Starting phenix.real_space_refine on Sun Aug 24 05:59:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g7a_29804/08_2025/8g7a_29804.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7a_29804/08_2025/8g7a_29804.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g7a_29804/08_2025/8g7a_29804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7a_29804/08_2025/8g7a_29804.map" model { file = "/net/cci-nas-00/data/ceres_data/8g7a_29804/08_2025/8g7a_29804.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7a_29804/08_2025/8g7a_29804.cif" } resolution = 3.3 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= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1380 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 10384 2.51 5 N 2723 2.21 5 O 3061 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16237 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 877 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "A" Number of atoms: 4526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4526 Classifications: {'peptide': 567} Link IDs: {'PTRANS': 31, 'TRANS': 535} Chain breaks: 2 Chain: "B" Number of atoms: 4526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4526 Classifications: {'peptide': 567} Link IDs: {'PTRANS': 31, 'TRANS': 535} Chain breaks: 2 Chain: "C" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 877 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "D" Number of atoms: 4526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4526 Classifications: {'peptide': 567} Link IDs: {'PTRANS': 31, 'TRANS': 535} Chain breaks: 2 Chain: "F" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 877 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.79, per 1000 atoms: 0.17 Number of scatterers: 16237 At special positions: 0 Unit cell: (164.25, 154.03, 124.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 3061 8.00 N 2723 7.00 C 10384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.04 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.02 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.06 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 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=1, symmetry=0 Links applied NAG-ASN " NAG B1301 " - " ASN B 331 " " NAG D1301 " - " ASN D 331 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 451.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3816 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 39 sheets defined 8.3% alpha, 32.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 372 removed outlier: 4.046A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.647A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 372 removed outlier: 4.393A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 4.108A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.665A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.726A pdb=" N LYS C 64 " --> pdb=" O ASN C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 365 through 370 Processing helix chain 'D' and resid 406 through 410 Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 438 through 443 removed outlier: 3.576A pdb=" N SER D 443 " --> pdb=" O ASN D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 505 Processing helix chain 'F' and resid 61 through 64 removed outlier: 3.908A pdb=" N LYS F 64 " --> pdb=" O ASN F 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 61 through 64' Processing helix chain 'F' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.166A pdb=" N GLY E 10 " --> pdb=" O THR E 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.605A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.362A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.607A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.877A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 68 through 69 removed outlier: 3.608A pdb=" N ARG A 78 " --> pdb=" O HIS A 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.475A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.680A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.622A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.703A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.715A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.230A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.915A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 68 through 70 Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.560A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.544A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N PHE B 565 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.677A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.276A pdb=" N GLY C 10 " --> pdb=" O THR C 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.607A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N MET C 34 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR C 104 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 28 through 30 removed outlier: 8.381A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 47 through 55 removed outlier: 3.777A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 68 through 69 Processing sheet with id=AD4, first strand: chain 'D' and resid 84 through 85 Processing sheet with id=AD5, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.594A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA D 243 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE D 101 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER D 172 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL D 130 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AD7, first strand: chain 'D' and resid 361 through 362 removed outlier: 7.005A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AD9, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.634A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AE2, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.218A pdb=" N GLY F 10 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL F 111 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG F 38 " --> pdb=" O MET F 47 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N MET F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.218A pdb=" N GLY F 10 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL F 111 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR F 104 " --> pdb=" O ALA F 97 " (cutoff:3.500A) 526 hydrogen bonds defined for protein. 1317 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: 2.37 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4697 1.33 - 1.46: 3928 1.46 - 1.58: 7942 1.58 - 1.70: 0 1.70 - 1.83: 84 Bond restraints: 16651 Sorted by residual: bond pdb=" N PHE D 329 " pdb=" CA PHE D 329 " ideal model delta sigma weight residual 1.453 1.484 -0.031 8.30e-03 1.45e+04 1.42e+01 bond pdb=" N GLN C 102 " pdb=" CA GLN C 102 " ideal model delta sigma weight residual 1.457 1.505 -0.048 1.29e-02 6.01e+03 1.37e+01 bond pdb=" CA PRO B 25 " pdb=" C PRO B 25 " ideal model delta sigma weight residual 1.514 1.496 0.019 5.50e-03 3.31e+04 1.13e+01 bond pdb=" N VAL D 524 " pdb=" CA VAL D 524 " ideal model delta sigma weight residual 1.458 1.495 -0.036 1.19e-02 7.06e+03 9.36e+00 bond pdb=" N PHE B 392 " pdb=" CA PHE B 392 " ideal model delta sigma weight residual 1.453 1.491 -0.037 1.22e-02 6.72e+03 9.35e+00 ... (remaining 16646 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 21663 1.91 - 3.82: 867 3.82 - 5.73: 79 5.73 - 7.65: 22 7.65 - 9.56: 9 Bond angle restraints: 22640 Sorted by residual: angle pdb=" N PRO B 295 " pdb=" CA PRO B 295 " pdb=" C PRO B 295 " ideal model delta sigma weight residual 113.40 103.84 9.56 1.34e+00 5.57e-01 5.09e+01 angle pdb=" CA PRO D 337 " pdb=" C PRO D 337 " pdb=" O PRO D 337 " ideal model delta sigma weight residual 121.31 116.93 4.38 7.40e-01 1.83e+00 3.50e+01 angle pdb=" C LYS B 424 " pdb=" N LEU B 425 " pdb=" CA LEU B 425 " ideal model delta sigma weight residual 121.76 113.11 8.65 1.74e+00 3.30e-01 2.47e+01 angle pdb=" C TRP D 353 " pdb=" N ASN D 354 " pdb=" CA ASN D 354 " ideal model delta sigma weight residual 122.41 115.18 7.23 1.47e+00 4.63e-01 2.42e+01 angle pdb=" CA GLN D 173 " pdb=" CB GLN D 173 " pdb=" CG GLN D 173 " ideal model delta sigma weight residual 114.10 122.69 -8.59 2.00e+00 2.50e-01 1.84e+01 ... (remaining 22635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8950 17.94 - 35.88: 709 35.88 - 53.82: 168 53.82 - 71.76: 16 71.76 - 89.70: 6 Dihedral angle restraints: 9849 sinusoidal: 3894 harmonic: 5955 Sorted by residual: dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 95 " pdb=" CB CYS C 95 " ideal model delta sinusoidal sigma weight residual -86.00 -156.60 70.60 1 1.00e+01 1.00e-02 6.41e+01 dihedral pdb=" CA TYR B 351 " pdb=" C TYR B 351 " pdb=" N ALA B 352 " pdb=" CA ALA B 352 " ideal model delta harmonic sigma weight residual 180.00 155.64 24.36 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA TYR D 351 " pdb=" C TYR D 351 " pdb=" N ALA D 352 " pdb=" CA ALA D 352 " ideal model delta harmonic sigma weight residual 180.00 156.06 23.94 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 9846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2026 0.066 - 0.132: 414 0.132 - 0.198: 42 0.198 - 0.264: 6 0.264 - 0.330: 3 Chirality restraints: 2491 Sorted by residual: chirality pdb=" CA VAL A 401 " pdb=" N VAL A 401 " pdb=" C VAL A 401 " pdb=" CB VAL A 401 " both_signs ideal model delta sigma weight residual False 2.44 2.77 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CA CYS D 525 " pdb=" N CYS D 525 " pdb=" C CYS D 525 " pdb=" CB CYS D 525 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA ILE B 332 " pdb=" N ILE B 332 " pdb=" C ILE B 332 " pdb=" CB ILE B 332 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.76e+00 ... (remaining 2488 not shown) Planarity restraints: 2935 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.127 2.00e-02 2.50e+03 1.35e-01 2.27e+02 pdb=" CG ASN B 331 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.232 2.00e-02 2.50e+03 pdb=" C1 NAG B1301 " 0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 353 " 0.045 2.00e-02 2.50e+03 2.77e-02 1.92e+01 pdb=" CG TRP D 353 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP D 353 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP D 353 " -0.017 2.00e-02 2.50e+03 pdb=" NE1 TRP D 353 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP D 353 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP D 353 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 353 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 353 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 353 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 423 " 0.038 2.00e-02 2.50e+03 3.05e-02 1.85e+01 pdb=" CG TYR B 423 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR B 423 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR B 423 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR B 423 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR B 423 " 0.033 2.00e-02 2.50e+03 pdb=" CZ TYR B 423 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR B 423 " -0.012 2.00e-02 2.50e+03 ... (remaining 2932 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 93 2.40 - 3.03: 9655 3.03 - 3.65: 23278 3.65 - 4.28: 35695 4.28 - 4.90: 59560 Nonbonded interactions: 128281 Sorted by model distance: nonbonded pdb=" O VAL A 350 " pdb=" CZ2 TRP A 353 " model vdw 1.778 3.340 nonbonded pdb=" O SER C 52 " pdb=" NH2 ARG C 71 " model vdw 1.810 3.120 nonbonded pdb=" O SER E 52 " pdb=" NH2 ARG E 71 " model vdw 1.886 3.120 nonbonded pdb=" CB SER E 101 " pdb=" OD1 ASN A 354 " model vdw 1.920 3.440 nonbonded pdb=" CD2 PHE A 347 " pdb=" OG SER A 399 " model vdw 1.934 3.340 ... (remaining 128276 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' selection = (chain 'B' and resid 14 through 592) selection = (chain 'D' and resid 14 through 592) } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' } 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: 5.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.300 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5151 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 : 0.008 0.468 16677 Z= 0.469 Angle : 0.860 18.334 22692 Z= 0.500 Chirality : 0.055 0.330 2491 Planarity : 0.008 0.079 2933 Dihedral : 13.256 89.705 5964 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 23.04 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.06 % Favored : 95.70 % Rotamer: Outliers : 0.67 % Allowed : 11.39 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.47 (0.18), residues: 2022 helix: -2.34 (0.44), residues: 115 sheet: -0.02 (0.20), residues: 652 loop : -1.41 (0.16), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 246 TYR 0.064 0.003 TYR B 423 PHE 0.059 0.002 PHE D 565 TRP 0.066 0.004 TRP D 353 HIS 0.008 0.001 HIS F 79 Details of bonding type rmsd covalent geometry : bond 0.00589 (16651) covalent geometry : angle 0.83213 (22640) SS BOND : bond 0.00707 ( 23) SS BOND : angle 1.85678 ( 46) hydrogen bonds : bond 0.14635 ( 517) hydrogen bonds : angle 8.08097 ( 1317) Misc. bond : bond 0.37715 ( 1) link_NAG-ASN : bond 0.33096 ( 2) link_NAG-ASN : angle 12.61763 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 181 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 THR cc_start: 0.7746 (m) cc_final: 0.7325 (p) REVERT: A 406 GLU cc_start: 0.6285 (mt-10) cc_final: 0.5943 (mm-30) REVERT: A 450 ASN cc_start: 0.6130 (OUTLIER) cc_final: 0.5905 (p0) REVERT: A 454 ARG cc_start: 0.6235 (mtt180) cc_final: 0.5881 (ptp-110) REVERT: A 462 LYS cc_start: 0.7954 (mttp) cc_final: 0.7723 (mttp) REVERT: B 66 HIS cc_start: 0.5942 (m-70) cc_final: 0.5525 (m90) REVERT: B 100 ILE cc_start: 0.8233 (pt) cc_final: 0.7545 (tp) REVERT: B 153 MET cc_start: -0.0618 (mtm) cc_final: -0.0962 (mmm) REVERT: B 177 MET cc_start: 0.2432 (mmp) cc_final: 0.2031 (mpp) REVERT: B 237 ARG cc_start: 0.7929 (mtm180) cc_final: 0.7374 (mtm110) REVERT: B 305 SER cc_start: 0.9042 (p) cc_final: 0.8777 (t) REVERT: B 537 LYS cc_start: 0.8498 (tttt) cc_final: 0.8213 (tttm) REVERT: B 558 LYS cc_start: 0.7227 (pttt) cc_final: 0.6527 (mmmm) REVERT: C 34 MET cc_start: 0.5565 (mpp) cc_final: 0.4678 (tpp) REVERT: C 100 LYS cc_start: 0.4649 (tptp) cc_final: 0.4161 (mtmm) REVERT: D 69 HIS cc_start: 0.4893 (p-80) cc_final: 0.4596 (p90) REVERT: D 100 ILE cc_start: 0.7285 (pt) cc_final: 0.6693 (mm) REVERT: D 177 MET cc_start: 0.1113 (mmp) cc_final: 0.0207 (mmt) REVERT: D 218 GLN cc_start: 0.6148 (mt0) cc_final: 0.5802 (pm20) REVERT: D 239 GLN cc_start: 0.8316 (tt0) cc_final: 0.7869 (tt0) REVERT: F 82 MET cc_start: 0.2163 (mmt) cc_final: 0.1468 (ptm) outliers start: 12 outliers final: 5 residues processed: 193 average time/residue: 0.1128 time to fit residues: 32.7337 Evaluate side-chains 111 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain D residue 331 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.0970 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.0020 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 58 GLN A 69 HIS A 207 HIS A 317 ASN A 501 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 207 HIS B 317 ASN B 532 ASN C 32 ASN C 44 GLN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN F 13 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.249006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.180585 restraints weight = 23071.654| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 3.15 r_work: 0.3785 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16677 Z= 0.136 Angle : 0.624 11.635 22692 Z= 0.331 Chirality : 0.048 0.178 2491 Planarity : 0.006 0.069 2933 Dihedral : 5.055 29.885 2279 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.71 % Favored : 96.14 % Rotamer: Outliers : 2.33 % Allowed : 12.00 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.35 (0.18), residues: 2022 helix: -2.06 (0.44), residues: 122 sheet: -0.09 (0.20), residues: 658 loop : -1.24 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 403 TYR 0.030 0.002 TYR B 423 PHE 0.036 0.002 PHE D 400 TRP 0.020 0.002 TRP B 353 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00314 (16651) covalent geometry : angle 0.62192 (22640) SS BOND : bond 0.00240 ( 23) SS BOND : angle 0.92328 ( 46) hydrogen bonds : bond 0.03966 ( 517) hydrogen bonds : angle 6.82759 ( 1317) Misc. bond : bond 0.01112 ( 1) link_NAG-ASN : bond 0.00554 ( 2) link_NAG-ASN : angle 2.54872 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 116 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 80 LEU cc_start: 0.3707 (OUTLIER) cc_final: 0.3328 (tp) REVERT: A 158 ARG cc_start: 0.7392 (mtt-85) cc_final: 0.7047 (mtp85) REVERT: A 236 THR cc_start: 0.8204 (m) cc_final: 0.7994 (p) REVERT: A 406 GLU cc_start: 0.6696 (mt-10) cc_final: 0.6277 (mm-30) REVERT: A 436 TRP cc_start: 0.5330 (OUTLIER) cc_final: 0.3871 (p-90) REVERT: A 462 LYS cc_start: 0.8302 (mttp) cc_final: 0.7996 (pttm) REVERT: B 66 HIS cc_start: 0.6000 (m-70) cc_final: 0.5755 (m90) REVERT: B 100 ILE cc_start: 0.8437 (pt) cc_final: 0.7854 (tp) REVERT: B 177 MET cc_start: 0.2742 (mmp) cc_final: 0.2163 (mpp) REVERT: B 537 LYS cc_start: 0.8961 (tttt) cc_final: 0.8753 (tttm) REVERT: B 558 LYS cc_start: 0.7595 (pttt) cc_final: 0.7229 (mmmm) REVERT: C 34 MET cc_start: 0.4562 (mpp) cc_final: 0.3884 (mmm) REVERT: C 100 LYS cc_start: 0.4851 (tptp) cc_final: 0.3509 (mtmt) REVERT: D 69 HIS cc_start: 0.4969 (p-80) cc_final: 0.3792 (p-80) REVERT: D 177 MET cc_start: 0.2020 (mmp) cc_final: 0.0769 (mmt) REVERT: D 429 PHE cc_start: 0.4649 (OUTLIER) cc_final: 0.4410 (t80) REVERT: F 82 MET cc_start: 0.2915 (mmt) cc_final: 0.0796 (ptm) outliers start: 42 outliers final: 17 residues processed: 155 average time/residue: 0.1010 time to fit residues: 24.5557 Evaluate side-chains 115 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 11 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 14 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 163 optimal weight: 0.4980 chunk 139 optimal weight: 4.9990 chunk 9 optimal weight: 40.0000 chunk 105 optimal weight: 9.9990 chunk 180 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 68 optimal weight: 0.0670 chunk 7 optimal weight: 3.9990 overall best weight: 1.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 5 GLN A 165 ASN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS B 121 ASN B 134 GLN C 44 GLN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN D 188 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.246067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.179421 restraints weight = 23118.393| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 3.25 r_work: 0.3672 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16677 Z= 0.146 Angle : 0.588 8.950 22692 Z= 0.310 Chirality : 0.047 0.205 2491 Planarity : 0.005 0.061 2933 Dihedral : 4.658 25.272 2268 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.21 % Favored : 96.64 % Rotamer: Outliers : 2.89 % Allowed : 13.50 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.26 (0.18), residues: 2022 helix: -1.79 (0.45), residues: 122 sheet: -0.08 (0.20), residues: 706 loop : -1.22 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 237 TYR 0.029 0.002 TYR A 160 PHE 0.023 0.002 PHE B 429 TRP 0.015 0.002 TRP B 353 HIS 0.003 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00351 (16651) covalent geometry : angle 0.58528 (22640) SS BOND : bond 0.00484 ( 23) SS BOND : angle 1.19353 ( 46) hydrogen bonds : bond 0.03569 ( 517) hydrogen bonds : angle 6.36333 ( 1317) Misc. bond : bond 0.00007 ( 1) link_NAG-ASN : bond 0.00355 ( 2) link_NAG-ASN : angle 2.06155 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 110 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.0433 (ptm) cc_final: -0.1230 (mmm) REVERT: E 80 LEU cc_start: 0.3650 (OUTLIER) cc_final: 0.3153 (tp) REVERT: A 158 ARG cc_start: 0.7337 (mtt-85) cc_final: 0.7087 (mtp85) REVERT: A 406 GLU cc_start: 0.6629 (mt-10) cc_final: 0.6186 (mm-30) REVERT: A 424 LYS cc_start: 0.8176 (mmmt) cc_final: 0.7788 (mmmt) REVERT: A 436 TRP cc_start: 0.5256 (OUTLIER) cc_final: 0.3892 (p-90) REVERT: A 462 LYS cc_start: 0.8251 (mttp) cc_final: 0.7934 (pttm) REVERT: B 66 HIS cc_start: 0.5935 (m-70) cc_final: 0.5656 (m90) REVERT: B 156 GLU cc_start: 0.6712 (mp0) cc_final: 0.4740 (tt0) REVERT: B 177 MET cc_start: 0.2639 (mmp) cc_final: 0.2021 (mpp) REVERT: B 558 LYS cc_start: 0.7605 (pttt) cc_final: 0.7313 (mmmm) REVERT: C 34 MET cc_start: 0.4293 (mpp) cc_final: 0.3614 (mmm) REVERT: C 47 MET cc_start: 0.1750 (OUTLIER) cc_final: 0.0862 (ptt) REVERT: D 69 HIS cc_start: 0.4912 (p-80) cc_final: 0.3642 (p-80) REVERT: D 177 MET cc_start: 0.2306 (mmp) cc_final: 0.1056 (mmt) REVERT: D 198 ASP cc_start: 0.8174 (t0) cc_final: 0.7957 (t0) REVERT: D 429 PHE cc_start: 0.4766 (OUTLIER) cc_final: 0.4555 (t80) REVERT: D 468 ILE cc_start: 0.4065 (OUTLIER) cc_final: 0.3714 (tt) REVERT: D 574 ASP cc_start: 0.8144 (t70) cc_final: 0.7629 (t0) REVERT: F 58 GLN cc_start: 0.2766 (OUTLIER) cc_final: 0.1087 (tt0) REVERT: F 82 MET cc_start: 0.3111 (mmt) cc_final: 0.0770 (ptm) outliers start: 52 outliers final: 30 residues processed: 155 average time/residue: 0.0977 time to fit residues: 24.0347 Evaluate side-chains 130 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 94 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 58 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 7 optimal weight: 0.0060 chunk 22 optimal weight: 0.9990 chunk 142 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 133 optimal weight: 20.0000 chunk 70 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 GLN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN F 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.246866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.176595 restraints weight = 22718.999| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 3.07 r_work: 0.3736 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16677 Z= 0.136 Angle : 0.561 8.186 22692 Z= 0.296 Chirality : 0.046 0.201 2491 Planarity : 0.004 0.058 2933 Dihedral : 4.504 23.985 2268 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.46 % Favored : 96.39 % Rotamer: Outliers : 3.00 % Allowed : 13.89 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.19 (0.18), residues: 2022 helix: -1.61 (0.46), residues: 123 sheet: 0.03 (0.20), residues: 693 loop : -1.22 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 237 TYR 0.019 0.001 TYR A 160 PHE 0.014 0.001 PHE A 86 TRP 0.014 0.001 TRP B 64 HIS 0.002 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00315 (16651) covalent geometry : angle 0.55852 (22640) SS BOND : bond 0.00495 ( 23) SS BOND : angle 1.03982 ( 46) hydrogen bonds : bond 0.03273 ( 517) hydrogen bonds : angle 6.15869 ( 1317) Misc. bond : bond 0.00045 ( 1) link_NAG-ASN : bond 0.00097 ( 2) link_NAG-ASN : angle 1.93161 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 103 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.0717 (ptm) cc_final: -0.1082 (mmm) REVERT: A 158 ARG cc_start: 0.7485 (mtt-85) cc_final: 0.7212 (mtp85) REVERT: A 357 ARG cc_start: 0.8122 (ttm-80) cc_final: 0.7785 (ttp80) REVERT: A 406 GLU cc_start: 0.6666 (mt-10) cc_final: 0.6216 (mm-30) REVERT: A 436 TRP cc_start: 0.5280 (OUTLIER) cc_final: 0.3929 (p-90) REVERT: A 462 LYS cc_start: 0.8305 (mttp) cc_final: 0.7958 (pttm) REVERT: B 66 HIS cc_start: 0.6010 (m-70) cc_final: 0.5773 (m90) REVERT: B 177 MET cc_start: 0.2611 (mmp) cc_final: 0.2057 (mpp) REVERT: B 558 LYS cc_start: 0.7718 (pttt) cc_final: 0.7341 (mmmm) REVERT: C 34 MET cc_start: 0.4077 (mpp) cc_final: 0.3541 (mmm) REVERT: C 100 LYS cc_start: 0.4749 (tptp) cc_final: 0.3707 (mtmt) REVERT: D 177 MET cc_start: 0.2228 (mmp) cc_final: 0.1087 (mmt) REVERT: D 198 ASP cc_start: 0.8283 (t0) cc_final: 0.8079 (t0) REVERT: D 369 TYR cc_start: 0.5240 (OUTLIER) cc_final: 0.3730 (t80) REVERT: D 468 ILE cc_start: 0.4042 (OUTLIER) cc_final: 0.3644 (tt) REVERT: D 574 ASP cc_start: 0.8429 (t70) cc_final: 0.7923 (t0) REVERT: F 58 GLN cc_start: 0.2714 (OUTLIER) cc_final: 0.1055 (tt0) REVERT: F 82 MET cc_start: 0.2994 (mmt) cc_final: 0.0656 (ptm) outliers start: 54 outliers final: 27 residues processed: 153 average time/residue: 0.0931 time to fit residues: 23.3036 Evaluate side-chains 128 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 369 TYR Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 58 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 127 optimal weight: 40.0000 chunk 78 optimal weight: 8.9990 chunk 68 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 128 optimal weight: 0.0020 chunk 146 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 43 optimal weight: 8.9990 chunk 185 optimal weight: 3.9990 overall best weight: 1.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.243938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.173171 restraints weight = 22585.065| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 3.08 r_work: 0.3716 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16677 Z= 0.139 Angle : 0.561 7.456 22692 Z= 0.294 Chirality : 0.046 0.206 2491 Planarity : 0.004 0.057 2933 Dihedral : 4.398 23.264 2268 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.66 % Favored : 96.19 % Rotamer: Outliers : 3.44 % Allowed : 13.78 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.12 (0.18), residues: 2022 helix: -1.51 (0.46), residues: 122 sheet: 0.14 (0.20), residues: 679 loop : -1.20 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 237 TYR 0.015 0.001 TYR B 265 PHE 0.015 0.001 PHE A 86 TRP 0.015 0.002 TRP B 64 HIS 0.004 0.001 HIS F 79 Details of bonding type rmsd covalent geometry : bond 0.00338 (16651) covalent geometry : angle 0.55971 (22640) SS BOND : bond 0.00611 ( 23) SS BOND : angle 0.77458 ( 46) hydrogen bonds : bond 0.03232 ( 517) hydrogen bonds : angle 5.98419 ( 1317) Misc. bond : bond 0.00035 ( 1) link_NAG-ASN : bond 0.00085 ( 2) link_NAG-ASN : angle 1.86505 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 106 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.0740 (ptm) cc_final: -0.1155 (mmm) REVERT: A 357 ARG cc_start: 0.8114 (ttm-80) cc_final: 0.7857 (ttp80) REVERT: A 361 CYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8173 (p) REVERT: A 406 GLU cc_start: 0.6662 (mt-10) cc_final: 0.6206 (mm-30) REVERT: A 436 TRP cc_start: 0.5327 (OUTLIER) cc_final: 0.3898 (p-90) REVERT: A 462 LYS cc_start: 0.8292 (mttp) cc_final: 0.7971 (pttm) REVERT: B 66 HIS cc_start: 0.6130 (m-70) cc_final: 0.5784 (m90) REVERT: B 100 ILE cc_start: 0.8539 (pt) cc_final: 0.7999 (tt) REVERT: B 156 GLU cc_start: 0.6470 (mp0) cc_final: 0.4658 (pt0) REVERT: B 177 MET cc_start: 0.2600 (mmp) cc_final: 0.2078 (mpp) REVERT: B 537 LYS cc_start: 0.8808 (tttm) cc_final: 0.8412 (tttp) REVERT: B 558 LYS cc_start: 0.7736 (pttt) cc_final: 0.7354 (mmmm) REVERT: C 47 MET cc_start: 0.1881 (OUTLIER) cc_final: 0.1040 (ptt) REVERT: C 100 LYS cc_start: 0.5032 (tptp) cc_final: 0.4015 (mtmt) REVERT: D 69 HIS cc_start: 0.5202 (OUTLIER) cc_final: 0.3732 (p-80) REVERT: D 177 MET cc_start: 0.2441 (mmp) cc_final: 0.1327 (mmt) REVERT: D 198 ASP cc_start: 0.8340 (t0) cc_final: 0.8136 (t0) REVERT: D 369 TYR cc_start: 0.5253 (OUTLIER) cc_final: 0.3717 (t80) REVERT: D 468 ILE cc_start: 0.4083 (OUTLIER) cc_final: 0.3661 (tt) REVERT: D 574 ASP cc_start: 0.8505 (t70) cc_final: 0.7964 (t0) REVERT: F 58 GLN cc_start: 0.3046 (OUTLIER) cc_final: 0.1338 (tt0) REVERT: F 82 MET cc_start: 0.2281 (mmt) cc_final: 0.0479 (ptm) outliers start: 62 outliers final: 38 residues processed: 159 average time/residue: 0.1014 time to fit residues: 25.7243 Evaluate side-chains 145 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 100 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 369 TYR Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain F residue 81 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 194 optimal weight: 30.0000 chunk 172 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 187 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN C 102 GLN F 44 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.240893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.169301 restraints weight = 22455.105| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 3.29 r_work: 0.3641 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 16677 Z= 0.227 Angle : 0.634 8.399 22692 Z= 0.331 Chirality : 0.049 0.282 2491 Planarity : 0.005 0.055 2933 Dihedral : 4.681 26.070 2268 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.55 % Favored : 95.30 % Rotamer: Outliers : 3.72 % Allowed : 14.17 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.23 (0.18), residues: 2022 helix: -1.65 (0.45), residues: 122 sheet: 0.02 (0.19), residues: 683 loop : -1.25 (0.17), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 45 TYR 0.021 0.002 TYR B 265 PHE 0.025 0.002 PHE A 86 TRP 0.017 0.002 TRP B 64 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00554 (16651) covalent geometry : angle 0.63296 (22640) SS BOND : bond 0.00457 ( 23) SS BOND : angle 0.92640 ( 46) hydrogen bonds : bond 0.03631 ( 517) hydrogen bonds : angle 6.05952 ( 1317) Misc. bond : bond 0.00036 ( 1) link_NAG-ASN : bond 0.00219 ( 2) link_NAG-ASN : angle 2.00789 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 101 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.0704 (ptm) cc_final: -0.1300 (mmm) REVERT: A 177 MET cc_start: 0.4667 (mmm) cc_final: 0.4465 (mmp) REVERT: A 357 ARG cc_start: 0.8233 (ttm-80) cc_final: 0.7966 (ttp80) REVERT: A 361 CYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8346 (p) REVERT: A 406 GLU cc_start: 0.6724 (mt-10) cc_final: 0.6023 (mm-30) REVERT: A 424 LYS cc_start: 0.8377 (mmmt) cc_final: 0.8052 (mmmt) REVERT: A 436 TRP cc_start: 0.5332 (OUTLIER) cc_final: 0.3743 (p-90) REVERT: A 462 LYS cc_start: 0.8274 (mttp) cc_final: 0.7919 (pttm) REVERT: A 505 TYR cc_start: 0.7572 (t80) cc_final: 0.7208 (t80) REVERT: B 66 HIS cc_start: 0.6285 (m-70) cc_final: 0.5846 (m90) REVERT: B 100 ILE cc_start: 0.8557 (pt) cc_final: 0.8030 (tt) REVERT: B 177 MET cc_start: 0.2743 (mmp) cc_final: 0.2290 (mpp) REVERT: B 537 LYS cc_start: 0.8949 (tttm) cc_final: 0.8698 (tttp) REVERT: B 558 LYS cc_start: 0.7816 (pttt) cc_final: 0.7456 (mmmm) REVERT: B 581 THR cc_start: 0.8304 (OUTLIER) cc_final: 0.7973 (p) REVERT: C 47 MET cc_start: 0.2254 (OUTLIER) cc_final: 0.1458 (ptt) REVERT: C 100 LYS cc_start: 0.5094 (tptp) cc_final: 0.4073 (mtmt) REVERT: D 69 HIS cc_start: 0.5135 (OUTLIER) cc_final: 0.3636 (p-80) REVERT: D 177 MET cc_start: 0.2818 (mmp) cc_final: 0.1731 (mmt) REVERT: D 369 TYR cc_start: 0.5262 (OUTLIER) cc_final: 0.3687 (t80) REVERT: D 468 ILE cc_start: 0.3997 (OUTLIER) cc_final: 0.3579 (tt) REVERT: D 574 ASP cc_start: 0.8619 (t70) cc_final: 0.8050 (t0) REVERT: F 44 GLN cc_start: 0.3856 (OUTLIER) cc_final: 0.3569 (mt0) REVERT: F 58 GLN cc_start: 0.3000 (OUTLIER) cc_final: 0.1468 (tt0) REVERT: F 81 GLN cc_start: 0.4830 (OUTLIER) cc_final: 0.4225 (tm-30) REVERT: F 82 MET cc_start: 0.2286 (mmt) cc_final: 0.0701 (ptm) outliers start: 67 outliers final: 46 residues processed: 158 average time/residue: 0.0976 time to fit residues: 24.9785 Evaluate side-chains 148 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 92 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 369 TYR Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain F residue 81 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 121 optimal weight: 1.9990 chunk 98 optimal weight: 0.0470 chunk 170 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 167 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN F 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.238778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.168765 restraints weight = 22238.475| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 2.97 r_work: 0.3645 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 16677 Z= 0.247 Angle : 0.647 7.794 22692 Z= 0.340 Chirality : 0.049 0.277 2491 Planarity : 0.005 0.054 2933 Dihedral : 4.803 23.546 2268 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.70 % Favored : 95.15 % Rotamer: Outliers : 3.50 % Allowed : 15.17 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.35 (0.18), residues: 2022 helix: -1.85 (0.44), residues: 122 sheet: -0.08 (0.19), residues: 685 loop : -1.30 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 45 TYR 0.029 0.002 TYR B 453 PHE 0.025 0.002 PHE A 86 TRP 0.020 0.002 TRP B 64 HIS 0.003 0.001 HIS D 519 Details of bonding type rmsd covalent geometry : bond 0.00601 (16651) covalent geometry : angle 0.64572 (22640) SS BOND : bond 0.00487 ( 23) SS BOND : angle 0.99214 ( 46) hydrogen bonds : bond 0.03691 ( 517) hydrogen bonds : angle 6.08169 ( 1317) Misc. bond : bond 0.00038 ( 1) link_NAG-ASN : bond 0.00163 ( 2) link_NAG-ASN : angle 1.98023 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 98 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.0742 (ptm) cc_final: -0.1617 (mmm) REVERT: A 133 PHE cc_start: 0.7103 (OUTLIER) cc_final: 0.6899 (t80) REVERT: A 304 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8495 (mtpt) REVERT: A 357 ARG cc_start: 0.8246 (ttm-80) cc_final: 0.8016 (ttp80) REVERT: A 361 CYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8433 (p) REVERT: A 406 GLU cc_start: 0.6744 (mt-10) cc_final: 0.6059 (mm-30) REVERT: A 436 TRP cc_start: 0.5330 (OUTLIER) cc_final: 0.3737 (p-90) REVERT: A 462 LYS cc_start: 0.8309 (mttp) cc_final: 0.7923 (pttm) REVERT: A 505 TYR cc_start: 0.7585 (t80) cc_final: 0.7213 (t80) REVERT: B 100 ILE cc_start: 0.8680 (pt) cc_final: 0.8142 (tt) REVERT: B 177 MET cc_start: 0.2872 (mmp) cc_final: 0.2508 (mpp) REVERT: B 558 LYS cc_start: 0.7922 (pttt) cc_final: 0.7616 (mmmm) REVERT: B 581 THR cc_start: 0.8264 (OUTLIER) cc_final: 0.7939 (p) REVERT: C 47 MET cc_start: 0.2210 (OUTLIER) cc_final: 0.1448 (ptt) REVERT: C 100 LYS cc_start: 0.5273 (tptp) cc_final: 0.4278 (mtmt) REVERT: D 177 MET cc_start: 0.2976 (mmp) cc_final: 0.2027 (mmt) REVERT: D 369 TYR cc_start: 0.5257 (OUTLIER) cc_final: 0.3686 (t80) REVERT: D 468 ILE cc_start: 0.4039 (OUTLIER) cc_final: 0.3594 (tt) REVERT: D 574 ASP cc_start: 0.8574 (t70) cc_final: 0.8002 (t0) REVERT: F 58 GLN cc_start: 0.3023 (OUTLIER) cc_final: 0.1662 (tt0) REVERT: F 81 GLN cc_start: 0.4858 (OUTLIER) cc_final: 0.4240 (tm-30) REVERT: F 82 MET cc_start: 0.2286 (mmt) cc_final: 0.0715 (ptm) outliers start: 63 outliers final: 49 residues processed: 151 average time/residue: 0.0860 time to fit residues: 21.6256 Evaluate side-chains 147 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 88 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 369 TYR Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain F residue 81 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 54 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 179 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 170 optimal weight: 20.0000 chunk 74 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN F 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.240834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.172929 restraints weight = 22580.597| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 3.24 r_work: 0.3683 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16677 Z= 0.143 Angle : 0.575 9.271 22692 Z= 0.299 Chirality : 0.046 0.208 2491 Planarity : 0.004 0.054 2933 Dihedral : 4.502 19.704 2268 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.76 % Favored : 96.09 % Rotamer: Outliers : 3.33 % Allowed : 15.72 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.24 (0.18), residues: 2022 helix: -1.82 (0.44), residues: 122 sheet: 0.08 (0.20), residues: 670 loop : -1.27 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 328 TYR 0.015 0.001 TYR B 265 PHE 0.021 0.001 PHE B 140 TRP 0.019 0.002 TRP B 64 HIS 0.002 0.001 HIS C 79 Details of bonding type rmsd covalent geometry : bond 0.00347 (16651) covalent geometry : angle 0.57365 (22640) SS BOND : bond 0.00315 ( 23) SS BOND : angle 0.80303 ( 46) hydrogen bonds : bond 0.03178 ( 517) hydrogen bonds : angle 5.86174 ( 1317) Misc. bond : bond 0.00024 ( 1) link_NAG-ASN : bond 0.00038 ( 2) link_NAG-ASN : angle 1.93440 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 97 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.0511 (ptm) cc_final: -0.1627 (mmm) REVERT: A 177 MET cc_start: 0.4093 (mmp) cc_final: 0.3725 (mmm) REVERT: A 357 ARG cc_start: 0.8118 (ttm-80) cc_final: 0.7865 (ttp80) REVERT: A 361 CYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8525 (p) REVERT: A 406 GLU cc_start: 0.6639 (mt-10) cc_final: 0.5942 (mm-30) REVERT: A 436 TRP cc_start: 0.5250 (OUTLIER) cc_final: 0.3709 (p-90) REVERT: A 505 TYR cc_start: 0.7563 (t80) cc_final: 0.7190 (t80) REVERT: B 100 ILE cc_start: 0.8609 (pt) cc_final: 0.8038 (tt) REVERT: B 177 MET cc_start: 0.2829 (mmp) cc_final: 0.2508 (mpp) REVERT: B 581 THR cc_start: 0.8093 (OUTLIER) cc_final: 0.7708 (p) REVERT: C 47 MET cc_start: 0.2301 (OUTLIER) cc_final: 0.1520 (ptt) REVERT: C 100 LYS cc_start: 0.5321 (tptp) cc_final: 0.4349 (mtmt) REVERT: D 177 MET cc_start: 0.2785 (mmp) cc_final: 0.2079 (mmt) REVERT: D 369 TYR cc_start: 0.5224 (OUTLIER) cc_final: 0.3699 (t80) REVERT: D 468 ILE cc_start: 0.4066 (OUTLIER) cc_final: 0.3659 (tt) REVERT: D 574 ASP cc_start: 0.8182 (t70) cc_final: 0.7583 (t0) REVERT: F 58 GLN cc_start: 0.3234 (OUTLIER) cc_final: 0.1917 (tt0) REVERT: F 81 GLN cc_start: 0.5003 (OUTLIER) cc_final: 0.4344 (tm-30) REVERT: F 82 MET cc_start: 0.2398 (mmt) cc_final: 0.0703 (ptm) outliers start: 60 outliers final: 37 residues processed: 150 average time/residue: 0.0893 time to fit residues: 22.3500 Evaluate side-chains 134 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 89 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 369 TYR Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain F residue 81 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 59 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 128 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 133 optimal weight: 20.0000 chunk 116 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN B 14 GLN D 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.235923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.198930 restraints weight = 22469.831| |-----------------------------------------------------------------------------| r_work (start): 0.4336 rms_B_bonded: 3.23 r_work: 0.3630 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 16677 Z= 0.318 Angle : 0.727 8.724 22692 Z= 0.379 Chirality : 0.052 0.311 2491 Planarity : 0.005 0.052 2933 Dihedral : 5.153 26.122 2268 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.38 % Favored : 93.47 % Rotamer: Outliers : 3.28 % Allowed : 15.44 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.54 (0.18), residues: 2022 helix: -1.93 (0.43), residues: 124 sheet: -0.11 (0.20), residues: 661 loop : -1.49 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 403 TYR 0.025 0.002 TYR B 265 PHE 0.029 0.003 PHE A 86 TRP 0.023 0.003 TRP B 64 HIS 0.005 0.001 HIS D 519 Details of bonding type rmsd covalent geometry : bond 0.00779 (16651) covalent geometry : angle 0.72451 (22640) SS BOND : bond 0.00505 ( 23) SS BOND : angle 1.13277 ( 46) hydrogen bonds : bond 0.04048 ( 517) hydrogen bonds : angle 6.21852 ( 1317) Misc. bond : bond 0.00040 ( 1) link_NAG-ASN : bond 0.00359 ( 2) link_NAG-ASN : angle 2.39498 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 90 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7134 (OUTLIER) cc_final: 0.6838 (t80) REVERT: A 177 MET cc_start: 0.3999 (mmp) cc_final: 0.3575 (mmm) REVERT: A 406 GLU cc_start: 0.6665 (mt-10) cc_final: 0.6254 (mm-30) REVERT: A 436 TRP cc_start: 0.5674 (OUTLIER) cc_final: 0.3941 (p-90) REVERT: B 100 ILE cc_start: 0.8580 (pt) cc_final: 0.8185 (tt) REVERT: B 581 THR cc_start: 0.8234 (OUTLIER) cc_final: 0.7899 (p) REVERT: C 47 MET cc_start: 0.3134 (OUTLIER) cc_final: 0.2201 (ptt) REVERT: C 100 LYS cc_start: 0.5604 (tptp) cc_final: 0.4804 (mtmt) REVERT: D 177 MET cc_start: 0.3233 (mmp) cc_final: 0.2579 (mmt) REVERT: D 369 TYR cc_start: 0.5072 (OUTLIER) cc_final: 0.3304 (t80) REVERT: D 468 ILE cc_start: 0.4617 (OUTLIER) cc_final: 0.4216 (tt) REVERT: D 574 ASP cc_start: 0.8289 (t70) cc_final: 0.7752 (t0) REVERT: D 592 PHE cc_start: 0.1000 (OUTLIER) cc_final: 0.0102 (t80) REVERT: F 58 GLN cc_start: 0.3513 (OUTLIER) cc_final: 0.2252 (tt0) REVERT: F 81 GLN cc_start: 0.5099 (OUTLIER) cc_final: 0.4485 (tm-30) REVERT: F 82 MET cc_start: 0.2573 (mmt) cc_final: 0.0830 (ptm) outliers start: 59 outliers final: 43 residues processed: 142 average time/residue: 0.0867 time to fit residues: 20.4767 Evaluate side-chains 135 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 83 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 369 TYR Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain F residue 81 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 53 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 166 optimal weight: 8.9990 chunk 113 optimal weight: 7.9990 chunk 188 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 168 optimal weight: 20.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** 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 = 0.4710 r_free = 0.4710 target = 0.237660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.196304 restraints weight = 22468.590| |-----------------------------------------------------------------------------| r_work (start): 0.4341 rms_B_bonded: 3.28 r_work: 0.3676 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16677 Z= 0.201 Angle : 0.642 8.867 22692 Z= 0.334 Chirality : 0.048 0.301 2491 Planarity : 0.004 0.053 2933 Dihedral : 4.917 24.615 2268 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.50 % Favored : 95.35 % Rotamer: Outliers : 3.06 % Allowed : 16.06 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.47 (0.18), residues: 2022 helix: -2.00 (0.43), residues: 126 sheet: -0.08 (0.20), residues: 665 loop : -1.42 (0.17), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 357 TYR 0.019 0.002 TYR B 265 PHE 0.022 0.002 PHE A 86 TRP 0.022 0.002 TRP B 64 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00489 (16651) covalent geometry : angle 0.64036 (22640) SS BOND : bond 0.00376 ( 23) SS BOND : angle 0.92606 ( 46) hydrogen bonds : bond 0.03523 ( 517) hydrogen bonds : angle 6.05573 ( 1317) Misc. bond : bond 0.00023 ( 1) link_NAG-ASN : bond 0.00186 ( 2) link_NAG-ASN : angle 2.13907 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 89 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: -0.1009 (ptm) cc_final: -0.1782 (mtt) REVERT: A 133 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.6979 (t80) REVERT: A 153 MET cc_start: 0.0425 (mtt) cc_final: 0.0131 (mtt) REVERT: A 177 MET cc_start: 0.3988 (mmp) cc_final: 0.3685 (mmm) REVERT: A 406 GLU cc_start: 0.6637 (mt-10) cc_final: 0.6215 (mm-30) REVERT: A 436 TRP cc_start: 0.5630 (OUTLIER) cc_final: 0.3898 (p-90) REVERT: B 100 ILE cc_start: 0.8557 (pt) cc_final: 0.8133 (tt) REVERT: B 437 ASN cc_start: 0.5327 (m-40) cc_final: 0.4926 (t0) REVERT: B 581 THR cc_start: 0.8293 (OUTLIER) cc_final: 0.7973 (p) REVERT: C 47 MET cc_start: 0.3138 (OUTLIER) cc_final: 0.2210 (ptt) REVERT: C 100 LYS cc_start: 0.5594 (tptp) cc_final: 0.4738 (mtmt) REVERT: D 177 MET cc_start: 0.3292 (mmp) cc_final: 0.2815 (mmt) REVERT: D 369 TYR cc_start: 0.5031 (OUTLIER) cc_final: 0.3384 (t80) REVERT: D 468 ILE cc_start: 0.4589 (OUTLIER) cc_final: 0.4217 (tt) REVERT: D 574 ASP cc_start: 0.8224 (t70) cc_final: 0.7720 (t0) REVERT: D 592 PHE cc_start: 0.1050 (OUTLIER) cc_final: 0.0192 (t80) REVERT: F 58 GLN cc_start: 0.3576 (OUTLIER) cc_final: 0.2438 (tt0) REVERT: F 81 GLN cc_start: 0.5245 (OUTLIER) cc_final: 0.4572 (tm-30) REVERT: F 82 MET cc_start: 0.2625 (mmt) cc_final: 0.0855 (ptm) outliers start: 55 outliers final: 43 residues processed: 137 average time/residue: 0.0849 time to fit residues: 19.8206 Evaluate side-chains 136 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 84 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 369 TYR Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain F residue 81 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 48 optimal weight: 4.9990 chunk 152 optimal weight: 0.2980 chunk 197 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 46 optimal weight: 0.1980 chunk 177 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.242643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.192067 restraints weight = 22352.290| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 3.19 r_work: 0.3685 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16677 Z= 0.117 Angle : 0.574 9.748 22692 Z= 0.298 Chirality : 0.046 0.224 2491 Planarity : 0.004 0.053 2933 Dihedral : 4.504 26.306 2268 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.10 % Favored : 95.75 % Rotamer: Outliers : 2.89 % Allowed : 16.22 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.31 (0.18), residues: 2022 helix: -1.88 (0.44), residues: 126 sheet: 0.12 (0.20), residues: 649 loop : -1.35 (0.17), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 357 TYR 0.014 0.001 TYR D 265 PHE 0.017 0.001 PHE B 140 TRP 0.022 0.002 TRP A 353 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00284 (16651) covalent geometry : angle 0.57266 (22640) SS BOND : bond 0.00255 ( 23) SS BOND : angle 0.68989 ( 46) hydrogen bonds : bond 0.02978 ( 517) hydrogen bonds : angle 5.79699 ( 1317) Misc. bond : bond 0.00012 ( 1) link_NAG-ASN : bond 0.00086 ( 2) link_NAG-ASN : angle 2.09475 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5124.97 seconds wall clock time: 87 minutes 57.19 seconds (5277.19 seconds total)