Starting phenix.real_space_refine on Fri Sep 19 01:55:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cuk_45936/09_2025/9cuk_45936.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cuk_45936/09_2025/9cuk_45936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cuk_45936/09_2025/9cuk_45936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cuk_45936/09_2025/9cuk_45936.map" model { file = "/net/cci-nas-00/data/ceres_data/9cuk_45936/09_2025/9cuk_45936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cuk_45936/09_2025/9cuk_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-2.0-5805/lib/python3.9/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, 347 Unusual residues: {' CA': 1, 'CLR': 1, 'PCW': 11, 'Y01': 2} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 346 Unresolved non-hydrogen angles: 418 Unresolved non-hydrogen dihedrals: 314 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PCW:plan-1': 8, 'PCW:plan-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, 348 Unusual residues: {' CA': 2, 'CLR': 1, 'PCW': 11, 'Y01': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 346 Unresolved non-hydrogen angles: 418 Unresolved non-hydrogen dihedrals: 314 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PCW:plan-1': 8, 'PCW:plan-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, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.95, per 1000 atoms: 0.26 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: 1.82 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.85 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: 4.00 Time building geometry restraints manager: 2.51 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: 1.320 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.920 Find NCS groups from input model: 0.550 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.216 22984 Z= 0.589 Angle : 1.374 17.235 30958 Z= 0.693 Chirality : 0.057 0.335 3424 Planarity : 0.014 0.293 3816 Dihedral : 16.398 164.413 9578 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.03 % Favored : 89.67 % Rotamer: Outliers : 0.44 % Allowed : 4.46 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.77 % Twisted General : 0.67 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 covalent geometry : bond 0.01272 (22984) covalent geometry : angle 1.37402 (30958) hydrogen bonds : bond 0.33124 ( 931) hydrogen bonds : angle 9.95960 ( 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 : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8238 (ttmt) cc_final: 0.7565 (mmtp) REVERT: A 130 MET cc_start: 0.7768 (tpt) cc_final: 0.7205 (ptt) REVERT: A 174 ASN cc_start: 0.8330 (t160) cc_final: 0.7771 (t0) REVERT: A 233 ASP cc_start: 0.8458 (p0) cc_final: 0.8039 (p0) REVERT: A 306 GLN cc_start: 0.8237 (mt0) cc_final: 0.7941 (mm-40) REVERT: A 340 ILE cc_start: 0.8761 (tp) cc_final: 0.8493 (tp) REVERT: A 379 THR cc_start: 0.8217 (t) cc_final: 0.7931 (m) REVERT: A 435 MET cc_start: 0.7795 (mmt) cc_final: 0.7491 (mmt) REVERT: A 481 MET cc_start: 0.8397 (mmm) cc_final: 0.7658 (mmt) REVERT: A 591 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7116 (mm-30) REVERT: A 618 ILE cc_start: 0.8886 (mp) cc_final: 0.8621 (mm) REVERT: B 59 GLN cc_start: 0.7803 (tt0) cc_final: 0.7512 (mp10) REVERT: B 168 SER cc_start: 0.8528 (m) cc_final: 0.7958 (t) REVERT: B 230 GLN cc_start: 0.6206 (tp40) cc_final: 0.5709 (mm-40) REVERT: B 371 LYS cc_start: 0.7552 (ptmt) cc_final: 0.7333 (ptpp) REVERT: B 381 LYS cc_start: 0.8109 (mttt) cc_final: 0.7907 (tttm) REVERT: B 474 MET cc_start: 0.8281 (ttm) cc_final: 0.8062 (ttm) REVERT: C 379 THR cc_start: 0.7181 (t) cc_final: 0.6871 (t) REVERT: D 80 GLU cc_start: 0.7790 (pm20) cc_final: 0.7428 (pm20) REVERT: D 90 ASP cc_start: 0.8611 (t70) cc_final: 0.8220 (t70) REVERT: D 177 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7786 (mm-30) REVERT: E 145 MET cc_start: 0.6709 (mmt) cc_final: 0.6177 (mmp) outliers start: 10 outliers final: 5 residues processed: 624 average time/residue: 0.1761 time to fit residues: 166.2374 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 : 0.876 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 118 GLN A 129 ASN A 174 ASN A 214 GLN A 228 HIS A 230 GLN A 267 GLN A 572 ASN B 84 HIS B 118 GLN B 129 ASN B 217 ASN B 228 HIS B 230 GLN B 572 ASN B 640 ASN C 118 GLN C 129 ASN C 158 ASN C 174 ASN C 228 HIS C 267 GLN C 464 ASN C 652 HIS C 694 ASN D 84 HIS D 91 ASN D 118 GLN D 129 ASN D 174 ASN D 206 GLN D 228 HIS D 230 GLN D 252 ASN D 258 HIS D 267 GLN D 572 ASN E 111 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.164661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.126876 restraints weight = 28877.501| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.08 r_work: 0.3268 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22984 Z= 0.144 Angle : 0.688 9.506 30958 Z= 0.352 Chirality : 0.043 0.214 3424 Planarity : 0.006 0.091 3816 Dihedral : 16.738 178.749 4483 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.69 % Favored : 91.16 % Rotamer: Outliers : 2.71 % Allowed : 9.93 % 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 aren not related in a simple way. whole: -3.81 (0.14), residues: 2623 helix: -2.01 (0.11), residues: 1571 sheet: -2.77 (0.49), residues: 84 loop : -3.23 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 628 TYR 0.022 0.001 TYR A 524 PHE 0.013 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 covalent geometry : bond 0.00318 (22984) covalent geometry : angle 0.68805 (30958) hydrogen bonds : bond 0.04910 ( 931) hydrogen bonds : angle 4.62205 ( 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 493 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 431 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8338 (ttmt) cc_final: 0.7598 (mmtp) REVERT: A 91 ASN cc_start: 0.6788 (m-40) cc_final: 0.6578 (m110) REVERT: A 174 ASN cc_start: 0.8430 (t0) cc_final: 0.8211 (t0) REVERT: A 211 PHE cc_start: 0.7957 (m-80) cc_final: 0.7491 (m-80) REVERT: A 216 TYR cc_start: 0.8639 (t80) cc_final: 0.8382 (t80) REVERT: A 303 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7888 (pt0) REVERT: A 306 GLN cc_start: 0.8466 (mt0) cc_final: 0.7970 (mm-40) REVERT: A 331 MET cc_start: 0.7779 (tpt) cc_final: 0.7434 (tpt) REVERT: A 435 MET cc_start: 0.7814 (mmt) cc_final: 0.7565 (mmt) REVERT: A 491 MET cc_start: 0.8628 (ttt) cc_final: 0.8376 (ttm) REVERT: A 616 SER cc_start: 0.8955 (m) cc_final: 0.8697 (p) REVERT: A 618 ILE cc_start: 0.8813 (mp) cc_final: 0.8566 (mm) REVERT: B 59 GLN cc_start: 0.7995 (tt0) cc_final: 0.7629 (mp10) REVERT: B 168 SER cc_start: 0.8309 (m) cc_final: 0.7873 (p) REVERT: B 230 GLN cc_start: 0.6369 (tp-100) cc_final: 0.5936 (mp-120) REVERT: B 270 TYR cc_start: 0.8204 (t80) cc_final: 0.7927 (t80) REVERT: B 371 LYS cc_start: 0.7480 (ptmt) cc_final: 0.7263 (ptpp) REVERT: B 381 LYS cc_start: 0.7912 (mttt) cc_final: 0.7419 (tttm) REVERT: B 485 MET cc_start: 0.8065 (mmt) cc_final: 0.7773 (mmt) REVERT: B 532 SER cc_start: 0.8333 (m) cc_final: 0.8048 (m) REVERT: B 587 HIS cc_start: 0.7581 (OUTLIER) cc_final: 0.6999 (m90) REVERT: C 62 ASN cc_start: 0.7352 (m110) cc_final: 0.7009 (p0) REVERT: C 63 LYS cc_start: 0.8209 (mtpt) cc_final: 0.7829 (mtpt) REVERT: C 104 GLU cc_start: 0.8355 (mp0) cc_final: 0.7782 (mp0) REVERT: C 108 GLU cc_start: 0.8094 (pt0) cc_final: 0.7707 (pp20) REVERT: C 184 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8328 (mm-30) REVERT: C 300 LYS cc_start: 0.8676 (mptt) cc_final: 0.8465 (mmmt) REVERT: C 628 ARG cc_start: 0.8321 (ptp-170) cc_final: 0.7942 (mtm-85) REVERT: D 80 GLU cc_start: 0.8135 (pm20) cc_final: 0.7678 (pm20) REVERT: D 294 GLU cc_start: 0.8225 (mp0) cc_final: 0.7721 (mp0) REVERT: D 295 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8204 (mp) REVERT: D 303 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7651 (mp0) REVERT: D 373 LEU cc_start: 0.6657 (OUTLIER) cc_final: 0.6151 (tt) REVERT: D 519 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6753 (mm-30) REVERT: E 11 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7491 (tp30) REVERT: E 51 MET cc_start: 0.8409 (mtt) cc_final: 0.7813 (mmm) REVERT: E 76 MET cc_start: 0.6661 (tpp) cc_final: 0.6051 (ptm) REVERT: E 109 MET cc_start: 0.6991 (mmt) cc_final: 0.6738 (mmm) REVERT: E 119 GLU cc_start: 0.7272 (tp30) cc_final: 0.6832 (tp30) outliers start: 62 outliers final: 34 residues processed: 471 average time/residue: 0.1607 time to fit residues: 119.1938 Evaluate side-chains 393 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 356 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 295 LEU 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 27 ILE 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: 0.9980 chunk 231 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 160 optimal weight: 20.0000 chunk 202 optimal weight: 9.9990 chunk 157 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN A 258 HIS B 206 GLN C 174 ASN C 214 GLN C 522 HIS C 640 ASN D 174 ASN D 522 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.166324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.125317 restraints weight = 28858.332| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.57 r_work: 0.3250 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22984 Z= 0.119 Angle : 0.615 8.372 30958 Z= 0.312 Chirality : 0.041 0.202 3424 Planarity : 0.005 0.093 3816 Dihedral : 15.034 164.950 4483 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.15 % Favored : 90.70 % Rotamer: Outliers : 3.33 % Allowed : 12.04 % Favored : 84.64 % 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 aren not related in a simple way. whole: -2.28 (0.16), residues: 2623 helix: -0.58 (0.13), residues: 1563 sheet: -2.48 (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 A 470 TYR 0.020 0.001 TYR A 524 PHE 0.015 0.001 PHE B 553 TRP 0.007 0.001 TRP C 613 HIS 0.005 0.001 HIS D 587 Details of bonding type rmsd covalent geometry : bond 0.00268 (22984) covalent geometry : angle 0.61519 (30958) hydrogen bonds : bond 0.03775 ( 931) hydrogen bonds : angle 4.10325 ( 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 462 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 386 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8236 (ttmt) cc_final: 0.7469 (mmtp) REVERT: A 91 ASN cc_start: 0.6636 (m-40) cc_final: 0.6422 (m110) REVERT: A 130 MET cc_start: 0.8058 (tpt) cc_final: 0.6570 (ptt) REVERT: A 174 ASN cc_start: 0.8472 (t0) cc_final: 0.8202 (t0) REVERT: A 181 LEU cc_start: 0.7426 (tp) cc_final: 0.7194 (tp) REVERT: A 211 PHE cc_start: 0.7870 (m-80) cc_final: 0.7469 (m-80) REVERT: A 216 TYR cc_start: 0.8524 (t80) cc_final: 0.8317 (t80) REVERT: A 255 MET cc_start: 0.8833 (mmm) cc_final: 0.8594 (mmm) REVERT: A 306 GLN cc_start: 0.8364 (mt0) cc_final: 0.7774 (mm-40) REVERT: A 345 MET cc_start: 0.8307 (mtm) cc_final: 0.8059 (mtp) REVERT: A 421 LEU cc_start: 0.6354 (OUTLIER) cc_final: 0.6103 (tt) REVERT: A 435 MET cc_start: 0.7618 (mmt) cc_final: 0.7364 (mmt) REVERT: A 618 ILE cc_start: 0.8651 (mp) cc_final: 0.8341 (mm) REVERT: A 628 ARG cc_start: 0.8129 (mtp85) cc_final: 0.7816 (mtp85) REVERT: B 59 GLN cc_start: 0.8093 (tt0) cc_final: 0.7614 (mp10) REVERT: B 129 ASN cc_start: 0.7916 (t0) cc_final: 0.7475 (t0) REVERT: B 168 SER cc_start: 0.8270 (m) cc_final: 0.7838 (p) REVERT: B 230 GLN cc_start: 0.6061 (OUTLIER) cc_final: 0.5815 (mp-120) REVERT: B 363 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7674 (pmt100) REVERT: B 381 LYS cc_start: 0.7816 (mttt) cc_final: 0.7295 (tttm) REVERT: B 405 PRO cc_start: 0.7754 (Cg_exo) cc_final: 0.7476 (Cg_endo) REVERT: B 448 SER cc_start: 0.8335 (p) cc_final: 0.8107 (t) REVERT: B 528 MET cc_start: 0.7771 (tpp) cc_final: 0.6935 (tpp) REVERT: B 532 SER cc_start: 0.8235 (m) cc_final: 0.7875 (m) REVERT: B 587 HIS cc_start: 0.7557 (OUTLIER) cc_final: 0.6911 (m90) REVERT: C 61 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7886 (mm) REVERT: C 104 GLU cc_start: 0.8286 (mp0) cc_final: 0.7710 (pm20) REVERT: C 108 GLU cc_start: 0.8153 (pt0) cc_final: 0.7893 (pp20) REVERT: C 136 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7777 (mp) REVERT: C 184 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8381 (mm-30) REVERT: C 300 LYS cc_start: 0.8662 (mptt) cc_final: 0.8434 (mmmt) REVERT: C 571 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8432 (mp) REVERT: C 628 ARG cc_start: 0.8330 (ptp-170) cc_final: 0.7854 (mtm-85) REVERT: D 80 GLU cc_start: 0.8094 (pm20) cc_final: 0.7521 (pm20) REVERT: D 90 ASP cc_start: 0.7784 (t0) cc_final: 0.7444 (t0) REVERT: D 96 MET cc_start: 0.8559 (mmm) cc_final: 0.8259 (mmm) REVERT: D 139 ARG cc_start: 0.7700 (mmt180) cc_final: 0.7444 (tpp80) REVERT: D 294 GLU cc_start: 0.8348 (mp0) cc_final: 0.7811 (mp0) REVERT: D 295 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8032 (mp) REVERT: D 303 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7560 (mp0) REVERT: D 368 LEU cc_start: 0.8050 (pt) cc_final: 0.7768 (tt) REVERT: D 373 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6054 (tt) REVERT: D 519 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6785 (mm-30) REVERT: E 51 MET cc_start: 0.8261 (mtt) cc_final: 0.7819 (mmt) REVERT: E 119 GLU cc_start: 0.7269 (tp30) cc_final: 0.6742 (tp30) outliers start: 76 outliers final: 38 residues processed: 440 average time/residue: 0.1667 time to fit residues: 115.4473 Evaluate side-chains 400 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 353 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 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 565 ILE Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 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 571 LEU Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain D residue 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: 3.9990 chunk 25 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 48 optimal weight: 0.0020 chunk 16 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 230 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 211 optimal weight: 10.0000 overall best weight: 3.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 HIS C 73 HIS C 426 HIS C 582 HIS C 645 GLN C 694 ASN D 174 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.161462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.124362 restraints weight = 28978.178| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.89 r_work: 0.3189 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 22984 Z= 0.198 Angle : 0.675 8.489 30958 Z= 0.338 Chirality : 0.044 0.210 3424 Planarity : 0.005 0.093 3816 Dihedral : 14.553 159.316 4481 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.57 % Favored : 90.28 % Rotamer: Outliers : 4.38 % Allowed : 12.30 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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 aren not related in a simple way. whole: -1.68 (0.16), residues: 2623 helix: -0.03 (0.13), residues: 1560 sheet: -2.53 (0.50), residues: 84 loop : -2.79 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 190 TYR 0.020 0.002 TYR A 524 PHE 0.017 0.002 PHE B 553 TRP 0.011 0.001 TRP D 613 HIS 0.005 0.001 HIS D 587 Details of bonding type rmsd covalent geometry : bond 0.00483 (22984) covalent geometry : angle 0.67528 (30958) hydrogen bonds : bond 0.04158 ( 931) hydrogen bonds : angle 4.22800 ( 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 453 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 353 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8664 (ttmt) cc_final: 0.7755 (mmtp) REVERT: A 91 ASN cc_start: 0.6866 (m-40) cc_final: 0.6585 (m110) REVERT: A 130 MET cc_start: 0.8207 (tpt) cc_final: 0.6821 (ptt) REVERT: A 174 ASN cc_start: 0.8724 (t0) cc_final: 0.8466 (t0) REVERT: A 181 LEU cc_start: 0.8172 (tp) cc_final: 0.7909 (tp) REVERT: A 211 PHE cc_start: 0.8065 (m-80) cc_final: 0.7727 (m-80) REVERT: A 306 GLN cc_start: 0.8540 (mt0) cc_final: 0.8312 (mm-40) REVERT: A 331 MET cc_start: 0.8256 (tpt) cc_final: 0.7972 (tpt) REVERT: B 139 ARG cc_start: 0.8148 (mtt180) cc_final: 0.7624 (mtt180) REVERT: B 363 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7568 (pmt100) REVERT: B 381 LYS cc_start: 0.8127 (mttt) cc_final: 0.7778 (tttm) REVERT: B 421 LEU cc_start: 0.4970 (OUTLIER) cc_final: 0.4341 (tt) REVERT: B 532 SER cc_start: 0.7974 (m) cc_final: 0.7765 (m) REVERT: C 136 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8318 (mp) REVERT: C 184 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8400 (mm-30) REVERT: D 90 ASP cc_start: 0.8122 (t0) cc_final: 0.7624 (t0) REVERT: D 294 GLU cc_start: 0.8576 (mp0) cc_final: 0.8343 (mp0) REVERT: D 373 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.6953 (tt) REVERT: D 519 GLU cc_start: 0.7364 (mt-10) cc_final: 0.7162 (mm-30) REVERT: E 11 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7535 (mm-30) REVERT: E 51 MET cc_start: 0.8380 (mtt) cc_final: 0.7843 (mmm) REVERT: E 76 MET cc_start: 0.6557 (tpp) cc_final: 0.6025 (ptm) REVERT: E 119 GLU cc_start: 0.7632 (tp30) cc_final: 0.7125 (tp30) REVERT: E 145 MET cc_start: 0.6208 (mmt) cc_final: 0.5894 (mmp) outliers start: 100 outliers final: 61 residues processed: 425 average time/residue: 0.1558 time to fit residues: 104.1426 Evaluate side-chains 398 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 333 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 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 235 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 546 ASN Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 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 502 LEU Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain D residue 58 VAL 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 627 ASP Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 112 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 96 optimal weight: 0.0670 chunk 225 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 197 optimal weight: 0.0010 chunk 235 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 chunk 213 optimal weight: 0.0870 chunk 146 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 overall best weight: 0.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN A 267 GLN C 267 GLN C 522 HIS D 118 GLN D 174 ASN D 267 GLN D 464 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.168504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.131459 restraints weight = 28458.708| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.79 r_work: 0.3308 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22984 Z= 0.099 Angle : 0.582 9.051 30958 Z= 0.293 Chirality : 0.040 0.187 3424 Planarity : 0.005 0.091 3816 Dihedral : 13.304 143.881 4481 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.58 % Favored : 91.27 % Rotamer: Outliers : 2.93 % Allowed : 13.87 % Favored : 83.19 % 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 aren not related in a simple way. whole: -0.97 (0.17), residues: 2623 helix: 0.62 (0.13), residues: 1549 sheet: -2.45 (0.50), residues: 84 loop : -2.60 (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 0.013 0.001 PHE B 553 TRP 0.010 0.001 TRP A 593 HIS 0.004 0.000 HIS D 587 Details of bonding type rmsd covalent geometry : bond 0.00208 (22984) covalent geometry : angle 0.58247 (30958) hydrogen bonds : bond 0.02948 ( 931) hydrogen bonds : angle 3.79798 ( 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 452 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 385 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8647 (ttmt) cc_final: 0.7739 (mmtp) REVERT: A 91 ASN cc_start: 0.6792 (m-40) cc_final: 0.6517 (m110) REVERT: A 130 MET cc_start: 0.8055 (tpt) cc_final: 0.6889 (mtm) REVERT: A 174 ASN cc_start: 0.8647 (t0) cc_final: 0.8377 (t0) REVERT: A 181 LEU cc_start: 0.8045 (tp) cc_final: 0.7783 (tp) REVERT: A 188 ASP cc_start: 0.7400 (t0) cc_final: 0.7190 (t0) REVERT: A 211 PHE cc_start: 0.8000 (m-80) cc_final: 0.7720 (m-80) REVERT: A 331 MET cc_start: 0.7965 (tpt) cc_final: 0.7671 (tpt) REVERT: A 373 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6498 (tt) REVERT: A 421 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6333 (tt) REVERT: B 257 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7770 (tp-100) REVERT: B 290 GLN cc_start: 0.7566 (mm-40) cc_final: 0.7255 (tp40) REVERT: B 381 LYS cc_start: 0.8075 (mttt) cc_final: 0.7806 (tttm) REVERT: B 421 LEU cc_start: 0.4717 (OUTLIER) cc_final: 0.4197 (tt) REVERT: C 104 GLU cc_start: 0.8308 (pm20) cc_final: 0.7881 (pm20) REVERT: C 136 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8280 (mp) REVERT: C 184 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8368 (mm-30) REVERT: C 215 MET cc_start: 0.9276 (mmm) cc_final: 0.8869 (tpt) REVERT: C 592 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8772 (mp) REVERT: D 373 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6825 (tt) REVERT: D 519 GLU cc_start: 0.7298 (mt-10) cc_final: 0.7088 (mm-30) REVERT: E 11 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7454 (mm-30) REVERT: E 51 MET cc_start: 0.8157 (mtt) cc_final: 0.7815 (mmm) outliers start: 67 outliers final: 38 residues processed: 432 average time/residue: 0.1501 time to fit residues: 102.3749 Evaluate side-chains 393 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 349 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 621 ARG Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 565 ILE 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 367 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 427 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 592 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 408 PHE Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 55 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 121 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 143 optimal weight: 0.0670 chunk 200 optimal weight: 6.9990 chunk 152 optimal weight: 0.4980 chunk 115 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 overall best weight: 1.5124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 HIS C 267 GLN C 640 ASN D 174 ASN D 464 ASN E 137 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.166829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.129939 restraints weight = 28565.001| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.82 r_work: 0.3281 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22984 Z= 0.121 Angle : 0.597 10.921 30958 Z= 0.298 Chirality : 0.041 0.191 3424 Planarity : 0.005 0.090 3816 Dihedral : 13.048 139.632 4481 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.42 % Favored : 90.43 % Rotamer: Outliers : 2.89 % Allowed : 15.14 % Favored : 81.97 % 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 aren not related in a simple way. whole: -0.71 (0.17), residues: 2623 helix: 0.89 (0.14), residues: 1544 sheet: -2.56 (0.49), residues: 84 loop : -2.55 (0.19), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 74 TYR 0.020 0.001 TYR C 524 PHE 0.019 0.001 PHE B 553 TRP 0.007 0.001 TRP A 45 HIS 0.004 0.000 HIS D 587 Details of bonding type rmsd covalent geometry : bond 0.00285 (22984) covalent geometry : angle 0.59698 (30958) hydrogen bonds : bond 0.03202 ( 931) hydrogen bonds : angle 3.85774 ( 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 421 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 355 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8664 (ttmt) cc_final: 0.7740 (mmtp) REVERT: A 91 ASN cc_start: 0.6758 (m-40) cc_final: 0.6497 (m110) REVERT: A 130 MET cc_start: 0.8140 (tpt) cc_final: 0.6864 (mtm) REVERT: A 174 ASN cc_start: 0.8682 (t0) cc_final: 0.8394 (t0) REVERT: A 181 LEU cc_start: 0.8034 (tp) cc_final: 0.7766 (tp) REVERT: A 211 PHE cc_start: 0.8004 (m-80) cc_final: 0.7675 (m-80) REVERT: A 421 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6356 (tt) REVERT: B 98 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8429 (mm) REVERT: B 139 ARG cc_start: 0.8171 (mtt180) cc_final: 0.7738 (mtt180) REVERT: B 257 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7780 (tp-100) REVERT: B 381 LYS cc_start: 0.8057 (mttt) cc_final: 0.7725 (tttm) REVERT: B 421 LEU cc_start: 0.4396 (OUTLIER) cc_final: 0.3876 (tt) REVERT: C 136 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8182 (mp) REVERT: C 184 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8304 (mm-30) REVERT: C 215 MET cc_start: 0.9290 (mmm) cc_final: 0.8865 (tpt) REVERT: D 308 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8421 (mp) REVERT: D 373 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6787 (tt) REVERT: E 51 MET cc_start: 0.8162 (mtt) cc_final: 0.7793 (mmm) REVERT: E 76 MET cc_start: 0.6401 (tpp) cc_final: 0.5794 (ptm) outliers start: 66 outliers final: 47 residues processed: 401 average time/residue: 0.1451 time to fit residues: 91.4202 Evaluate side-chains 394 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 341 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 131 ASN 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 474 MET 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 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 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 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 308 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 571 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 125 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 182 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 237 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 187 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 HIS C 572 ASN D 118 GLN D 174 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.157377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.116979 restraints weight = 29011.222| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.20 r_work: 0.3150 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 22984 Z= 0.248 Angle : 0.714 11.666 30958 Z= 0.354 Chirality : 0.046 0.227 3424 Planarity : 0.005 0.094 3816 Dihedral : 13.830 155.403 4481 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.99 % Favored : 89.86 % Rotamer: Outliers : 3.50 % Allowed : 16.02 % Favored : 80.48 % 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 aren not related in a simple way. whole: -0.90 (0.17), residues: 2623 helix: 0.72 (0.13), residues: 1536 sheet: -2.59 (0.51), residues: 84 loop : -2.57 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 74 TYR 0.025 0.002 TYR A 524 PHE 0.020 0.002 PHE B 553 TRP 0.011 0.001 TRP B 29 HIS 0.006 0.001 HIS D 587 Details of bonding type rmsd covalent geometry : bond 0.00612 (22984) covalent geometry : angle 0.71357 (30958) hydrogen bonds : bond 0.04216 ( 931) hydrogen bonds : angle 4.23165 ( 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 415 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 335 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: A 174 ASN cc_start: 0.8725 (t0) cc_final: 0.8440 (t0) REVERT: A 211 PHE cc_start: 0.7893 (m-80) cc_final: 0.7435 (m-80) REVERT: A 421 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6285 (tt) REVERT: A 591 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7436 (mm-30) REVERT: B 98 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8164 (mm) REVERT: B 139 ARG cc_start: 0.8201 (mtt180) cc_final: 0.7679 (mmt90) REVERT: B 257 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7637 (tp-100) REVERT: B 381 LYS cc_start: 0.7800 (mttt) cc_final: 0.7359 (tttm) REVERT: B 382 ASP cc_start: 0.6890 (p0) cc_final: 0.6486 (p0) REVERT: B 405 PRO cc_start: 0.7979 (Cg_exo) cc_final: 0.7735 (Cg_endo) REVERT: B 421 LEU cc_start: 0.4513 (OUTLIER) cc_final: 0.4042 (tt) REVERT: C 35 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7692 (tm-30) REVERT: C 136 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7705 (mp) REVERT: C 215 MET cc_start: 0.9135 (mmm) cc_final: 0.8716 (tpt) REVERT: D 90 ASP cc_start: 0.8001 (t0) cc_final: 0.7583 (t0) REVERT: D 176 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8105 (mt-10) REVERT: D 308 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8259 (mp) REVERT: D 373 LEU cc_start: 0.6783 (OUTLIER) cc_final: 0.6265 (tt) REVERT: E 51 MET cc_start: 0.8147 (mtt) cc_final: 0.7587 (mmm) outliers start: 80 outliers final: 55 residues processed: 391 average time/residue: 0.1450 time to fit residues: 89.3217 Evaluate side-chains 380 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 319 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 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 235 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 546 ASN Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain 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 222 TYR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 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 604 LEU Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 502 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 39 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 117 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 59 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 180 optimal weight: 0.3980 chunk 196 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 231 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN A 267 GLN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.161474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.121660 restraints weight = 28766.597| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.23 r_work: 0.3193 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22984 Z= 0.150 Angle : 0.633 9.196 30958 Z= 0.316 Chirality : 0.042 0.198 3424 Planarity : 0.005 0.091 3816 Dihedral : 13.253 145.274 4481 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.57 % Favored : 90.28 % Rotamer: Outliers : 2.89 % Allowed : 16.98 % Favored : 80.13 % 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 aren not related in a simple way. whole: -0.69 (0.17), residues: 2623 helix: 0.88 (0.14), residues: 1545 sheet: -2.68 (0.50), residues: 86 loop : -2.48 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 74 TYR 0.026 0.001 TYR A 524 PHE 0.019 0.001 PHE D 434 TRP 0.009 0.001 TRP A 593 HIS 0.004 0.001 HIS D 587 Details of bonding type rmsd covalent geometry : bond 0.00360 (22984) covalent geometry : angle 0.63254 (30958) hydrogen bonds : bond 0.03504 ( 931) hydrogen bonds : angle 3.98399 ( 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 407 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 341 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.8085 (tpt) cc_final: 0.6411 (ptt) REVERT: A 174 ASN cc_start: 0.8668 (t0) cc_final: 0.8395 (t0) REVERT: A 211 PHE cc_start: 0.7878 (m-80) cc_final: 0.7411 (m-80) REVERT: A 297 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.8037 (tp) REVERT: A 331 MET cc_start: 0.7573 (tpt) cc_final: 0.7287 (tpt) REVERT: A 421 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.6245 (tt) REVERT: A 591 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7572 (mm-30) REVERT: B 98 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8142 (mm) REVERT: B 139 ARG cc_start: 0.8200 (mtt180) cc_final: 0.7826 (mtt180) REVERT: B 257 GLN cc_start: 0.7966 (mm-40) cc_final: 0.7612 (tp-100) REVERT: B 381 LYS cc_start: 0.7786 (mttt) cc_final: 0.7338 (tttm) REVERT: B 382 ASP cc_start: 0.6916 (p0) cc_final: 0.6493 (p0) REVERT: B 405 PRO cc_start: 0.7989 (Cg_exo) cc_final: 0.7749 (Cg_endo) REVERT: B 421 LEU cc_start: 0.3846 (OUTLIER) cc_final: 0.3412 (tt) REVERT: C 136 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7732 (mp) REVERT: C 215 MET cc_start: 0.9181 (mmm) cc_final: 0.8776 (tpt) REVERT: D 134 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7436 (tpp-160) REVERT: D 176 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8091 (mt-10) REVERT: D 308 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8263 (mp) REVERT: D 373 LEU cc_start: 0.6777 (OUTLIER) cc_final: 0.6215 (tt) REVERT: E 11 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7366 (mm-30) REVERT: E 51 MET cc_start: 0.8112 (mtt) cc_final: 0.7601 (mmm) REVERT: E 119 GLU cc_start: 0.7204 (mp0) cc_final: 0.6883 (tt0) outliers start: 66 outliers final: 46 residues processed: 388 average time/residue: 0.1574 time to fit residues: 95.5773 Evaluate side-chains 372 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 318 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 297 ILE 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 90 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 546 ASN Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 222 TYR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 363 ARG Chi-restraints excluded: chain C residue 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 604 LEU Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 502 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 89 optimal weight: 3.9990 chunk 259 optimal weight: 10.0000 chunk 193 optimal weight: 0.7980 chunk 228 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 244 optimal weight: 0.1980 chunk 249 optimal weight: 7.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 267 GLN C 640 ASN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.162982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.121889 restraints weight = 28923.590| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.38 r_work: 0.3221 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22984 Z= 0.118 Angle : 0.606 8.521 30958 Z= 0.304 Chirality : 0.041 0.190 3424 Planarity : 0.005 0.090 3816 Dihedral : 12.622 135.071 4479 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.80 % Favored : 90.05 % Rotamer: Outliers : 2.54 % Allowed : 17.42 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: -0.46 (0.17), residues: 2623 helix: 1.11 (0.14), residues: 1536 sheet: -2.64 (0.50), residues: 86 loop : -2.43 (0.20), residues: 1001 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 0.018 0.001 PHE B 553 TRP 0.009 0.001 TRP A 593 HIS 0.004 0.000 HIS D 587 Details of bonding type rmsd covalent geometry : bond 0.00273 (22984) covalent geometry : angle 0.60571 (30958) hydrogen bonds : bond 0.03158 ( 931) hydrogen bonds : angle 3.85263 ( 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 399 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 341 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7990 (tpt) cc_final: 0.6366 (ptt) REVERT: A 174 ASN cc_start: 0.8639 (t0) cc_final: 0.8352 (t0) REVERT: A 211 PHE cc_start: 0.7831 (m-80) cc_final: 0.7378 (m-80) REVERT: A 303 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7660 (mp0) REVERT: A 373 LEU cc_start: 0.6094 (OUTLIER) cc_final: 0.5539 (tt) REVERT: A 421 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6272 (tt) REVERT: B 80 GLU cc_start: 0.7813 (pm20) cc_final: 0.6968 (pm20) REVERT: B 98 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8172 (mm) REVERT: B 139 ARG cc_start: 0.8173 (mtt180) cc_final: 0.7773 (mpt180) REVERT: B 257 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7549 (tp-100) REVERT: B 381 LYS cc_start: 0.7739 (mttt) cc_final: 0.7313 (tttm) REVERT: B 382 ASP cc_start: 0.6931 (p0) cc_final: 0.6461 (p0) REVERT: B 421 LEU cc_start: 0.4003 (OUTLIER) cc_final: 0.3574 (tt) REVERT: B 454 MET cc_start: 0.7266 (mtt) cc_final: 0.6903 (mtt) REVERT: C 78 MET cc_start: 0.7456 (mmp) cc_final: 0.6999 (mmp) REVERT: C 136 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7661 (mp) REVERT: C 215 MET cc_start: 0.9157 (mmm) cc_final: 0.8766 (tpt) REVERT: C 378 MET cc_start: 0.7049 (mtm) cc_final: 0.6803 (mtm) REVERT: D 80 GLU cc_start: 0.7766 (pm20) cc_final: 0.7472 (pm20) REVERT: D 134 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7454 (tpp-160) REVERT: D 176 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8068 (mt-10) REVERT: D 308 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8230 (mp) REVERT: D 373 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6184 (tt) REVERT: E 11 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7349 (mm-30) REVERT: E 51 MET cc_start: 0.7945 (mtt) cc_final: 0.7541 (mmm) REVERT: E 76 MET cc_start: 0.6449 (tpp) cc_final: 0.5843 (ptm) REVERT: E 119 GLU cc_start: 0.7189 (mp0) cc_final: 0.6850 (tt0) outliers start: 58 outliers final: 41 residues processed: 380 average time/residue: 0.1584 time to fit residues: 94.8332 Evaluate side-chains 375 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 326 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 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 235 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 546 ASN Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 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 368 LEU Chi-restraints excluded: chain C residue 373 LEU 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 604 LEU Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 571 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 125 optimal weight: 8.9990 chunk 129 optimal weight: 0.3980 chunk 145 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 chunk 112 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 182 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.165253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.124584 restraints weight = 28896.005| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.40 r_work: 0.3244 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22984 Z= 0.102 Angle : 0.599 13.102 30958 Z= 0.298 Chirality : 0.040 0.183 3424 Planarity : 0.005 0.091 3816 Dihedral : 12.079 124.613 4479 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.96 % Favored : 90.89 % Rotamer: Outliers : 2.06 % Allowed : 18.38 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: -0.25 (0.17), residues: 2623 helix: 1.29 (0.14), residues: 1537 sheet: -2.58 (0.51), residues: 86 loop : -2.38 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 140 TYR 0.026 0.001 TYR A 524 PHE 0.021 0.001 PHE B 553 TRP 0.009 0.001 TRP A 593 HIS 0.003 0.000 HIS D 587 Details of bonding type rmsd covalent geometry : bond 0.00225 (22984) covalent geometry : angle 0.59887 (30958) hydrogen bonds : bond 0.02945 ( 931) hydrogen bonds : angle 3.80361 ( 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 394 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 347 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7963 (tpt) cc_final: 0.6358 (ptt) REVERT: A 153 ARG cc_start: 0.7689 (mtt180) cc_final: 0.7251 (mtt-85) REVERT: A 174 ASN cc_start: 0.8623 (t0) cc_final: 0.8343 (t0) REVERT: A 211 PHE cc_start: 0.7824 (m-80) cc_final: 0.7368 (m-80) REVERT: A 303 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7695 (mp0) REVERT: A 373 LEU cc_start: 0.6252 (OUTLIER) cc_final: 0.5635 (tt) REVERT: A 421 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6303 (tt) REVERT: A 434 PHE cc_start: 0.7452 (t80) cc_final: 0.7234 (t80) REVERT: B 98 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8181 (mm) REVERT: B 222 TYR cc_start: 0.7131 (OUTLIER) cc_final: 0.6693 (t80) REVERT: B 257 GLN cc_start: 0.7799 (mm-40) cc_final: 0.7475 (tp-100) REVERT: B 381 LYS cc_start: 0.7682 (mttt) cc_final: 0.7290 (tttm) REVERT: B 382 ASP cc_start: 0.6938 (p0) cc_final: 0.6381 (p0) REVERT: B 421 LEU cc_start: 0.3593 (OUTLIER) cc_final: 0.3187 (tt) REVERT: B 454 MET cc_start: 0.7202 (mtt) cc_final: 0.6837 (mtt) REVERT: C 136 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7613 (mp) REVERT: C 215 MET cc_start: 0.9166 (mmm) cc_final: 0.8774 (tpt) REVERT: D 80 GLU cc_start: 0.7718 (pm20) cc_final: 0.7427 (pm20) REVERT: D 134 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7501 (tpp-160) REVERT: E 11 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7339 (mm-30) REVERT: E 26 THR cc_start: 0.7815 (p) cc_final: 0.7582 (t) REVERT: E 51 MET cc_start: 0.7867 (mtt) cc_final: 0.7545 (mmm) REVERT: E 76 MET cc_start: 0.6423 (tpp) cc_final: 0.5805 (ptm) REVERT: E 119 GLU cc_start: 0.7195 (mp0) cc_final: 0.6828 (tt0) outliers start: 47 outliers final: 34 residues processed: 382 average time/residue: 0.1628 time to fit residues: 97.0626 Evaluate side-chains 369 residues out of total 2285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 328 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 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 222 TYR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 421 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 274 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 363 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 48 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 217 optimal weight: 0.9980 chunk 247 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 113 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 244 optimal weight: 0.3980 chunk 17 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 134 optimal weight: 0.0040 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.164475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.122138 restraints weight = 28881.263| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.36 r_work: 0.3249 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22984 Z= 0.109 Angle : 0.610 11.867 30958 Z= 0.302 Chirality : 0.041 0.187 3424 Planarity : 0.005 0.092 3816 Dihedral : 11.881 121.798 4479 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.34 % Favored : 90.51 % Rotamer: Outliers : 2.19 % Allowed : 18.47 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: -0.17 (0.17), residues: 2623 helix: 1.36 (0.14), residues: 1539 sheet: -2.61 (0.51), residues: 86 loop : -2.34 (0.20), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 74 TYR 0.026 0.001 TYR A 524 PHE 0.021 0.001 PHE B 553 TRP 0.011 0.001 TRP A 593 HIS 0.004 0.000 HIS D 587 Details of bonding type rmsd covalent geometry : bond 0.00249 (22984) covalent geometry : angle 0.61002 (30958) hydrogen bonds : bond 0.03002 ( 931) hydrogen bonds : angle 3.82303 ( 2709) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6738.17 seconds wall clock time: 115 minutes 39.59 seconds (6939.59 seconds total)