Starting phenix.real_space_refine on Fri Sep 27 23:29:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7a_29804/09_2024/8g7a_29804.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7a_29804/09_2024/8g7a_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7a_29804/09_2024/8g7a_29804.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7a_29804/09_2024/8g7a_29804.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7a_29804/09_2024/8g7a_29804.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7a_29804/09_2024/8g7a_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-5461/modules/chem_data/mon_lib" Total number of atoms: 16237 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 877 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "A" Number of atoms: 4526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4526 Classifications: {'peptide': 567} Link IDs: {'PTRANS': 31, 'TRANS': 535} Chain breaks: 2 Chain: "B" Number of atoms: 4526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4526 Classifications: {'peptide': 567} Link IDs: {'PTRANS': 31, 'TRANS': 535} Chain breaks: 2 Chain: "C" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 877 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "D" Number of atoms: 4526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4526 Classifications: {'peptide': 567} Link IDs: {'PTRANS': 31, 'TRANS': 535} Chain breaks: 2 Chain: "F" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 877 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.83, per 1000 atoms: 0.67 Number of scatterers: 16237 At special positions: 0 Unit cell: (164.25, 154.03, 124.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 3061 8.00 N 2723 7.00 C 10384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.04 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.02 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.06 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B1301 " - " ASN B 331 " " NAG D1301 " - " ASN D 331 " Time building additional restraints: 3.96 Conformation dependent library (CDL) restraints added in 2.1 seconds 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3816 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 39 sheets defined 8.3% alpha, 32.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 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: 6.00 Time building geometry restraints manager: 4.68 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: 95 2.40 - 3.03: 9656 3.03 - 3.65: 23278 3.65 - 4.28: 35695 4.28 - 4.90: 59560 Nonbonded interactions: 128284 Sorted by model distance: nonbonded pdb=" O VAL A 350 " pdb=" CZ2 TRP A 353 " model vdw 1.778 3.340 nonbonded pdb=" CG2 ILE E 51 " pdb=" NH2 ARG E 71 " model vdw 1.807 3.540 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 ... (remaining 128279 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 14 through 592) selection = (chain 'D' and resid 14 through 592) } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 39.540 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.300 ------------------------------------------------------------------------------- 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 : 0.006 0.052 16651 Z= 0.384 Angle : 0.832 9.557 22640 Z= 0.494 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 *********************** 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 fitting. rotamer outliers: 12 poor density : 181 time to evaluate : 1.761 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: 0.3164 time to fit residues: 92.0520 Evaluate side-chains 111 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 2.032 ------------------------------------------------------------------------------- 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: 0.9990 chunk 182 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 44 GLN ** 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5187 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16651 Z= 0.269 Angle : 0.642 11.866 22640 Z= 0.341 Chirality : 0.048 0.205 2491 Planarity : 0.006 0.071 2933 Dihedral : 5.145 29.942 2279 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.91 % Favored : 95.94 % Rotamer: Outliers : 2.72 % Allowed : 11.78 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.18), residues: 2022 helix: -2.08 (0.43), residues: 126 sheet: -0.18 (0.20), residues: 676 loop : -1.28 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 353 HIS 0.003 0.001 HIS B 207 PHE 0.036 0.002 PHE D 400 TYR 0.030 0.002 TYR B 423 ARG 0.017 0.001 ARG D 403 *********************** 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 160 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 111 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.6669 (mtt-85) cc_final: 0.6235 (mtp85) REVERT: A 236 THR cc_start: 0.7903 (m) cc_final: 0.7524 (p) REVERT: A 406 GLU cc_start: 0.6383 (mt-10) cc_final: 0.5777 (mm-30) REVERT: A 421 TYR cc_start: 0.8140 (m-10) cc_final: 0.7930 (m-10) REVERT: A 436 TRP cc_start: 0.4355 (OUTLIER) cc_final: 0.3350 (p-90) REVERT: A 454 ARG cc_start: 0.5893 (mtt180) cc_final: 0.5534 (ptp-110) REVERT: A 462 LYS cc_start: 0.7761 (mttp) cc_final: 0.7456 (pttm) REVERT: B 66 HIS cc_start: 0.5998 (m-70) cc_final: 0.5530 (m90) REVERT: B 127 VAL cc_start: 0.6961 (t) cc_final: 0.6711 (m) REVERT: B 153 MET cc_start: -0.0693 (mtm) cc_final: -0.1000 (mmm) REVERT: B 177 MET cc_start: 0.2265 (mmp) cc_final: 0.1743 (mpp) REVERT: B 287 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8255 (m-30) REVERT: B 305 SER cc_start: 0.9021 (p) cc_final: 0.8784 (t) REVERT: B 537 LYS cc_start: 0.8620 (tttt) cc_final: 0.7954 (tttp) REVERT: B 558 LYS cc_start: 0.7297 (pttt) cc_final: 0.6584 (mmmm) REVERT: C 100 LYS cc_start: 0.4629 (tptp) cc_final: 0.4229 (mtmt) REVERT: D 69 HIS cc_start: 0.4901 (p-80) cc_final: 0.3807 (p-80) REVERT: D 100 ILE cc_start: 0.7463 (pt) cc_final: 0.7122 (mm) REVERT: D 177 MET cc_start: 0.1541 (mmp) cc_final: 0.0381 (mmt) REVERT: D 218 GLN cc_start: 0.6241 (mt0) cc_final: 0.5869 (pm20) REVERT: D 239 GLN cc_start: 0.8025 (tt0) cc_final: 0.7584 (tt0) REVERT: F 44 GLN cc_start: 0.3813 (OUTLIER) cc_final: 0.3406 (mm-40) REVERT: F 82 MET cc_start: 0.2155 (mmt) cc_final: 0.1379 (ptm) outliers start: 49 outliers final: 23 residues processed: 156 average time/residue: 0.2372 time to fit residues: 59.1486 Evaluate side-chains 125 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 99 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 SER 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 90 VAL Chi-restraints excluded: chain B residue 94 SER 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 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 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 101 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 182 optimal weight: 10.0000 chunk 197 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5229 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16651 Z= 0.287 Angle : 0.609 9.209 22640 Z= 0.322 Chirality : 0.048 0.240 2491 Planarity : 0.005 0.058 2933 Dihedral : 4.816 27.186 2268 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.86 % Favored : 95.99 % Rotamer: Outliers : 3.11 % Allowed : 12.61 % 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: -1.34 (0.18), residues: 2022 helix: -1.88 (0.44), residues: 128 sheet: -0.14 (0.19), residues: 716 loop : -1.27 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 353 HIS 0.003 0.001 HIS A 69 PHE 0.022 0.002 PHE B 429 TYR 0.024 0.002 TYR A 160 ARG 0.006 0.001 ARG A 466 *********************** 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 171 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 115 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: -0.1374 (ptm) cc_final: -0.1872 (mmm) REVERT: A 158 ARG cc_start: 0.6814 (mtt-85) cc_final: 0.6381 (mtp85) REVERT: A 236 THR cc_start: 0.8148 (m) cc_final: 0.7805 (p) REVERT: A 406 GLU cc_start: 0.6431 (mt-10) cc_final: 0.5850 (mm-30) REVERT: A 436 TRP cc_start: 0.4259 (OUTLIER) cc_final: 0.3328 (p-90) REVERT: A 462 LYS cc_start: 0.7732 (mttp) cc_final: 0.7441 (pttm) REVERT: B 66 HIS cc_start: 0.6157 (m-70) cc_final: 0.5572 (m90) REVERT: B 127 VAL cc_start: 0.7030 (t) cc_final: 0.6799 (m) REVERT: B 153 MET cc_start: -0.0822 (mtm) cc_final: -0.1111 (mmm) REVERT: B 177 MET cc_start: 0.2205 (mmp) cc_final: 0.1679 (mpp) REVERT: B 224 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7641 (mt-10) REVERT: B 233 ILE cc_start: 0.6219 (pt) cc_final: 0.5989 (pt) REVERT: B 305 SER cc_start: 0.9003 (p) cc_final: 0.8754 (t) REVERT: B 537 LYS cc_start: 0.8684 (tttt) cc_final: 0.8052 (tttp) REVERT: B 558 LYS cc_start: 0.7340 (pttt) cc_final: 0.6663 (mmmm) REVERT: D 100 ILE cc_start: 0.7518 (pt) cc_final: 0.7169 (mm) REVERT: D 177 MET cc_start: 0.1844 (mmp) cc_final: 0.0733 (mmt) REVERT: D 198 ASP cc_start: 0.8211 (t0) cc_final: 0.8008 (t0) REVERT: D 218 GLN cc_start: 0.6255 (mt0) cc_final: 0.5939 (pm20) REVERT: D 239 GLN cc_start: 0.8074 (tt0) cc_final: 0.7673 (tt0) REVERT: D 468 ILE cc_start: 0.3381 (OUTLIER) cc_final: 0.3112 (tt) REVERT: D 574 ASP cc_start: 0.7642 (t70) cc_final: 0.6954 (t0) REVERT: F 58 GLN cc_start: 0.2594 (OUTLIER) cc_final: 0.1890 (tt0) REVERT: F 82 MET cc_start: 0.2181 (mmt) cc_final: 0.1347 (ptm) outliers start: 56 outliers final: 32 residues processed: 165 average time/residue: 0.2521 time to fit residues: 64.7853 Evaluate side-chains 141 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 105 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 118 LEU 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 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 90 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 224 GLU 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 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 387 LEU 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 180 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 122 optimal weight: 0.5980 chunk 183 optimal weight: 0.0050 chunk 194 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 134 GLN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5205 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16651 Z= 0.183 Angle : 0.555 8.911 22640 Z= 0.292 Chirality : 0.046 0.198 2491 Planarity : 0.004 0.057 2933 Dihedral : 4.517 22.692 2268 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.36 % Favored : 96.49 % Rotamer: Outliers : 2.83 % Allowed : 13.44 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.18), residues: 2022 helix: -1.77 (0.44), residues: 129 sheet: 0.01 (0.20), residues: 690 loop : -1.22 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 64 HIS 0.003 0.001 HIS A 69 PHE 0.014 0.001 PHE A 329 TYR 0.021 0.001 TYR A 160 ARG 0.015 0.001 ARG E 38 *********************** 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 167 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 116 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: -0.1439 (ptm) cc_final: -0.1838 (mmm) REVERT: A 158 ARG cc_start: 0.6877 (mtt-85) cc_final: 0.6587 (mtp85) REVERT: A 236 THR cc_start: 0.8106 (m) cc_final: 0.7777 (p) REVERT: A 357 ARG cc_start: 0.8030 (ttm-80) cc_final: 0.7390 (ttp80) REVERT: A 396 TYR cc_start: 0.6418 (m-80) cc_final: 0.6146 (m-80) REVERT: A 406 GLU cc_start: 0.6381 (mt-10) cc_final: 0.5977 (mm-30) REVERT: A 436 TRP cc_start: 0.4390 (OUTLIER) cc_final: 0.3270 (p-90) REVERT: A 462 LYS cc_start: 0.7742 (mttp) cc_final: 0.7454 (pttm) REVERT: A 505 TYR cc_start: 0.7510 (m-80) cc_final: 0.7235 (t80) REVERT: B 66 HIS cc_start: 0.6197 (m-70) cc_final: 0.5685 (m90) REVERT: B 127 VAL cc_start: 0.7007 (t) cc_final: 0.6784 (m) REVERT: B 153 MET cc_start: -0.0909 (mtm) cc_final: -0.1169 (mmm) REVERT: B 177 MET cc_start: 0.2170 (mmp) cc_final: 0.1673 (mpp) REVERT: B 305 SER cc_start: 0.9022 (p) cc_final: 0.8731 (t) REVERT: B 537 LYS cc_start: 0.8656 (tttt) cc_final: 0.8287 (tttp) REVERT: B 558 LYS cc_start: 0.7326 (pttt) cc_final: 0.6658 (mmmm) REVERT: C 47 MET cc_start: 0.1660 (OUTLIER) cc_final: 0.1438 (ptt) REVERT: D 100 ILE cc_start: 0.7495 (pt) cc_final: 0.7165 (mm) REVERT: D 177 MET cc_start: 0.1790 (mmp) cc_final: 0.0744 (mmt) REVERT: D 218 GLN cc_start: 0.6186 (mt0) cc_final: 0.5872 (pm20) REVERT: D 239 GLN cc_start: 0.8033 (tt0) cc_final: 0.7642 (tt0) REVERT: D 369 TYR cc_start: 0.5201 (OUTLIER) cc_final: 0.3938 (t80) REVERT: D 468 ILE cc_start: 0.3246 (OUTLIER) cc_final: 0.2998 (tt) REVERT: D 574 ASP cc_start: 0.7726 (t70) cc_final: 0.7034 (t0) REVERT: F 44 GLN cc_start: 0.3696 (OUTLIER) cc_final: 0.3491 (mm-40) REVERT: F 58 GLN cc_start: 0.2753 (OUTLIER) cc_final: 0.2072 (tt0) REVERT: F 82 MET cc_start: 0.2167 (mmt) cc_final: 0.1303 (ptm) outliers start: 51 outliers final: 26 residues processed: 163 average time/residue: 0.2317 time to fit residues: 61.8037 Evaluate side-chains 136 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 104 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 118 LEU Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain 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 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 369 TYR Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 58 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 161 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 144 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 165 optimal weight: 8.9990 chunk 134 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 174 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 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** B 544 ASN C 44 GLN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5341 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.082 16651 Z= 0.675 Angle : 0.804 8.787 22640 Z= 0.422 Chirality : 0.056 0.382 2491 Planarity : 0.006 0.055 2933 Dihedral : 5.411 31.876 2268 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.69 % Favored : 94.16 % Rotamer: Outliers : 4.39 % Allowed : 13.50 % 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: -1.64 (0.18), residues: 2022 helix: -2.13 (0.41), residues: 133 sheet: -0.23 (0.19), residues: 688 loop : -1.52 (0.17), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 104 HIS 0.007 0.002 HIS A 66 PHE 0.033 0.003 PHE A 86 TYR 0.028 0.003 TYR A 266 ARG 0.007 0.001 ARG B 466 *********************** 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 185 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 106 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: -0.1238 (ptm) cc_final: -0.1843 (mmm) REVERT: A 133 PHE cc_start: 0.5873 (OUTLIER) cc_final: 0.5637 (t80) REVERT: A 357 ARG cc_start: 0.8019 (ttm-80) cc_final: 0.7574 (ttp80) REVERT: A 361 CYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7160 (p) REVERT: A 396 TYR cc_start: 0.6467 (m-80) cc_final: 0.6169 (m-80) REVERT: A 406 GLU cc_start: 0.6469 (mt-10) cc_final: 0.5986 (mm-30) REVERT: A 436 TRP cc_start: 0.4349 (OUTLIER) cc_final: 0.3286 (p-90) REVERT: A 505 TYR cc_start: 0.7496 (m-80) cc_final: 0.7293 (t80) REVERT: B 100 ILE cc_start: 0.8455 (pt) cc_final: 0.7838 (tt) REVERT: B 153 MET cc_start: -0.0861 (mtm) cc_final: -0.1075 (mmt) REVERT: B 177 MET cc_start: 0.2816 (mmp) cc_final: 0.2477 (mpp) REVERT: B 305 SER cc_start: 0.9091 (p) cc_final: 0.8854 (t) REVERT: B 537 LYS cc_start: 0.8698 (tttt) cc_final: 0.8428 (tttp) REVERT: B 558 LYS cc_start: 0.7443 (pttt) cc_final: 0.6812 (mmmm) REVERT: B 581 THR cc_start: 0.7268 (OUTLIER) cc_final: 0.6981 (p) REVERT: D 100 ILE cc_start: 0.7859 (pt) cc_final: 0.7425 (mm) REVERT: D 177 MET cc_start: 0.2541 (mmp) cc_final: 0.1563 (mmt) REVERT: D 218 GLN cc_start: 0.6635 (mt0) cc_final: 0.6106 (pm20) REVERT: D 369 TYR cc_start: 0.5335 (OUTLIER) cc_final: 0.3916 (t80) REVERT: D 468 ILE cc_start: 0.3469 (OUTLIER) cc_final: 0.3142 (tt) REVERT: D 574 ASP cc_start: 0.7864 (t70) cc_final: 0.7042 (t0) REVERT: D 592 PHE cc_start: -0.0746 (OUTLIER) cc_final: -0.1436 (t80) REVERT: F 58 GLN cc_start: 0.3036 (OUTLIER) cc_final: 0.2300 (tt0) REVERT: F 82 MET cc_start: 0.1933 (mmt) cc_final: 0.1330 (ptm) outliers start: 79 outliers final: 49 residues processed: 170 average time/residue: 0.2356 time to fit residues: 64.0589 Evaluate side-chains 154 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 97 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 133 PHE 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 361 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain 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 197 ILE 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 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 B residue 581 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 54 LEU 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 236 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 369 TYR Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 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 D residue 592 PHE Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 58 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 65 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 114 optimal weight: 0.0040 chunk 47 optimal weight: 3.9990 chunk 194 optimal weight: 30.0000 chunk 161 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 16 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5255 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16651 Z= 0.196 Angle : 0.581 8.927 22640 Z= 0.306 Chirality : 0.047 0.196 2491 Planarity : 0.004 0.055 2933 Dihedral : 4.712 21.810 2268 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.51 % Favored : 96.34 % Rotamer: Outliers : 2.67 % Allowed : 15.50 % Favored : 81.83 % 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: -1.40 (0.18), residues: 2022 helix: -1.91 (0.44), residues: 122 sheet: -0.13 (0.19), residues: 684 loop : -1.33 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 64 HIS 0.005 0.001 HIS C 79 PHE 0.014 0.001 PHE D 86 TYR 0.018 0.001 TYR B 495 ARG 0.003 0.000 ARG A 328 *********************** 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 155 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 107 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: -0.1338 (ptm) cc_final: -0.1877 (mmm) REVERT: A 158 ARG cc_start: 0.6785 (mtt-85) cc_final: 0.6384 (mtp85) REVERT: A 236 THR cc_start: 0.8186 (m) cc_final: 0.7892 (p) REVERT: A 357 ARG cc_start: 0.8081 (ttm-80) cc_final: 0.7352 (ttp80) REVERT: A 361 CYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7306 (p) REVERT: A 406 GLU cc_start: 0.6358 (mt-10) cc_final: 0.5768 (mm-30) REVERT: A 436 TRP cc_start: 0.4386 (OUTLIER) cc_final: 0.3297 (p-90) REVERT: A 462 LYS cc_start: 0.7683 (mttp) cc_final: 0.7482 (pttm) REVERT: A 505 TYR cc_start: 0.7538 (m-80) cc_final: 0.7302 (t80) REVERT: A 583 GLU cc_start: 0.6984 (tp30) cc_final: 0.6518 (pt0) REVERT: B 100 ILE cc_start: 0.8279 (pt) cc_final: 0.7603 (tt) REVERT: B 127 VAL cc_start: 0.7110 (t) cc_final: 0.6841 (m) REVERT: B 177 MET cc_start: 0.2706 (mmp) cc_final: 0.2488 (mpp) REVERT: B 305 SER cc_start: 0.9023 (p) cc_final: 0.8756 (t) REVERT: B 537 LYS cc_start: 0.8633 (tttt) cc_final: 0.8404 (tttm) REVERT: B 558 LYS cc_start: 0.7466 (pttt) cc_final: 0.6829 (mmmm) REVERT: B 581 THR cc_start: 0.7446 (OUTLIER) cc_final: 0.7137 (p) REVERT: D 69 HIS cc_start: 0.4894 (OUTLIER) cc_final: 0.3609 (p-80) REVERT: D 100 ILE cc_start: 0.7725 (pt) cc_final: 0.7386 (mm) REVERT: D 177 MET cc_start: 0.2240 (mmp) cc_final: 0.1437 (mmt) REVERT: D 218 GLN cc_start: 0.6379 (mt0) cc_final: 0.5928 (pm20) REVERT: D 369 TYR cc_start: 0.5206 (OUTLIER) cc_final: 0.3921 (t80) REVERT: D 468 ILE cc_start: 0.3355 (OUTLIER) cc_final: 0.3050 (tt) REVERT: D 574 ASP cc_start: 0.7827 (t70) cc_final: 0.7052 (t0) REVERT: F 58 GLN cc_start: 0.3184 (OUTLIER) cc_final: 0.2514 (tt0) REVERT: F 82 MET cc_start: 0.1853 (mmt) cc_final: 0.1151 (ptm) outliers start: 48 outliers final: 24 residues processed: 149 average time/residue: 0.2308 time to fit residues: 55.9837 Evaluate side-chains 130 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 99 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 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 A residue 534 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 369 TYR Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 58 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 187 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 142 optimal weight: 4.9990 chunk 163 optimal weight: 0.0030 chunk 108 optimal weight: 10.0000 chunk 193 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 207 HIS ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5271 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16651 Z= 0.236 Angle : 0.579 9.180 22640 Z= 0.302 Chirality : 0.046 0.205 2491 Planarity : 0.004 0.055 2933 Dihedral : 4.561 22.838 2268 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.10 % Favored : 95.75 % Rotamer: Outliers : 2.56 % Allowed : 16.56 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.96 (0.43), residues: 128 sheet: -0.07 (0.19), residues: 680 loop : -1.35 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 64 HIS 0.002 0.001 HIS B 207 PHE 0.016 0.002 PHE A 86 TYR 0.015 0.001 TYR B 265 ARG 0.003 0.000 ARG A 328 *********************** 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 157 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 111 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: -0.1341 (ptm) cc_final: -0.1856 (mmm) REVERT: A 158 ARG cc_start: 0.6755 (mtt-85) cc_final: 0.6357 (mtp85) REVERT: A 236 THR cc_start: 0.8254 (m) cc_final: 0.7965 (p) REVERT: A 281 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: A 357 ARG cc_start: 0.8082 (ttm-80) cc_final: 0.7552 (ttp80) REVERT: A 361 CYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7344 (p) REVERT: A 396 TYR cc_start: 0.6477 (m-80) cc_final: 0.6221 (m-80) REVERT: A 406 GLU cc_start: 0.6325 (mt-10) cc_final: 0.5737 (mm-30) REVERT: A 436 TRP cc_start: 0.4352 (OUTLIER) cc_final: 0.3265 (p-90) REVERT: A 505 TYR cc_start: 0.7525 (m-80) cc_final: 0.7299 (t80) REVERT: A 583 GLU cc_start: 0.6980 (tp30) cc_final: 0.6489 (pt0) REVERT: B 100 ILE cc_start: 0.8323 (pt) cc_final: 0.7638 (tt) REVERT: B 127 VAL cc_start: 0.7113 (t) cc_final: 0.6873 (m) REVERT: B 177 MET cc_start: 0.2875 (mmp) cc_final: 0.2569 (mpp) REVERT: B 305 SER cc_start: 0.9048 (p) cc_final: 0.8773 (t) REVERT: B 523 THR cc_start: 0.7564 (p) cc_final: 0.7296 (t) REVERT: B 537 LYS cc_start: 0.8632 (tttt) cc_final: 0.8366 (tttm) REVERT: B 558 LYS cc_start: 0.7460 (pttt) cc_final: 0.6858 (mmmm) REVERT: B 581 THR cc_start: 0.7435 (OUTLIER) cc_final: 0.7004 (p) REVERT: D 100 ILE cc_start: 0.7703 (pt) cc_final: 0.7293 (mm) REVERT: D 177 MET cc_start: 0.2358 (mmp) cc_final: 0.1541 (mmt) REVERT: D 218 GLN cc_start: 0.6390 (mt0) cc_final: 0.5945 (pm20) REVERT: D 239 GLN cc_start: 0.8092 (tt0) cc_final: 0.7733 (tt0) REVERT: D 369 TYR cc_start: 0.5232 (OUTLIER) cc_final: 0.3901 (t80) REVERT: D 468 ILE cc_start: 0.3342 (OUTLIER) cc_final: 0.3038 (tt) REVERT: D 574 ASP cc_start: 0.7792 (t70) cc_final: 0.6978 (t0) REVERT: F 58 GLN cc_start: 0.3280 (OUTLIER) cc_final: 0.2668 (tt0) REVERT: F 82 MET cc_start: 0.1903 (mmt) cc_final: 0.1119 (ptm) outliers start: 46 outliers final: 32 residues processed: 154 average time/residue: 0.2613 time to fit residues: 64.6587 Evaluate side-chains 144 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 105 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 581 THR 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 266 TYR Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 369 TYR Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 77 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 123 optimal weight: 20.0000 chunk 131 optimal weight: 10.0000 chunk 95 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 chunk 176 optimal weight: 20.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** D 317 ASN F 32 ASN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5254 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16651 Z= 0.195 Angle : 0.559 9.524 22640 Z= 0.293 Chirality : 0.046 0.189 2491 Planarity : 0.004 0.054 2933 Dihedral : 4.424 25.211 2268 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.41 % Favored : 96.44 % Rotamer: Outliers : 2.89 % Allowed : 16.22 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.88 (0.43), residues: 128 sheet: 0.04 (0.20), residues: 676 loop : -1.26 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 64 HIS 0.003 0.001 HIS D 207 PHE 0.019 0.001 PHE B 140 TYR 0.014 0.001 TYR B 265 ARG 0.003 0.000 ARG B 466 *********************** 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 162 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 110 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: -0.1388 (ptm) cc_final: -0.1885 (mmm) REVERT: A 168 PHE cc_start: 0.7788 (t80) cc_final: 0.7571 (t80) REVERT: A 236 THR cc_start: 0.8143 (m) cc_final: 0.7870 (p) REVERT: A 281 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: A 357 ARG cc_start: 0.8104 (ttm-80) cc_final: 0.7577 (ttp80) REVERT: A 361 CYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7212 (p) REVERT: A 396 TYR cc_start: 0.6474 (m-80) cc_final: 0.6230 (m-80) REVERT: A 406 GLU cc_start: 0.6290 (mt-10) cc_final: 0.5688 (mm-30) REVERT: A 424 LYS cc_start: 0.6865 (mmmt) cc_final: 0.6111 (mmmt) REVERT: A 436 TRP cc_start: 0.4358 (OUTLIER) cc_final: 0.3254 (p-90) REVERT: A 583 GLU cc_start: 0.7023 (tp30) cc_final: 0.6557 (pt0) REVERT: B 100 ILE cc_start: 0.8345 (pt) cc_final: 0.7672 (tt) REVERT: B 177 MET cc_start: 0.2923 (mmp) cc_final: 0.2672 (mpp) REVERT: B 305 SER cc_start: 0.9040 (p) cc_final: 0.8754 (t) REVERT: B 523 THR cc_start: 0.7757 (p) cc_final: 0.7476 (t) REVERT: B 537 LYS cc_start: 0.8610 (tttt) cc_final: 0.8332 (tttm) REVERT: B 558 LYS cc_start: 0.7479 (pttt) cc_final: 0.6900 (mmmm) REVERT: D 100 ILE cc_start: 0.7636 (pt) cc_final: 0.7217 (mm) REVERT: D 177 MET cc_start: 0.2235 (mmp) cc_final: 0.1498 (mmt) REVERT: D 369 TYR cc_start: 0.5241 (OUTLIER) cc_final: 0.3961 (t80) REVERT: D 468 ILE cc_start: 0.3314 (OUTLIER) cc_final: 0.3030 (tt) REVERT: D 574 ASP cc_start: 0.7655 (t70) cc_final: 0.6829 (t0) REVERT: F 58 GLN cc_start: 0.3606 (OUTLIER) cc_final: 0.2996 (tt0) REVERT: F 82 MET cc_start: 0.1789 (mmt) cc_final: 0.1024 (ptm) outliers start: 52 outliers final: 36 residues processed: 156 average time/residue: 0.2280 time to fit residues: 57.7645 Evaluate side-chains 145 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 103 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 281 GLU 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 A residue 534 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 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 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 136 CYS Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 369 TYR Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 185 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 180 optimal weight: 20.0000 chunk 108 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 141 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 163 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 chunk 179 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN B 14 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5327 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 16651 Z= 0.477 Angle : 0.685 10.824 22640 Z= 0.358 Chirality : 0.050 0.298 2491 Planarity : 0.005 0.053 2933 Dihedral : 4.941 22.808 2268 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.89 % Favored : 93.97 % Rotamer: Outliers : 3.06 % Allowed : 16.11 % Favored : 80.83 % 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: -1.48 (0.18), residues: 2022 helix: -1.91 (0.43), residues: 124 sheet: -0.15 (0.19), residues: 676 loop : -1.41 (0.17), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 64 HIS 0.005 0.001 HIS B 245 PHE 0.030 0.003 PHE B 79 TYR 0.025 0.002 TYR B 265 ARG 0.008 0.001 ARG B 78 *********************** 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 154 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 99 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 THR cc_start: 0.8446 (m) cc_final: 0.8146 (p) REVERT: A 281 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: A 357 ARG cc_start: 0.8088 (ttm-80) cc_final: 0.7603 (ttp80) REVERT: A 361 CYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7316 (p) REVERT: A 406 GLU cc_start: 0.6434 (mt-10) cc_final: 0.5854 (mm-30) REVERT: A 436 TRP cc_start: 0.4404 (OUTLIER) cc_final: 0.3319 (p-90) REVERT: B 100 ILE cc_start: 0.8531 (pt) cc_final: 0.7963 (tt) REVERT: B 177 MET cc_start: 0.3214 (mmp) cc_final: 0.2989 (mpp) REVERT: B 305 SER cc_start: 0.9072 (p) cc_final: 0.8766 (t) REVERT: B 523 THR cc_start: 0.7733 (p) cc_final: 0.7451 (t) REVERT: B 558 LYS cc_start: 0.7518 (pttt) cc_final: 0.6949 (mmmm) REVERT: B 581 THR cc_start: 0.7315 (OUTLIER) cc_final: 0.7012 (p) REVERT: D 100 ILE cc_start: 0.7808 (pt) cc_final: 0.7411 (mm) REVERT: D 177 MET cc_start: 0.2689 (mmp) cc_final: 0.2001 (mmt) REVERT: D 239 GLN cc_start: 0.8149 (tt0) cc_final: 0.7833 (tt0) REVERT: D 369 TYR cc_start: 0.5195 (OUTLIER) cc_final: 0.3947 (t80) REVERT: D 468 ILE cc_start: 0.3396 (OUTLIER) cc_final: 0.3071 (tt) REVERT: D 574 ASP cc_start: 0.7821 (t0) cc_final: 0.6871 (t0) REVERT: F 58 GLN cc_start: 0.3591 (OUTLIER) cc_final: 0.3008 (tt0) REVERT: F 82 MET cc_start: 0.1776 (mmt) cc_final: 0.0990 (ptm) outliers start: 55 outliers final: 40 residues processed: 147 average time/residue: 0.2316 time to fit residues: 54.9030 Evaluate side-chains 142 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 95 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 281 GLU 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 A residue 534 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 227 VAL 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 581 THR 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 289 VAL Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 369 TYR Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 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 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 190 optimal weight: 30.0000 chunk 116 optimal weight: 0.0000 chunk 90 optimal weight: 0.0980 chunk 132 optimal weight: 20.0000 chunk 200 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN B 317 ASN C 58 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5261 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16651 Z= 0.188 Angle : 0.568 9.377 22640 Z= 0.296 Chirality : 0.046 0.224 2491 Planarity : 0.004 0.053 2933 Dihedral : 4.544 27.550 2268 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.36 % Favored : 96.49 % Rotamer: Outliers : 2.56 % Allowed : 16.56 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.84 (0.44), residues: 120 sheet: 0.04 (0.20), residues: 670 loop : -1.33 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 353 HIS 0.003 0.001 HIS D 207 PHE 0.020 0.001 PHE B 140 TYR 0.013 0.001 TYR B 265 ARG 0.003 0.000 ARG B 319 ********************** 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 155 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 109 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.7762 (t80) cc_final: 0.7524 (t80) REVERT: A 236 THR cc_start: 0.8194 (m) cc_final: 0.7929 (p) REVERT: A 281 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: A 357 ARG cc_start: 0.8094 (ttm-80) cc_final: 0.7356 (ttp80) REVERT: A 361 CYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7285 (p) REVERT: A 406 GLU cc_start: 0.6333 (mt-10) cc_final: 0.5740 (mm-30) REVERT: A 436 TRP cc_start: 0.4324 (OUTLIER) cc_final: 0.3233 (p-90) REVERT: A 583 GLU cc_start: 0.7081 (tp30) cc_final: 0.6651 (pt0) REVERT: B 100 ILE cc_start: 0.8442 (pt) cc_final: 0.7819 (tt) REVERT: B 305 SER cc_start: 0.9035 (p) cc_final: 0.8746 (t) REVERT: B 437 ASN cc_start: 0.4962 (m-40) cc_final: 0.4507 (t0) REVERT: B 523 THR cc_start: 0.7762 (p) cc_final: 0.7479 (t) REVERT: B 537 LYS cc_start: 0.8404 (tttm) cc_final: 0.8083 (tttp) REVERT: B 551 VAL cc_start: 0.8385 (OUTLIER) cc_final: 0.8123 (p) REVERT: B 558 LYS cc_start: 0.7482 (pttt) cc_final: 0.6939 (mmmm) REVERT: B 581 THR cc_start: 0.7469 (OUTLIER) cc_final: 0.7152 (p) REVERT: C 100 LYS cc_start: 0.5112 (tptp) cc_final: 0.4732 (mtmt) REVERT: D 100 ILE cc_start: 0.7707 (pt) cc_final: 0.7288 (mm) REVERT: D 177 MET cc_start: 0.2583 (mmp) cc_final: 0.1958 (mmt) REVERT: D 218 GLN cc_start: 0.6360 (mt0) cc_final: 0.5887 (pm20) REVERT: D 369 TYR cc_start: 0.5203 (OUTLIER) cc_final: 0.3983 (t80) REVERT: D 468 ILE cc_start: 0.3313 (OUTLIER) cc_final: 0.3046 (tt) REVERT: D 574 ASP cc_start: 0.7643 (t0) cc_final: 0.6775 (t0) REVERT: F 58 GLN cc_start: 0.3675 (OUTLIER) cc_final: 0.3124 (tt0) REVERT: F 82 MET cc_start: 0.1834 (mmm) cc_final: 0.1033 (ptm) outliers start: 46 outliers final: 33 residues processed: 149 average time/residue: 0.2376 time to fit residues: 57.7441 Evaluate side-chains 145 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 104 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 281 GLU 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 A residue 534 VAL 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 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 581 THR Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 369 TYR Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 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 169 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 159 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 HIS ** 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 218 GLN C 76 ASN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.244175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.215145 restraints weight = 22391.048| |-----------------------------------------------------------------------------| r_work (start): 0.4477 rms_B_bonded: 2.02 r_work: 0.4195 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work: 0.4153 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16651 Z= 0.221 Angle : 0.575 10.908 22640 Z= 0.298 Chirality : 0.046 0.253 2491 Planarity : 0.004 0.053 2933 Dihedral : 4.472 25.208 2268 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.20 % Favored : 95.65 % Rotamer: Outliers : 2.50 % Allowed : 16.72 % Favored : 80.78 % 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: -1.24 (0.18), residues: 2022 helix: -1.59 (0.47), residues: 113 sheet: 0.08 (0.20), residues: 676 loop : -1.31 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 353 HIS 0.006 0.001 HIS B 207 PHE 0.018 0.001 PHE B 140 TYR 0.015 0.001 TYR A 160 ARG 0.003 0.000 ARG B 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3626.10 seconds wall clock time: 65 minutes 42.56 seconds (3942.56 seconds total)