Starting phenix.real_space_refine on Sun May 18 20:33:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g7a_29804/05_2025/8g7a_29804.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7a_29804/05_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_29804/05_2025/8g7a_29804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7a_29804/05_2025/8g7a_29804.map" model { file = "/net/cci-nas-00/data/ceres_data/8g7a_29804/05_2025/8g7a_29804.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7a_29804/05_2025/8g7a_29804.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.94, per 1000 atoms: 0.67 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: 4.29 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.61 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: 5.81 Time building geometry restraints manager: 4.95 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: 8.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.810 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 40.160 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.190 ------------------------------------------------------------------------------- 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 : 23.01 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (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 TRP 0.066 0.004 TRP D 353 HIS 0.008 0.001 HIS F 79 PHE 0.059 0.002 PHE D 565 TYR 0.064 0.003 TYR B 423 ARG 0.015 0.001 ARG B 246 Details of bonding type rmsd link_NAG-ASN : bond 0.33096 ( 2) link_NAG-ASN : angle 12.61763 ( 6) hydrogen bonds : bond 0.14635 ( 517) hydrogen bonds : angle 8.08097 ( 1317) SS BOND : bond 0.00707 ( 23) SS BOND : angle 1.85678 ( 46) covalent geometry : bond 0.00589 (16651) covalent geometry : angle 0.83213 (22640) Misc. bond : bond 0.37715 ( 1) *********************** 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 : 1.716 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: 0.2866 time to fit residues: 83.0403 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 : 1.653 ------------------------------------------------------------------------------- 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 169 optimal weight: 7.9990 chunk 152 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 157 optimal weight: 20.0000 chunk 60 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 182 optimal weight: 5.9990 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN F 44 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.247472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.177597 restraints weight = 23135.135| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 3.35 r_work: 0.3733 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16677 Z= 0.169 Angle : 0.641 11.480 22692 Z= 0.340 Chirality : 0.048 0.203 2491 Planarity : 0.006 0.068 2933 Dihedral : 5.131 30.349 2279 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.91 % Favored : 95.94 % Rotamer: Outliers : 2.72 % Allowed : 11.83 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.18), residues: 2022 helix: -2.06 (0.43), residues: 126 sheet: -0.17 (0.20), residues: 674 loop : -1.26 (0.17), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 436 HIS 0.003 0.001 HIS B 207 PHE 0.035 0.002 PHE D 400 TYR 0.031 0.002 TYR B 423 ARG 0.016 0.001 ARG D 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 2) link_NAG-ASN : angle 2.36634 ( 6) hydrogen bonds : bond 0.04284 ( 517) hydrogen bonds : angle 6.88982 ( 1317) SS BOND : bond 0.00352 ( 23) SS BOND : angle 0.98100 ( 46) covalent geometry : bond 0.00406 (16651) covalent geometry : angle 0.63902 (22640) Misc. bond : bond 0.00155 ( 1) *********************** 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 163 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 114 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 80 LEU cc_start: 0.3703 (OUTLIER) cc_final: 0.3254 (tp) REVERT: A 158 ARG cc_start: 0.7297 (mtt-85) cc_final: 0.7076 (mtp85) REVERT: A 406 GLU cc_start: 0.6631 (mt-10) cc_final: 0.6020 (mm-30) REVERT: A 436 TRP cc_start: 0.5222 (OUTLIER) cc_final: 0.3819 (p-90) REVERT: A 462 LYS cc_start: 0.8216 (mttp) cc_final: 0.7891 (pttm) REVERT: B 66 HIS cc_start: 0.5871 (m-70) cc_final: 0.5503 (m90) REVERT: B 177 MET cc_start: 0.2636 (mmp) cc_final: 0.2130 (mpp) REVERT: B 305 SER cc_start: 0.9238 (p) cc_final: 0.9024 (t) REVERT: B 537 LYS cc_start: 0.8899 (tttt) cc_final: 0.8658 (tttp) REVERT: B 558 LYS cc_start: 0.7572 (pttt) cc_final: 0.7251 (mmmm) REVERT: C 34 MET cc_start: 0.4624 (mpp) cc_final: 0.4408 (mmm) REVERT: C 100 LYS cc_start: 0.4792 (tptp) cc_final: 0.3624 (mtmt) REVERT: D 69 HIS cc_start: 0.4868 (p-80) cc_final: 0.3719 (p-80) REVERT: D 177 MET cc_start: 0.2043 (mmp) cc_final: 0.0851 (mmt) REVERT: D 239 GLN cc_start: 0.8556 (tt0) cc_final: 0.8334 (tt0) REVERT: D 429 PHE cc_start: 0.4658 (OUTLIER) cc_final: 0.4410 (t80) REVERT: F 44 GLN cc_start: 0.3664 (OUTLIER) cc_final: 0.2733 (mm-40) REVERT: F 82 MET cc_start: 0.2901 (mmt) cc_final: 0.0822 (ptm) outliers start: 49 outliers final: 24 residues processed: 159 average time/residue: 0.2508 time to fit residues: 63.2303 Evaluate side-chains 125 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 1.784 ------------------------------------------------------------------------------- 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 B residue 42 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 236 THR 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 63 THR Chi-restraints excluded: chain D residue 114 THR 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 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 44 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 73 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 188 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 124 optimal weight: 0.0670 chunk 187 optimal weight: 0.9980 chunk 183 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.242034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.171519 restraints weight = 22385.307| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 3.31 r_work: 0.3646 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16677 Z= 0.219 Angle : 0.661 12.359 22692 Z= 0.348 Chirality : 0.049 0.272 2491 Planarity : 0.005 0.058 2933 Dihedral : 5.027 29.215 2268 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.45 % Favored : 95.40 % Rotamer: Outliers : 3.94 % Allowed : 11.94 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.18), residues: 2022 helix: -1.94 (0.44), residues: 128 sheet: -0.21 (0.19), residues: 719 loop : -1.32 (0.17), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 353 HIS 0.004 0.001 HIS A 66 PHE 0.025 0.002 PHE A 86 TYR 0.025 0.002 TYR A 160 ARG 0.011 0.001 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 2) link_NAG-ASN : angle 1.92280 ( 6) hydrogen bonds : bond 0.03983 ( 517) hydrogen bonds : angle 6.53703 ( 1317) SS BOND : bond 0.00532 ( 23) SS BOND : angle 1.46127 ( 46) covalent geometry : bond 0.00529 (16651) covalent geometry : angle 0.65820 (22640) Misc. bond : bond 0.00009 ( 1) *********************** 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 187 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 116 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.7424 (mtt-85) cc_final: 0.7019 (mtp85) REVERT: A 357 ARG cc_start: 0.8053 (ttm-80) cc_final: 0.7714 (ttp80) REVERT: A 406 GLU cc_start: 0.6751 (mt-10) cc_final: 0.6107 (mm-30) REVERT: A 436 TRP cc_start: 0.5156 (OUTLIER) cc_final: 0.3688 (p-90) REVERT: A 454 ARG cc_start: 0.7030 (ptp-110) cc_final: 0.6662 (ptm160) REVERT: A 462 LYS cc_start: 0.8246 (mttp) cc_final: 0.7905 (pttm) REVERT: B 66 HIS cc_start: 0.6008 (m-70) cc_final: 0.5650 (m90) REVERT: B 156 GLU cc_start: 0.6823 (mp0) cc_final: 0.4940 (pt0) REVERT: B 177 MET cc_start: 0.2625 (mmp) cc_final: 0.2206 (mpp) REVERT: B 233 ILE cc_start: 0.6834 (pt) cc_final: 0.6583 (pt) REVERT: B 305 SER cc_start: 0.9300 (p) cc_final: 0.9073 (t) REVERT: B 537 LYS cc_start: 0.9016 (tttt) cc_final: 0.8675 (tttp) REVERT: B 558 LYS cc_start: 0.7676 (pttt) cc_final: 0.7431 (mmmm) REVERT: C 34 MET cc_start: 0.4642 (mpp) cc_final: 0.4299 (mmm) REVERT: D 177 MET cc_start: 0.2401 (mmp) cc_final: 0.1262 (mmt) REVERT: D 369 TYR cc_start: 0.5343 (OUTLIER) cc_final: 0.3701 (t80) REVERT: D 429 PHE cc_start: 0.4796 (OUTLIER) cc_final: 0.4575 (t80) REVERT: D 468 ILE cc_start: 0.3952 (OUTLIER) cc_final: 0.3568 (tt) REVERT: D 574 ASP cc_start: 0.8272 (t70) cc_final: 0.7740 (t0) REVERT: F 58 GLN cc_start: 0.2723 (OUTLIER) cc_final: 0.1024 (tt0) REVERT: F 82 MET cc_start: 0.3003 (mmt) cc_final: 0.0729 (ptm) outliers start: 71 outliers final: 42 residues processed: 179 average time/residue: 0.2559 time to fit residues: 70.2301 Evaluate side-chains 148 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 101 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain A residue 18 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 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 236 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 465 GLU 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 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 505 TYR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 18 LEU 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 114 THR Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 236 THR 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 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 15 optimal weight: 0.8980 chunk 133 optimal weight: 7.9990 chunk 165 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 173 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 67 optimal weight: 20.0000 chunk 137 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.243462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.154786 restraints weight = 22688.166| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 3.79 r_work: 0.3585 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16677 Z= 0.127 Angle : 0.572 8.014 22692 Z= 0.301 Chirality : 0.046 0.214 2491 Planarity : 0.004 0.058 2933 Dihedral : 4.653 23.140 2268 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.46 % Favored : 96.39 % Rotamer: Outliers : 2.44 % Allowed : 14.06 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.18), residues: 2022 helix: -1.82 (0.44), residues: 129 sheet: -0.04 (0.20), residues: 682 loop : -1.27 (0.17), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 64 HIS 0.003 0.001 HIS A 69 PHE 0.015 0.001 PHE A 329 TYR 0.021 0.002 TYR A 160 ARG 0.006 0.001 ARG F 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00029 ( 2) link_NAG-ASN : angle 1.87281 ( 6) hydrogen bonds : bond 0.03301 ( 517) hydrogen bonds : angle 6.24127 ( 1317) SS BOND : bond 0.00486 ( 23) SS BOND : angle 0.96553 ( 46) covalent geometry : bond 0.00301 (16651) covalent geometry : angle 0.57011 (22640) Misc. bond : bond 0.00026 ( 1) *********************** 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 153 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 109 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.0621 (ptm) cc_final: -0.1036 (mmm) REVERT: A 357 ARG cc_start: 0.8056 (ttm-80) cc_final: 0.7733 (ttp80) REVERT: A 406 GLU cc_start: 0.6597 (mt-10) cc_final: 0.5897 (mm-30) REVERT: A 436 TRP cc_start: 0.4915 (OUTLIER) cc_final: 0.3591 (p-90) REVERT: A 454 ARG cc_start: 0.6954 (ptp-110) cc_final: 0.6449 (ptm160) REVERT: A 462 LYS cc_start: 0.8007 (mttp) cc_final: 0.7678 (pttm) REVERT: A 554 GLU cc_start: 0.6774 (mm-30) cc_final: 0.6412 (mt-10) REVERT: B 66 HIS cc_start: 0.6176 (m-70) cc_final: 0.5753 (m90) REVERT: B 100 ILE cc_start: 0.8476 (pt) cc_final: 0.7892 (tt) REVERT: B 177 MET cc_start: 0.2646 (mmp) cc_final: 0.2144 (mpp) REVERT: B 305 SER cc_start: 0.9328 (p) cc_final: 0.9102 (t) REVERT: B 537 LYS cc_start: 0.8958 (tttt) cc_final: 0.8642 (tttp) REVERT: B 558 LYS cc_start: 0.7684 (pttt) cc_final: 0.7231 (mmmm) REVERT: C 47 MET cc_start: 0.1543 (OUTLIER) cc_final: 0.0940 (ptt) REVERT: C 100 LYS cc_start: 0.4341 (tptp) cc_final: 0.3352 (mtmt) REVERT: D 177 MET cc_start: 0.2297 (mmp) cc_final: 0.1213 (mmt) REVERT: D 429 PHE cc_start: 0.4737 (OUTLIER) cc_final: 0.4478 (t80) REVERT: D 468 ILE cc_start: 0.3823 (OUTLIER) cc_final: 0.3431 (tt) REVERT: D 574 ASP cc_start: 0.8308 (t70) cc_final: 0.7732 (t0) REVERT: F 58 GLN cc_start: 0.2625 (OUTLIER) cc_final: 0.1085 (tt0) REVERT: F 82 MET cc_start: 0.2905 (mmt) cc_final: 0.0716 (ptm) outliers start: 44 outliers final: 24 residues processed: 148 average time/residue: 0.2318 time to fit residues: 55.1776 Evaluate side-chains 128 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 1.584 ------------------------------------------------------------------------------- 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 133 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 90 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 47 MET Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 429 PHE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 74 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 57 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 0.0770 chunk 88 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.241285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.168687 restraints weight = 22764.845| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 3.23 r_work: 0.3642 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16677 Z= 0.206 Angle : 0.612 7.695 22692 Z= 0.321 Chirality : 0.048 0.264 2491 Planarity : 0.005 0.057 2933 Dihedral : 4.705 25.245 2268 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.85 % Favored : 95.00 % Rotamer: Outliers : 3.39 % Allowed : 14.33 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.18), residues: 2022 helix: -1.71 (0.45), residues: 122 sheet: -0.01 (0.20), residues: 680 loop : -1.29 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 64 HIS 0.004 0.001 HIS A 66 PHE 0.020 0.002 PHE A 86 TYR 0.019 0.002 TYR B 265 ARG 0.004 0.001 ARG B 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00172 ( 2) link_NAG-ASN : angle 1.94803 ( 6) hydrogen bonds : bond 0.03570 ( 517) hydrogen bonds : angle 6.19664 ( 1317) SS BOND : bond 0.00566 ( 23) SS BOND : angle 0.91697 ( 46) covalent geometry : bond 0.00504 (16651) covalent geometry : angle 0.61070 (22640) Misc. bond : bond 0.00052 ( 1) *********************** 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 165 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 104 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.0663 (ptm) cc_final: -0.1424 (mmm) REVERT: A 177 MET cc_start: 0.4301 (mmp) cc_final: 0.4056 (mmm) REVERT: A 357 ARG cc_start: 0.8206 (ttm-80) cc_final: 0.7979 (ttp80) REVERT: A 361 CYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8275 (p) REVERT: A 406 GLU cc_start: 0.6721 (mt-10) cc_final: 0.6038 (mm-30) REVERT: A 436 TRP cc_start: 0.5294 (OUTLIER) cc_final: 0.3729 (p-90) REVERT: A 454 ARG cc_start: 0.7182 (ptp-110) cc_final: 0.6473 (ptm160) REVERT: A 462 LYS cc_start: 0.8309 (mttp) cc_final: 0.7936 (pttm) REVERT: B 66 HIS cc_start: 0.6239 (m-70) cc_final: 0.5785 (m90) REVERT: B 100 ILE cc_start: 0.8551 (pt) cc_final: 0.8012 (tt) REVERT: B 177 MET cc_start: 0.2882 (mmp) cc_final: 0.2550 (mpp) REVERT: B 305 SER cc_start: 0.9378 (p) cc_final: 0.9140 (t) REVERT: B 523 THR cc_start: 0.7847 (p) cc_final: 0.7449 (t) REVERT: B 558 LYS cc_start: 0.7786 (pttt) cc_final: 0.7435 (mmmm) REVERT: B 581 THR cc_start: 0.8156 (OUTLIER) cc_final: 0.7914 (p) REVERT: C 47 MET cc_start: 0.1754 (OUTLIER) cc_final: 0.1037 (ptt) REVERT: D 69 HIS cc_start: 0.5087 (OUTLIER) cc_final: 0.3548 (p-80) REVERT: D 177 MET cc_start: 0.2795 (mmp) cc_final: 0.1710 (mmt) REVERT: D 369 TYR cc_start: 0.5354 (OUTLIER) cc_final: 0.3731 (t80) REVERT: D 429 PHE cc_start: 0.4796 (OUTLIER) cc_final: 0.4539 (t80) REVERT: D 468 ILE cc_start: 0.4001 (OUTLIER) cc_final: 0.3599 (tt) REVERT: D 574 ASP cc_start: 0.8552 (t70) cc_final: 0.7995 (t0) REVERT: F 58 GLN cc_start: 0.3060 (OUTLIER) cc_final: 0.1406 (tt0) REVERT: F 82 MET cc_start: 0.2372 (mmt) cc_final: 0.0612 (ptm) outliers start: 61 outliers final: 39 residues processed: 156 average time/residue: 0.2506 time to fit residues: 61.9810 Evaluate side-chains 144 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 96 time to evaluate : 1.883 ------------------------------------------------------------------------------- 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 114 THR Chi-restraints excluded: chain A residue 133 PHE 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 392 PHE 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 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 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 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 299 THR Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 369 TYR Chi-restraints excluded: chain D residue 429 PHE 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 54 ILE Chi-restraints excluded: chain F residue 58 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 39 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 157 optimal weight: 0.9990 chunk 158 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 86 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 176 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.241877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.170356 restraints weight = 22404.717| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 2.94 r_work: 0.3688 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16677 Z= 0.144 Angle : 0.573 8.346 22692 Z= 0.299 Chirality : 0.046 0.219 2491 Planarity : 0.004 0.056 2933 Dihedral : 4.525 21.898 2268 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.46 % Favored : 96.39 % Rotamer: Outliers : 3.44 % Allowed : 14.89 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.18), residues: 2022 helix: -1.79 (0.44), residues: 122 sheet: 0.02 (0.20), residues: 676 loop : -1.28 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 64 HIS 0.003 0.001 HIS C 79 PHE 0.016 0.001 PHE A 86 TYR 0.017 0.001 TYR A 423 ARG 0.003 0.000 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00051 ( 2) link_NAG-ASN : angle 1.85653 ( 6) hydrogen bonds : bond 0.03239 ( 517) hydrogen bonds : angle 6.05090 ( 1317) SS BOND : bond 0.00366 ( 23) SS BOND : angle 0.74199 ( 46) covalent geometry : bond 0.00343 (16651) covalent geometry : angle 0.57148 (22640) Misc. bond : bond 0.00030 ( 1) *********************** 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 163 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 101 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.0660 (ptm) cc_final: -0.1317 (mmm) REVERT: A 177 MET cc_start: 0.4264 (mmp) cc_final: 0.4023 (mmm) REVERT: A 361 CYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8286 (p) REVERT: A 406 GLU cc_start: 0.6616 (mt-10) cc_final: 0.5955 (mm-30) REVERT: A 436 TRP cc_start: 0.5287 (OUTLIER) cc_final: 0.3705 (p-90) REVERT: B 66 HIS cc_start: 0.6199 (m-70) cc_final: 0.5807 (m90) REVERT: B 100 ILE cc_start: 0.8552 (pt) cc_final: 0.7994 (tt) REVERT: B 177 MET cc_start: 0.2878 (mmp) cc_final: 0.2605 (mpp) REVERT: B 305 SER cc_start: 0.9354 (p) cc_final: 0.9108 (t) REVERT: B 523 THR cc_start: 0.7998 (p) cc_final: 0.7611 (t) REVERT: B 558 LYS cc_start: 0.7799 (pttt) cc_final: 0.7483 (mmmm) REVERT: B 581 THR cc_start: 0.8143 (OUTLIER) cc_final: 0.7880 (p) REVERT: C 47 MET cc_start: 0.1807 (OUTLIER) cc_final: 0.1104 (ptt) REVERT: D 69 HIS cc_start: 0.5084 (OUTLIER) cc_final: 0.3579 (p-80) REVERT: D 177 MET cc_start: 0.2662 (mmp) cc_final: 0.1662 (mmt) REVERT: D 369 TYR cc_start: 0.5232 (OUTLIER) cc_final: 0.3669 (t80) REVERT: D 429 PHE cc_start: 0.4835 (OUTLIER) cc_final: 0.4598 (t80) REVERT: D 468 ILE cc_start: 0.4055 (OUTLIER) cc_final: 0.3668 (tt) REVERT: D 574 ASP cc_start: 0.8425 (t70) cc_final: 0.7849 (t0) REVERT: F 58 GLN cc_start: 0.3118 (OUTLIER) cc_final: 0.1550 (tt0) REVERT: F 81 GLN cc_start: 0.4892 (OUTLIER) cc_final: 0.4266 (tm-30) REVERT: F 82 MET cc_start: 0.2297 (mmt) cc_final: 0.0710 (ptm) outliers start: 62 outliers final: 40 residues processed: 155 average time/residue: 0.2409 time to fit residues: 59.8754 Evaluate side-chains 143 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 93 time to evaluate : 1.738 ------------------------------------------------------------------------------- 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 136 CYS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 392 PHE 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 143 VAL Chi-restraints excluded: chain B residue 224 GLU 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 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 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 326 ILE Chi-restraints excluded: chain D residue 369 TYR Chi-restraints excluded: chain D residue 429 PHE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 63 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 chunk 199 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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** A 99 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN D 207 HIS ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.235299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.205077 restraints weight = 22241.948| |-----------------------------------------------------------------------------| r_work (start): 0.4399 rms_B_bonded: 2.09 r_work: 0.3742 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.081 16677 Z= 0.444 Angle : 0.849 8.709 22692 Z= 0.444 Chirality : 0.056 0.359 2491 Planarity : 0.006 0.053 2933 Dihedral : 5.723 28.333 2268 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.22 % Favored : 92.63 % Rotamer: Outliers : 4.94 % Allowed : 14.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.18), residues: 2022 helix: -2.22 (0.40), residues: 131 sheet: -0.36 (0.20), residues: 646 loop : -1.66 (0.16), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 104 HIS 0.007 0.002 HIS A 66 PHE 0.037 0.003 PHE A 400 TYR 0.034 0.003 TYR B 495 ARG 0.008 0.001 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00513 ( 2) link_NAG-ASN : angle 2.79404 ( 6) hydrogen bonds : bond 0.04771 ( 517) hydrogen bonds : angle 6.75217 ( 1317) SS BOND : bond 0.00748 ( 23) SS BOND : angle 1.47184 ( 46) covalent geometry : bond 0.01068 (16651) covalent geometry : angle 0.84620 (22640) Misc. bond : bond 0.00060 ( 1) *********************** 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 185 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 96 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7896 (t0) cc_final: 0.7591 (m-40) REVERT: A 406 GLU cc_start: 0.6561 (mt-10) cc_final: 0.6289 (mm-30) REVERT: A 436 TRP cc_start: 0.5668 (OUTLIER) cc_final: 0.3986 (p-90) REVERT: B 100 ILE cc_start: 0.8486 (pt) cc_final: 0.8109 (tt) REVERT: B 305 SER cc_start: 0.9163 (p) cc_final: 0.8891 (t) REVERT: B 574 ASP cc_start: 0.8383 (p0) cc_final: 0.8139 (p0) REVERT: B 581 THR cc_start: 0.7963 (OUTLIER) cc_final: 0.7651 (p) REVERT: C 47 MET cc_start: 0.2914 (OUTLIER) cc_final: 0.2111 (ptt) REVERT: D 177 MET cc_start: 0.3245 (mmp) cc_final: 0.2547 (mmt) REVERT: D 369 TYR cc_start: 0.5045 (OUTLIER) cc_final: 0.3198 (t80) REVERT: D 468 ILE cc_start: 0.4736 (OUTLIER) cc_final: 0.4324 (tt) REVERT: D 574 ASP cc_start: 0.8209 (t0) cc_final: 0.7629 (t0) REVERT: D 592 PHE cc_start: 0.0828 (OUTLIER) cc_final: -0.0045 (t80) REVERT: F 58 GLN cc_start: 0.3649 (OUTLIER) cc_final: 0.2229 (tt0) REVERT: F 81 GLN cc_start: 0.4861 (OUTLIER) cc_final: 0.4473 (tm-30) REVERT: F 82 MET cc_start: 0.2642 (mmt) cc_final: 0.0896 (ptm) outliers start: 89 outliers final: 60 residues processed: 173 average time/residue: 0.2268 time to fit residues: 63.6702 Evaluate side-chains 156 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 88 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 86 ILE 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 136 CYS Chi-restraints excluded: chain A residue 176 LEU 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 392 PHE 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 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 136 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 157 PHE 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 505 TYR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 69 ILE 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 136 CYS Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 236 THR 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 534 VAL Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 568 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 54 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 188 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 147 optimal weight: 0.2980 chunk 28 optimal weight: 0.6980 chunk 135 optimal weight: 0.2980 chunk 163 optimal weight: 0.2980 chunk 193 optimal weight: 20.0000 chunk 92 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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** A 99 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN C 44 GLN D 317 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.242225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.211231 restraints weight = 22411.564| |-----------------------------------------------------------------------------| r_work (start): 0.4451 rms_B_bonded: 2.05 r_work: 0.4088 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work: 0.4033 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16677 Z= 0.123 Angle : 0.602 9.434 22692 Z= 0.316 Chirality : 0.046 0.235 2491 Planarity : 0.004 0.054 2933 Dihedral : 4.891 29.639 2268 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.41 % Favored : 96.44 % Rotamer: Outliers : 2.67 % Allowed : 16.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.18), residues: 2022 helix: -2.11 (0.42), residues: 126 sheet: -0.22 (0.20), residues: 671 loop : -1.47 (0.17), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 64 HIS 0.004 0.001 HIS B 245 PHE 0.018 0.002 PHE E 37 TYR 0.020 0.001 TYR A 423 ARG 0.005 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 2) link_NAG-ASN : angle 2.26441 ( 6) hydrogen bonds : bond 0.03203 ( 517) hydrogen bonds : angle 6.20809 ( 1317) SS BOND : bond 0.00349 ( 23) SS BOND : angle 0.84023 ( 46) covalent geometry : bond 0.00284 (16651) covalent geometry : angle 0.60058 (22640) Misc. bond : bond 0.00028 ( 1) *********************** 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 149 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 101 time to evaluate : 1.711 Fit side-chains revert: symmetry clash REVERT: A 177 MET cc_start: 0.3702 (mmp) cc_final: 0.3369 (mmm) REVERT: A 436 TRP cc_start: 0.5756 (OUTLIER) cc_final: 0.4068 (p-90) REVERT: B 305 SER cc_start: 0.9144 (p) cc_final: 0.8932 (t) REVERT: B 581 THR cc_start: 0.7844 (OUTLIER) cc_final: 0.7602 (p) REVERT: C 47 MET cc_start: 0.3045 (OUTLIER) cc_final: 0.2269 (ptt) REVERT: C 100 LYS cc_start: 0.5346 (tptp) cc_final: 0.4767 (mtmt) REVERT: D 177 MET cc_start: 0.2827 (mmp) cc_final: 0.2588 (mmt) REVERT: D 369 TYR cc_start: 0.4215 (OUTLIER) cc_final: 0.2716 (t80) REVERT: D 574 ASP cc_start: 0.7985 (t0) cc_final: 0.7576 (t0) REVERT: D 592 PHE cc_start: 0.0972 (OUTLIER) cc_final: 0.0245 (t80) REVERT: F 58 GLN cc_start: 0.3172 (OUTLIER) cc_final: 0.2715 (tt0) REVERT: F 82 MET cc_start: 0.2649 (mmt) cc_final: 0.1149 (ptm) outliers start: 48 outliers final: 29 residues processed: 142 average time/residue: 0.2049 time to fit residues: 49.3659 Evaluate side-chains 119 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 84 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 143 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 281 GLU 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 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 581 THR Chi-restraints excluded: chain C residue 47 MET 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 114 THR Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 369 TYR 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 11 LEU Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 58 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 109 optimal weight: 20.0000 chunk 177 optimal weight: 8.9990 chunk 165 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 164 optimal weight: 0.8980 chunk 149 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 0.0060 chunk 128 optimal weight: 9.9990 chunk 160 optimal weight: 1.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- 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** A 99 ASN ** B 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 = 0.4725 r_free = 0.4725 target = 0.240524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.213593 restraints weight = 22378.013| |-----------------------------------------------------------------------------| r_work (start): 0.4491 rms_B_bonded: 1.73 r_work: 0.4016 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16677 Z= 0.166 Angle : 0.627 13.920 22692 Z= 0.324 Chirality : 0.047 0.247 2491 Planarity : 0.004 0.054 2933 Dihedral : 4.827 26.316 2268 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.80 % Favored : 95.05 % Rotamer: Outliers : 2.67 % Allowed : 16.78 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.18), residues: 2022 helix: -2.03 (0.43), residues: 126 sheet: -0.09 (0.20), residues: 669 loop : -1.44 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 64 HIS 0.005 0.001 HIS B 207 PHE 0.018 0.002 PHE B 238 TYR 0.024 0.002 TYR A 423 ARG 0.004 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 2) link_NAG-ASN : angle 2.14521 ( 6) hydrogen bonds : bond 0.03333 ( 517) hydrogen bonds : angle 6.08021 ( 1317) SS BOND : bond 0.00535 ( 23) SS BOND : angle 1.03192 ( 46) covalent geometry : bond 0.00403 (16651) covalent geometry : angle 0.62493 (22640) Misc. bond : bond 0.00048 ( 1) *********************** 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 136 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 88 time to evaluate : 1.616 Fit side-chains revert: symmetry clash REVERT: A 177 MET cc_start: 0.3777 (mmp) cc_final: 0.3462 (mmm) REVERT: A 436 TRP cc_start: 0.5720 (OUTLIER) cc_final: 0.4007 (p-90) REVERT: B 581 THR cc_start: 0.7496 (OUTLIER) cc_final: 0.7267 (p) REVERT: C 47 MET cc_start: 0.2826 (OUTLIER) cc_final: 0.2052 (ptt) REVERT: C 100 LYS cc_start: 0.5323 (tptp) cc_final: 0.4633 (mtmt) REVERT: D 177 MET cc_start: 0.2848 (mmp) cc_final: 0.2532 (mmt) REVERT: D 369 TYR cc_start: 0.4555 (OUTLIER) cc_final: 0.2984 (t80) REVERT: D 574 ASP cc_start: 0.7777 (t0) cc_final: 0.7322 (t0) REVERT: D 592 PHE cc_start: 0.0858 (OUTLIER) cc_final: 0.0195 (t80) REVERT: F 58 GLN cc_start: 0.3219 (OUTLIER) cc_final: 0.2681 (tt0) REVERT: F 82 MET cc_start: 0.2771 (mmt) cc_final: 0.0894 (ptm) outliers start: 48 outliers final: 36 residues processed: 129 average time/residue: 0.2059 time to fit residues: 45.1109 Evaluate side-chains 124 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 82 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 143 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 281 GLU 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 63 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 157 PHE 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 581 THR Chi-restraints excluded: chain C residue 47 MET 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 114 THR Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 369 TYR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 163 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 161 optimal weight: 0.6980 chunk 56 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 194 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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** A 99 ASN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 GLN C 76 ASN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.240090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.210771 restraints weight = 22664.824| |-----------------------------------------------------------------------------| r_work (start): 0.4477 rms_B_bonded: 1.97 r_work: 0.4103 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work: 0.4060 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16677 Z= 0.126 Angle : 0.594 12.787 22692 Z= 0.306 Chirality : 0.046 0.219 2491 Planarity : 0.004 0.054 2933 Dihedral : 4.620 27.119 2268 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.61 % Favored : 96.24 % Rotamer: Outliers : 2.17 % Allowed : 17.11 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.18), residues: 2022 helix: -1.95 (0.44), residues: 126 sheet: -0.03 (0.20), residues: 696 loop : -1.35 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 64 HIS 0.004 0.001 HIS B 207 PHE 0.016 0.001 PHE E 37 TYR 0.024 0.001 TYR A 423 ARG 0.004 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00110 ( 2) link_NAG-ASN : angle 2.03454 ( 6) hydrogen bonds : bond 0.03083 ( 517) hydrogen bonds : angle 5.91776 ( 1317) SS BOND : bond 0.00303 ( 23) SS BOND : angle 0.84597 ( 46) covalent geometry : bond 0.00303 (16651) covalent geometry : angle 0.59249 (22640) Misc. bond : bond 0.00029 ( 1) ********************** 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 133 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 94 time to evaluate : 1.658 Fit side-chains revert: symmetry clash REVERT: E 47 MET cc_start: 0.0956 (mmm) cc_final: -0.0653 (ptm) REVERT: A 177 MET cc_start: 0.3605 (mmp) cc_final: 0.3354 (mmm) REVERT: A 436 TRP cc_start: 0.5706 (OUTLIER) cc_final: 0.4034 (p-90) REVERT: B 581 THR cc_start: 0.7803 (OUTLIER) cc_final: 0.7484 (p) REVERT: C 47 MET cc_start: 0.2961 (OUTLIER) cc_final: 0.2207 (ptt) REVERT: C 100 LYS cc_start: 0.5356 (tptp) cc_final: 0.4798 (mtmt) REVERT: D 177 MET cc_start: 0.2970 (mmp) cc_final: 0.2654 (mmt) REVERT: D 369 TYR cc_start: 0.4272 (OUTLIER) cc_final: 0.2899 (t80) REVERT: D 574 ASP cc_start: 0.7831 (t0) cc_final: 0.7420 (t0) REVERT: F 58 GLN cc_start: 0.3103 (OUTLIER) cc_final: 0.2774 (pt0) REVERT: F 82 MET cc_start: 0.2549 (mmt) cc_final: 0.0814 (ptm) outliers start: 39 outliers final: 32 residues processed: 127 average time/residue: 0.2106 time to fit residues: 44.9578 Evaluate side-chains 129 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 92 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 143 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 281 GLU 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 94 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 157 PHE 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 581 THR Chi-restraints excluded: chain C residue 47 MET 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 114 THR Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 369 TYR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 96 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 185 optimal weight: 0.5980 chunk 149 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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** A 99 ASN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.238565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.197810 restraints weight = 22593.039| |-----------------------------------------------------------------------------| r_work (start): 0.4328 rms_B_bonded: 3.18 r_work: 0.3673 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16677 Z= 0.150 Angle : 0.599 12.689 22692 Z= 0.309 Chirality : 0.046 0.241 2491 Planarity : 0.004 0.054 2933 Dihedral : 4.602 25.443 2268 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.60 % Favored : 95.25 % Rotamer: Outliers : 2.50 % Allowed : 16.78 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.18), residues: 2022 helix: -1.72 (0.46), residues: 119 sheet: 0.00 (0.20), residues: 686 loop : -1.34 (0.17), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 64 HIS 0.004 0.001 HIS B 207 PHE 0.016 0.002 PHE B 238 TYR 0.023 0.001 TYR A 423 ARG 0.004 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00144 ( 2) link_NAG-ASN : angle 1.96705 ( 6) hydrogen bonds : bond 0.03208 ( 517) hydrogen bonds : angle 5.85575 ( 1317) SS BOND : bond 0.00327 ( 23) SS BOND : angle 0.81345 ( 46) covalent geometry : bond 0.00366 (16651) covalent geometry : angle 0.59774 (22640) Misc. bond : bond 0.00033 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10368.77 seconds wall clock time: 179 minutes 46.57 seconds (10786.57 seconds total)