REVERT: E 51 MET cc_start: 0.8270 (mtt) cc_final: 0.7805 (mmt) REVERT: E 119 GLU cc_start: 0.7314 (tp30) cc_final: 0.6785 (tp30) outliers start: 77 outliers final: 37 residues processed: 447 average time/residue: 0.1398 time to fit residues: 98.6915 Evaluate side-chains 400 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 355 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 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 367 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain E residue 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 174 optimal weight: 8.9990 chunk 240 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 48 optimal weight: 0.2980 chunk 16 optimal weight: 8.9990 chunk 221 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 230 optimal weight: 4.9990 chunk 179 optimal weight: 0.9990 chunk 211 optimal weight: 10.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN B 74 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 C 426 HIS C 582 HIS D 174 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.164640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.127294 restraints weight = 28942.307| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.85 r_work: 0.3248 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22984 Z= 0.143 Angle : 0.625 8.640 30958 Z= 0.313 Chirality : 0.042 0.199 3424 Planarity : 0.005 0.092 3816 Dihedral : 14.153 154.017 4481 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.26 % Favored : 90.58 % Rotamer: Outliers : 3.89 % Allowed : 12.65 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.83 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.16), residues: 2623 helix: 0.07 (0.13), residues: 1566 sheet: -2.47 (0.51), residues: 84 loop : -2.76 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 190 TYR 0.020 0.001 TYR A 524 PHE 0.016 0.001 PHE B 553 TRP 0.011 0.001 TRP D 613 HIS 0.005 0.001 HIS D 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (22984) covalent geometry : angle 0.62457 / 0.31 (30958) hydrogen bonds : bond 0.03632 / 2.37 ( 931) hydrogen bonds : angle 4.03143 / 2.86 ( 2709) *********************** 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 452 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 363 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8626 (ttmt) cc_final: 0.7716 (mmtp) REVERT: A 91 ASN cc_start: 0.6807 (m-40) cc_final: 0.6546 (m110) REVERT: A 130 MET cc_start: 0.8145 (tpt) cc_final: 0.6805 (ptt) REVERT: A 174 ASN cc_start: 0.8647 (t0) cc_final: 0.8370 (t0) REVERT: A 211 PHE cc_start: 0.8028 (m-80) cc_final: 0.7693 (m-80) REVERT: A 306 GLN cc_start: 0.8424 (mt0) cc_final: 0.8218 (mm-40) REVERT: A 345 MET cc_start: 0.8461 (mtm) cc_final: 0.8215 (mtp) REVERT: A 592 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8243 (mt) REVERT: A 618 ILE cc_start: 0.9130 (mp) cc_final: 0.8769 (mm) REVERT: B 222 TYR cc_start: 0.7553 (OUTLIER) cc_final: 0.6790 (t80) REVERT: B 363 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7501 (pmt100) REVERT: B 381 LYS cc_start: 0.8075 (mttt) cc_final: 0.7774 (tttm) REVERT: B 528 MET cc_start: 0.7931 (tpp) cc_final: 0.7240 (tpp) REVERT: B 532 SER cc_start: 0.7883 (m) cc_final: 0.7660 (m) REVERT: C 104 GLU cc_start: 0.8295 (mp0) cc_final: 0.7852 (pm20) REVERT: C 136 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8301 (mp) REVERT: C 184 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8382 (mm-30) REVERT: C 215 MET cc_start: 0.9242 (mmm) cc_final: 0.8805 (tpt) REVERT: C 571 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8456 (mp) REVERT: D 96 MET cc_start: 0.8719 (mmm) cc_final: 0.8506 (mmm) REVERT: D 373 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.6897 (tt) REVERT: D 592 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8706 (mp) REVERT: D 603 MET cc_start: 0.8877 (ttp) cc_final: 0.8656 (ttp) REVERT: E 11 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7583 (mm-30) REVERT: E 51 MET cc_start: 0.8239 (mtt) cc_final: 0.7762 (mmm) REVERT: E 76 MET cc_start: 0.6530 (tpp) cc_final: 0.5972 (ptm) REVERT: E 119 GLU cc_start: 0.7647 (tp30) cc_final: 0.7266 (tp30) outliers start: 89 outliers final: 55 residues processed: 424 average time/residue: 0.1351 time to fit residues: 91.1554 Evaluate side-chains 394 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 332 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 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 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 269 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 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 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 112 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 96 optimal weight: 7.9990 chunk 225 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 197 optimal weight: 9.9990 chunk 235 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 213 optimal weight: 0.8980 chunk 146 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 GLN A 267 GLN C 174 ASN D 174 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.164382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.127381 restraints weight = 28615.285| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.86 r_work: 0.3223 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22984 Z= 0.135 Angle : 0.608 8.839 30958 Z= 0.304 Chirality : 0.042 0.201 3424 Planarity : 0.005 0.089 3816 Dihedral : 13.591 146.679 4481 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.45 % Favored : 90.39 % Rotamer: Outliers : 3.89 % Allowed : 13.09 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.17), residues: 2623 helix: 0.51 (0.13), residues: 1553 sheet: -2.51 (0.50), residues: 84 loop : -2.60 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 190 TYR 0.020 0.001 TYR A 524 PHE 0.015 0.001 PHE B 553 TRP 0.007 0.001 TRP D 613 HIS 0.005 0.001 HIS D 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (22984) covalent geometry : angle 0.60836 / 0.30 (30958) hydrogen bonds : bond 0.03408 / 2.23 ( 931) hydrogen bonds : angle 3.93248 / 2.78 ( 2709) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 354 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8672 (ttmt) cc_final: 0.7753 (mmtp) REVERT: A 91 ASN cc_start: 0.6851 (m-40) cc_final: 0.6575 (m110) REVERT: A 130 MET cc_start: 0.8181 (tpt) cc_final: 0.6958 (mtm) REVERT: A 174 ASN cc_start: 0.8676 (t0) cc_final: 0.8409 (t0) REVERT: A 188 ASP cc_start: 0.7455 (t0) cc_final: 0.7229 (t0) REVERT: A 211 PHE cc_start: 0.8007 (m-80) cc_final: 0.7684 (m-80) REVERT: A 331 MET cc_start: 0.8151 (tpt) cc_final: 0.7872 (tpt) REVERT: A 345 MET cc_start: 0.8434 (mtm) cc_final: 0.8177 (mtp) REVERT: A 421 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6415 (tt) REVERT: A 592 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8272 (mt) REVERT: B 98 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8438 (mm) REVERT: B 222 TYR cc_start: 0.7553 (OUTLIER) cc_final: 0.6927 (t80) REVERT: B 363 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.7402 (pmt100) REVERT: B 381 LYS cc_start: 0.8078 (mttt) cc_final: 0.7803 (tttm) REVERT: B 421 LEU cc_start: 0.5060 (OUTLIER) cc_final: 0.4563 (tt) REVERT: B 528 MET cc_start: 0.7910 (tpp) cc_final: 0.7206 (tpp) REVERT: B 532 SER cc_start: 0.7921 (m) cc_final: 0.7698 (m) REVERT: C 118 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8489 (tt0) REVERT: C 136 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8330 (mp) REVERT: C 184 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8362 (mm-30) REVERT: C 215 MET cc_start: 0.9262 (mmm) cc_final: 0.8844 (tpt) REVERT: C 297 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8418 (mm) REVERT: C 571 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8321 (mp) REVERT: D 373 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.6898 (tt) REVERT: D 592 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8716 (mp) REVERT: E 11 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7542 (mm-30) REVERT: E 51 MET cc_start: 0.8242 (mtt) cc_final: 0.7887 (mmm) REVERT: E 119 GLU cc_start: 0.7694 (tp30) cc_final: 0.7281 (tp30) outliers start: 89 outliers final: 54 residues processed: 417 average time/residue: 0.1415 time to fit residues: 92.7843 Evaluate side-chains 394 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 328 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 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 421 LEU Chi-restraints excluded: chain B residue 546 ASN Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 118 GLN 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 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 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 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 491 MET Chi-restraints excluded: chain D residue 571 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 121 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 200 optimal weight: 0.5980 chunk 152 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 582 HIS B 257 GLN C 267 GLN D 174 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.168806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.132329 restraints weight = 28561.438| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.83 r_work: 0.3310 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22984 Z= 0.100 Angle : 0.576 7.704 30958 Z= 0.290 Chirality : 0.040 0.183 3424 Planarity : 0.005 0.091 3816 Dihedral : 12.853 139.250 4481 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.15 % Favored : 90.70 % Rotamer: Outliers : 3.24 % Allowed : 14.53 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.17), residues: 2623 helix: 0.91 (0.14), residues: 1549 sheet: -2.48 (0.49), residues: 84 loop : -2.55 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 140 TYR 0.021 0.001 TYR A 524 PHE 0.015 0.001 PHE B 553 TRP 0.009 0.001 TRP D 593 HIS 0.004 0.000 HIS D 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (22984) covalent geometry : angle 0.57625 / 0.29 (30958) hydrogen bonds : bond 0.02935 / 1.92 ( 931) hydrogen bonds : angle 3.77016 / 2.68 ( 2709) *********************** 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 446 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 372 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8630 (ttmt) cc_final: 0.7720 (mmtp) REVERT: A 91 ASN cc_start: 0.6707 (m-40) cc_final: 0.6450 (m110) REVERT: A 130 MET cc_start: 0.8075 (tpt) cc_final: 0.6893 (mtm) REVERT: A 174 ASN cc_start: 0.8655 (t0) cc_final: 0.8364 (t0) REVERT: A 211 PHE cc_start: 0.7969 (m-80) cc_final: 0.7635 (m-80) REVERT: A 331 MET cc_start: 0.7894 (tpt) cc_final: 0.7580 (tpt) REVERT: A 373 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6287 (tt) REVERT: A 421 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6349 (tt) REVERT: B 98 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8258 (mm) REVERT: B 139 ARG cc_start: 0.8042 (mtt180) cc_final: 0.7781 (mmt90) REVERT: B 222 TYR cc_start: 0.7405 (OUTLIER) cc_final: 0.6958 (t80) REVERT: B 381 LYS cc_start: 0.8028 (mttt) cc_final: 0.7740 (tttm) REVERT: B 421 LEU cc_start: 0.4572 (OUTLIER) cc_final: 0.4139 (tt) REVERT: B 528 MET cc_start: 0.7841 (tpp) cc_final: 0.7132 (tpp) REVERT: B 532 SER cc_start: 0.7987 (m) cc_final: 0.7747 (m) REVERT: C 78 MET cc_start: 0.7955 (mmt) cc_final: 0.7548 (mmp) REVERT: C 136 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8180 (mp) REVERT: C 215 MET cc_start: 0.9285 (mmm) cc_final: 0.8875 (tpt) REVERT: D 373 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6719 (tt) REVERT: E 11 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7454 (mm-30) REVERT: E 37 ARG cc_start: 0.7715 (mpp80) cc_final: 0.7409 (mpp80) REVERT: E 51 MET cc_start: 0.8142 (mtt) cc_final: 0.7790 (mmm) REVERT: E 74 ARG cc_start: 0.7973 (mmm-85) cc_final: 0.7739 (mtt90) REVERT: E 76 MET cc_start: 0.6424 (tpp) cc_final: 0.5826 (ptm) outliers start: 74 outliers final: 42 residues processed: 422 average time/residue: 0.1374 time to fit residues: 91.6458 Evaluate side-chains 389 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 340 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 98 LEU 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 367 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 546 ASN Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain 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 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 410 MET Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 427 VAL 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 174 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 631 LEU Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 48 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 125 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 237 optimal weight: 5.9990 chunk 235 optimal weight: 0.3980 chunk 87 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN C 640 ASN D 174 ASN ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.159846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.118138 restraints weight = 29027.215| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.49 r_work: 0.3167 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 22984 Z= 0.193 Angle : 0.665 7.633 30958 Z= 0.332 Chirality : 0.044 0.212 3424 Planarity : 0.005 0.094 3816 Dihedral : 13.331 145.225 4479 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.87 % Favored : 89.97 % Rotamer: Outliers : 3.37 % Allowed : 15.19 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.17), residues: 2623 helix: 0.83 (0.14), residues: 1545 sheet: -2.55 (0.51), residues: 84 loop : -2.54 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 355 TYR 0.025 0.002 TYR A 524 PHE 0.021 0.002 PHE E 65 TRP 0.008 0.001 TRP B 29 HIS 0.005 0.001 HIS D 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.19 (22984) covalent geometry : angle 0.66545 / 0.33 (30958) hydrogen bonds : bond 0.03855 / 2.50 ( 931) hydrogen bonds : angle 4.08973 / 2.89 ( 2709) *********************** 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 411 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 334 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.8048 (tpt) cc_final: 0.6745 (mtm) REVERT: A 174 ASN cc_start: 0.8691 (t0) cc_final: 0.8392 (t0) REVERT: A 211 PHE cc_start: 0.7863 (m-80) cc_final: 0.7383 (m-80) REVERT: A 331 MET cc_start: 0.7594 (tpt) cc_final: 0.7307 (tpt) REVERT: A 421 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6225 (tt) REVERT: A 628 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7669 (mtp85) REVERT: B 98 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8063 (mm) REVERT: B 139 ARG cc_start: 0.8182 (mtt180) cc_final: 0.7688 (mpt-90) REVERT: B 222 TYR cc_start: 0.7276 (OUTLIER) cc_final: 0.6987 (t80) REVERT: B 308 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8629 (mt) REVERT: B 381 LYS cc_start: 0.7528 (mttt) cc_final: 0.7173 (tttm) REVERT: B 421 LEU cc_start: 0.4880 (OUTLIER) cc_final: 0.4411 (tt) REVERT: B 532 SER cc_start: 0.8225 (m) cc_final: 0.7961 (m) REVERT: C 118 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8279 (tt0) REVERT: C 136 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7749 (mp) REVERT: C 215 MET cc_start: 0.9136 (mmm) cc_final: 0.8724 (tpt) REVERT: D 373 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6251 (tt) REVERT: D 587 HIS cc_start: 0.7320 (t70) cc_final: 0.7113 (t70) REVERT: E 11 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7307 (mm-30) REVERT: E 51 MET cc_start: 0.8136 (mtt) cc_final: 0.7620 (mmm) outliers start: 77 outliers final: 53 residues processed: 389 average time/residue: 0.1355 time to fit residues: 83.6761 Evaluate side-chains 385 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 323 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 408 PHE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain A residue 628 ARG 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 307 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 546 ASN Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 118 GLN 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 222 TYR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 363 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 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 174 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 397 ILE 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 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 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 59 optimal weight: 9.9990 chunk 248 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 196 optimal weight: 0.9980 chunk 138 optimal weight: 8.9990 chunk 231 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 127 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 GLN A 267 GLN ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 HIS C 572 ASN D 174 ASN D 464 ASN ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.160822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.121573 restraints weight = 28813.584| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.16 r_work: 0.3178 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22984 Z= 0.180 Angle : 0.652 11.062 30958 Z= 0.325 Chirality : 0.044 0.208 3424 Planarity : 0.005 0.091 3816 Dihedral : 13.250 142.364 4479 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.45 % Favored : 90.39 % Rotamer: Outliers : 3.28 % Allowed : 15.75 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.17), residues: 2623 helix: 0.85 (0.14), residues: 1543 sheet: -2.61 (0.50), residues: 84 loop : -2.47 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 74 TYR 0.027 0.001 TYR A 524 PHE 0.021 0.001 PHE D 434 TRP 0.010 0.001 TRP D 593 HIS 0.005 0.001 HIS D 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.18 (22984) covalent geometry : angle 0.65237 / 0.32 (30958) hydrogen bonds : bond 0.03676 / 2.37 ( 931) hydrogen bonds : angle 4.04868 / 2.87 ( 2709) *********************** 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 404 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 329 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.7979 (tpt) cc_final: 0.6788 (mtm) REVERT: A 174 ASN cc_start: 0.8704 (t0) cc_final: 0.8398 (t0) REVERT: A 211 PHE cc_start: 0.7898 (m-80) cc_final: 0.7442 (m-80) REVERT: A 297 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.8028 (tp) REVERT: A 421 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.6217 (tt) REVERT: A 591 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7429 (mm-30) REVERT: B 98 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8176 (mm) REVERT: B 139 ARG cc_start: 0.8157 (mtt180) cc_final: 0.7874 (mpt-90) REVERT: B 308 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8623 (mt) REVERT: B 381 LYS cc_start: 0.7658 (mttt) cc_final: 0.7247 (tttm) REVERT: B 421 LEU cc_start: 0.4216 (OUTLIER) cc_final: 0.3783 (tt) REVERT: B 528 MET cc_start: 0.7866 (tpp) cc_final: 0.7045 (tpp) REVERT: B 532 SER cc_start: 0.8203 (m) cc_final: 0.7894 (m) REVERT: C 35 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7701 (tm-30) REVERT: C 136 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7769 (mp) REVERT: C 215 MET cc_start: 0.9166 (mmm) cc_final: 0.8766 (tpt) REVERT: D 373 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6253 (tt) REVERT: D 587 HIS cc_start: 0.7216 (t70) cc_final: 0.7011 (t70) REVERT: D 604 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7433 (mm) REVERT: E 11 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7339 (mm-30) REVERT: E 51 MET cc_start: 0.8100 (mtt) cc_final: 0.7612 (mmm) REVERT: E 119 GLU cc_start: 0.7225 (mp0) cc_final: 0.6896 (tt0) outliers start: 75 outliers final: 55 residues processed: 381 average time/residue: 0.1333 time to fit residues: 80.5870 Evaluate side-chains 381 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 318 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 274 THR Chi-restraints excluded: chain A residue 297 ILE 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 421 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 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 136 LEU Chi-restraints excluded: chain C residue 222 TYR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 363 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 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 367 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 604 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 89 optimal weight: 0.0970 chunk 259 optimal weight: 9.9990 chunk 193 optimal weight: 6.9990 chunk 228 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 121 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 244 optimal weight: 8.9990 chunk 249 optimal weight: 10.0000 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.161459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.121528 restraints weight = 28937.687| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.31 r_work: 0.3190 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22984 Z= 0.155 Angle : 0.644 10.543 30958 Z= 0.319 Chirality : 0.043 0.204 3424 Planarity : 0.005 0.091 3816 Dihedral : 13.011 138.722 4479 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.03 % Favored : 89.82 % Rotamer: Outliers : 3.24 % Allowed : 15.97 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.17), residues: 2623 helix: 0.94 (0.14), residues: 1537 sheet: -2.55 (0.51), residues: 84 loop : -2.43 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 140 TYR 0.027 0.001 TYR A 524 PHE 0.019 0.001 PHE B 553 TRP 0.010 0.001 TRP D 593 HIS 0.005 0.001 HIS D 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.15 (22984) covalent geometry : angle 0.64445 / 0.32 (30958) hydrogen bonds : bond 0.03521 / 2.28 ( 931) hydrogen bonds : angle 4.02612 / 2.86 ( 2709) *********************** 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 408 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 334 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7975 (tpt) cc_final: 0.6797 (mtm) REVERT: A 174 ASN cc_start: 0.8682 (t0) cc_final: 0.8391 (t0) REVERT: A 211 PHE cc_start: 0.7879 (m-80) cc_final: 0.7403 (m-80) REVERT: A 297 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.8033 (tp) REVERT: A 421 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6215 (tt) REVERT: A 591 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7524 (mm-30) REVERT: B 80 GLU cc_start: 0.7786 (pm20) cc_final: 0.7439 (pm20) REVERT: B 98 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8206 (mm) REVERT: B 308 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8622 (mt) REVERT: B 381 LYS cc_start: 0.7600 (mttt) cc_final: 0.7242 (tttm) REVERT: B 421 LEU cc_start: 0.4557 (OUTLIER) cc_final: 0.3996 (tt) REVERT: B 528 MET cc_start: 0.7876 (tpp) cc_final: 0.7051 (tpp) REVERT: B 532 SER cc_start: 0.8183 (m) cc_final: 0.7874 (m) REVERT: C 136 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7747 (mp) REVERT: C 215 MET cc_start: 0.9179 (mmm) cc_final: 0.8765 (tpt) REVERT: C 217 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.7939 (m-40) REVERT: C 481 MET cc_start: 0.8779 (tpp) cc_final: 0.8365 (mmt) REVERT: D 80 GLU cc_start: 0.7767 (pm20) cc_final: 0.7461 (pm20) REVERT: D 373 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6223 (tt) REVERT: D 403 GLU cc_start: 0.8241 (tp30) cc_final: 0.7757 (mm-30) REVERT: D 604 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7371 (mm) REVERT: D 637 GLN cc_start: 0.7992 (pt0) cc_final: 0.7781 (pm20) REVERT: E 11 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7342 (mm-30) REVERT: E 51 MET cc_start: 0.8019 (mtt) cc_final: 0.7579 (mmm) REVERT: E 76 MET cc_start: 0.6483 (tpp) cc_final: 0.5876 (ptm) REVERT: E 119 GLU cc_start: 0.7213 (mp0) cc_final: 0.6904 (tt0) outliers start: 74 outliers final: 60 residues processed: 382 average time/residue: 0.1388 time to fit residues: 83.3994 Evaluate side-chains 393 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 324 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 235 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 297 ILE 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 421 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 546 ASN Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 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 269 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 363 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 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 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 397 ILE 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 571 LEU Chi-restraints excluded: chain D residue 604 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 125 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 145 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 112 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 182 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 GLN ** 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 = 0.3829 r_free = 0.3829 target = 0.162092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.121211 restraints weight = 28927.043| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.50 r_work: 0.3195 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22984 Z= 0.145 Angle : 0.644 12.011 30958 Z= 0.319 Chirality : 0.043 0.200 3424 Planarity : 0.005 0.091 3816 Dihedral : 12.829 135.774 4479 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.34 % Favored : 90.51 % Rotamer: Outliers : 2.93 % Allowed : 16.54 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.17), residues: 2623 helix: 0.98 (0.14), residues: 1539 sheet: -2.60 (0.51), residues: 86 loop : -2.37 (0.20), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 140 TYR 0.027 0.001 TYR A 524 PHE 0.022 0.001 PHE D 434 TRP 0.011 0.001 TRP D 593 HIS 0.003 0.001 HIS D 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (22984) covalent geometry : angle 0.64437 / 0.32 (30958) hydrogen bonds : bond 0.03444 / 2.23 ( 931) hydrogen bonds : angle 4.00808 / 2.85 ( 2709) ********************** 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: 67 poor density : 333 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7973 (tpt) cc_final: 0.6750 (mtm) REVERT: A 174 ASN cc_start: 0.8668 (t0) cc_final: 0.8392 (t0) REVERT: A 211 PHE cc_start: 0.7851 (m-80) cc_final: 0.7369 (m-80) REVERT: A 303 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7674 (mp0) REVERT: A 421 LEU cc_start: 0.6684 (OUTLIER) cc_final: 0.6217 (tt) REVERT: B 80 GLU cc_start: 0.7612 (pm20) cc_final: 0.6929 (pm20) REVERT: B 98 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8128 (mm) REVERT: B 230 GLN cc_start: 0.6386 (mp10) cc_final: 0.5994 (mt0) REVERT: B 308 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8557 (mt) REVERT: B 381 LYS cc_start: 0.7542 (mttt) cc_final: 0.7162 (tttm) REVERT: B 421 LEU cc_start: 0.3817 (OUTLIER) cc_final: 0.3312 (tt) REVERT: B 528 MET cc_start: 0.7754 (tpp) cc_final: 0.6906 (tpp) REVERT: B 532 SER cc_start: 0.8178 (m) cc_final: 0.7858 (m) REVERT: C 136 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7663 (mp) REVERT: C 215 MET cc_start: 0.9094 (mmm) cc_final: 0.8713 (tpt) REVERT: C 217 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7921 (m-40) REVERT: C 481 MET cc_start: 0.8747 (tpp) cc_final: 0.8364 (mmt) REVERT: D 80 GLU cc_start: 0.7730 (pm20) cc_final: 0.7415 (pm20) REVERT: D 134 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7441 (tpp-160) REVERT: D 373 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.6139 (tt) REVERT: D 403 GLU cc_start: 0.8202 (tp30) cc_final: 0.7728 (mm-30) REVERT: D 604 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7267 (mm) REVERT: D 637 GLN cc_start: 0.8010 (pt0) cc_final: 0.7763 (pm20) REVERT: E 11 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7315 (mm-30) REVERT: E 51 MET cc_start: 0.7962 (mtt) cc_final: 0.7545 (mmm) REVERT: E 76 MET cc_start: 0.6507 (tpp) cc_final: 0.5911 (ptm) REVERT: E 119 GLU cc_start: 0.7178 (mp0) cc_final: 0.6858 (tt0) outliers start: 67 outliers final: 54 residues processed: 377 average time/residue: 0.1272 time to fit residues: 76.0047 Evaluate side-chains 382 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 319 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 235 VAL 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 421 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 546 ASN Chi-restraints excluded: chain B residue 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 269 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 363 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 502 LEU 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 367 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 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 571 LEU Chi-restraints excluded: chain D residue 604 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 217 optimal weight: 0.9980 chunk 247 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 244 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 166 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 134 optimal weight: 0.0470 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN C 267 GLN D 174 ASN D 483 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.163698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.121688 restraints weight = 28888.869| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.35 r_work: 0.3244 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22984 Z= 0.107 Angle : 0.611 12.370 30958 Z= 0.302 Chirality : 0.041 0.262 3424 Planarity : 0.005 0.089 3816 Dihedral : 12.247 124.537 4479 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.26 % Favored : 90.58 % Rotamer: Outliers : 2.49 % Allowed : 17.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.17), residues: 2623 helix: 1.18 (0.14), residues: 1540 sheet: -2.56 (0.51), residues: 86 loop : -2.32 (0.20), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 140 TYR 0.027 0.001 TYR A 524 PHE 0.020 0.001 PHE B 553 TRP 0.015 0.001 TRP D 593 HIS 0.002 0.000 HIS C 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (22984) covalent geometry : angle 0.61088 / 0.30 (30958) hydrogen bonds : bond 0.03002 / 1.97 ( 931) hydrogen bonds : angle 3.87417 / 2.77 ( 2709) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5552.37 seconds wall clock time: 95 minutes 29.44 seconds (5729.44 seconds total)