Starting phenix.real_space_refine on Sun Jun 15 15:05:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g7a_29804/06_2025/8g7a_29804.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7a_29804/06_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_29804/06_2025/8g7a_29804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7a_29804/06_2025/8g7a_29804.map" model { file = "/net/cci-nas-00/data/ceres_data/8g7a_29804/06_2025/8g7a_29804.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7a_29804/06_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-5710/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: 13.33, per 1000 atoms: 0.82 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: 4.46 Conformation dependent library (CDL) restraints added in 2.5 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: 2.21 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: 5.87 Time building geometry restraints manager: 5.13 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: 0.010 Normalize map: mean=0, sd=1: 444.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 0.790 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 42.830 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 492.920 ------------------------------------------------------------------------------- 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 : 1.695 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: 0.2922 time to fit residues: 84.1584 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 : 1.406 ------------------------------------------------------------------------------- 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 = 0.247473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.178406 restraints weight = 23135.138| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 3.29 r_work: 0.3736 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 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 2.36636 ( 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 : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 80 LEU cc_start: 0.3695 (OUTLIER) cc_final: 0.3248 (tp) REVERT: A 158 ARG cc_start: 0.7311 (mtt-85) cc_final: 0.7090 (mtp85) REVERT: A 406 GLU cc_start: 0.6636 (mt-10) cc_final: 0.6023 (mm-30) REVERT: A 436 TRP cc_start: 0.5201 (OUTLIER) cc_final: 0.3811 (p-90) REVERT: A 454 ARG cc_start: 0.6158 (mtt180) cc_final: 0.5956 (ptp-110) REVERT: A 462 LYS cc_start: 0.8220 (mttp) cc_final: 0.7894 (pttm) REVERT: B 66 HIS cc_start: 0.5863 (m-70) cc_final: 0.5498 (m90) REVERT: B 177 MET cc_start: 0.2643 (mmp) cc_final: 0.2139 (mpp) REVERT: B 305 SER cc_start: 0.9228 (p) cc_final: 0.9014 (t) REVERT: B 537 LYS cc_start: 0.8901 (tttt) cc_final: 0.8659 (tttp) REVERT: B 558 LYS cc_start: 0.7566 (pttt) cc_final: 0.7263 (mmmm) REVERT: C 34 MET cc_start: 0.4617 (mpp) cc_final: 0.4400 (mmm) REVERT: C 100 LYS cc_start: 0.4812 (tptp) cc_final: 0.3641 (mtmt) REVERT: D 69 HIS cc_start: 0.4875 (p-80) cc_final: 0.3726 (p-80) REVERT: D 177 MET cc_start: 0.2044 (mmp) cc_final: 0.0854 (mmt) REVERT: D 239 GLN cc_start: 0.8550 (tt0) cc_final: 0.8331 (tt0) REVERT: D 429 PHE cc_start: 0.4662 (OUTLIER) cc_final: 0.4416 (t80) REVERT: F 44 GLN cc_start: 0.3665 (OUTLIER) cc_final: 0.2741 (mm-40) REVERT: F 82 MET cc_start: 0.2920 (mmt) cc_final: 0.0824 (ptm) outliers start: 49 outliers final: 24 residues processed: 159 average time/residue: 0.2452 time to fit residues: 61.6719 Evaluate side-chains 127 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 1.868 ------------------------------------------------------------------------------- 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: 10.0000 chunk 102 optimal weight: 9.9990 chunk 188 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 107 optimal weight: 20.0000 chunk 83 optimal weight: 4.9990 chunk 124 optimal weight: 0.0970 chunk 187 optimal weight: 0.9990 chunk 183 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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 44 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.241992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.170268 restraints weight = 22375.683| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 3.16 r_work: 0.3668 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16677 Z= 0.222 Angle : 0.650 9.574 22692 Z= 0.342 Chirality : 0.049 0.266 2491 Planarity : 0.005 0.060 2933 Dihedral : 4.993 29.128 2268 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.40 % Favored : 95.45 % Rotamer: Outliers : 3.78 % Allowed : 11.94 % Favored : 84.28 % 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: -1.41 (0.18), residues: 2022 helix: -1.93 (0.44), residues: 128 sheet: -0.19 (0.19), residues: 717 loop : -1.31 (0.17), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 64 HIS 0.004 0.001 HIS A 66 PHE 0.024 0.002 PHE A 86 TYR 0.028 0.002 TYR A 160 ARG 0.015 0.001 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 2) link_NAG-ASN : angle 1.96919 ( 6) hydrogen bonds : bond 0.03987 ( 517) hydrogen bonds : angle 6.54131 ( 1317) SS BOND : bond 0.00587 ( 23) SS BOND : angle 1.36908 ( 46) covalent geometry : bond 0.00538 (16651) covalent geometry : angle 0.64658 (22640) Misc. bond : bond 0.00040 ( 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 183 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 115 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.7504 (mtt-85) cc_final: 0.7064 (mtp85) REVERT: A 357 ARG cc_start: 0.8168 (ttm-80) cc_final: 0.7913 (mtp-110) REVERT: A 406 GLU cc_start: 0.6810 (mt-10) cc_final: 0.6153 (mm-30) REVERT: A 436 TRP cc_start: 0.5221 (OUTLIER) cc_final: 0.3736 (p-90) REVERT: A 462 LYS cc_start: 0.8297 (mttp) cc_final: 0.7958 (pttm) REVERT: B 66 HIS cc_start: 0.6141 (m-70) cc_final: 0.5770 (m90) REVERT: B 156 GLU cc_start: 0.6852 (mp0) cc_final: 0.4996 (pt0) REVERT: B 177 MET cc_start: 0.2752 (mmp) cc_final: 0.2198 (mpp) REVERT: B 233 ILE cc_start: 0.6935 (pt) cc_final: 0.6674 (pt) REVERT: B 305 SER cc_start: 0.9368 (p) cc_final: 0.9158 (t) REVERT: B 537 LYS cc_start: 0.9094 (tttt) cc_final: 0.8747 (tttp) REVERT: B 558 LYS cc_start: 0.7798 (pttt) cc_final: 0.7441 (mmmm) REVERT: C 34 MET cc_start: 0.4638 (mpp) cc_final: 0.4301 (mmm) REVERT: D 177 MET cc_start: 0.2466 (mmp) cc_final: 0.1255 (mmt) REVERT: D 369 TYR cc_start: 0.5299 (OUTLIER) cc_final: 0.3636 (t80) REVERT: D 429 PHE cc_start: 0.4803 (OUTLIER) cc_final: 0.4593 (t80) REVERT: D 468 ILE cc_start: 0.3999 (OUTLIER) cc_final: 0.3613 (tt) REVERT: D 574 ASP cc_start: 0.8531 (t70) cc_final: 0.8045 (t0) REVERT: F 58 GLN cc_start: 0.2703 (OUTLIER) cc_final: 0.1001 (tt0) REVERT: F 82 MET cc_start: 0.2999 (mmt) cc_final: 0.0745 (ptm) outliers start: 68 outliers final: 42 residues processed: 174 average time/residue: 0.2604 time to fit residues: 71.0902 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 : 1.904 ------------------------------------------------------------------------------- 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 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 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 465 GLU Chi-restraints excluded: chain B residue 42 VAL 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 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: 1.9990 chunk 133 optimal weight: 20.0000 chunk 165 optimal weight: 10.0000 chunk 167 optimal weight: 8.9990 chunk 173 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 67 optimal weight: 20.0000 chunk 137 optimal weight: 0.7980 chunk 144 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4775 r_free = 0.4775 target = 0.243816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.172126 restraints weight = 22549.925| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 3.02 r_work: 0.3699 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16677 Z= 0.141 Angle : 0.583 8.121 22692 Z= 0.307 Chirality : 0.047 0.230 2491 Planarity : 0.004 0.058 2933 Dihedral : 4.702 24.361 2268 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.61 % Favored : 96.24 % Rotamer: Outliers : 3.06 % Allowed : 13.39 % Favored : 83.56 % 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: -1.31 (0.18), residues: 2022 helix: -1.80 (0.44), residues: 129 sheet: -0.07 (0.20), residues: 684 loop : -1.26 (0.17), residues: 1209 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 0.002 PHE D 86 TYR 0.022 0.002 TYR A 160 ARG 0.005 0.001 ARG E 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00058 ( 2) link_NAG-ASN : angle 1.87349 ( 6) hydrogen bonds : bond 0.03382 ( 517) hydrogen bonds : angle 6.25767 ( 1317) SS BOND : bond 0.00385 ( 23) SS BOND : angle 0.97416 ( 46) covalent geometry : bond 0.00333 (16651) covalent geometry : angle 0.58085 (22640) Misc. bond : bond 0.00034 ( 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 162 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 107 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.0667 (ptm) cc_final: -0.1083 (mmm) REVERT: A 357 ARG cc_start: 0.8162 (ttm-80) cc_final: 0.7827 (ttp80) REVERT: A 406 GLU cc_start: 0.6745 (mt-10) cc_final: 0.6057 (mm-30) REVERT: A 436 TRP cc_start: 0.5238 (OUTLIER) cc_final: 0.3715 (p-90) REVERT: A 462 LYS cc_start: 0.8290 (mttp) cc_final: 0.7949 (pttm) REVERT: A 554 GLU cc_start: 0.6902 (mm-30) cc_final: 0.6506 (mt-10) REVERT: B 66 HIS cc_start: 0.6147 (m-70) cc_final: 0.5797 (m90) REVERT: B 100 ILE cc_start: 0.8530 (pt) cc_final: 0.7992 (tt) REVERT: B 177 MET cc_start: 0.2692 (mmp) cc_final: 0.2222 (mpp) REVERT: B 305 SER cc_start: 0.9358 (p) cc_final: 0.9150 (t) REVERT: B 537 LYS cc_start: 0.9056 (tttt) cc_final: 0.8820 (tttp) REVERT: B 558 LYS cc_start: 0.7775 (pttt) cc_final: 0.7397 (mmmm) REVERT: C 34 MET cc_start: 0.4477 (mpp) cc_final: 0.4274 (mmm) REVERT: C 47 MET cc_start: 0.1894 (OUTLIER) cc_final: 0.1204 (ptt) REVERT: C 100 LYS cc_start: 0.4573 (tptp) cc_final: 0.3532 (mtmt) REVERT: D 177 MET cc_start: 0.2365 (mmp) cc_final: 0.1253 (mmt) REVERT: D 429 PHE cc_start: 0.4824 (OUTLIER) cc_final: 0.4582 (t80) REVERT: D 468 ILE cc_start: 0.4020 (OUTLIER) cc_final: 0.3633 (tt) REVERT: D 574 ASP cc_start: 0.8492 (t70) cc_final: 0.7989 (t0) REVERT: F 58 GLN cc_start: 0.2705 (OUTLIER) cc_final: 0.1062 (tt0) REVERT: F 82 MET cc_start: 0.3031 (mmt) cc_final: 0.0743 (ptm) outliers start: 55 outliers final: 32 residues processed: 157 average time/residue: 0.2418 time to fit residues: 61.0798 Evaluate side-chains 135 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 304 LYS 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 68 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 SER 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 63 THR Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 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: 0.7980 chunk 101 optimal weight: 0.2980 chunk 5 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 81 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** D 501 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 = 0.4770 r_free = 0.4770 target = 0.242883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.171114 restraints weight = 22928.934| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 2.98 r_work: 0.3705 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3556 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16677 Z= 0.140 Angle : 0.572 7.925 22692 Z= 0.300 Chirality : 0.046 0.209 2491 Planarity : 0.004 0.058 2933 Dihedral : 4.473 22.300 2268 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.45 % Favored : 95.40 % Rotamer: Outliers : 3.00 % Allowed : 14.22 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.20 (0.18), residues: 2022 helix: -1.58 (0.46), residues: 122 sheet: -0.01 (0.20), residues: 675 loop : -1.19 (0.17), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 64 HIS 0.004 0.001 HIS F 79 PHE 0.015 0.002 PHE A 86 TYR 0.018 0.002 TYR A 160 ARG 0.009 0.001 ARG F 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00077 ( 2) link_NAG-ASN : angle 1.85209 ( 6) hydrogen bonds : bond 0.03227 ( 517) hydrogen bonds : angle 6.00203 ( 1317) SS BOND : bond 0.00425 ( 23) SS BOND : angle 0.85238 ( 46) covalent geometry : bond 0.00337 (16651) covalent geometry : angle 0.57044 (22640) Misc. bond : bond 0.00046 ( 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 164 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 110 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.0606 (ptm) cc_final: -0.1336 (mmm) REVERT: A 177 MET cc_start: 0.4172 (mmp) cc_final: 0.3945 (mmm) REVERT: A 361 CYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8236 (p) REVERT: A 406 GLU cc_start: 0.6670 (mt-10) cc_final: 0.6012 (mm-30) REVERT: A 436 TRP cc_start: 0.5338 (OUTLIER) cc_final: 0.3732 (p-90) REVERT: A 462 LYS cc_start: 0.8277 (mttp) cc_final: 0.7911 (pttm) REVERT: B 66 HIS cc_start: 0.6151 (m-70) cc_final: 0.5790 (m90) REVERT: B 100 ILE cc_start: 0.8546 (pt) cc_final: 0.8008 (tt) REVERT: B 156 GLU cc_start: 0.6485 (mp0) cc_final: 0.4696 (pt0) REVERT: B 177 MET cc_start: 0.2893 (mmp) cc_final: 0.2554 (mpp) REVERT: B 305 SER cc_start: 0.9353 (p) cc_final: 0.9148 (t) REVERT: B 558 LYS cc_start: 0.7753 (pttt) cc_final: 0.7431 (mmmm) REVERT: B 581 THR cc_start: 0.8302 (OUTLIER) cc_final: 0.7557 (p) REVERT: B 583 GLU cc_start: 0.7877 (pt0) cc_final: 0.7638 (pm20) REVERT: C 34 MET cc_start: 0.4239 (mpp) cc_final: 0.4027 (mmm) REVERT: C 47 MET cc_start: 0.1796 (OUTLIER) cc_final: 0.1093 (ptt) REVERT: D 69 HIS cc_start: 0.5122 (OUTLIER) cc_final: 0.3604 (p-80) REVERT: D 177 MET cc_start: 0.2599 (mmp) cc_final: 0.1498 (mmt) REVERT: D 369 TYR cc_start: 0.5236 (OUTLIER) cc_final: 0.3686 (t80) REVERT: D 429 PHE cc_start: 0.4834 (OUTLIER) cc_final: 0.4588 (t80) REVERT: D 468 ILE cc_start: 0.3983 (OUTLIER) cc_final: 0.3605 (tt) REVERT: D 574 ASP cc_start: 0.8430 (t70) cc_final: 0.7887 (t0) REVERT: F 58 GLN cc_start: 0.2999 (OUTLIER) cc_final: 0.1359 (tt0) REVERT: F 82 MET cc_start: 0.2249 (mmt) cc_final: 0.0515 (ptm) outliers start: 54 outliers final: 32 residues processed: 157 average time/residue: 0.2771 time to fit residues: 70.0601 Evaluate side-chains 144 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 103 time to evaluate : 1.961 ------------------------------------------------------------------------------- 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 361 CYS Chi-restraints excluded: chain A residue 436 TRP 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 90 VAL Chi-restraints excluded: chain B residue 94 SER 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 114 THR 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: 9.9990 chunk 46 optimal weight: 10.0000 chunk 157 optimal weight: 0.1980 chunk 158 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 86 optimal weight: 0.6980 chunk 162 optimal weight: 0.8980 chunk 176 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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** F 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.242917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.170014 restraints weight = 22536.553| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 3.10 r_work: 0.3698 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16677 Z= 0.143 Angle : 0.566 9.164 22692 Z= 0.295 Chirality : 0.046 0.219 2491 Planarity : 0.004 0.056 2933 Dihedral : 4.441 22.470 2268 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.76 % Favored : 96.09 % Rotamer: Outliers : 3.56 % Allowed : 14.33 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.16 (0.18), residues: 2022 helix: -1.60 (0.46), residues: 122 sheet: 0.05 (0.20), residues: 682 loop : -1.19 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 64 HIS 0.002 0.001 HIS C 79 PHE 0.015 0.001 PHE A 86 TYR 0.018 0.001 TYR A 423 ARG 0.004 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00082 ( 2) link_NAG-ASN : angle 1.85436 ( 6) hydrogen bonds : bond 0.03213 ( 517) hydrogen bonds : angle 5.95214 ( 1317) SS BOND : bond 0.00342 ( 23) SS BOND : angle 0.73909 ( 46) covalent geometry : bond 0.00346 (16651) covalent geometry : angle 0.56482 (22640) Misc. bond : bond 0.00022 ( 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 168 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 104 time to evaluate : 2.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.0646 (ptm) cc_final: -0.1331 (mmm) REVERT: A 177 MET cc_start: 0.4234 (mmp) cc_final: 0.4026 (mmm) REVERT: A 361 CYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8204 (p) REVERT: A 406 GLU cc_start: 0.6648 (mt-10) cc_final: 0.5974 (mm-30) REVERT: A 436 TRP cc_start: 0.5298 (OUTLIER) cc_final: 0.3716 (p-90) REVERT: B 66 HIS cc_start: 0.6170 (m-70) cc_final: 0.5805 (m90) REVERT: B 100 ILE cc_start: 0.8536 (pt) cc_final: 0.7984 (tt) REVERT: B 153 MET cc_start: 0.1832 (mmm) cc_final: 0.1629 (mmm) REVERT: B 156 GLU cc_start: 0.6607 (mp0) cc_final: 0.4738 (pt0) REVERT: B 177 MET cc_start: 0.2828 (mmp) cc_final: 0.2524 (mpp) REVERT: B 305 SER cc_start: 0.9350 (p) cc_final: 0.9112 (t) REVERT: B 537 LYS cc_start: 0.8887 (tttm) cc_final: 0.8532 (tttp) REVERT: B 558 LYS cc_start: 0.7802 (pttt) cc_final: 0.7486 (mmmm) REVERT: B 581 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.7972 (p) REVERT: C 34 MET cc_start: 0.4279 (mpp) cc_final: 0.4033 (mmm) REVERT: C 47 MET cc_start: 0.1709 (OUTLIER) cc_final: 0.1024 (ptt) REVERT: D 69 HIS cc_start: 0.5097 (OUTLIER) cc_final: 0.3626 (p-80) REVERT: D 177 MET cc_start: 0.2700 (mmp) cc_final: 0.1632 (mmt) REVERT: D 369 TYR cc_start: 0.5229 (OUTLIER) cc_final: 0.3695 (t80) REVERT: D 429 PHE cc_start: 0.4818 (OUTLIER) cc_final: 0.4558 (t80) REVERT: D 468 ILE cc_start: 0.4009 (OUTLIER) cc_final: 0.3619 (tt) REVERT: D 574 ASP cc_start: 0.8407 (t70) cc_final: 0.7838 (t0) REVERT: F 58 GLN cc_start: 0.3074 (OUTLIER) cc_final: 0.1523 (tt0) REVERT: F 82 MET cc_start: 0.2318 (mmt) cc_final: 0.0535 (ptm) outliers start: 64 outliers final: 47 residues processed: 159 average time/residue: 0.2940 time to fit residues: 79.0432 Evaluate side-chains 154 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 98 time to evaluate : 1.653 ------------------------------------------------------------------------------- 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 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 118 LEU Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 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 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 224 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 266 TYR 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 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: 9.9990 chunk 129 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 chunk 199 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 200 optimal weight: 6.9990 chunk 67 optimal weight: 0.0060 chunk 142 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 overall best weight: 2.9802 ------------------------------------------------------------------------------- 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 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 207 HIS ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.237680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.167148 restraints weight = 22259.135| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.93 r_work: 0.3617 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 16677 Z= 0.299 Angle : 0.706 7.878 22692 Z= 0.370 Chirality : 0.051 0.325 2491 Planarity : 0.005 0.054 2933 Dihedral : 5.116 25.515 2268 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.13 % Favored : 93.72 % Rotamer: Outliers : 4.50 % Allowed : 14.06 % Favored : 81.44 % 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: -1.52 (0.18), residues: 2022 helix: -1.96 (0.41), residues: 132 sheet: -0.10 (0.20), residues: 675 loop : -1.48 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 64 HIS 0.005 0.001 HIS A 66 PHE 0.028 0.003 PHE A 86 TYR 0.026 0.002 TYR B 265 ARG 0.006 0.001 ARG A 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00339 ( 2) link_NAG-ASN : angle 2.39223 ( 6) hydrogen bonds : bond 0.04017 ( 517) hydrogen bonds : angle 6.28268 ( 1317) SS BOND : bond 0.00529 ( 23) SS BOND : angle 1.13625 ( 46) covalent geometry : bond 0.00724 (16651) covalent geometry : angle 0.70414 (22640) Misc. bond : bond 0.00024 ( 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 176 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 95 time to evaluate : 2.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 CYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8418 (p) REVERT: A 406 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6200 (mm-30) REVERT: A 436 TRP cc_start: 0.5281 (OUTLIER) cc_final: 0.3706 (p-90) REVERT: B 100 ILE cc_start: 0.8699 (pt) cc_final: 0.8203 (tt) REVERT: B 153 MET cc_start: 0.1638 (mmm) cc_final: 0.1404 (mmm) REVERT: B 305 SER cc_start: 0.9390 (p) cc_final: 0.9136 (t) REVERT: B 558 LYS cc_start: 0.7912 (pttt) cc_final: 0.7605 (mmmm) REVERT: B 581 THR cc_start: 0.8237 (OUTLIER) cc_final: 0.7903 (p) REVERT: C 34 MET cc_start: 0.4490 (mpp) cc_final: 0.4280 (mmm) REVERT: C 47 MET cc_start: 0.1817 (OUTLIER) cc_final: 0.1105 (ptt) REVERT: D 117 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7710 (tp) REVERT: D 177 MET cc_start: 0.3152 (mmp) cc_final: 0.2357 (mmt) REVERT: D 369 TYR cc_start: 0.5214 (OUTLIER) cc_final: 0.3713 (t80) REVERT: D 429 PHE cc_start: 0.4764 (OUTLIER) cc_final: 0.4514 (t80) REVERT: D 468 ILE cc_start: 0.4042 (OUTLIER) cc_final: 0.3587 (tt) REVERT: D 574 ASP cc_start: 0.8628 (t70) cc_final: 0.7981 (t0) REVERT: D 592 PHE cc_start: 0.0454 (OUTLIER) cc_final: -0.0632 (t80) REVERT: F 58 GLN cc_start: 0.3154 (OUTLIER) cc_final: 0.1685 (tt0) REVERT: F 81 GLN cc_start: 0.4800 (OUTLIER) cc_final: 0.4178 (tm-30) REVERT: F 82 MET cc_start: 0.2317 (mmt) cc_final: 0.0753 (ptm) outliers start: 81 outliers final: 50 residues processed: 166 average time/residue: 0.2834 time to fit residues: 81.1412 Evaluate side-chains 143 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 82 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 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 289 VAL 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 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 126 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 391 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 369 TYR Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 553 THR 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: 0.0070 chunk 62 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 147 optimal weight: 0.0870 chunk 28 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 193 optimal weight: 20.0000 chunk 92 optimal weight: 0.7980 chunk 120 optimal weight: 0.5980 overall best weight: 0.4776 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.240951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.170938 restraints weight = 22442.839| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 3.26 r_work: 0.3687 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16677 Z= 0.112 Angle : 0.575 9.043 22692 Z= 0.301 Chirality : 0.046 0.194 2491 Planarity : 0.004 0.054 2933 Dihedral : 4.593 25.976 2268 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.46 % Favored : 96.39 % Rotamer: Outliers : 2.72 % Allowed : 15.94 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.32 (0.18), residues: 2022 helix: -1.93 (0.42), residues: 128 sheet: 0.07 (0.20), residues: 664 loop : -1.34 (0.17), residues: 1230 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 0.017 0.001 PHE B 140 TYR 0.023 0.001 TYR B 453 ARG 0.004 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 2) link_NAG-ASN : angle 2.07524 ( 6) hydrogen bonds : bond 0.03131 ( 517) hydrogen bonds : angle 5.93989 ( 1317) SS BOND : bond 0.00292 ( 23) SS BOND : angle 1.10359 ( 46) covalent geometry : bond 0.00264 (16651) covalent geometry : angle 0.57276 (22640) Misc. bond : bond 0.00029 ( 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 152 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 103 time to evaluate : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4069 (mmp) cc_final: 0.3769 (mmm) REVERT: A 361 CYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8444 (p) REVERT: A 406 GLU cc_start: 0.6604 (mt-10) cc_final: 0.5935 (mm-30) REVERT: A 423 TYR cc_start: 0.8276 (t80) cc_final: 0.8014 (t80) REVERT: A 436 TRP cc_start: 0.5227 (OUTLIER) cc_final: 0.3679 (p-90) REVERT: B 100 ILE cc_start: 0.8592 (pt) cc_final: 0.8090 (tt) REVERT: B 305 SER cc_start: 0.9275 (p) cc_final: 0.9013 (t) REVERT: B 437 ASN cc_start: 0.5148 (m-40) cc_final: 0.4595 (t0) REVERT: B 537 LYS cc_start: 0.8861 (tttm) cc_final: 0.8638 (tttp) REVERT: B 551 VAL cc_start: 0.8917 (OUTLIER) cc_final: 0.8706 (p) REVERT: B 581 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7734 (p) REVERT: C 47 MET cc_start: 0.1900 (OUTLIER) cc_final: 0.1171 (ptt) REVERT: D 177 MET cc_start: 0.2840 (mmp) cc_final: 0.2172 (mmt) REVERT: D 198 ASP cc_start: 0.8234 (t0) cc_final: 0.8023 (t0) REVERT: D 369 TYR cc_start: 0.5222 (OUTLIER) cc_final: 0.3723 (t80) REVERT: D 429 PHE cc_start: 0.4832 (OUTLIER) cc_final: 0.4580 (t80) REVERT: D 468 ILE cc_start: 0.4050 (OUTLIER) cc_final: 0.3641 (tt) REVERT: D 574 ASP cc_start: 0.8167 (t70) cc_final: 0.7525 (t0) REVERT: F 58 GLN cc_start: 0.3273 (OUTLIER) cc_final: 0.1917 (tt0) REVERT: F 81 GLN cc_start: 0.4836 (OUTLIER) cc_final: 0.4183 (tm-30) REVERT: F 82 MET cc_start: 0.2333 (mmt) cc_final: 0.0686 (ptm) outliers start: 49 outliers final: 33 residues processed: 144 average time/residue: 0.2304 time to fit residues: 54.7145 Evaluate side-chains 135 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 92 time to evaluate : 1.680 ------------------------------------------------------------------------------- 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 136 CYS Chi-restraints excluded: chain A residue 143 VAL 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 402 ILE Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 551 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 C residue 69 ILE 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 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 553 THR Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain F residue 81 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 109 optimal weight: 9.9990 chunk 177 optimal weight: 5.9990 chunk 165 optimal weight: 0.7980 chunk 106 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 chunk 149 optimal weight: 0.0570 chunk 183 optimal weight: 7.9990 chunk 4 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 overall best weight: 1.9704 ------------------------------------------------------------------------------- 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 14 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.239487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.216050 restraints weight = 22256.205| |-----------------------------------------------------------------------------| r_work (start): 0.4502 rms_B_bonded: 1.60 r_work: 0.4058 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16677 Z= 0.206 Angle : 0.627 8.510 22692 Z= 0.326 Chirality : 0.048 0.290 2491 Planarity : 0.004 0.053 2933 Dihedral : 4.742 26.405 2268 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.14 % Favored : 94.71 % Rotamer: Outliers : 2.94 % Allowed : 16.11 % 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: -1.37 (0.18), residues: 2022 helix: -1.88 (0.43), residues: 126 sheet: -0.04 (0.20), residues: 676 loop : -1.35 (0.17), residues: 1220 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 0.020 0.002 PHE B 238 TYR 0.020 0.002 TYR B 265 ARG 0.004 0.001 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 2) link_NAG-ASN : angle 2.12337 ( 6) hydrogen bonds : bond 0.03464 ( 517) hydrogen bonds : angle 5.95103 ( 1317) SS BOND : bond 0.00361 ( 23) SS BOND : angle 1.04780 ( 46) covalent geometry : bond 0.00500 (16651) covalent geometry : angle 0.62456 (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 145 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 92 time to evaluate : 2.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 MET cc_start: 0.3162 (mmm) cc_final: 0.2405 (mpp) REVERT: A 177 MET cc_start: 0.3756 (mmp) cc_final: 0.3389 (mmm) REVERT: A 436 TRP cc_start: 0.5666 (OUTLIER) cc_final: 0.3978 (p-90) REVERT: B 100 ILE cc_start: 0.8123 (pt) cc_final: 0.7886 (tt) REVERT: B 581 THR cc_start: 0.7601 (OUTLIER) cc_final: 0.7329 (p) REVERT: C 47 MET cc_start: 0.2878 (OUTLIER) cc_final: 0.2148 (ptt) REVERT: C 100 LYS cc_start: 0.5218 (tptp) cc_final: 0.4661 (mtmt) REVERT: D 177 MET cc_start: 0.2736 (mmp) cc_final: 0.2310 (mmt) REVERT: D 369 TYR cc_start: 0.4555 (OUTLIER) cc_final: 0.2906 (t80) REVERT: D 574 ASP cc_start: 0.7700 (t70) cc_final: 0.7269 (t0) REVERT: F 58 GLN cc_start: 0.3442 (OUTLIER) cc_final: 0.2836 (tt0) REVERT: F 82 MET cc_start: 0.2641 (mmt) cc_final: 0.1060 (ptm) outliers start: 53 outliers final: 40 residues processed: 136 average time/residue: 0.2344 time to fit residues: 53.7288 Evaluate side-chains 133 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 88 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 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 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 B residue 63 THR Chi-restraints excluded: chain B residue 68 ILE 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 551 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 69 ILE 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 266 TYR 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 553 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 163 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 161 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 194 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.241640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.216272 restraints weight = 22648.266| |-----------------------------------------------------------------------------| r_work (start): 0.4514 rms_B_bonded: 1.61 r_work: 0.4156 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16677 Z= 0.149 Angle : 0.589 8.598 22692 Z= 0.307 Chirality : 0.047 0.272 2491 Planarity : 0.004 0.053 2933 Dihedral : 4.604 25.970 2268 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.56 % Favored : 96.29 % Rotamer: Outliers : 2.56 % Allowed : 16.39 % Favored : 81.06 % 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: -1.26 (0.18), residues: 2022 helix: -1.80 (0.45), residues: 120 sheet: 0.09 (0.20), residues: 663 loop : -1.30 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 353 HIS 0.004 0.001 HIS B 207 PHE 0.017 0.002 PHE B 79 TYR 0.024 0.001 TYR A 423 ARG 0.007 0.000 ARG B 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00116 ( 2) link_NAG-ASN : angle 2.00870 ( 6) hydrogen bonds : bond 0.03161 ( 517) hydrogen bonds : angle 5.93270 ( 1317) SS BOND : bond 0.00305 ( 23) SS BOND : angle 0.88830 ( 46) covalent geometry : bond 0.00363 (16651) covalent geometry : angle 0.58714 (22640) Misc. bond : bond 0.00036 ( 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 139 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 93 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: -0.0360 (ptm) cc_final: -0.1413 (mtt) REVERT: A 177 MET cc_start: 0.3655 (mmp) cc_final: 0.3358 (mmm) REVERT: A 436 TRP cc_start: 0.5587 (OUTLIER) cc_final: 0.3888 (p-90) REVERT: B 581 THR cc_start: 0.7569 (OUTLIER) cc_final: 0.7291 (p) REVERT: C 47 MET cc_start: 0.2856 (OUTLIER) cc_final: 0.2152 (ptt) REVERT: C 100 LYS cc_start: 0.5247 (tptp) cc_final: 0.4711 (mtmt) REVERT: D 177 MET cc_start: 0.2774 (mmp) cc_final: 0.2505 (mmt) REVERT: D 369 TYR cc_start: 0.4292 (OUTLIER) cc_final: 0.2868 (t80) REVERT: D 574 ASP cc_start: 0.7619 (t70) cc_final: 0.7180 (t0) REVERT: F 58 GLN cc_start: 0.3311 (OUTLIER) cc_final: 0.2952 (tt0) REVERT: F 82 MET cc_start: 0.2691 (mmt) cc_final: 0.0987 (ptm) outliers start: 46 outliers final: 36 residues processed: 130 average time/residue: 0.2212 time to fit residues: 48.8373 Evaluate side-chains 131 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 90 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 289 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 69 ILE 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 266 TYR 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 553 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 59 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 163 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 chunk 185 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.238001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.203882 restraints weight = 22664.101| |-----------------------------------------------------------------------------| r_work (start): 0.4397 rms_B_bonded: 2.40 r_work: 0.3738 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16677 Z= 0.195 Angle : 0.624 11.901 22692 Z= 0.323 Chirality : 0.048 0.294 2491 Planarity : 0.004 0.053 2933 Dihedral : 4.724 24.140 2268 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.14 % Favored : 94.71 % Rotamer: Outliers : 2.83 % Allowed : 16.22 % 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: -1.32 (0.18), residues: 2022 helix: -1.86 (0.43), residues: 126 sheet: 0.06 (0.20), residues: 660 loop : -1.34 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 353 HIS 0.005 0.001 HIS B 207 PHE 0.020 0.002 PHE A 86 TYR 0.023 0.002 TYR A 423 ARG 0.004 0.000 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00224 ( 2) link_NAG-ASN : angle 1.99262 ( 6) hydrogen bonds : bond 0.03417 ( 517) hydrogen bonds : angle 5.98770 ( 1317) SS BOND : bond 0.00357 ( 23) SS BOND : angle 0.83475 ( 46) covalent geometry : bond 0.00476 (16651) covalent geometry : angle 0.62295 (22640) Misc. bond : bond 0.00044 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13101.23 seconds wall clock time: 230 minutes 53.79 seconds (13853.79 seconds total)