Starting phenix.real_space_refine on Thu Feb 5 06:26:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ei0_48072/02_2026/9ei0_48072.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ei0_48072/02_2026/9ei0_48072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ei0_48072/02_2026/9ei0_48072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ei0_48072/02_2026/9ei0_48072.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ei0_48072/02_2026/9ei0_48072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ei0_48072/02_2026/9ei0_48072.map" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 60 5.16 5 C 9912 2.51 5 N 2568 2.21 5 O 2708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15252 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2919 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 20, 'TRANS': 337} Chain breaks: 2 Chain: "E" Number of atoms: 893 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Conformer: "B" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} bond proxies already assigned to first conformer: 894 Chain: "F" Number of atoms: 893 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Conformer: "B" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} bond proxies already assigned to first conformer: 894 Chain: "G" Number of atoms: 893 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Conformer: "B" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} bond proxies already assigned to first conformer: 894 Chain: "H" Number of atoms: 893 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Conformer: "B" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} bond proxies already assigned to first conformer: 894 Chain: "B" Number of atoms: 2919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2919 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 20, 'TRANS': 337} Chain breaks: 2 Chain: "C" Number of atoms: 2919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2919 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 20, 'TRANS': 337} Chain breaks: 2 Chain: "D" Number of atoms: 2919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2919 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 20, 'TRANS': 337} Chain breaks: 2 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.36, per 1000 atoms: 0.29 Number of scatterers: 15252 At special positions: 0 Unit cell: (100.43, 100.43, 149.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 60 16.00 O 2708 8.00 N 2568 7.00 C 9912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 96 " 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 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 824.1 milliseconds 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3512 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 20 sheets defined 50.5% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 154 through 165 removed outlier: 4.299A pdb=" N ALA A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 188 Processing helix chain 'A' and resid 190 through 202 removed outlier: 3.504A pdb=" N MET A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 226 Processing helix chain 'A' and resid 231 through 254 Processing helix chain 'A' and resid 293 through 317 removed outlier: 3.557A pdb=" N VAL A 298 " --> pdb=" O PRO A 294 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 removed outlier: 3.534A pdb=" N PHE A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 335 removed outlier: 3.957A pdb=" N ASP A 332 " --> pdb=" O MET A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 347 removed outlier: 3.510A pdb=" N PHE A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 370 Processing helix chain 'A' and resid 371 through 378 removed outlier: 3.679A pdb=" N PHE A 375 " --> pdb=" O PHE A 372 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS A 376 " --> pdb=" O ARG A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 394 Processing helix chain 'A' and resid 394 through 419 Processing helix chain 'A' and resid 434 through 443 Processing helix chain 'A' and resid 454 through 474 removed outlier: 3.586A pdb=" N ALA A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 489 Processing helix chain 'E' and resid 29 through 33 Processing helix chain 'F' and resid 29 through 33 Processing helix chain 'G' and resid 29 through 33 Processing helix chain 'H' and resid 29 through 33 Processing helix chain 'B' and resid 119 through 123 Processing helix chain 'B' and resid 154 through 165 removed outlier: 4.299A pdb=" N ALA B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 188 Processing helix chain 'B' and resid 190 through 202 removed outlier: 3.503A pdb=" N MET B 194 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 226 Processing helix chain 'B' and resid 231 through 254 Processing helix chain 'B' and resid 293 through 317 removed outlier: 3.557A pdb=" N VAL B 298 " --> pdb=" O PRO B 294 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 324 removed outlier: 3.534A pdb=" N PHE B 323 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 335 removed outlier: 3.957A pdb=" N ASP B 332 " --> pdb=" O MET B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 347 removed outlier: 3.510A pdb=" N PHE B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 370 Processing helix chain 'B' and resid 371 through 378 removed outlier: 3.679A pdb=" N PHE B 375 " --> pdb=" O PHE B 372 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS B 376 " --> pdb=" O ARG B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 394 Processing helix chain 'B' and resid 394 through 419 Processing helix chain 'B' and resid 434 through 443 Processing helix chain 'B' and resid 454 through 474 removed outlier: 3.587A pdb=" N ALA B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 Processing helix chain 'C' and resid 119 through 123 Processing helix chain 'C' and resid 154 through 165 removed outlier: 4.299A pdb=" N ALA C 158 " --> pdb=" O PRO C 154 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR C 163 " --> pdb=" O ILE C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 188 Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.504A pdb=" N MET C 194 " --> pdb=" O GLY C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 226 Processing helix chain 'C' and resid 231 through 254 Processing helix chain 'C' and resid 293 through 317 removed outlier: 3.556A pdb=" N VAL C 298 " --> pdb=" O PRO C 294 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 324 removed outlier: 3.534A pdb=" N PHE C 323 " --> pdb=" O SER C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 335 removed outlier: 3.958A pdb=" N ASP C 332 " --> pdb=" O MET C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 347 removed outlier: 3.510A pdb=" N PHE C 340 " --> pdb=" O ILE C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 370 Processing helix chain 'C' and resid 371 through 378 removed outlier: 3.678A pdb=" N PHE C 375 " --> pdb=" O PHE C 372 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS C 376 " --> pdb=" O ARG C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 394 Processing helix chain 'C' and resid 394 through 419 Processing helix chain 'C' and resid 434 through 443 Processing helix chain 'C' and resid 454 through 474 removed outlier: 3.586A pdb=" N ALA C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C 466 " --> pdb=" O SER C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 489 Processing helix chain 'D' and resid 119 through 123 Processing helix chain 'D' and resid 154 through 165 removed outlier: 4.299A pdb=" N ALA D 158 " --> pdb=" O PRO D 154 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR D 163 " --> pdb=" O ILE D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 188 Processing helix chain 'D' and resid 190 through 202 removed outlier: 3.504A pdb=" N MET D 194 " --> pdb=" O GLY D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 226 Processing helix chain 'D' and resid 231 through 254 Processing helix chain 'D' and resid 293 through 317 removed outlier: 3.557A pdb=" N VAL D 298 " --> pdb=" O PRO D 294 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 324 removed outlier: 3.534A pdb=" N PHE D 323 " --> pdb=" O SER D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 335 removed outlier: 3.957A pdb=" N ASP D 332 " --> pdb=" O MET D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 347 removed outlier: 3.510A pdb=" N PHE D 340 " --> pdb=" O ILE D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 370 Processing helix chain 'D' and resid 371 through 378 removed outlier: 3.679A pdb=" N PHE D 375 " --> pdb=" O PHE D 372 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS D 376 " --> pdb=" O ARG D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 394 Processing helix chain 'D' and resid 394 through 419 Processing helix chain 'D' and resid 434 through 443 Processing helix chain 'D' and resid 454 through 474 removed outlier: 3.587A pdb=" N ALA D 465 " --> pdb=" O GLY D 461 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE D 466 " --> pdb=" O SER D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 489 Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 118 removed outlier: 8.622A pdb=" N TYR A 147 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL A 107 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N PHE A 149 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASN A 109 " --> pdb=" O PHE A 149 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 4 through 8 removed outlier: 3.671A pdb=" N GLN E 4 " --> pdb=" O SER E 26 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER E 22 " --> pdb=" O SER E 8 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER E 71 " --> pdb=" O TYR E 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 47 through 48 Processing sheet with id=AA4, first strand: chain 'E' and resid 47 through 48 Processing sheet with id=AA5, first strand: chain 'E' and resid 50 through 51 Processing sheet with id=AA6, first strand: chain 'F' and resid 4 through 8 removed outlier: 3.671A pdb=" N GLN F 4 " --> pdb=" O SER F 26 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER F 22 " --> pdb=" O SER F 8 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER F 71 " --> pdb=" O TYR F 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 47 through 48 Processing sheet with id=AA8, first strand: chain 'F' and resid 47 through 48 Processing sheet with id=AA9, first strand: chain 'F' and resid 50 through 51 Processing sheet with id=AB1, first strand: chain 'G' and resid 4 through 8 removed outlier: 3.670A pdb=" N GLN G 4 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER G 22 " --> pdb=" O SER G 8 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER G 71 " --> pdb=" O TYR G 80 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 47 through 48 Processing sheet with id=AB3, first strand: chain 'G' and resid 47 through 48 Processing sheet with id=AB4, first strand: chain 'G' and resid 50 through 51 Processing sheet with id=AB5, first strand: chain 'H' and resid 4 through 8 removed outlier: 3.671A pdb=" N GLN H 4 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER H 22 " --> pdb=" O SER H 8 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 47 through 48 Processing sheet with id=AB7, first strand: chain 'H' and resid 47 through 48 Processing sheet with id=AB8, first strand: chain 'H' and resid 50 through 51 Processing sheet with id=AB9, first strand: chain 'B' and resid 113 through 118 removed outlier: 8.622A pdb=" N TYR B 147 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL B 107 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N PHE B 149 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASN B 109 " --> pdb=" O PHE B 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 113 through 118 removed outlier: 8.622A pdb=" N TYR C 147 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL C 107 " --> pdb=" O TYR C 147 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N PHE C 149 " --> pdb=" O VAL C 107 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASN C 109 " --> pdb=" O PHE C 149 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 113 through 118 removed outlier: 8.623A pdb=" N TYR D 147 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL D 107 " --> pdb=" O TYR D 147 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N PHE D 149 " --> pdb=" O VAL D 107 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASN D 109 " --> pdb=" O PHE D 149 " (cutoff:3.500A) 816 hydrogen bonds defined for protein. 2268 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2396 1.32 - 1.44: 4496 1.44 - 1.56: 8644 1.56 - 1.68: 0 1.68 - 1.81: 92 Bond restraints: 15628 Sorted by residual: bond pdb=" CA ALA B 465 " pdb=" CB ALA B 465 " ideal model delta sigma weight residual 1.528 1.457 0.071 1.59e-02 3.96e+03 2.01e+01 bond pdb=" CA ALA A 465 " pdb=" CB ALA A 465 " ideal model delta sigma weight residual 1.528 1.458 0.071 1.59e-02 3.96e+03 1.98e+01 bond pdb=" CA ALA C 465 " pdb=" CB ALA C 465 " ideal model delta sigma weight residual 1.528 1.458 0.071 1.59e-02 3.96e+03 1.98e+01 bond pdb=" CA ALA D 465 " pdb=" CB ALA D 465 " ideal model delta sigma weight residual 1.528 1.458 0.071 1.59e-02 3.96e+03 1.98e+01 bond pdb=" CA ALA C 438 " pdb=" CB ALA C 438 " ideal model delta sigma weight residual 1.528 1.464 0.064 1.59e-02 3.96e+03 1.64e+01 ... (remaining 15623 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 20212 1.65 - 3.30: 707 3.30 - 4.95: 204 4.95 - 6.59: 33 6.59 - 8.24: 8 Bond angle restraints: 21164 Sorted by residual: angle pdb=" CA HIS B 451 " pdb=" C HIS B 451 " pdb=" N PRO B 452 " ideal model delta sigma weight residual 117.95 122.22 -4.27 7.70e-01 1.69e+00 3.07e+01 angle pdb=" CA HIS A 451 " pdb=" C HIS A 451 " pdb=" N PRO A 452 " ideal model delta sigma weight residual 117.95 122.22 -4.27 7.70e-01 1.69e+00 3.07e+01 angle pdb=" CA HIS C 451 " pdb=" C HIS C 451 " pdb=" N PRO C 452 " ideal model delta sigma weight residual 117.95 122.22 -4.27 7.70e-01 1.69e+00 3.07e+01 angle pdb=" CA HIS D 451 " pdb=" C HIS D 451 " pdb=" N PRO D 452 " ideal model delta sigma weight residual 117.95 122.22 -4.27 7.70e-01 1.69e+00 3.07e+01 angle pdb=" N LEU C 463 " pdb=" CA LEU C 463 " pdb=" CB LEU C 463 " ideal model delta sigma weight residual 110.40 102.38 8.02 1.63e+00 3.76e-01 2.42e+01 ... (remaining 21159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 8463 17.14 - 34.28: 609 34.28 - 51.42: 132 51.42 - 68.56: 12 68.56 - 85.70: 8 Dihedral angle restraints: 9224 sinusoidal: 3748 harmonic: 5476 Sorted by residual: dihedral pdb=" N LEU B 463 " pdb=" C LEU B 463 " pdb=" CA LEU B 463 " pdb=" CB LEU B 463 " ideal model delta harmonic sigma weight residual 122.80 113.37 9.43 0 2.50e+00 1.60e-01 1.42e+01 dihedral pdb=" N LEU C 463 " pdb=" C LEU C 463 " pdb=" CA LEU C 463 " pdb=" CB LEU C 463 " ideal model delta harmonic sigma weight residual 122.80 113.38 9.42 0 2.50e+00 1.60e-01 1.42e+01 dihedral pdb=" N LEU A 463 " pdb=" C LEU A 463 " pdb=" CA LEU A 463 " pdb=" CB LEU A 463 " ideal model delta harmonic sigma weight residual 122.80 113.38 9.42 0 2.50e+00 1.60e-01 1.42e+01 ... (remaining 9221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1607 0.047 - 0.094: 546 0.094 - 0.140: 135 0.140 - 0.187: 16 0.187 - 0.234: 20 Chirality restraints: 2324 Sorted by residual: chirality pdb=" CB VAL C 440 " pdb=" CA VAL C 440 " pdb=" CG1 VAL C 440 " pdb=" CG2 VAL C 440 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CB VAL B 440 " pdb=" CA VAL B 440 " pdb=" CG1 VAL B 440 " pdb=" CG2 VAL B 440 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB VAL A 440 " pdb=" CA VAL A 440 " pdb=" CG1 VAL A 440 " pdb=" CG2 VAL A 440 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 2321 not shown) Planarity restraints: 2696 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 445 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.89e+00 pdb=" C VAL B 445 " 0.049 2.00e-02 2.50e+03 pdb=" O VAL B 445 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY B 446 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 445 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.89e+00 pdb=" C VAL A 445 " -0.049 2.00e-02 2.50e+03 pdb=" O VAL A 445 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY A 446 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 445 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.89e+00 pdb=" C VAL D 445 " -0.049 2.00e-02 2.50e+03 pdb=" O VAL D 445 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY D 446 " 0.016 2.00e-02 2.50e+03 ... (remaining 2693 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.79: 3884 2.79 - 3.38: 16783 3.38 - 3.97: 28711 3.97 - 4.55: 42070 4.55 - 5.14: 61819 Nonbonded interactions: 153267 Sorted by model distance: nonbonded pdb=" OD1 ASN G 33 " pdb=" OH TYR G 104 " model vdw 2.209 3.040 nonbonded pdb=" OD1 ASN F 33 " pdb=" OH TYR F 104 " model vdw 2.209 3.040 nonbonded pdb=" OD1 ASN H 33 " pdb=" OH TYR H 104 " model vdw 2.209 3.040 nonbonded pdb=" OD1 ASN E 33 " pdb=" OH TYR E 104 " model vdw 2.209 3.040 nonbonded pdb=" O VAL C 409 " pdb=" OG SER C 413 " model vdw 2.258 3.040 ... (remaining 153262 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 103 through 490) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 2 through 31 or resid 33 through 116)) selection = (chain 'F' and (resid 2 through 31 or resid 33 through 116)) selection = (chain 'G' and (resid 2 through 31 or resid 33 through 116)) selection = (chain 'H' and (resid 2 through 31 or resid 33 through 116)) } 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=0.35 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 16.000 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 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 : 0.007 0.071 15632 Z= 0.357 Angle : 0.776 8.243 21172 Z= 0.493 Chirality : 0.052 0.234 2324 Planarity : 0.006 0.059 2696 Dihedral : 12.329 85.698 5700 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.94 % Allowed : 7.83 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.21), residues: 1864 helix: 0.17 (0.18), residues: 924 sheet: -2.14 (0.36), residues: 212 loop : -0.22 (0.26), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 370 TYR 0.027 0.002 TYR D 447 PHE 0.018 0.002 PHE B 406 TRP 0.014 0.002 TRP B 437 HIS 0.010 0.002 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00678 (15628) covalent geometry : angle 0.77599 (21164) SS BOND : bond 0.00071 ( 4) SS BOND : angle 0.35288 ( 8) hydrogen bonds : bond 0.17420 ( 784) hydrogen bonds : angle 7.03299 ( 2268) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 TYR cc_start: 0.7957 (t80) cc_final: 0.7757 (t80) REVERT: A 212 PRO cc_start: 0.7505 (Cg_exo) cc_final: 0.7186 (Cg_endo) REVERT: A 262 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7844 (mm-30) REVERT: F 77 ASN cc_start: 0.7885 (t0) cc_final: 0.7668 (t0) REVERT: G 77 ASN cc_start: 0.7869 (t0) cc_final: 0.7647 (t0) REVERT: H 53 ARG cc_start: 0.8061 (mtp85) cc_final: 0.7807 (mtm180) REVERT: H 77 ASN cc_start: 0.7883 (t0) cc_final: 0.7674 (t0) REVERT: B 212 PRO cc_start: 0.7518 (Cg_exo) cc_final: 0.7201 (Cg_endo) REVERT: B 261 ASP cc_start: 0.7182 (t70) cc_final: 0.6941 (t0) REVERT: B 262 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7829 (mm-30) REVERT: C 162 TYR cc_start: 0.7953 (t80) cc_final: 0.7753 (t80) REVERT: C 212 PRO cc_start: 0.7515 (Cg_exo) cc_final: 0.7198 (Cg_endo) REVERT: C 261 ASP cc_start: 0.7183 (t70) cc_final: 0.6942 (t0) REVERT: C 262 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7814 (mm-30) REVERT: D 162 TYR cc_start: 0.7950 (t80) cc_final: 0.7735 (t80) REVERT: D 212 PRO cc_start: 0.7515 (Cg_exo) cc_final: 0.7195 (Cg_endo) REVERT: D 261 ASP cc_start: 0.7181 (t70) cc_final: 0.6942 (t0) REVERT: D 262 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7828 (mm-30) outliers start: 32 outliers final: 24 residues processed: 211 average time/residue: 0.3743 time to fit residues: 91.7367 Evaluate side-chains 191 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 416 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 0.0570 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.0170 chunk 149 optimal weight: 0.9980 overall best weight: 0.3734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 40 GLN F 40 GLN G 40 GLN H 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.217838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.131675 restraints weight = 21658.297| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.93 r_work: 0.3249 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15632 Z= 0.117 Angle : 0.547 5.915 21172 Z= 0.286 Chirality : 0.042 0.135 2324 Planarity : 0.005 0.047 2696 Dihedral : 4.406 26.288 2144 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.43 % Allowed : 12.56 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.21), residues: 1864 helix: 0.89 (0.18), residues: 940 sheet: -1.71 (0.37), residues: 212 loop : 0.01 (0.26), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 209 TYR 0.010 0.001 TYR H 38 PHE 0.016 0.001 PHE A 186 TRP 0.011 0.001 TRP B 436 HIS 0.004 0.001 HIS D 427 Details of bonding type rmsd covalent geometry : bond 0.00251 (15628) covalent geometry : angle 0.54656 (21164) SS BOND : bond 0.00323 ( 4) SS BOND : angle 0.56440 ( 8) hydrogen bonds : bond 0.04494 ( 784) hydrogen bonds : angle 4.73996 ( 2268) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 PRO cc_start: 0.7395 (Cg_exo) cc_final: 0.7021 (Cg_endo) REVERT: A 262 GLU cc_start: 0.8466 (mt-10) cc_final: 0.7836 (mm-30) REVERT: A 466 ILE cc_start: 0.8258 (mt) cc_final: 0.7901 (mp) REVERT: F 39 ARG cc_start: 0.6842 (ptp90) cc_final: 0.6606 (ptp-170) REVERT: G 39 ARG cc_start: 0.6836 (ptp90) cc_final: 0.6612 (ptp-170) REVERT: H 39 ARG cc_start: 0.6867 (ptp90) cc_final: 0.6621 (ptp-170) REVERT: B 212 PRO cc_start: 0.7411 (Cg_exo) cc_final: 0.7046 (Cg_endo) REVERT: B 466 ILE cc_start: 0.8257 (mt) cc_final: 0.7912 (mp) REVERT: C 212 PRO cc_start: 0.7414 (Cg_exo) cc_final: 0.7044 (Cg_endo) REVERT: C 466 ILE cc_start: 0.8263 (mt) cc_final: 0.7919 (mp) REVERT: D 212 PRO cc_start: 0.7409 (Cg_exo) cc_final: 0.7038 (Cg_endo) REVERT: D 466 ILE cc_start: 0.8257 (mt) cc_final: 0.7913 (mp) outliers start: 40 outliers final: 24 residues processed: 203 average time/residue: 0.4495 time to fit residues: 103.7740 Evaluate side-chains 186 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 395 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 108 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.215956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.142502 restraints weight = 29973.798| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 3.22 r_work: 0.3147 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15632 Z= 0.165 Angle : 0.550 5.409 21172 Z= 0.289 Chirality : 0.043 0.140 2324 Planarity : 0.005 0.051 2696 Dihedral : 4.079 19.545 2132 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.43 % Allowed : 14.08 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.21), residues: 1864 helix: 0.98 (0.17), residues: 940 sheet: -1.74 (0.37), residues: 212 loop : 0.08 (0.26), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 209 TYR 0.016 0.001 TYR B 162 PHE 0.021 0.002 PHE D 186 TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS D 427 Details of bonding type rmsd covalent geometry : bond 0.00399 (15628) covalent geometry : angle 0.54945 (21164) SS BOND : bond 0.00187 ( 4) SS BOND : angle 0.81022 ( 8) hydrogen bonds : bond 0.04606 ( 784) hydrogen bonds : angle 4.57420 ( 2268) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 PRO cc_start: 0.7430 (Cg_exo) cc_final: 0.7073 (Cg_endo) REVERT: A 262 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7906 (mm-30) REVERT: A 466 ILE cc_start: 0.8477 (mt) cc_final: 0.8154 (mp) REVERT: F 39 ARG cc_start: 0.7162 (ptp90) cc_final: 0.6901 (ptp-170) REVERT: H 39 ARG cc_start: 0.7167 (ptp90) cc_final: 0.6903 (ptp-170) REVERT: B 212 PRO cc_start: 0.7440 (Cg_exo) cc_final: 0.7085 (Cg_endo) REVERT: B 466 ILE cc_start: 0.8469 (mt) cc_final: 0.8144 (mp) REVERT: C 212 PRO cc_start: 0.7446 (Cg_exo) cc_final: 0.7092 (Cg_endo) REVERT: C 261 ASP cc_start: 0.7310 (t70) cc_final: 0.7085 (t0) REVERT: C 466 ILE cc_start: 0.8470 (mt) cc_final: 0.8148 (mp) REVERT: D 212 PRO cc_start: 0.7429 (Cg_exo) cc_final: 0.7076 (Cg_endo) REVERT: D 466 ILE cc_start: 0.8471 (mt) cc_final: 0.8148 (mp) outliers start: 40 outliers final: 32 residues processed: 194 average time/residue: 0.3600 time to fit residues: 81.5192 Evaluate side-chains 200 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 395 MET Chi-restraints excluded: chain D residue 416 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 160 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 58 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 150 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.217342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.138782 restraints weight = 25567.448| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.59 r_work: 0.3233 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15632 Z= 0.127 Angle : 0.512 5.406 21172 Z= 0.268 Chirality : 0.041 0.131 2324 Planarity : 0.005 0.048 2696 Dihedral : 3.946 18.913 2132 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.43 % Allowed : 14.26 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.21), residues: 1864 helix: 1.22 (0.18), residues: 940 sheet: -1.56 (0.36), residues: 212 loop : 0.11 (0.26), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 209 TYR 0.014 0.001 TYR D 162 PHE 0.023 0.001 PHE D 186 TRP 0.007 0.001 TRP D 436 HIS 0.003 0.001 HIS C 427 Details of bonding type rmsd covalent geometry : bond 0.00297 (15628) covalent geometry : angle 0.51232 (21164) SS BOND : bond 0.00163 ( 4) SS BOND : angle 0.68351 ( 8) hydrogen bonds : bond 0.04089 ( 784) hydrogen bonds : angle 4.35412 ( 2268) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 PRO cc_start: 0.7279 (Cg_exo) cc_final: 0.6945 (Cg_endo) REVERT: A 466 ILE cc_start: 0.8397 (mt) cc_final: 0.8147 (mp) REVERT: F 39 ARG cc_start: 0.7209 (ptp90) cc_final: 0.7004 (ptp90) REVERT: H 39 ARG cc_start: 0.7243 (ptp90) cc_final: 0.7034 (ptp90) REVERT: B 212 PRO cc_start: 0.7377 (Cg_exo) cc_final: 0.7033 (Cg_endo) REVERT: B 466 ILE cc_start: 0.8397 (mt) cc_final: 0.8145 (mp) REVERT: C 212 PRO cc_start: 0.7378 (Cg_exo) cc_final: 0.7032 (Cg_endo) REVERT: C 466 ILE cc_start: 0.8390 (mt) cc_final: 0.8138 (mp) REVERT: D 212 PRO cc_start: 0.7371 (Cg_exo) cc_final: 0.7020 (Cg_endo) REVERT: D 466 ILE cc_start: 0.8399 (mt) cc_final: 0.8148 (mp) outliers start: 40 outliers final: 31 residues processed: 197 average time/residue: 0.3593 time to fit residues: 81.9790 Evaluate side-chains 198 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 395 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 102 optimal weight: 0.0770 chunk 156 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 101 optimal weight: 0.0980 chunk 34 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.216272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.140863 restraints weight = 30987.991| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 4.08 r_work: 0.3080 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15632 Z= 0.116 Angle : 0.504 5.963 21172 Z= 0.262 Chirality : 0.041 0.125 2324 Planarity : 0.005 0.048 2696 Dihedral : 3.868 19.061 2132 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.43 % Allowed : 15.05 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.21), residues: 1864 helix: 1.37 (0.18), residues: 944 sheet: -1.57 (0.36), residues: 212 loop : 0.05 (0.26), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 209 TYR 0.011 0.001 TYR B 162 PHE 0.025 0.001 PHE A 186 TRP 0.007 0.001 TRP C 436 HIS 0.002 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00268 (15628) covalent geometry : angle 0.50432 (21164) SS BOND : bond 0.00119 ( 4) SS BOND : angle 0.77153 ( 8) hydrogen bonds : bond 0.03879 ( 784) hydrogen bonds : angle 4.22438 ( 2268) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 PRO cc_start: 0.7271 (Cg_exo) cc_final: 0.6924 (Cg_endo) REVERT: A 466 ILE cc_start: 0.8350 (mt) cc_final: 0.8102 (mp) REVERT: B 212 PRO cc_start: 0.7275 (Cg_exo) cc_final: 0.6944 (Cg_endo) REVERT: B 466 ILE cc_start: 0.8346 (mt) cc_final: 0.8096 (mp) REVERT: C 212 PRO cc_start: 0.7276 (Cg_exo) cc_final: 0.6939 (Cg_endo) REVERT: C 466 ILE cc_start: 0.8350 (mt) cc_final: 0.8100 (mp) REVERT: D 212 PRO cc_start: 0.7268 (Cg_exo) cc_final: 0.6923 (Cg_endo) REVERT: D 466 ILE cc_start: 0.8355 (mt) cc_final: 0.8105 (mp) outliers start: 40 outliers final: 28 residues processed: 200 average time/residue: 0.3649 time to fit residues: 85.6429 Evaluate side-chains 199 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 416 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 175 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 135 optimal weight: 0.2980 chunk 19 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 161 optimal weight: 0.8980 chunk 181 optimal weight: 0.9990 chunk 143 optimal weight: 0.6980 chunk 157 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.216372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.145815 restraints weight = 35262.863| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 4.70 r_work: 0.3059 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15632 Z= 0.123 Angle : 0.508 6.409 21172 Z= 0.263 Chirality : 0.041 0.126 2324 Planarity : 0.005 0.048 2696 Dihedral : 3.846 19.401 2132 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.73 % Allowed : 15.59 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.21), residues: 1864 helix: 1.42 (0.18), residues: 944 sheet: -1.59 (0.35), residues: 212 loop : 0.08 (0.26), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 209 TYR 0.016 0.001 TYR D 162 PHE 0.025 0.001 PHE B 186 TRP 0.007 0.001 TRP B 436 HIS 0.002 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00288 (15628) covalent geometry : angle 0.50756 (21164) SS BOND : bond 0.00082 ( 4) SS BOND : angle 0.76478 ( 8) hydrogen bonds : bond 0.03895 ( 784) hydrogen bonds : angle 4.16344 ( 2268) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 170 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 PRO cc_start: 0.7172 (Cg_exo) cc_final: 0.6812 (Cg_endo) REVERT: A 258 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6673 (pt0) REVERT: A 366 ILE cc_start: 0.6714 (OUTLIER) cc_final: 0.6473 (mt) REVERT: A 466 ILE cc_start: 0.8084 (mt) cc_final: 0.7812 (mp) REVERT: H 39 ARG cc_start: 0.6614 (ptp90) cc_final: 0.6401 (ptp90) REVERT: B 212 PRO cc_start: 0.7186 (Cg_exo) cc_final: 0.6831 (Cg_endo) REVERT: B 366 ILE cc_start: 0.6737 (OUTLIER) cc_final: 0.6493 (mt) REVERT: B 466 ILE cc_start: 0.8087 (mt) cc_final: 0.7810 (mp) REVERT: C 212 PRO cc_start: 0.7192 (Cg_exo) cc_final: 0.6839 (Cg_endo) REVERT: C 366 ILE cc_start: 0.6752 (OUTLIER) cc_final: 0.6507 (mt) REVERT: C 466 ILE cc_start: 0.8083 (mt) cc_final: 0.7811 (mp) REVERT: D 212 PRO cc_start: 0.7190 (Cg_exo) cc_final: 0.6832 (Cg_endo) REVERT: D 366 ILE cc_start: 0.6751 (OUTLIER) cc_final: 0.6508 (mt) REVERT: D 466 ILE cc_start: 0.8093 (mt) cc_final: 0.7822 (mp) outliers start: 45 outliers final: 31 residues processed: 199 average time/residue: 0.3965 time to fit residues: 91.6089 Evaluate side-chains 196 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 395 MET Chi-restraints excluded: chain D residue 416 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 62 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 114 optimal weight: 4.9990 chunk 10 optimal weight: 0.0470 chunk 142 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 144 optimal weight: 0.4980 chunk 49 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 121 optimal weight: 0.0020 overall best weight: 0.3686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.219490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.147307 restraints weight = 29263.986| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 3.32 r_work: 0.3183 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15632 Z= 0.101 Angle : 0.491 6.810 21172 Z= 0.253 Chirality : 0.040 0.119 2324 Planarity : 0.004 0.047 2696 Dihedral : 3.758 19.321 2131 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.61 % Allowed : 16.32 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.21), residues: 1864 helix: 1.73 (0.18), residues: 928 sheet: -1.53 (0.34), residues: 212 loop : 0.02 (0.25), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 209 TYR 0.015 0.001 TYR B 162 PHE 0.028 0.001 PHE A 186 TRP 0.008 0.001 TRP A 436 HIS 0.002 0.001 HIS B 427 Details of bonding type rmsd covalent geometry : bond 0.00223 (15628) covalent geometry : angle 0.49122 (21164) SS BOND : bond 0.00079 ( 4) SS BOND : angle 0.65975 ( 8) hydrogen bonds : bond 0.03608 ( 784) hydrogen bonds : angle 4.02664 ( 2268) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 167 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.8080 (tpp) cc_final: 0.7874 (tpp) REVERT: A 212 PRO cc_start: 0.7278 (Cg_exo) cc_final: 0.6948 (Cg_endo) REVERT: A 366 ILE cc_start: 0.7323 (OUTLIER) cc_final: 0.7051 (mt) REVERT: A 466 ILE cc_start: 0.8447 (mt) cc_final: 0.8219 (mp) REVERT: B 137 MET cc_start: 0.8099 (tpp) cc_final: 0.7893 (tpp) REVERT: B 212 PRO cc_start: 0.7305 (Cg_exo) cc_final: 0.6975 (Cg_endo) REVERT: B 258 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6891 (pt0) REVERT: B 366 ILE cc_start: 0.7344 (OUTLIER) cc_final: 0.7073 (mt) REVERT: B 466 ILE cc_start: 0.8440 (mt) cc_final: 0.8211 (mp) REVERT: C 137 MET cc_start: 0.8134 (tpp) cc_final: 0.7933 (tpp) REVERT: C 212 PRO cc_start: 0.7294 (Cg_exo) cc_final: 0.6967 (Cg_endo) REVERT: C 366 ILE cc_start: 0.7332 (OUTLIER) cc_final: 0.7061 (mt) REVERT: C 466 ILE cc_start: 0.8443 (mt) cc_final: 0.8214 (mp) REVERT: D 137 MET cc_start: 0.8100 (tpp) cc_final: 0.7892 (tpp) REVERT: D 212 PRO cc_start: 0.7291 (Cg_exo) cc_final: 0.6958 (Cg_endo) REVERT: D 366 ILE cc_start: 0.7342 (OUTLIER) cc_final: 0.7067 (mt) REVERT: D 466 ILE cc_start: 0.8450 (mt) cc_final: 0.8228 (mp) outliers start: 43 outliers final: 26 residues processed: 195 average time/residue: 0.3961 time to fit residues: 89.7332 Evaluate side-chains 194 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 395 MET Chi-restraints excluded: chain D residue 416 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 95 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 67 optimal weight: 0.3980 chunk 97 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.217513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.149637 restraints weight = 37314.470| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 4.17 r_work: 0.3134 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15632 Z= 0.142 Angle : 0.515 6.300 21172 Z= 0.269 Chirality : 0.042 0.132 2324 Planarity : 0.005 0.048 2696 Dihedral : 3.818 20.027 2130 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.22 % Allowed : 16.38 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.21), residues: 1864 helix: 1.60 (0.18), residues: 928 sheet: -1.42 (0.35), residues: 212 loop : 0.01 (0.25), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 209 TYR 0.020 0.001 TYR C 162 PHE 0.031 0.001 PHE B 186 TRP 0.006 0.001 TRP D 436 HIS 0.002 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00342 (15628) covalent geometry : angle 0.51517 (21164) SS BOND : bond 0.00059 ( 4) SS BOND : angle 0.76573 ( 8) hydrogen bonds : bond 0.03955 ( 784) hydrogen bonds : angle 4.01863 ( 2268) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 165 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 PRO cc_start: 0.7308 (Cg_exo) cc_final: 0.6962 (Cg_endo) REVERT: A 258 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6894 (pt0) REVERT: A 328 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.8004 (mtm) REVERT: A 366 ILE cc_start: 0.7374 (OUTLIER) cc_final: 0.7116 (mt) REVERT: A 466 ILE cc_start: 0.8494 (mt) cc_final: 0.8259 (mp) REVERT: B 212 PRO cc_start: 0.7319 (Cg_exo) cc_final: 0.6980 (Cg_endo) REVERT: B 258 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6863 (pt0) REVERT: B 261 ASP cc_start: 0.7239 (t70) cc_final: 0.7036 (t0) REVERT: B 366 ILE cc_start: 0.7396 (OUTLIER) cc_final: 0.7134 (mt) REVERT: B 466 ILE cc_start: 0.8482 (mt) cc_final: 0.8254 (mp) REVERT: C 212 PRO cc_start: 0.7319 (Cg_exo) cc_final: 0.6976 (Cg_endo) REVERT: C 258 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6869 (pt0) REVERT: C 366 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.7115 (mt) REVERT: C 466 ILE cc_start: 0.8491 (mt) cc_final: 0.8256 (mp) REVERT: D 212 PRO cc_start: 0.7315 (Cg_exo) cc_final: 0.6972 (Cg_endo) REVERT: D 258 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6880 (pt0) REVERT: D 366 ILE cc_start: 0.7398 (OUTLIER) cc_final: 0.7135 (mt) REVERT: D 466 ILE cc_start: 0.8498 (mt) cc_final: 0.8263 (mp) outliers start: 53 outliers final: 28 residues processed: 199 average time/residue: 0.3893 time to fit residues: 89.5459 Evaluate side-chains 197 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 395 MET Chi-restraints excluded: chain D residue 416 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 145 optimal weight: 0.4980 chunk 72 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.213102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.129213 restraints weight = 25149.023| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 3.59 r_work: 0.3124 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 15632 Z= 0.309 Angle : 0.642 7.128 21172 Z= 0.335 Chirality : 0.049 0.175 2324 Planarity : 0.006 0.053 2696 Dihedral : 4.237 20.802 2129 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.16 % Allowed : 16.50 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.20), residues: 1864 helix: 0.79 (0.17), residues: 944 sheet: -1.42 (0.36), residues: 212 loop : -0.08 (0.26), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 209 TYR 0.023 0.002 TYR C 162 PHE 0.032 0.002 PHE A 186 TRP 0.010 0.002 TRP A 437 HIS 0.004 0.001 HIS D 427 Details of bonding type rmsd covalent geometry : bond 0.00779 (15628) covalent geometry : angle 0.64161 (21164) SS BOND : bond 0.00012 ( 4) SS BOND : angle 0.98731 ( 8) hydrogen bonds : bond 0.05249 ( 784) hydrogen bonds : angle 4.35968 ( 2268) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 166 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 PRO cc_start: 0.7473 (Cg_exo) cc_final: 0.7147 (Cg_endo) REVERT: A 258 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6929 (pt0) REVERT: A 466 ILE cc_start: 0.8400 (mt) cc_final: 0.8124 (mp) REVERT: B 147 TYR cc_start: 0.7567 (m-80) cc_final: 0.7360 (m-80) REVERT: B 212 PRO cc_start: 0.7484 (Cg_exo) cc_final: 0.7156 (Cg_endo) REVERT: B 258 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6810 (pt0) REVERT: B 466 ILE cc_start: 0.8394 (mt) cc_final: 0.8118 (mp) REVERT: C 212 PRO cc_start: 0.7476 (Cg_exo) cc_final: 0.7146 (Cg_endo) REVERT: C 258 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6871 (pt0) REVERT: C 466 ILE cc_start: 0.8385 (mt) cc_final: 0.8107 (mp) REVERT: D 137 MET cc_start: 0.8035 (tpp) cc_final: 0.7825 (tpp) REVERT: D 212 PRO cc_start: 0.7476 (Cg_exo) cc_final: 0.7146 (Cg_endo) REVERT: D 258 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6863 (pt0) REVERT: D 466 ILE cc_start: 0.8388 (mt) cc_final: 0.8111 (mp) outliers start: 52 outliers final: 32 residues processed: 195 average time/residue: 0.3434 time to fit residues: 78.2708 Evaluate side-chains 201 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 395 MET Chi-restraints excluded: chain D residue 416 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 115 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 153 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.216626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.143801 restraints weight = 34107.017| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 3.64 r_work: 0.3134 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15632 Z= 0.144 Angle : 0.536 6.839 21172 Z= 0.282 Chirality : 0.042 0.132 2324 Planarity : 0.005 0.048 2696 Dihedral : 3.971 18.828 2129 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.73 % Allowed : 17.17 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.21), residues: 1864 helix: 1.13 (0.17), residues: 940 sheet: -1.35 (0.36), residues: 212 loop : 0.09 (0.26), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 209 TYR 0.023 0.001 TYR A 162 PHE 0.036 0.001 PHE B 186 TRP 0.008 0.001 TRP A 305 HIS 0.002 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00347 (15628) covalent geometry : angle 0.53571 (21164) SS BOND : bond 0.00017 ( 4) SS BOND : angle 0.81572 ( 8) hydrogen bonds : bond 0.04171 ( 784) hydrogen bonds : angle 4.14412 ( 2268) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 163 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 PRO cc_start: 0.7438 (Cg_exo) cc_final: 0.7110 (Cg_endo) REVERT: A 466 ILE cc_start: 0.8420 (mt) cc_final: 0.8155 (mp) REVERT: B 212 PRO cc_start: 0.7441 (Cg_exo) cc_final: 0.7115 (Cg_endo) REVERT: B 466 ILE cc_start: 0.8411 (mt) cc_final: 0.8144 (mp) REVERT: C 212 PRO cc_start: 0.7409 (Cg_exo) cc_final: 0.7079 (Cg_endo) REVERT: C 466 ILE cc_start: 0.8420 (mt) cc_final: 0.8153 (mp) REVERT: D 137 MET cc_start: 0.8074 (tpp) cc_final: 0.7860 (tpp) REVERT: D 212 PRO cc_start: 0.7401 (Cg_exo) cc_final: 0.7063 (Cg_endo) REVERT: D 466 ILE cc_start: 0.8425 (mt) cc_final: 0.8159 (mp) outliers start: 45 outliers final: 34 residues processed: 187 average time/residue: 0.3410 time to fit residues: 74.4262 Evaluate side-chains 193 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 395 MET Chi-restraints excluded: chain D residue 416 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 25 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 75 optimal weight: 0.0670 chunk 103 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.216745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.141568 restraints weight = 28477.016| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 3.03 r_work: 0.3195 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15632 Z= 0.139 Angle : 0.529 6.609 21172 Z= 0.278 Chirality : 0.042 0.131 2324 Planarity : 0.005 0.049 2696 Dihedral : 3.888 19.515 2129 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.25 % Allowed : 17.84 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.21), residues: 1864 helix: 1.22 (0.18), residues: 940 sheet: -1.33 (0.36), residues: 212 loop : 0.11 (0.26), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 209 TYR 0.007 0.001 TYR B 187 PHE 0.034 0.001 PHE C 186 TRP 0.007 0.001 TRP C 436 HIS 0.002 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00333 (15628) covalent geometry : angle 0.52895 (21164) SS BOND : bond 0.00007 ( 4) SS BOND : angle 0.78759 ( 8) hydrogen bonds : bond 0.04047 ( 784) hydrogen bonds : angle 4.07433 ( 2268) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5710.02 seconds wall clock time: 98 minutes 2.49 seconds (5882.49 seconds total)